Publications from Section for Biomolecular Sciences

Total publications from unit:



Lau Dalby Nielsen, Christian Parsbæk Pedersen, Simon Erlendsson and Kaare Teilum. (2019) The Capsid Domain of Arc Changes Its Oligomerization Propensity through Direct Interaction with the NMDA Receptor Structure(112):157-166.


Lau D Nielsen, Mads M Foged, Anastasia Albert, Andreas B Bertelsen, Cecilie L Søltoft, Samuel D Robinson, Steen V Petersen, Anthony W Purcell, Baldomero M Olivera, Raymond S Norton, Terje Vasskog, Helena Safavi-Hemami, Kaare Teilum and Lars Ellgaard. (2019) The three-dimensional structure of an H-superfamily conotoxin reveals a granulin fold arising from a common ICK cysteine framework The Journal of Biological Chemistry 15(1):77-82.


Michael Lückmann, Mette Trauelsen, Marie A Bentsen, Tinne A D Nissen, Joao Martins, Zohreh Fallah, Mads M Nygaard, Elena Papaleo, Kresten Lindorff-Larsen, Thue W Schwartz and Thomas M Frimurer. (2019) Molecular dynamics-guided discovery of an ago-allosteric modulator for GPR40/FFAR1 Proceedings of the National Academy of Sciences of the United States of America 116(14):7123-7128.


Amelie Stein, Douglas M. Fowler, Rasmus Hartmann-Petersen and Kresten Lindorff-Larsen. (2019) Biophysical and Mechanistic Models for Disease-Causing Protein Variants Trends in Biochemical Sciences 207(2):1-14.


Emil G. P. Stender, Johnny Birch, Christian Kjeldsen, Lau D. Nielsen, Jens Ø. Duus, Birthe B. Kragelund and Birte Svensson. (2019) Alginate Trisaccharide Binding Sites on the Surface of ß-Lactoglobulin Identified by NMR Spectroscopy ACS Omega 4(4):6165-6174.


Ida Marie Zobbe Sjøgaard, Simon Bressendorff, Andreas Prestel, Swathi Kausika, Emilie Oksbjerg, Birthe B. Kragelund and Peter Brodersen. (2019) The transmembrane autophagy cargo receptors ATI1 and ATI2 interact with ATG8 through intrinsically disordered regions with distinct biophysical properties Biochemical Journal 476(3):449-465.


Lene Clausen, Amanda Bering Abildgaard, Sarah K. Gersing, Amelie Stein, Kresten Lindorff-Larsen and Rasmus Hartmann-Petersen. (2019) Protein stability and degradation in health and disease Molecular Chaperones in Human Disorders 40(4):444-457.


Niels Hadrup, Kristina Bram Knudsen, Trine Berthing, Henrik Wolff, Stefan Bengtson, Christian Kofoed, Roall Espersen, Casper Højgaard, Jakob Rahr Winther, Martin Willemoës, Irene Wedin, Markus Nuopponen, Harri Alenius, Hannu Norppa, Håkan Wallin and Ulla Vogel. (2019) Pulmonary effects of nanofibrillated celluloses in mice suggest that carboxylation lowers the inflammatory and acute phase responses Environmental Toxicology and Pharmacology 66(2):116-125.


Rasmus Scheller, Amelie Stein, Sofie V. Nielsen, Frederikke I. Marin, Anne-Marie Gerdes, Miriam Di Marco, Elena Papaleo, Kresten Lindorff-Larsen and Rasmus Hartmann-Petersen. (2019) Toward mechanistic models for genotype-phenotype correlations in phenylketonuria using protein stability calculations Human Mutation 40(4):444-457.


S. Jephthah, L. Staby, B. B. Kragelund and M. Skepö. (2019) Temperature Dependence of Intrinsically Disordered Proteins in Simulations Journal of Chemical Theory and Computation 15(4):2672-2683.


Sandro Bottaro, Giovanni Bussi, Giovanni Pinamonti, Sabine Reisser, Wouter Boomsma and Kresten Lindorff-Larsen. (2019) Barnaba RNA 25(2):219-231.


Simon Erlendsson, Thor Seneca Thorsen, Georges Vauquelin, Ina Ammendrup-Johnsen, Volker Wirth, Karen L. Martinez, Kaare Teilum, Ulrik Gether and Kenneth Lindegaard Madsen. (2019) Mechanisms of PDZ domain scaffold assembly illuminated by use of supported cell membrane sheets eLife 8(112):1-27.


Simon Riis, Britt Christensen, Birgitte Nellemann, Andreas Ruch Moller, Anna Sofie Husted, Steen B. Pedersen, Thue W. Schwartz, Jens Otto Lunde Jorgensen and Niels Jessen. (2019) Molecular adaptations in human subcutaneous adipose tissue after ten weeks of endurance exercise training in healthy males Journal of Applied Physiology 126(3):569-577.


Steen Pedersen, Thilde Bagger Terkelsen, Mette Eriksen, Magnus Krarup Hauge, Casper Carstens Lund, Kim Sneppen and Namiko Mitarai. (2019) Fast Translation within the First 45 Codons Decreases mRNA Stability and Increases Premature Transcription Termination in E. coli Journal of Molecular Biology 431(6):1088-1097.



Joao Henriques, Lise Arleth, Kresten Lindorff-Larsen and Marie Skepo. (2018) On the Calculation of SAXS Profiles of Folded and Intrinsically Disordered Proteins from Computer Simulations Journal of Molecular Biology 430:2521-2539.


Tone Bengtsen, Viktor Lindahl Holm, Søren Roi Midtgaard, Lise Arleth and Kresten Lindorff-Larsen. (2018) A Combined Simulation and SAXS Study of the Dynamics of Lipid Nanodiscs Biophysical Journal 114:559A-559A.


Anil Kurut, Rasmus Fonseca and Wouter Boomsma. (2018) Driving Structural Transitions in Molecular Simulations Using the Nonequilibrium Candidate Monte Carlo Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces & Biophysical 122(3):1195-1204.


Lars Ellgaard, Carolyn S. Sevier and Neil J. Bulleid. (2018) How are proteins reduced in the endoplasmic reticulum? Trends in Biochemical Sciences 43(1):32-43.


Line V. Kristensen, Felix S. Oppermann, Matthias J. Rauen, Karina Fog, Thorsten Schmidt, Jana Schmidt, Tina Harmuth, Rasmus Hartmann-Petersen and Kenneth Thirstrup. (2018) Mass spectrometry analyses of normal and polyglutamine expanded ataxin-3 reveal novel interaction partners involved in mitochondrial function Neurochemistry International 112(4):5-17.


Rasmus Skytte Eriksen, Sine Lo Svenningsen, Kim Sneppen and Namiko Mitarai. (2018) A growing microcolony can survive and support persistent propagation of virulent phages Proceedings of the National Academy of Sciences USA (PNAS) 115(2):337-342.


Alessandro Borgia, Madeleine B. Borgia, Katrine Østergaard Bugge, Vera M. Kissling, Pétur O. Heidarsson, Catarina B. Fernandes, Andrea Sottini, Andrea Soranno, Karin J. Buholzer, Daniel Nettels, Birthe Brandt Kragelund, Robert B. Best and Benjamin Schuler. (2018) Extreme disorder in an ultrahigh-affinity protein complex Nature 555(4):61-66.


Andreas Prestel, Katrine Bugge, Lasse Staby, Ruth Hendus-Altenburger and Birthe B. Kragelund. (2018) Characterization of Dynamic IDP Complexes by NMR Spectroscopy Intrinsically Disordered Proteins 48(4):74-82.


Birte Hoecker and Jakob R. Winther. (2018) Editorial overview: A perspective on protein evolution Current Opinion in Structural Biology 48(11):viii-ix.


Casper Højgaard, Henrik Vinther Sørensen, Jan Skov Pedersen, Jakob Rahr Winther and Daniel Erik Otzen. (2018) Can a Charged Surfactant Unfold an Uncharged Protein? Biophysical Journal 115(11):2081-2086.


Chao Li, Tegan M. Haslam, Anna Krüger, Lizette Marais Schneider, Kohei Mishina, Lacey Samuels, Hongxing Yan, Ljerka Kunst, Ulrich Schaffrath, Christiane Nawrath, Guoxiong Chen, Takao Komatsuda and Penny von Wettstein. (2018) The ß-Ketoacyl-CoA Synthase HvKCS1, Encoded by Cer-zh, Plays a Key Role in Synthesis of Barley Leaf Wax and Germination of Barley Powdery Mildew Plant and Cell Physiology 59(4):811-827.


Elena Papaleo, Carlo Camilloni, Kaare Teilum, Michele Vendruscolo and Kresten Lindorff-Larsen. (2018) Molecular dynamics ensemble refinement of the heterogeneous native state of NCBD using chemical shifts and NOEs PeerJ 6(2):1-24.


Elissa D. Pastuzyn, Cameron E. Day, Rachel B. Kearns, Madeleine Kyrke-Smith, Andrew V. Taibi, John McCormick, Nathan Yoder, David M. Belnap, Simon Erlendsson, Dustin R. Morado, John A. G. Briggs, Cédric Feschotte and Jason D. Shepherd. (2018) The Neuronal Gene Arc Encodes a Repurposed Retrotransposon Gag Protein that Mediates Intercellular RNA Transfer Cell 172:275-288, E18.


Helena Safavi-Hemami, Mads Møller Foged and Lars Ellgaard. (2018) Evolutionary Adaptations to Cysteine-rich Peptide Folding Oxidative Folding of Proteins 43(1):32-43.


Henrik O'Brien, Shingo Kanemura, Masaki Okumura, Robert P. Baskin, Pradip K. Bandyopadhyay, Baldomero M. Olivera, Lars Ellgaard, Kenji Inaba and Helena Safavi-Hemami. (2018) Ero1-Mediated Reoxidation of Protein Disulfide Isomerase Accelerates the Folding of Cone Snail Toxins International Journal of Molecular Sciences 19(11):1-15.


Jill J. Bouchard, Joel H. Otero, Daniel C. Scott, Elzbieta Szulc, Erik W. Martin, Nafiseh Sabri, Daniele Granata, Melissa R. Marzahn, Kresten Lindorff-Larsen, Xavier Salvatella, Brenda A. Schulman and Tanja Mittag. (2018) Cancer Mutations of the Tumor Suppressor SPOP Disrupt the Formation of Active, Phase-Separated Compartments Molecular Cell 72(1):19-36, e1-e8.


Katharina Weinhaupl, Caroline Lindau, Audrey Hessel, Yong Wang, Conny Schültze, Tobias Jores, Laura Melchionda, Birgit Schönfisch, Hubert Kalbacher, Beate Bersch, Doron Rapaport, Martha Brennich, Kresten Lindorff-Larsen, Nils Wiedemann and Paul Schanda. (2018) Structural Basis of Membrane Protein Chaperoning through the Mitochondrial Intermembrane Space Cell 175(5):1365-1379, e25.


Katrine Østergaard Bugge, Lasse Staby, Katherine Rosemary Kemplen, Charlotte O'Shea, Sidsel Krogh Bendsen, Mikael Kryger Jensen, Johan Gotthardt Olsen, Karen Skriver and Birthe Brandt Kragelund. (2018) Structure of radical-induced cell death1 hub domain reveals a common aa-scaffold for disorder in transcriptional networks Structure 26(5):734-746.


Kim Krighaar Rasmussen, Maria Hansen Falkesgaard, Malene Winther, Nikolaj Kulahin Roed, Christine Louise Ander Quistgaard, Marie Nygaard Teisen, Sofie Marie Edslev, David Leander Petersen, Ali Aljubouri, Claus Christensen, Peter Waaben Thulstrup, Leila Lo Leggio, Kaare Teilum and Peter Schledermann Walmod. (2018) NCAM2 Fibronectin type-III domains form a rigid structure that binds and activates the Fibroblast Growth Factor Receptor Scientific Reports 8(2):1-27.


Kristian Kølby Kristensen, Søren Roi Midtgaard, Simon Mysling, Oleg Kovrov, Lars Bo Hansen, Nicholas Skar-Gislinge, Anne P. Beigneux, Birthe Brandt Kragelund, Gunilla Olivecrona, Stephen G. Young, Thomas J. D. Jørgensen, Loren G. Fong and Michael Ploug. (2018) A disordered acidic domain in GPIHBP1 harboring a sulfated tyrosine regulates lipoprotein lipase Proceedings of the National Academy of Sciences of the United States of America 115(26):E6020-E6029.


Kristoffer Enøe Johansson and Jakob R. Winther. (2018) Protein evolution Nature Chemical Biology 14(3):202-204.


Maher M. Kassem, Lars B. Christoffersen, Andrea Cavalli and Kresten Lindorff-Larsen. (2018) Enhancing coevolution-based contact prediction by imposing structural self-consistency of the contacts Scientific Reports 8(5):74-82.


Manoj K. Singh, Sandra Richter, Hauke Beckmann, Marika Kientz, York-Dieter Stierhof, Nadine Anders, Florian Fäßler, Michael Nielsen, Christian Knöll, Alexis Thomann, Mirita Franz-Wachtel, Boris Macek, Karen Skriver, Peter Pimpl and Gerd Jürgens. (2018) A single class of ARF GTPase activated by several pathway-specific ARF-GEFs regulates essential membrane traffic in Arabidopsis PLoS Genetics 14(11):1-36.


Maria Louise Mønster Jørgensen, Babatunde Ekundayo, Mikel Zaratiegui, Karen Skriver, Genevieve Thon and Thomas Schalch. (2018) Structure of the replication regulator Sap1 reveals functionally important interfaces Scientific Reports 8(5):734-746.


Marit Ilves, Sara Vilske, Kukka Aimonen, Hanna K. Lindberg, Saila Pesonen, Irene Wedin, Markus Nuopponen, Esa Vanhala, Casper Højgaard, Jakob R. Winther, Martin Willemoës, Ulla Vogel, Henrik Wolff, Hannu Norppa, Kai Savolainen and Harri Alenius. (2018) Nanofibrillated cellulose causes acute pulmonary inflammation that subsides within a month Nanotoxicology 12(7):729-746.


Michael Askvad Sørensen, Annaleigh Ohrt Fehler and Sine Lo Svenningsen. (2018) Transfer RNA instability as a stress response in Escherichia coli RNA Biology 15:586-593.


Mustapha Carab Hussein Ahmed, Elena Papaleo and Kresten Lindorff-Larsen. (2018) How well do force fields capture the strength of salt bridges in proteins? PeerJ 6(1):19-36, e1-e8.


Paul Santner, Joao Miguel da Silva Martins, Caroline Kampmeyer, Rasmus Hartmann-Petersen, Jonas S. Laursen, Amelie Stein, Christian A Olsen, Isaiah T Arkin, Jakob R. Winther, Martin Willemoës and Kresten Lindorff-Larsen. (2018) Random mutagenesis analysis of the Influenza A M2 proton channel reveals novel resistance mutants Biochemistry 57(41):5957-5968.


Paul Santner, João Miguel da Silva Martins, Jonas S. Laursen, Lars Behrendt, Leise Riber, Christian A Olsen, Isaiah T. Arkin, Jakob R. Winther, Martin Willemoës and Kresten Lindorff-Larsen. (2018) A Robust Proton Flux (pHlux) Assay for Studying the Function and Inhibition of the Influenza A M2 Proton Channel Biochemistry 57(41):5949-5956.


Rasmus Herlo, Viktor K. Lund, Matthew D. Lycas, Anna M. Jansen, George Khelashvili, Rita Chan Andersen, Vikram Bhatia, Thomas S. Pedersen, Pedro B. C. Albornoz, Niklaus Johner, Ina Ammendrup-Johnsen, Nikolaj R. Christensen, Simon Erlendsson, Mikkel Stoklund, Jannik B. Larsen, Harel Weinstein, Ole Kjærulff, Dimitrios Stamou, Ulrik Gether and Kenneth Lindegaard Madsen. (2018) An Amphipathic Helix Directs Cellular Membrane Curvature Sensing and Function of the BAR Domain Protein PICK1 Cell Reports 23(7):2056-2069.


Robert B. Best and Kresten Lindorff-Larsen. (2018) Editorial overview: Theory and simulation: Interpreting experimental data at the molecular level Current Opinion in Structural Biology 49(5):iv-v.


Ryan William Paerl, John Sundh, Demeng Tan, Sine Lo Svenningsen, Samuel Hylander, Jarone Pinhassi, Anders F. Andersson and Lasse Riemann. (2018) Prevalent reliance of bacterioplankton on exogenous vitamin B1 and precursor availability Proceedings of the National Academy of Sciences of the United States of America 115(44):E10447-E10456.


Sandro Bottaro and Kresten Lindorff-Larsen. (2018) Biophysical experiments and biomolecular simulations Science 361(6400):355-360.


Sandro Bottaro, Giovanni Bussi, Scott D. Kennedy, Douglas H. Turner and Kresten Lindorff-Larsen. (2018) Conformational ensembles of RNA oligonucleotides from integrating NMR and molecular simulations Science Advances 4(5):19-36, e1-e8.


Signe Marie Schenstrøm, Caio A. Rebula, Michael H. Tatham, Ruth Hendus-Altenburger, Isabelle Jourdain, Ronald T. Hay, Birthe B. Kragelund and Rasmus Hartmann-Petersen. (2018) Expanded Interactome of the Intrinsically Disordered Protein Dss1 Cell Reports 25(4):862-870.


Sine Lo Svenningsen. (2018) Small RNA-Based Regulation of Bacterial Quorum Sensing and Biofilm Formation Microbiology Spectrum 6(4):337-342.


Thomas Prossliner, Kristoffer Skovbo Winther, Michael Askvad Sørensen and Kenn Gerdes. (2018) Ribosome Hibernation Annual Review of Genetics 52(25):321-348.


Y. Chhabra, H. Y. Wong, Louise Fletcher Nikolajsen, Helena Steinocher, A. Papadopulos, K. A. Tunny, F. A. Meunier, A. G. Smith, Birthe Brandt Kragelund, A. J. Brooks and M. J. Waters. (2018) A growth hormone receptor SNP promotes lung cancer by impairment of SOCS2-mediated degradation Oncogene 37(5):489-501.


Yong Wang, Katrine Østergaard Bugge, Birthe Brandt Kragelund and Kresten Lindorff-Larsen. (2018) Role of protein dynamics in transmembrane receptor signalling Current Opinion in Structural Biology 48(5):74-82.


Yong Wang, Omar Valsson, Pratyush Tiwary, Michele Parrinello and Kresten Lindorff-Larsen. (2018) Frequency adaptive metadynamics for the calculation of rare-event kinetics Journal of Chemical Physics 149(7):1-7.


Yong Wang, Pengfei Tian, Wouter Boomsma and Kresten Lindorff-Larsen. (2018) Monte Carlo Sampling of Protein Folding by Combining an All-Atom Physics-Based Model with a Native State Bias Journal of Physical Chemistry B 122(49):11174-11185.



Alexander Harms, Cinzia Fino, Michael Askvad Sørensen, Szabolcs Semsey and Kenn Gerdes. (2017) Prophages and growth dynamics confound experimental results with antibiotic-tolerant persister cells mBio 8(6):586-593.


Caroline Kampmeyer, Sofie V. Nielsen, Lene Clausen, Amelie Stein, Anne-Marie Axø Gerdes, Kresten Lindorff-Larsen and Rasmus Hartmann-Petersen. (2017) Blocking protein quality control to counter hereditary cancers Genes, Chromosomes & Cancer 56(12):823-831.


Alise J. Ponsero, Aeid Igbaria, Maxwell A. Darch, Samia Miled, Caryn E. Outten, Jakob R. Winther, Gael Palais, Benoit D'Autréaux, Agnès Delaunay-Moisan and Michel B. Toledano. (2017) Endoplasmic reticulum transport of glutathione by Sec61 is regulated by Ero1 and Bip Molecular Cell 67(6):962-973.e5.


Caroline Kampmeyer, Antonina Karakostova, Signe Marie Schenstrøm, Amanda B. Abildgaard, Anne Marie Lauridsen, Isabelle Jourdain and Rasmus Hartmann-Petersen. (2017) The exocyst subunit Sec3 is regulated by a protein quality control pathway Journal of Biological Chemistry 292(37):15240-15253.


Daniel Stiefler-Jensen, Troels Schwarz-Linnet, Casper de Lichtenberg, Tam T. T. N. Nguyen, Kasper Dyrberg Rand, Li Huang, Qunxin She and Kaare Teilum. (2017) The extraordinary thermal stability of EstA from S. islandicus is independent of post translational modifications Protein Science 26(9):1819-1827.


Johan Gotthardt Olsen, Kaare Teilum and Birthe Brandt Kragelund. (2017) Behaviour of intrinsically disordered proteins in protein-protein complexes with an emphasis on fuzziness Cellular and Molecular Life Sciences 74(17):3175-3183.


Li He, Helena Steinocher, Ashish Shelar, Emily B. Cohen, Erin N. Heim, Birthe Brandt Kragelund, Gevorg Grigoryan and Daniel DiMaio. (2017) Single methyl groups can act as toggle switches to specify transmembrane protein-protein interactions eLife 6(26):E6020-E6029.


Magnus Kjærgaard and Birthe Brandt Kragelund. (2017) Functions of intrinsic disorder in transmembrane proteins Cellular and Molecular Life Sciences 74(17):3205-3224.


Penny von Wettstein. (2017) The polyketide components of waxes and the Cer-cqu gene cluster encoding a novel polyketide synthase, the ß-diketone synthase, DKS Plants 6(3):811-827.


Ruth Hendus-Altenburger, Matteo Lambrughi, Thilde Bagger Terkelsen, Stine Helene Falsig Pedersen, Elena Papaleo, Kresten Lindorff-Larsen and Birthe Brandt Kragelund. (2017) A phosphorylation-motif for tuneable helix stabilisation in intrinsically disordered proteins - Lessons from the sodium proton exchanger 1 (NHE1) Cellular Signalling 37(9):40-51.


Yong Wang, João Martins and Kresten Lindorff-Larsen. (2017) Biomolecular conformational changes and ligand binding Chemical Science 8(9):6466-6473.


Farah Deeba, Tasawar Sultana, Tariq Mahmood, Charlotte O'Shea, Karen Skriver and S. M. Saqlan Naqvi. (2017) Involvement of WRKY, MYB and DOF DNA-binding proteins in interaction with a rice germin-like protein gene promoter Acta Physiologiae Plantarum 39(11):1-36.


Mads Nygaard, Birthe Brandt Kragelund, Elena Papaleo and Kresten Lindorff-Larsen. (2017) An efficient method for estimating the hydrodynamic radius of disordered protein conformations Biophysical Journal 113(3):550-557.


Sandra Muschiol, Simon Erlendsson, Marie-Stephanie Aschtgen, Vitor Oliveira, Peter Schmieder, Casper de Lichtenberg, Kaare Teilum, Thomas Boesen, Umit Akbey and Birgitta Henriques-Normark. (2017) Structure of the competence pilus major pilin ComGC in Streptococcus pneumoniae Journal of Biological Chemistry 292(34):14134-14146.


Thomas Søndergaard Stenum, Michael Askvad Sørensen and Sine Lo Svenningsen. (2017) Quantification of the abundance and charging levels of transfer RNAs in Escherichia coli Journal of Visualized Experiments 126:586-593.


Lasse Staby, Charlotte O'Shea, Martin Willemoës, Frederik Theisen, Birthe Brandt Kragelund and Karen Skriver. (2017) Eukaryotic transcription factors Biochemical Journal 474(15):2509-2532.


Sandro Bottaro and Kresten Lindorff-Larsen. (2017) Mapping the universe of RNA tetraloop folds Biophysical Journal 113(2):257-267.


Vaibhhav Sinha, Akshit Goyal, Sine Lo Svenningsen, Szabolcs Semsey and Sandeep Krishna. (2017) In silico evolution of lysis-lysogeny strategies reproduces observed lysogeny propensities in temperate bacteriophages Frontiers in Microbiology 8:586-593.


E.C. dos Santos, Z. Rozynek, E.L. Hansen, Rasmus Hartmann-Petersen, R.N. Klitgaard, Anders Løbner-Olesen, L. Michels, A. Mikkelsen, Heloisa Nunes Bordallo and J.O. Fossum. (2017) Ciprofloxacin intercalated in fluorohectorite clay R S C Advances 7(43):26537-26545.


Line V. Kristensen, Felix S. Oppermann, Matthias J. Rauen, Rasmus Hartmann-Petersen and Kenneth Thirstrup. (2017) Polyglutamine expansion of ataxin-3 alters its degree of ubiquitination and phosphorylation at specific sites Neurochemistry International 105(43):42-50.


Mark K Nøhr, Natalia Bobba, Bjørn Richelsen, Sten Lund and Steen B Pedersen. (2017) Inflammation Downregulates UCP1 Expression in Brown Adipocytes Potentially via SIRT1 and DBC1 Interaction International Journal of Molecular Sciences (CD-ROM) 18(5):1088-1097.


Oliver Fleck, Ulrik Fahnøe, Katrine Vyff Løvschal, Marie-Fabrice Uwamahoro Gasasira, Irina Nikolaeva Marinova, Birthe Brandt Kragelund, Antony M. Carr, Edgar Hartsuiker, Christian Holmberg and Olaf Nielsen. (2017) Deoxynucleoside salvage in fission yeast allows rescue of ribonucleotide reductase deficiency but not Spd1-mediated inhibition of replication Genes 8(5):2509-2532.


Sirke Virkkunen, Henrik Wolff, Caj Haglund, Casper Højgaard, Jakob R. Winther, Martin Willemoës, Ulla Vogel and Jaana Hagström. (2017) Positive staining for cellulose in oral pulse granuloma Oral Surgery, Oral Medicine, Oral Pathology and Oral Radiology 123(4):464-467.


Sofie V, Nielsen, Amelie Stein, Alexander B. Dinitzen, Elena Papaleo, Michael H. Tatham, Esben Guldahl Poulsen, Maher Mahmoud Kassem, Lene Juel Rasmussen, Kresten Lindorff-Larsen and Rasmus Hartmann-Petersen. (2017) Predicting the impact of Lynch syndrome-causing missense mutations from structural calculations PLoS Genetics 13(4):42-50.


Bjarne Hove-Jensen, Kasper R. Andersen, Mogens Kilstrup, Jan Martinussen, Robert L. Switzer and Martin Willemoës. (2017) Phosphoribosyl diphosphate (PRPP) Microbiology and Molecular Biology Reviews 81(1):464-467.


Kaare Teilum, Micha Ben Achim Kunze, Simon Erlendsson and Birthe Brandt Kragelund. (2017) (S)Pinning down protein interactions by NMR Protein Science 26(3):436-451.


Mette Eriksen, Kim Sneppen, Steen Pedersen and Namiko Mitarai. (2017) Occlusion of the ribosome binding site connects the translational initiation frequency, mRNA stability and premature transcription termination Frontiers in Microbiology 8(5):1088-1097.


Thu Phuong Tran, Christian Ørnbøl Larsen, Tobias Røndbjerg, Martina de Foresta, Micha Ben Achim Kunze, Ales Marek, Jacob Hartvig Løper, Lotte-Emilie Boyhus, Astrid Knuhtsen, Kresten Lindorff-Larsen and Daniel Sejer Pedersen. (2017) Diversity-oriented peptide stapling Chemistry: A European Journal 23(14):3490-3495.


Tina Mostrup Kousted, Otto Kalliokoski, Sofie Kjellerup Christensen, Jakob R. Winther and Jann Hau. (2017) Exploring the antigenic response to multiplexed immunizations in a chicken model of antibody production Heliyon 3(3):464-467.


Heike Ilona Rösner, Martina Caldarini, Andreas Prestel, Maria Antonietta Vanoni, Ricardo Americo Broglia, Alessandro Aliverti, Guido Tiana and Birthe Brandt Kragelund. (2017) Cold denaturation of the HIV-1 protease monomer Biochemistry 56(8):1029-1032.


Meng S. Choy, Yang Li, Luciana E. S. F. Machado, Micha Ben Achim Kunze, Christopher R. Connors, Xingyu Wei, Kresten Lindorff-Larsen, Rebecca Page and Wolfgang Peti. (2017) Conformational rigidity and protein dynamics at distinct timescales regulate PTP1B activity and allostery Molecular Cell 65(4):644-658.


Charlotte O'Shea, Lasse Staby, Sidsel Krogh Bendsen, Frederik Grønbæk Tidemand, Andreas Redsted, Martin Willemoës, Birthe Brandt Kragelund and Karen Skriver. (2017) Structures and short linear motif of disordered transcription factor regions provide clues to the interactome of the cellular hub radical-induced cell death1 Journal of Biological Chemistry 292(2):512-527.


Esben Guldahl Poulsen, Caroline Kampmeyer, Franziska Kriegenburg, Jens Vilstrup Johansen, Kay Hofmann, Christian Holmberg and Rasmus Hartmann-Petersen. (2017) UBL/BAG-domain co-chaperones cause cellular stress upon overexpression through constitutive activation of Hsf1 Cell Stress & Chaperones 22(1):143-154.


Julia Catalán, Elina Rydman, Kukka Aimonen, Kati-Susanna Hannukainen, Satu Suhonen, Esa Vanhala, Carlos Moreno, Valérie Meyer, Denilson da Silva Perez, Asko Sneck, Ulla Forsström, Casper Højgaard, Martin Willemoës, Jacob R. Winther, Ulla Vogel, Henrik Wolff, Harri Alenius, Kai M. Savolainen and Hannu Norppa. (2017) Genotoxic and inflammatory effects of nanofibrillated cellulose in murine lungs Mutagenesis 32(1):23-31.


Sine Lo Svenningsen, Mette Kongstad, Thomas Søndergaard Stenum, Ana Josefa Muñoz Gomez and Michael Askvad Sørensen. (2017) Transfer RNA is highly unstable during early amino acid starvation in Escherichia coli Nucleic Acids Research 45(2):793-804.


Arun Kumar Somavarapu, Fei Shen, Kaare Teilum, Jingdong Zhang, Susanne Mossin, Peter W. Thulstrup, Morten J. Bjerrum, Manish K. Tiwari, Daniel Szunyogh, Peter M. Søtofte, Kasper P. Kepp and Lars Hemmingsen. (2017) The Pathogenic A2V Mutant Exhibits Distinct Aggregation Kinetics, Metal Site Structure, and Metal Exchange of the Cu2+-Aß Complex Chemistry - A European Journal 23(55):13591-13595.


Birthe Brandt Kragelund. (2017) Choreography by Structural Disorder in Membrane Proteins Biophysical Society. Annual Meeting. Abstracts 112:12A.


Helena Steinocher, Katrine Østergaard Bugge, Louise Fletcher Nikolajsen, Kresten Lindorff-Larsen, Andrew Brooks and Birthe Brandt Kragelund. (2017) Class I Cytokine Receptors Biophysical Society. Annual Meeting. Abstracts 112:171A.


Lucia Marri, Anita M. Jansson, Caspar Elo Christensen and Ole Hindsgaul. (2017) An enzyme-linked immunosorbent assay for the detection of diacetyl (2,3-butanedione) Analytical Biochemistry 535(230):12-18.


Lucia Marri, Anita M. Jansson, Caspar Elo Christensen and Ole Hindsgaul. (2017) Synthesis of 1,2-phenylenediamine capturing molecule for the detection of diacetyl Data in Brief 15(230):483-490.


Simon Erlendsson, Kamil Gotfryd, Flemming Hofmann Larsen, Jonas Sigurd Mortensen, Michel-Andreas Geiger, Barth-Jan van Rossum, Hartmut Oschkinat, Ulrik Gether, Kaare Teilum and Claus Juul Løland. (2017) Direct assessment of substrate binding to the Neurotransmitter:Sodium Symporter LeuT by solid state NMR eLife 6(3):436-451.


Troels Rahbek-Clemmensen, Matthew D. Lycas, Simon Erlendsson, Jacob Eriksen, Mia Apuschkin, Frederik Vilhardt, Trine N. Jorgensen, Freja H. Hansen and Ulrik Gether. (2017) Super-resolution microscopy reveals functional organization of dopamine transporters into cholesterol and neuronal activity-dependent nanodomains Nature Communications 8(3):436-451.


Wouter Krogh Boomsma and Jes Frellsen. (2017) Spherical convolutions and their application in molecular modelling Neural Information Processing Systems 2017 122(49):11174-11185.



Katrine Østergaard Bugge, Kresten Lindorff-Larsen and Birthe Brandt Kragelund. (2016) Understanding single-pass transmembrane receptor signaling from a structural viewpoint—what are we missing? The F E B S Journal 283(24):4424-4451.


Chengzhe Tian, Mohammad Roghanian, Mikkel Girke Jørgensen, Kim Sneppen, Michael Askvad Sørensen, Kenn Gerdes and Namiko Mitarai. (2016) Rapid Curtailing of the Stringent Response by Toxin-Antitoxin Encoded mRNases Journal of Bacteriology 198(14):1918-1926.


Lars Ellgaard, Nicholas McCaul, Anna Chatsisvili and Ineke Braakman. (2016) Co- and post-translational protein folding in the ER Traffic (Malden) 17(6):615-638.


Birthe Brandt Kragelund, Eric Weterings, Rasmus Hartmann-Petersen and Guido Keijzers. (2016) The Ku70/80 ring in Non-Homologous End-Joining Frontiers in Bioscience 21(3):514-527.


Birthe Brandt Kragelund, Signe Marie Schenstrøm, Caio A. Rebula, Vikram Govind Panse and Rasmus Hartmann-Petersen. (2016) DSS1/Sem1, a multifunctional and intrinsically disordered protein Trends in Biochemical Sciences 41(5):446-459.


Casper Højgaard, Christian Kofoed, Roall Espersen, Kristoffer Enøe Johansson, Mara Villa, Martin Willemoës, Kresten Lindorff-Larsen, Kaare Teilum and Jakob R. Winther. (2016) A soluble, folded protein without charged amino acid residues Biochemistry 55(28):3949–3956.


Casper Wilkens, Susan Andersen, Bent O. Petersen, An Li, Marta Busse-Wicher, Johnny Birch, Darrell Cockburn, Hiroyuki Nakai, Hans Erik Mølager Christensen, Birthe Brandt Kragelund, Paul Dupree, Barry McCleary, Ole Hindsgaul, Maher Abou Hachem and Birte Svensson. (2016) An efficient arabinoxylan-debranching a-L-arabinofuranosidase of family GH62 from Aspergillus nidulans contains a secondary carbohydrate binding site Applied Microbiology and Biotechnology 100(14):6265-6277.


Ditte H. Welner, Farah Deeba, Leila Lo Leggio and Karen Skriver. (2016) NAC transcription factors Plant transcription factors 67(17):5259-5273.


Elena Pedraz Cuesta, Jacob Fredsted, Helene H. Jensen, Annika Bornebusch, Lene N. Nejsum, Birthe Brandt Kragelund and Stine Helene Falsig Pedersen. (2016) Prolactin signaling stimulates invasion via Na+/H+ exchanger NHE1 in T47D human breast cancer cells Molecular Endocrinology 30(7):693-708.


Esben Guldahl Poulsen, Sofie V. Nielsen, Elin J. Pietras, Jens Vilstrup Johansen, Cornelia Steinhauer and Rasmus Hartmann-Petersen. (2016) High-throughput siRNA screening applied to the ubiquitin-proteasome system Proteostasis 4(3):514-527.


Helena Safavi-Hemami, Qing Li, Ronneshia L. Jackson, Albert S. Song, Wouter Krogh Boomsma, Pradip K. Bandyopadhyay, Christian W. Gruber, Anthony W. Purcell, Mark Yandell, Baldomero M. Olivera and Lars Ellgaard. (2016) Rapid expansion of the protein disulfide isomerase gene family facilitates the folding of venom peptides Proceedings of the National Academy of Sciences of the United States of America 113(12):3227-3232.


Jeppe Trudslev Pedersen, Serene W. Chen, Christian Bernsen Borg, Samuel Ness, Justyna M. Bahl, Niels H. H. Heegard, Christopher M. Dobson, Lars Bo Stegeager Hemmingsen, Nunilo Cremades and Kaare Teilum. (2016) Amyloid-ß and a-synuclein decrease the level of metal-catalyzed reactive oxygen species by radical scavenging and redox silencing Journal of the American Chemical Society 138(12):3966-3969.


Katrine Østergaard Bugge, Elena Papaleo, Gitte Wolfsberg Haxholm, Jonathan T.S. Hopper, Carol V. Robinson, Johan Gotthardt Olsen, Kresten Lindorff-Larsen and Birthe Brandt Kragelund. (2016) A combined computational and structural model of the full-length human prolactin receptor Nature Communications 7(21):4361-4377.


Kresten Lindorff-Larsen, Paul Maragakis, Stefano Piana and David E Shaw. (2016) Picosecond to Millisecond Structural Dynamics in Human Ubiquitin Journal of Physical Chemistry B 120(33):8313-8320.


Kristoffer Enøe Johansson, Nicolai Tidemand Johansen, Signe Christensen, Scott Horowitz, James C. A. Bardwell, Johan Gotthardt Olsen, Martin Willemoës, Kresten Lindorff-Larsen, Jesper Ferkinghoff-Borg, Thomas Wim Hamelryck and Jakob R. Winther. (2016) Computational redesign of thioredoxin is hypersensitive towards minor conformational changes in the backbone template Journal of Molecular Biology 428(21):4361-4377.


Lizette Marais Schneider, Nikolai M. Adamski, Caspar Elo Christensen, David B. Stuart, Sonia Vautrin, Mats Hansson, Cristobal Uauy and Penny von Wettstein. (2016) The Cer-cqu gene cluster determines three key players in a ß-diketone synthase polyketide pathway synthesizing aliphatics in epicuticular waxes Journal of Experimental Botany 67(9):2715-2730.


Lubomir Dimitrov Antonov, S. Olsson, Wouter Krogh Boomsma and Thomas Wim Hamelryck. (2016) Bayesian inference of protein ensembles from SAXS data Physical Chemistry Chemical Physics 18(8):5832-5838.


Maher Mahmoud Kassem, Yong Wang, Wouter Krogh Boomsma and Kresten Lindorff-Larsen. (2016) Structure of the bacterial cytoskeleton protein bactofilin by NMR chemical shifts and sequence variation Biophysical Journal 110(11):2342-2348.


Michael W. Christiansen, Colette Matthewman, Dagmara Agata Podzimska-Sroka, Charlotte O'Shea, Søren Lindemose, Niels Erik Møllegaard, Inger Bæksted Holme, Kim Hebelstrup, Karen Skriver and Per L. Gregersen. (2016) Barley plants over-expressing the NAC transcription factor gene HvNAC005 show stunting and delay in development combined with early senescence Journal of Experimental Botany 67(17):5259-5273.


Michael May, Karen Skriver and Gert Dandanell. (2016) Towards a cognitive semiotics of science Meaning, mind and communication 67(17):5259-5273.


Nicholas Peter Schafer, Ha H. Truong, Daniel E. Otzen, Kresten Lindorff-Larsen and Peter G. Wolynes. (2016) Topological constraints and modular structure in the folding and functional motions of GlpG, an intramembrane protease Proceedings of the National Academy of Sciences of the United States of America 113(8):2098-2103.


Pengfei Tian, Kresten Lindorff-Larsen, Wouter Krogh Boomsma, Mogens Hogh Jensen and Daniel Erik Otzen. (2016) A Monte Carlo study of the early steps of functional amyloid formation P L o S One 11(1):2342-2348.


Richard T. Timms, Sam A. Menzies, Iva A. Tchasovnikarova, Lea Cecilie Christensen, James C. Williamson, Robin Antrobus, Gordon Dougan, Lars Ellgaard and Paul J. Lehner. (2016) Genetic dissection of mammalian ERAD through comparative haploid and CRISPR forward genetic screens Nature Communications 7(6):615-638.


Ruth Hendus-Altenburger, Elena Pedraz Cuesta, Christina Wilkens Olesen, Elena Papaleo, Jeff Alexander Schnell, Jonathan T. S. Hopper, Carol V. Robinson, Stine Helene Falsig Pedersen and Birthe Brandt Kragelund. (2016) The human Na+/H+ exchanger 1 is a membrane scaffold protein for extracellular signal-regulated kinase 2 BMC Biology 14(7):693-708.


Troels Schwarz-Linnet and Kaare Teilum. (2016) Non-uniform sampling of NMR relaxation data Journal of Biomolecular N M R 64(2):165-173.


Wouter Krogh Boomsma, Sofie Vincents Nielsen, Kresten Lindorff-Larsen, Rasmus Hartmann-Petersen and Lars Ellgaard. (2016) Bioinformatics analysis identifies several intrinsically disordered human E3 ubiquitin-protein ligases PeerJ 4(49):11174-11185.


Yong Wang, Elena Papaleo and Kresten Lindorff-Larsen. (2016) Mapping transiently formed and sparsely populated conformations on a complex energy landscape eLife 5(24):4424-4451.



Simon Erlendsson and Kenneth Lindegaard Madsen. (2015) Membrane Binding and Modulation of the PDZ Domain of PICK1 Membranes 5(4):597-615.


Szabolcs Semsey, Christopher Campion, Abdu Mohamed and Sine Lo Svenningsen. (2015) How long can bacteriophage ? change its mind? Bacteriophage 5(1):e1012930.


Morten L. Karlsen, Thor S. Thorsen, Niklaus Johner, Ina Ammendrup-Johnsen, Simon Erlendsson, Xinsheng Tian, Jens B. Simonsen, Rasmus Hoiberg-Nielsen, Nikolaj M. Christensen, George Khelashvili, Werner Streicher, Kaare Teilum, Bente Vestergaard, Harel Weinstein, Ulrik Gether, Lise Arleth and Kenneth L. Madsen. (2015) Structure of dimeric and tetrameric complexes of the BAR domain protein PICK1 determined by small-angle X-Ray scattering Structure 23(7):1258-1270.


Sabine Hansen, Sandeep Krishna, Szabolcs Semsey and Sine Lo Svenningsen. (2015) Effects of Four Different Regulatory Mechanisms on the Dynamics of Gene Regulatory Cascades Scientific Reports 5(1):e1012930.


Karen Skriver, Gert Dandanell, Jakob Hjorth von Stemann and Michael May. (2015) Udfordringer ved undervisning i enzymer MONA - Matematik- og Naturfagsdidaktik 2015(1):49-65.


Charlotte O'Shea, Mikael Kryger Jensen, Emil G.P. Stender, Birthe Brandt Kragelund, Martin Willemoës and Karen Skriver. (2015) Protein intrinsic disorder in Arabidopsis NAC transcription factors Biochemical Journal 465(2):281-294.


Chi Zhang, Ibtissem Cherifi, Mads Nygaard, Gitte Wolfsberg Haxholm, Roman L. Bogorad, Marie Bernadet, Patrick England, Isabelle Broutin, Birthe Brandt Kragelund, Jacques-Emmanuel Guidotti and Vincent Goffin. (2015) Residue 146 regulates prolactin receptor folding, basal activity and ligand-responsiveness Molecular and Cellular Endocrinology 401(3):173-188.


Chi Zhang, Mads Nygaard, Gitte Wolfsberg Haxholm, Florence Boutillon, Marie Bernadet, Sylviane Hoos, Patrick England, Isabelle Broutin, Birthe Brandt Kragelund and Vincent Goffin. (2015) A residue quartet in the extracellular domain of the prolactin receptor selectively controls mitogen-activated protein kinase signaling Journal of Biological Chemistry 290(19):11890-11904.


Christian Berg Oehlenschlæger, Monika Nøhr Løvgreen, Eva Reinauer, Emilia Lehtinen, Marie-Louise Lindberg Pind, Pernille Harris, Jan Martinussen and Martin Willemoës. (2015) Bacillus halodurans strain C125 encodes and synthesizes enzymes from both known pathways to form dUMP directly from Cytosine Deoxyribonucleotides Applied and Environmental Microbiology 81(10):3395-3404.


Dagmara Podzimska-Sroka, Charlotte O'Shea, Per L. Gregersen and Karen Skriver. (2015) NAC transcription factors in senescence Plants 4(3):412-448.


Demeng Tan, Sine Lo Svenningsen and Mathias Middelboe. (2015) Quorum sensing determines the choice of antiphage defense strategy in Vibrio anguillarum mBio 6(3):e1012930.


Dennis Hansen, Helen Webb, Jonas Willum Nielsen, Pernille Harris, Jakob R. Winther and Martin Willemoës. (2015) Mutational analysis of divalent metal ion binding in the active site of class II a-mannosidase from Sulfolobus solfataricus Biochemistry 54(11):2032-2039.


Emil G. Stender, Charlotte O'Shea and Karen Skriver. (2015) Subgroup-specific intrinsic disorder profiles of arabidopsis NAC transcription factors Plant Signalling & Behavior 10(6):412-448.


Fernando Martin-García, Elena Papaleo, Paulino Gomez-Puertas, Wouter Krogh Boomsma and Kresten Lindorff-Larsen. (2015) Comparing molecular dynamics force fields in the essential subspace PLoS ONE 10(3):227a.


Gitte Wolfsberg Haxholm, Louise Fletcher Nikolajsen, Johan Gotthardt Olsen, Jacob Fredsted, Flemming Hofmann Larsen, Vincent Goffin, Stine Helene Falsig Pedersen, Andrew J Brooks, Michael J Waters and Birthe Brandt Kragelund. (2015) Intrinsically disordered cytoplasmic domains of two cytokine receptors mediate conserved interactions with membranes Biochemical Journal 468(3):495-506.


Helena Safavi-Hemami, Joanna Gajewiak, Santhosh Karanth, Samuel D. Robinson, Beatrix Ueberheide, Adam D. Douglass, Amnon Schlegel, Julita S. Imperial, Maren Watkins, Pradip K. Bandyopadhyay, Mark Yandell, Qing Li, Anthony W. Purcell, Raymond S. Norton, Lars Ellgaard and Baldomero M. Olivera. (2015) Specialized insulin is used for chemical warfare by fish-hunting cone snails Proceedings of the National Academy of Sciences of the United States of America 112(6):1743-1748.


Irene Gonzalez-Thuillier, Monica Venegas-Caleron, Rafael Garces, Penny von Wettstein and Enrique Martinez-Force. (2015) Sunflower (Helianthus annuus) fatty acid synthase complex Planta 241(1):43-56.


Irina Nikolaeva Marinova, Jacob Engelbrecht, Adrian Ewald, Lasse L. Langholm, Christian Henrik Holmberg, Birthe Brandt Kragelund, Colin Gordon, Olaf Nielsen and Rasmus Hartmann-Petersen. (2015) Single site suppressors of a fission yeast temperature-sensitive mutant in cdc48 identified by whole genome sequencing P L o S One 10(2):21141-21153.


Jeppe Trudslev Pedersen, Christian Bernsen Borg, Thomas C. T. Michaels, Tuomas P. J. Knowles, Peter Faller, Kaare Teilum and Lars Bo Stegeager Hemmingsen. (2015) Aggregation prone amyloid-߷CuII Species formed on the millisecond timescale at mildly acidic conditions ChemBioChem 16(9):1293-1297.


Katrine Østergaard Bugge, Helena Steinocher, Andrew J. Brooks, Kresten Lindorff-Larsen and Birthe Brandt Kragelund. (2015) Exploiting hydrophobicity for efficient production of transmembrane helices for structure determination by NMR spectroscopy Analytical Chemistry 87(18):9126–9131.


Kristina Bram Knudsen, Christian Kofoed, Roall Espersen, Casper Højgaard, Jakob R. Winther, Martin Willemoës, Irene Wedin, Markus Nuopponen, Sara Vilske, Kukka Aimonen, Ingrid Elise Konow Weydahl, Harri Alenius, Hannu Norppa, Henrik Wolff, Erik Håkan Richard Wallin and Ulla Vogel. (2015) Visualization of nanofibrillar cellulose in biological tissues using a biotinylated carbohydrate binding module of ß-1,4-Glycanase Chemical Research in Toxicology 28(8):1627-1635.


Kaare Teilum, Johan Gotthardt Olsen and Birthe Brandt Kragelund. (2015) Globular and disordered-the non-identical twins in protein-protein interactions Frontiers in Bioscience 2(7):1258-1270.


Leila Malik, Jesper Nygård, Niels Johan Christensen, Charlotte Stahl Madsen, Heike Ilona Rösner, Birthe Brandt Kragelund, Rasmus Høiberg-Nielsen, Werner Streicher, Lise Arleth, Peter Waaben Thulstrup and Knud Jørgen Jensen. (2015) A de novo designed monomeric, compact three helix bundle protein on a carbohydrate template ChemBioChem 16(13):1905-1918.


Lorenzo Sborgi, Abhinav Verma, Stefano Piana, Kresten Lindorff-Larsen, Michele Cerminara, Clara M. Santiveri, David E. Shaw, Eva De Alba and Victor Muñoz. (2015) Interaction networks in protein folding via atomic-resolution experiments and long-time-scale molecular dynamics simulations Journal of the American Chemical Society 137(20):6506-6516.


Matteo Tiberti, Elena Papaleo, Tone Bengtsen, Wouter Krogh Boomsma and Kresten Lindorff-Larsen. (2015) ENCORE PloS Computational Biology 11(10):227a.


Mohsin M Naqvi, Pétur Orri Heiðarsson, Mariela R Otazo, Alessandro Mossa, Birthe Brandt Kragelund and Ciro Cecconi. (2015) Single-molecule folding mechanisms of the apo- and Mg2+-bound states of human neuronal calcium sensor-1 Biophysical Journal 109(1):113-123.


Pengfei Tian, Wouter Krogh Boomsma, Yong Wang, Daniel Erik Otzen, Mogens Høgh Jensen and Kresten Lindorff-Larsen. (2015) What does evolution tell us about the structure of a functional amyloid protein? Biophysical Journal 108:227a.


Pengfei Tian, Wouter Krogh Boomsma, Yong Wang, Daniel Otzen, Mogens Høgh Jensen and Kresten Lindorff-Larsen. (2015) Structure of a functional amyloid protein subunit computed using sequence variation Journal of the American Chemical Society 137(1):22–25.


Simon Erlendsson, Lise Arleth and Kenneth Lindegaard Madsen. (2015) Response to the challenges of Polydisperse SAXS data analysis Structure 23(11):1969-1970.


Sophie R Beeren, Caspar Elo Christensen, Hidenori Tanaka, Morten G. Jensen, Iain Donaldson and Ole Hindsgaul. (2015) Direct study of fluorescently-labelled barley ß-glucan fate in an in vitro human colon digestion model Carbohydrate Polymers 115(9):88-92.


Søs Grønbæk Mathiassen, Ida B. Larsen, Esben Guldahl Poulsen, Christian Toft Madsen, Elena Papaleo, Kresten Lindorff-Larsen, Birthe Brandt Kragelund, Michael Lund Nielsen, Franziska Kriegenburg and Rasmus Hartmann-Petersen. (2015) A two-step protein quality control pathway for a misfolded DJ-1 variant in fission yeast The Journal of Biological Chemistry 290(34):21141-21153.


Thomas Wim Hamelryck, Wouter Krogh Boomsma, Jesper Ferkinghoff-Borg, Jesper Illemann Foldager, Jes Frellsen, John Haslett and Douglas Theobald. (2015) Proteins, physics and probability kinematics Geometry driven statistics 113(12):3227-3232.


Yang Guo, Birthe Brandt Kragelund, Malcolm F. White and Xu Peng. (2015) Functional characterization of a conserved archaeal viral operon revealing single-stranded DNA binding, annealing and nuclease activities Journal of Molecular Biology 427(12):2179-2191.



Caspar Elo Christensen, Magnus Karlsson, Jakob R. Winther, Pernille Rose Jensen and Mathilde H. Lerche. (2014) Non-invasive in-cell determination of free cytosolic [NAD+]/[NADH] ratios using hyperpolarized glucose show large variations in metabolic phenotypes The Journal of Biological Chemistry 289(4):2344-2352.


Darrell Cockburn, Casper Wilkens, Christian Ruzanski, Susan Andersen, Jonas Willum Nielsen, Alison M. Smith, Robert A. Field, Martin Willemoës, Maher Abou Hachem and Birte Svensson. (2014) Analysis of surface binding sites (SBSs) in carbohydrate active enzymes with focus on glycoside hydrolase families 13 and 77 - a mini-review Biologia 69(6):705-712.


Elena Papaleo, Ludovico Sutto, Francesco Luigi Gervasio and Kresten Lindorff-Larsen. (2014) Conformational changes and free energies in a Proline isomerase Journal of Chemical Theory and Computation 10(9):4169-4174.


Franziska Kriegenburg, Visnja Jakopec, Esben Guldahl Poulsen, Sofie Vincents Nielsen, Assen Roguev, Nevan Krogan, Colin Gordon, Ursula Fleig and Rasmus Hartmann-Petersen. (2014) A chaperone-assisted degradation pathway targets kinetochore proteins to ensure genome stability P L o S Genetics 10(1):21141-21153.


Gaetano Invernizzi, Matteo Tiberti, Matteo Lambrughi, Kresten Lindorff-Larsen and Elena Papaleo. (2014) Communication routes in ARID domains between distal residues in Helix 5 and the DNA-binding loops P L o S Computational Biology (Online) 10(9):4169-4174.


Henning Gram Hansen, Cecilie Lützen Søltoft, Jonas Damgård Schmidt, Julia Birk, Christian Appenzeller-Herzog and Lars Ellgaard. (2014) Biochemical evidence that regulation of Ero1ß activity in human cells does not involve the isoform-specific cysteine 262 Bioscience Reports 34(2):106-116.


Jakob R. Winther and Colin Thorpe. (2014) Quantification of thiols and disulfides BBA General Subjects 1840(2):838-846.


Jan Halborg Jensen, Martin Willemoës, Jakob R. Winther and Luca De Vico. (2014) In Silico prediction of mutant HIV-1 proteases cleaving a target sequence P L o S One 9(5):281-294.


Jan Valentin, Christian Andreetta, Wouter Krogh Boomsma, Sandro Bottaro, Jesper Ferkinghoff-Borg, Jes Frellsen, Kanti V. Mardia, Pengfei Tian and Thomas Wim Hamelryck. (2014) Formulation of probabilistic models of protein structure in atomic detail using the reference ratio method Proteins: Structure, Function, and Bioinformatics 82(2):288-299.


Jeppe Trudslev Pedersen, Christian B. Borg, Kaare Teilum and Lars Bo Stegeager Hemmingsen. (2014) pH dependence of amyloid-ß-Cu(II) binding and oligomerization kinetics Journal of Biological Inorganic Chemistry 19:S755.


Jitka Petrlova, Arnab Bhattacherjee, Wouter Krogh Boomsma, Stefan Wallin, Jens O. Lagerstedt and Anders Irbäck. (2014) Conformational and aggregation properties of the 1-93 fragment of apolipoprotein A-I Protein Science 23(11):1559-1571.


Johan Gotthardt Olsen and Birthe Brandt Kragelund. (2014) Who climbs the tryptophan ladder? On the structure and function of the WSXWS motif in cytokine receptors and thrombospondin repeats Cytokine & Growth Factor Reviews 25(3):337-341.


Konstantinos Paraskevopoulos, Franziska Kriegenburg, Michael H. Tatham, Heike Ilona Rösner, Bethan Medina, Ida B. Larsen, Rikke Brandstrup, Kevin G. Hardwick, Ronald T. Hay, Birthe Brandt Kragelund, Rasmus Hartmann-Petersen and Colin Gordon. (2014) Dss1 is a 26S proteasome ubiquitin receptor Molecular Cell 56(3):453-461.


Kristine Steen Jensen, Jeppe Trudslev Pedersen, Jakob R. Winther and Kaare Teilum. (2014) The pKa value and accessibility of cysteine residues are key determinants for protein substrate discrimination by glutaredoxin Biochemistry 53(15):2533-2540.


Lars Behrendt, Jeppe Lund Nielsen, Søren Johannes Sørensen, Anthony W. D. Larkum, Jakob R. Winther and Michael Kühl. (2014) Rapid TaqMan-based quantification of chlorophyll d-containing cyanobacteria in the genus Acaryochloris Applied and Environmental Microbiology 80(10):3244-3249.


Louise Madsen, Karen Molbæk Hansen, Ida B. Larsen, Sofie V. Nielsen, Esben Guldahl Poulsen, Peter Schledermann Walmod, Kay Hofmann, Michael Seeger, Chen-Ying Chien, Rey-Huei Chen, Franziska Kriegenburg and Rasmus Hartmann-Petersen. (2014) Human ASPL/TUG interacts with p97 and complements the proteasome mislocalization of a yeast ubx4 mutant, but not the ER-associated degradation defect B M C Cell Biology 15(3):453-461.


Marie Bøjstrup, Caspar Elo Christensen, Michael Skovbo Windahl, Anette Henriksen and Ole Hindsgaul. (2014) A chromogenic assay for limit dextrinase and pullulanase activity Analytical Biochemistry 449(9):45-51.


Michael Henrik Hagemann-Jensen, Franziska Katharina Uhlenbrock, Stephanie Kehlet, Lars Andresen, Charlotte Gabel-Jensen, Lars Ellgaard, Bente Gammelgaard and Søren Skov. (2014) The selenium metabolite methylselenol regulates the expression of ligands that trigger immune activation through the lymphocyte receptor NKG2D The Journal of Biological Chemistry 289(6):31576-31590.


Michael Krogh Jensen and Karen Skriver. (2014) NAC transcription factor gene regulatory and protein-protein interaction networks in plant stress responses and senescence I U B M B Life 66(3):156-166.


Michael Riis Hansen, Eric W. Barr, Kaj Frank Jensen, Martin Willemoës, Charles Grubmeyer and Jakob R. Winther. (2014) Catalytic site interactions in yeast OMP synthase Archives of Biochemistry and Biophysics 542(6):28-38.


Pengfei Tian, Sigurður Ægir Jónsson, Jesper Ferkinghoff-Borg, Sergei V . Krivov, Kresten Lindorff-Larsen, Anders Irbäck and Wouter Krogh Boomsma. (2014) Robust estimation of diffusion-optimized ensembles for enhanced sampling Journal of Chemical Theory and Computation 10(2):543–553.


Pétur Orri Heiðarsson, Mohsin M. Naqvi, Mariela R. Otazo, Alessandro Mossa, Birthe Brandt Kragelund and Ciro Cecconi. (2014) Direct single-molecule observation of calcium-dependent misfolding in human neuronal calcium sensor-1 Proceedings of the National Academy of Sciences U.S.A. 111(36):13069-13074.


Rasmus Vejrup-Hansen, Oliver Fleck, Katrine Landvad, Ulrik Fahnøe, Sebastian S. Broendum, Ann-Sofie Schreurs, Birthe Brandt Kragelund, Antony M. Carr, Christian Henrik Holmberg and Olaf Nielsen. (2014) Spd2 assists Spd1 in the modulation of ribonucleotide reductase architecture but does not regulate deoxynucleotide pools Journal of Cell Science 127(3):2460-2470.


Rebecca Bolt Ettlinger, Michael Askvad Sørensen and Lene Broeng Oddershede. (2014) Force spectroscopy of DNA and RNA Nucleic Acid Nanotechnology 198(14):1918-1926.


Ruth Hendus-Altenburger, Birthe Brandt Kragelund and Stine Helene Falsig Pedersen. (2014) Structural dynamics and regulation of the mammalian SLC9A family of Na+/H+ exchangers Current Topics in Membranes 56(3):453-461.


Sebastien Morin, Troels Emtekær Linnet, Mathilde Lescanne, Paul Schanda, Gary S. Thompson, Martin Tollinger, Kaare Teilum, Stephane Gagne, Dominique Marion, Christian Griesinger, Martin Blackledge and Edward J. d’Auvergne. (2014) relax: the analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data Bioinformatics 30(15):2219-2220.


Simon Erlendsson, Mette Rathje, Pétur Orri Heiðarsson, Flemming Martin Poulsen, Kenneth Lindegaard Madsen, Kaare Teilum and Ulrik Gether. (2014) Protein interacting with C-kinase 1 (PICK1) binding promiscuity relies on unconventional PSD-95/Discs-Large/ZO-1 homology (PDZ) binding modes for nonclass II PDZ ligands Journal of Biological Chemistry 289(36):25327-25340.


Simon Olsson, Beat Rolf Vögeli, Andrea Cavalli, Wouter Krogh Boomsma, Jesper Ferkinghoff-Borg, Kresten Lindorff-Larsen and Thomas Wim Hamelryck. (2014) Probabilistic determination of native state ensembles of proteins Journal of Chemical Theory and Computation 10(8):3484-3491.


Sine Lo Svenningsen and Szabolcs Semsey. (2014) Commitment to lysogeny is preceded by a prolonged period of sensitivity to the late lytic regulator Q in bacteriophage ? Journal of Bacteriology 196(20):3582-3588.


Søren Lindemose, Michael K. Jensen, Jan Van de Velde, Charlotte O'Shea, Ken S. Heyndrickx, Christopher Workman, Klaas Vandepoele, Karen Skriver and Federico De Masi. (2014) A DNA-binding-site landscape and regulatory network analysis for NAC transcription factors in Arabidopsis thaliana Nucleic Acids Research 42(12):7681-7693.


Thomas Ramming, Henning Gram Hansen, Kazuhiro Nagata, Lars Ellgaard and Christian Appenzeller-Herzog. (2014) GPx8 peroxidase prevents leakage of H2O2 from the endoplasmic reticulum Free Radical Biology & Medicine 70(6):106-116.


Ulrich Weininger, Ulrika Brath, Kristofer Modig, Kaare Teilum and Mikael Akke. (2014) Off-resonance rotating-frame relaxation dispersion experiment for 13C in aromatic side chains using L-optimized TROSY-selection Journal of Biomolecular NMR 59(1):23-29.


Valéry Ozenne, Jeffrey K. Noel, Pétur Orri Heiðarsson, Søren Brander, Flemming Martin Poulsen, Malene Ringkjøbing Jensen, Birthe Brandt Kragelund, Martin Blackledge and Jens Albert Danielsson. (2014) Exploring the minimally frustrated energy landscape of unfolded ACBP Journal of Molecular Biology 426(3):722-734.


Vytautas Iesmantavicius, Jakob Dogan, Per Jemth, Kaare Teilum and Magnus Kjærgaard. (2014) Helical propensity in an intrinsically disordered protein accelerates ligand binding Angewandte Chemie (International ed. in English) 53(6):1548-1551.


Wouter Krogh Boomsma, Jesper Ferkinghoff-Borg and Kresten Lindorff-Larsen. (2014) Combining experiments and simulations using the maximum entropy principle PloS Computational Biology 10(2):543–553.


Wouter Krogh Boomsma, Pengfei Tian, Jes Frellsen, Jesper Ferkinghoff-Borg, Thomas Wim Hamelryck, Kresten Lindorff-Larsen and Michele Vendruscolo. (2014) Equilibrium simulations of proteins using molecular fragment replacement and NMR chemical shifts Proceedings of the National Academy of Sciences of the United States of America 111(38):13852-13857.



Namiko Mitarai and Steen Pedersen. (2013) Control of ribosome traffic by position-dependent choice of synonymous codons Physical Biology 10(5):1088-1097.


Anders Steen Christensen, Troels Emtekær Linnet, Mikael Borg, Wouter Krogh Boomsma, Kresten Lindorff-Larsen, Thomas Wim Hamelryck and Jan Halborg Jensen. (2013) Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics PLoS ONE 8(12):13852-13857.


Chandra Kenchappa, Pétur Orri Heiðarsson, Birthe Kragelund, Roger Garrett and Flemming Poulsen. (2013) Solution properties of the archaeal CRISPR DNA repeat-binding homeodomain protein Cbp2 Nucleic Acids Research 41(5):3424-3435.


Davide Montero, Christine Tachibana, Jakob R. Winther and Christian Appenzeller-Herzog. (2013) Intracellular glutathione pools are heterogeneously concentrated Redox Biology 1(1):508-513.


Jakob R. Winther and Ursula Jakob. (2013) Redox control Nature Chemical Biology 9(2):69-70.


Jean O'Donoghue, Dawadschargal Bech-Otschir, Ida Larsen, Mairi Wallace, Rasmus Hartmann-Petersen and Colin Gordon. (2013) Nedd8 processing enzymes in Schizosaccharomyces pombe B M C Biochemistry 14(8):1-6.


Lea Ellegaard-Jensen, Jens Aamand, Birthe Brandt Kragelund, A.H. Johnsen and Søren Rosendahl. (2013) Strains of the soil fungus Mortierella show different degradation potentials for the phenylurea herbicide diuron Biodegradation 24(6):765-774.


Magnus Kjaergaard, Lisbeth Andersen, Lau Dalby Nielsen and Kaare Teilum. (2013) A Folded Excited State of Ligand-Free Nuclear Coactivator Binding Domain (NCBD) Underlies Plasticity in Ligand Recognition. Biochemistry 52(10):1686-1693.


Mette Eriksen, Peter Horvath, Michael Askvad Sørensen, Szabolcs Semsey, Lene Broeng Oddershede and Liselotte Jauffred Pedersen. (2013) A novel complex Journal of Nanomaterials 2013(14):1918-1926.


Michael Krogh Jensen, Søren Lindemose, Federico de Masi, Julia J. Reimer, Michael Nielsen, Venura Perera, Chris T. Workman, Franziska Turck, Murray R. Grant, John Mundy, Morten Petersen and Karen Skriver. (2013) ATAF1 transcription factor directly regulates abscisic acid biosynthetic gene NCED3 in Arabidopsis thaliana FEBS Open Bio 3(12):321-327.


Michael May, Karen Skriver and Gert Dandanell. (2013) Technical and didactic problems of virtual lab exercises in biochemistry and biotechnology education False 23(1):81-90.


Naoyuki Umemoto, Takayuki Ohnuma, Mamiko Mizuhara, Hirokazu Sato, Karen Skriver and Tamo Fukamizo. (2013) Introduction of a tryptophan side chain into subsite +1 enhances transglycosylation activity of a GH-18 chitinase from Arabidopsis thaliana, AtChiC Glycobiology 23(1):81-90.


Nikolai Adamski, Maxwell Bush, James Simmonds, Adrian Turner, Sarah Mugford, Alan Jones, Kim Findlay, Nikolai Pedentchouk, Penelope Margaret von Wettstein and Cristobal Uauy. (2013) The Inhibitor of wax 1 locus (Iw1) prevents formation of ß- and OH-ß-diketones in wheat cuticular waxes and maps to a sub-cM interval on chromosome arm 2BS Plant Journal 74(6):989-1002.


Nina Molin Høyland-Kroghsbo, Rasmus Baadsgaard Mærkedahl and Sine Svenningsen. (2013) A quorum-sensing-induced bacteriophage defense mechanism mBio 4(1):1-9.


Paola Pietroni, Nishi Vasisht, Jonathan P Cook, David M Roberts, J Michael Lord, Rasmus Hartmann-Petersen, Lynne M Roberts and Robert A Spooner. (2013) The proteasome cap RPT5/Rpt5p subunit prevents aggregation of unfolded ricin A chain Biochemical Journal 453(3):435-445.


Pétur Orri Heiðarsson, Mariela R. Otazo, Luca Bellucci, Alessandro Mossa, Alberto Imparato, Emanuele Paci, Stefano Corni, Rosa Di Felice, Birthe Brandt Kragelund and Ciro Cecconi. (2013) Single-molecule folding mechanism of an EF-hand neuronal calcium sensor Structure 21(10):1812-1821.


Predrag Kukic, Damien Farrell, Lawrence P. McIntosh, Bertrand García-Moreno E., Kristine Steen Jensen, Zigmantas Toleikis, Kaare Teilum and Jens Erik Nielsen. (2013) Protein dielectric constants determined from NMR chemical shift perturbations Journal of the American Chemical Society 135(45):16968–16976.


Robert Dagil, Charlotte O'Shea, Anders Nykjær, Alexandre M J J Bonvin and Birthe B Kragelund. (2013) Gentamicin binds to the megalin receptor as a competitive inhibitor using the common ligand binding motif of complement type repeats The Journal of Biological Chemistry 288(6):4424-35.


Rosa Rebecca Erritzøe Hansen, Mieko Otsu, Ineke Braakman and Jakob R. Winther. (2013) Quantifying changes in the cellular thiol-disulfide status during differentiation of B cells into antibody-secreting plasma cells International Journal of Cell Biology 2013(2):69-70.


Sandro Bottaro, Kresten Lindorff-Larsen and Robert B. Best. (2013) Variational optimization of an all-atom implicit solvent force field to match explicit solvent simulation data Journal of Chemical Theory and Computation 9(12):5641-5652.


Simon Olsson, Jes Frellsen, Wouter Krogh Boomsma, Kanti V. Mardia and Thomas Wim Hamelryck. (2013) Inference of structure ensembles of flexible biomolecules from sparse, averaged data PLoS ONE 8(11):1697-1705.


Stefan Klumpp, Matthew Scott, Steen Pedersen and Terence Hwa. (2013) Molecular crowding limits translation and cell growth Proceedings of the National Academy of Sciences of the United States of America 110(42):16754-16759.


Stefano Piana, Kresten Lindorff-Larsen and David E. Shaw. (2013) Atomistic description of the folding of a dimeric protein Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces & Biophysical 117(42):12935-12942.


Søren Lindemose, Charlotte O'Shea, Michael Krogh Jensen and Karen Skriver. (2013) Structure, function and networks of transcription factors involved in abiotic stress responses International Journal of Molecular Sciences (Online) 14(3):5842-78.


Wouter Krogh Boomsma, Jes Frellsen, Tim Philipp Harder, Sandro Bottaro, Kristoffer Enøe Johansson, Pengfei Tian, Kasper Stovgaard, Christian Andreetta, Simon Olsson, Jan Valentin, Lubomir Dimitrov Antonov, Anders Steen Christensen, Mikael Borg, Jan Halborg Jensen, Kresten Lindorff-Larsen, Jesper Ferkinghoff-Borg and Thomas Wim Hamelryck. (2013) PHAISTOS Journal of Computational Chemistry 34(19):1697-1705.



Anna Mosbech, Ian Gibbs-Seymour, Konstantinos Kagias, Tina Thorslund, Petra Beli, Lou Povlsen, Sofie Vincents Nielsen, Stine Smedegaard, Garry Sedgwick, Claudia Lukas, Rasmus Hartmann-Petersen, Jiri Lukas, Chuna Ram Choudhary, Roger David John Pocock, Simon Bekker-Jensen and Niels Mailand. (2012) DVC1 (C1orf124) is a DNA damage-targeting p97 adaptor that promotes ubiquitin-dependent responses to replication blocks Nature Structural and Molecular Biology 19(11):1084-92.


Anneli Edström Hägerwall, Victoria Rydengård, Per Fernlund, Matthias Mörgelin, Maria Baumgarten, Alexander M. Cole, Martin Malmsten, Birthe Kragelund and Ole E. Sørensen. (2012) ß-Microseminoprotein endows post coital seminal plasma with potent candidacidal activity by a calcium- and pH-dependent mechanism. P L o S Pathogens 8(4):1-12.


Birthe Brandt Kragelund, Michael Krogh Jensen and Karen Skriver. (2012) Order by disorder in plant signaling Trends in Plant Science 17(11):625-632.


Ditte Hededam Welner, Søren Lindemose, J. Günter Grossmann, Niels Erik Møllegaard, Addie Nina Olsen, Charlotte Helgstrand, Karen Skriver and Leila Lo Leggio. (2012) DNA binding by the plant-specific NAC transcription factors in crystal and solution Biochemical Journal 444(1):395-404.


Elena Papaleo, Kresten Lindorff-Larsen and Luca De Gioia. (2012) Paths of long-range communication in the E2 enzymes of family 3 Physical Chemistry Chemical Physics 14(44):12515-12525.


Emily M. Lynes, Michael Bui, Megan C. Yap, Matthew D. Benson, Bobbie Schneider, Lars Ellgaard, Luc G. Berthiaume and Thomas Simmen. (2012) Palmitoylated TMX and calnexin target to the mitochondria-associated membrane E M B O Journal 31(2):457-470.


Esben G Poulsen, Cornelia Steinhauer, Michael Lees, Anne-Marie Lauridsen, Lars Ellgaard and Rasmus Hartmann-Petersen. (2012) HUWE1 and TRIP12 Collaborate in Degradation of Ubiquitin-Fusion Proteins and Misframed Ubiquitin P L o S One 7(11):532-542.


Franziska Kriegenburg, Lars Ellgaard and Rasmus Hartmann-Petersen. (2012) Molecular chaperones in targeting misfolded proteins for ubiquitin-dependent degradation F E B S Journal 279(4):532-542.


Heike Rösner and Birthe Kragelund. (2012) Structure and Dynamic Properties of Membrane Proteins using NMR Comprehensive Physiology 2(2):1491-1539.


Henning Gram Hansen, Jonas Damgård Schmidt, Cecilie Lützen Søltoft, Thomas Ramming, Henrik Marcus Geertz-Hansen, Brian Christensen, Esben Skipper Sørensen, Agnieszka Juncker, Christian Andreas Appenzeller and Lars Ellgaard. (2012) Hyperactivity of the Ero1a oxidase elicits endoplasmic reticulum stress but no broad antioxidant response Journal of Biological Chemistry 287(47):39513-39523.


Jesper Tholstrup Hansen, Lene Broeng Oddershede and Michael Askvad Sørensen. (2012) mRNA pseudoknot structures can act as ribosomal roadblocks Nucleic Acids Research 40(1):303-313.


Jonas Willum Nielsen, Karina Krarup Sand, Christian Schack Pedersen, L. Z. Lakshtanov, Jakob R. Winther, Martin Willemoës and Susan Louise Svane Stipp. (2012) Polysaccharide effects on calcite growth Crystal Growth & Design 12(10):4906-4910.


Jonas Willum Nielsen, Kristine Steen Jensen, Rosa Rebecca Erritzøe Hansen, Charlotte Held Gotfredsen and Jakob R. Winther. (2012) A fluorescent probe which allows highly specific thiol labeling at low pH Analytical Biochemistry 421(1):115-120.


Jonas Willum Nielsen, Nina Rødtness Poulsen, Anna Margit Susanne Johnsson, Jakob R. Winther, Susan Louise Svane Stipp and Martin Willemoës. (2012) Metal-ion dependent catalytic properties of Sulfolobus solfataricus class II a-mannosidase Biochemistry 51(40):8039-8046.


Kresten Lindorff-Larsen, Nikola Trbovic, Paul Maragakis, Stefano Piana and David E Shaw. (2012) Structure and dynamics of an unfolded protein examined by molecular dynamics simulation Journal of the American Chemical Society 134(8):3787-3791.


Kresten Lindorff-Larsen, Paul Maragakis, Stefano Piana, Michael P Eastwood, Ron O Dror and David E Shaw. (2012) Systematic validation of protein force fields against experimental data P L o S One 7(2):5641-5652.


Lea Cecilie Christensen, Njal Winther Jensen, Andrea Lages Lino Vala, Jurate Kamarauskaite, Linda Christina Johansson, Jakob R. Winther, Kay Hofmann, Kaare Teilum and Lars Ellgaard. (2012) The human selenoprotein VCP-interacting membrane protein (VIMP) is non-globular and harbors a reductase function in an intrinsically disordered region Journal of Biological Chemistry 287(31):26388-26399.


Magnus Kjærgaard, Flemming Martin Poulsen and Birthe Brandt Kragelund. (2012) Analyzing temperature-induced transitions in disordered proteins by NMR spectroscopy and secondary chemical shift analyses Intrinsically disordered protein analysis 2(2):1491-1539.


Magnus Kjærgaard, Flemming Martin Poulsen and Birthe Brandt Kragelund. (2012) Temperature-induced transitions in disordered proteins probed by NMR spectroscopy Intrinsically disordered protein analysis 2(2):1491-1539.


Magnus Kjærgaard, Flemming Martin Poulsen and Kaare Teilum. (2012) Is a malleable protein necessarily highly dynamic? Biophysical Journal 102(7):1627-1635.


Mary Penney, Itaru Samejima, Caroline Wilkinson, Christopher McInerny, Søs Mathiassen, Mairi Wallace, Takashi Toda, Rasmus Hartmann-Petersen and Colin Gordon. (2012) Fission yeast 26S proteasome mutants are multi-drug resistant due to stabilization of the Pap1transcription factor. P L o S One 7(11):1084-92.


Penelope Margaret von Wettstein. (2012) Plant waxes eLS 74(6):989-1002.


Pétur Orri Heiðarsson, Ida Jannike Bjerrum-Bohr, Gitte A. Jensen, Olaf Pongs, Bryan E. Finn, Flemming Martin Poulsen and Birthe Brandt Kragelund. (2012) The C-terminal tail of human neuronal calcium sensor 1 regulates the conformational stability of the Ca2+-activated state Journal of Molecular Biology 417:51-64.


Pétur Orri Heiðarsson, Immanuel Valpapuram, Carlo Camilloni, Alberto Imparato, Guido Tiana, Flemming Martin Poulsen, Birthe Brandt Kragelund and Ciro Cecconi. (2012) A highly compliant protein native state with a spontaneous-like mechanical unfolding pathway Journal of the American Chemical Society 134(41):17068-17075.


Robert Dagil, Maiken J. Knudsen, Johan Gotthardt Olsen, Charlotte O'Shea, Magnus Franzmann, Vincent Goffin, Kaare Teilum, Jens Breinholt and Birthe Brandt Kragelund. (2012) The WSXWS motif in cytokine receptors is a molecular switch involved in receptor activation Structure 20(2):270-282.


Sandro Bottaro, Wouter Krogh Boomsma, Kristoffer Enøe Johansson, Christian Andreetta, Thomas Wim Hamelryck and Jesper Ferkinghoff-Borg. (2012) Subtle Monte Carlo updates in dense molecular systems Journal of Chemical Theory and Computation 8(2):695-702.


Stefano Piana, Kresten Lindorff-Larsen and David E. Shaw. (2012) Protein folding kinetics and thermodynamics from atomistic simulation Proceedings of the National Academy of Sciences of the United States of America 109(44):17845-17850.


Stefano Piana, Kresten Lindorff-Larsen, Robert M Dirks, John K Salmon, Ron O Dror and David E Shaw. (2012) Evaluating the effects of cutoffs and treatment of long-range electrostatics in protein folding simulations P L o S One 7(6):3787-3791.


Tim Philipp Harder, Mikael Borg, Wouter Krogh Boomsma, Peter Røgen and Thomas Wim Hamelryck. (2012) Fast large-scale clustering of protein structures using Gauss integrals Bioinformatics 28(4):510-515.


Tim Philipp Harder, Sandro Bottaro, Wouter Krogh Boomsma, Simon Olsson, Jesper Ferkinghoff-Borg and Thomas Wim Hamelryck. (2012) An efficient null model for conformational fluctuations in proteins Structure 20(6):1028-1039.


Wouter Krogh Boomsma, Jes Frellsen and Thomas Wim Hamelryck. (2012) Probabilistic models of local biomolecular structure and their applications Bayesian methods in structural bioinformatics 28(4):510-515.



Jan Martinussen, Martin Willemoës and Mogens Kilstrup. (2011) The Biochemical Basis | Nucleotide Metabolism Comprehensive Biotechnology. 51(40):8039-8046.


Stefano Piana, Krishnarjun Sarkar, Kresten Lindorff-Larsen, Minghao Guo, Martin Gruebele and David E Shaw. (2011) Computational design and experimental testing of the fastest-folding ß-sheet protein Journal of Molecular Biology 405(1):43-48.


Ann-Beth Nørholm, Ruth Hendus-Altenburger, Gabriel Bjerre, Magnus Kjærgaard, Stine Helene Falsig Pedersen and Birthe B Kragelund. (2011) The Intracellular Distal Tail of the Na+/H+ Exchanger NHE1 Is Intrinsically Disordered Biochemistry 50(17):3469-80.


Brian K Hammer and Sine Lo Svenningsen. (2011) Small RNA target genes and regulatory connections in the Vibrio cholerae quorum sensing system Quorum sensing 407(1):35-44.


Franziska Kriegenburg, Esben G Poulsen, Annett Koch, Elke Krüger and Rasmus Hartmann-Petersen. (2011) Redox control of the ubiquitin-proteasome system Antioxidants & Redox Signaling 15(8):2265-99.


Helen Webb, Barbara Mary Tynan-Connolly, Gregory M Lee, Damien Farrell, Fergal O'Meara, Chresten R Søndergaard, Kaare Teilum, Chandralal Hewage, Lawrence P McIntosh and Jens Erik Nielsen. (2011) Remeasuring HEWL pKa values by NMR spectroscopy  Proteins: Structure, Function, and Bioinformatics 79(3):685-702.


Iben H. Lauritsen, Martin Willemoës, Kaj Frank Jensen, Eva Johansson and Pernille Harris. (2011) Structure of the dimeric form of CTP synthase from Sulfolobus solfataricus Acta Crystallographica. Section F : Structural Biology and Crystallization Communications 67(2):201-208.


Jan Riemer, Henning G Hansen, C. Appenzeller-Herzog, Christian Appenzeller-Herzog, Linda Johansson and Lars Ellgaard. (2011) Identification of the PDI-family member ERp90 as an interaction partner of ERFAD P L o S One 6(2):485-92.


Jeppe Trudslev Pedersen, Kaare Teilum, Niels H. H. Heegaard, Jesper Østergaard, Hans-Werner Adolph and Lars Bo Stegeager Hemmingsen. (2011) Rapid formation of a preoligomeric peptide-metal-peptide complex following copper(II) binding to amyloid ß peptides Angewandte Chemie International Edition 50(11):2532-2535.


Katrine M Andersen, Camilla Jensen, Franziska Kriegenburg, Anne-Marie B Lauridsen, Colin Gordon and Rasmus Hartmann-Petersen. (2011) Txl1 and Txc1 are co-factors of the 26S proteasome in fission yeast Antioxidants & Redox Signaling 14(9):1601-8.


Kresten Lindorff-Larsen, Stefano Piana, Ron O Dror and David E Shaw. (2011) How fast-folding proteins fold Science (New York, N.Y.) 334(6055):517-20.


Kristian Moss Bendtsen, Janos Erdossy, Zsolt Csiszovski, Sine Lo Svenningsen, Kim Sneppen, Sandeep Krishna and Szabolcs Semsey. (2011) Direct and indirect effects in the regulation of overlapping promoters Nucleic Acids Research 39(16):6879-6885.


Kristine Steen Jensen, Jakob R Winther and Kaare Teilum. (2011) Millisecond dynamics in glutaredoxin during catalytic turnover is dependent on substrate binding and absent in the resting states Journal of the American Chemical Society 133(9):3034-42.


Kaare Teilum, Johan G Olsen and Birthe B Kragelund. (2011) Protein stability, flexibility and function B B A - Proteins and Proteomics 1814(8):969-76.


Louise Meinert Niclasen, Johan G Olsen, Robert Dagil, Zhang Qing, Ole E Sørensen and Birthe B Kragelund. (2011) Streptococcal pyogenic exotoxin B (SpeB) boosts the contact system via binding of a-1 antitrypsin Biochemical Journal 434(1):123-32.


Margit Pedersen, Søren Nissen, Namiko Mitarai, Sine Lo Svenningsen, Kim Sneppen and Steen Pedersen. (2011) The functional half-life of an mRNA depends on the ribosome spacing in an early coding region Journal of Molecular Biology 407(1):35-44.


Mathilde Johanne Kaas Hansen, Johan Gotthardt Olsen, Sophie Bernichtein, Charlotte O'Shea, Bent Walther Sigurskjold, Vincent Goffin and Birthe Brandt Kragelund. (2011) Development of prolactin receptor antagonists with reduced pH-dependence of receptor binding. Journal of Molecular Recognition 24(4):533-547.


Melanie Kny, Sybille Standera, Rasmus Hartmann-Petersen, Peter-Michael Kloetzel and Michael Seeger. (2011) Herp regulates Hrd1-mediated ubiquitylation in a ubiquitin-like domain-dependent manner Journal of Biological Chemistry 286(7):5151-6.


Neil J Bulleid and Lars Ellgaard. (2011) Multiple ways to make disulfides Trends in Biochemical Sciences 36(9):485-92.


Rasmus W. Nielsen, Christine Tachibana, Niels Erik Hansen and Jakob R Winther. (2011) Trisulfides in Proteins Antioxidants & Redox Signaling 15(1):67-75.


Simon Olsson, Wouter Krogh Boomsma, Jes Frellsen, Sandro Bottaro, Tim Philipp Harder, Jesper Ferkinghoff-Borg and Thomas Wim Hamelryck. (2011) Generative probabilistic models extend the scope of inferential structure determination Journal of Magnetic Resonance 213(1):182-186.


Stefano Piana, Kresten Lindorff-Larsen and David E Shaw. (2011) How robust are protein folding simulations with respect to force field parameterization? Biophysical Journal (2011) 100(9):L47-L49.


T. Letzel, E. Sahmel-Schneide, K. Skriver, T. Ohnuma and T. Fukamizo. (2011) Chitinase-catalyzed hydrolysis of 4-nitrophenyl penta-N-acetyl-B-chitopentaoside as determined by real-time ESI-MS Carbohydrate Research 346(6):863-866.


Takayuki Ohnuma, Tomoyuki Numata, Takuo Osawa, Mamiko Mizuhara, Outi Lampela, André H Juffer, Karen Skriver and Tamo Fukamizo. (2011) A class V chitinase from Arabidopsis thaliana: gene responses, enzymatic properties, and crystallographic analysis Planta 234(1):123-37.


Trine Kjaersgaard, Michael K Jensen, Michael W Christiansen, Per L. Gregersen, Birthe B Kragelund and Karen Skriver. (2011) Senescence-associated barley NAC (NAM, ATAF1,2, CUC) transcription factor interacts with radical-induced cell death 1 through a disordered regulatory domain Journal of Biological Chemistry 286(41):35418-29.



Christian Appenzeller-Herzog, Jan Riemer, Ester Zito, King-Tung Chin, David Ron, Martin Spiess and Lars Ellgaard. (2010) Disulphide production by Ero1a-PDI relay is rapid and effectively regulated EMBO Journal 29(19):3318-29.


Kim Sneppen, Steen Pedersen, Sandeep Krishna, Ian Burwell Dodd and Szabolcs Semsey. (2010) Economy of operon formation Microbe 1(4):e00177-10.


Magnus Kjærgaard, Ann-Beth Nørholm, Ruth Hendus-Altenburger, Stine Helene Falsig Pedersen, Flemming M Poulsen and Birthe B Kragelund. (2010) Temperature-dependent structural changes in intrinsically disordered proteins: formation of alpha-helices or loss of polyproline II? Protein Science 19(8):1555-64.


Susan Arent, Caspar Elo Christensen, Valerie E Pye, Allan Nørgaard and Anette Henriksen. (2010) The multifunctional protein in peroxisomal beta-oxidation The Journal of Biological Chemistry 285(31):24066-77.


Valerie E Pye, Caspar Elo Christensen, James H Dyer, Susan Arent and Anette Henriksen. (2010) Peroxisomal plant 3-ketoacyl-CoA thiolase structure and activity are regulated by a sensitive redox switch The Journal of Biological Chemistry 285(31):24078-88.


Konstantinos Nestoras, Asma Hadi Mohammed, Ann-Sofie Schreurs, Oliver Fleck, Adam T Watson, Marius Poitelea, Charlotte O'Shea, Charly Chahwan, Christian Holmberg, Birthe B Kragelund, Olaf Nielsen, Mark Osborne, Antony M Carr and Cong Liu. (2010) Regulation of ribonucleotide reductase by Spd1 involves multiple mechanisms Genes & Development 24(11):1145-1159.


Kresten Lindorff-Larsen, Stefano Piana, Kim Palmo, Paul Maragakis, John L Klepeis, Ron O Dror and David E Shaw. (2010) Improved side-chain torsion potentials for the Amber ff99SB protein force field Proteins: Structure, Function, and Bioinformatics 78(8):1950-8.


Michael K Jensen, Trine Kjaersgaard, Michael M. Nielsen, Pernille Galberg, Klaus Petersen, Charlotte O'Shea and Karen Skriver. (2010) The Arabidopsis thaliana NAC transcription factor family: structure-function relationships and determinants of ANAC019 stress signalling Biochemical Journal 426(2):183-96.


Kimberly C. Tu, Tao Long, Sine Lo Svenningsen, Ned S. Wingreen and Bonnie L. Bassler. (2010) Negative feedback loops involving small regulatory RNAs precisely control the Vibrio harveyi qourum-sensing response Molecular Cell 37(4):567-579.


Tim Harder, Wouter Krogh Boomsma, Martin Paluszewski, Jes Frellsen, Kristoffer Enøe Johansson and Thomas Wim Hamelryck. (2010) Beyond rotamers B M C Bioinformatics 11(1):306.


Bjarne Hove-Jensen, Tina J. Rosenkrantz, David L. Zechel and Martin Willemoës. (2010) Accumulation of intermediates of the carbon-phosphorus lyase pathway for phosphonate degradation in phn mutants of Escherichia coli Journal of Bacteriology 192(1):370-374.


Damián González-Mellado, Penny von Wettstein, Rafael Garcés and Enrique Martínez-Force. (2010) The role of ß-ketoacyl-acyl carrier protein synthase III in the condensation steps of fatty acid biosynthesis in sunflower Planta 231(6):1277-1289.


David E Shaw, Paul Maragakis, Kresten Lindorff-Larsen, Stefano Piana, Ron O Dror, Michael P Eastwood, Joseph A Bank, John M Jumper, John K Salmon, Yibing Shan and Willy Wriggers. (2010) Atomic-level characterization of the structural dynamics of proteins Science (New York, N.Y.) 330(6002):341-6.


Doris Roth, Emily Lynes, Jan Riemer, Henning Gram Hansen, Nils Althaus, Thomas Simmen and Lars Ellgaard. (2010) A di-arginine motif contributes to the ER localization of the type I transmembrane ER oxidoreductase TMX4 Biochemical Journal 425(1):195-205.


Franziska Kriegenburg and Rasmus Hartmann-Petersen. (2010) Cdc48 connects with eIF3 Cell Cycle 9(1):22-27.


Isabelle Broutin, Jean-Baptiste Jomain, Estelle Tallet, Jan Van Agthoven, Bertand Raynal, Sylviane Hoos, Birthe Brandt Kragelund, Paul Kelly, Alexandre Ducroix, Patrick England and Vincent Goffin. (2010) Crystal structure of an affinity-matured prolactin complexed to its dimerized receptor reveals the topology of hormone binding site 2. Journal of Biological Chemistry 285(11):8422-8433.


Kenji Maeda, Per Hägglund, Olof Björnberg, Jakob R Winther and Birte Svensson. (2010) Kinetic and thermodynamic properties of two barley thioredoxin h isozymes, HvTrxh1 and HvTrxh2 FEBS Letters 584(15):3376-3380.


Magnus Kjærgaard, Kaare Teilum and Flemming M Poulsen. (2010) Conformational selection in the molten globule state of the nuclear coactivator binding domain of CBP Proceedings of the National Academy of Science of the United States of America 107(28):12535-40.


Michael Krogh Jensen, Trine Kjærsgaard, Klaus Petersen and Karen Skriver. (2010) NAC genes: Time-specific regulators of hormonal signaling in Arabidopsis Plant Signalling & Behavior 5(7):183-96.


Morten ؠJensen, David W Borhani, Kresten Lindorff-Larsen, Paul Maragakis, Vishwanath Jogini, Michael P Eastwood, Ron O Dror and David E Shaw. (2010) Principles of conduction and hydrophobic gating in K+ channels Proceedings of the National Academy of Sciences of the United States of America 107(13):5833-8.


Rasmus Iversen, Peter Anders Andersen, Kristine Steen Jensen, Jakob R. Winther and Bent Walther Sigurskjold. (2010) Thiol-Disulfide Exchange between Glutaredoxin and Glutathione Biochemistry 49(4):810-820.


Rodrigo Cabrera, Zhe Sha, Tegy J. Vadakkan, Joel Otero, Franziska Kriegenburg, Rasmus Hartmann-Petersen, Mary E. Dickinson and Eric C. Chang. (2010) Proteasome nuclear import mediated by Arc3 can influence efficient DNA damage repair and mitosis in Schizosaccharomyces pombe Molecular Biology of the Cell 21(18):3125-3136.


Ryan Chao, Linda Nevin, Pooja Agarwal, Jan Riemer, Xiaoyang Bai, Allen Delaney, Matthew Akana, Nelson JimenezLopez, Tanya Bardakjian, Adele Schneider, Nicolas Chassaing, Daniel F Schorderet, David FitzPatrick, Pui-yan Kwok, Lars Ellgaard, Douglas B Gould, Yan Zhang, Jarema Malicki, Herwig Baier and Anne Slavotinek. (2010) A male with unilateral microphthalmia reveals a role for TMX3 in eye development PLoS ONE 5(5):e10565.


Thomas Hamelryck, Mikael Borg, Martin Paluszewski, Jonas Paulsen, Jes Frellsen, Christian Andreetta, Wouter Krogh Boomsma, Sandro Bottaro and Jesper Ferkinghoff-Borg. (2010) Potentials of mean force for protein structure prediction vindicated, formalized and generalized PLoS ONE 5(11):306.


Tuhina Mazumdar, F Murat Gorgun, Youbao Sha, Alexey Tyryshkin, Shenyan Zeng, Rasmus Hartmann-Petersen, Jakob Ploug Jørgensen, Klavs B Hendil and N Tony Eissa. (2010) Regulation of NF-kappaB activity and inducible nitric oxide synthase by regulatory particle non-ATPase subunit 13 (Rpn13) Proceedings of the National Academy of Science of the United States of America 107(31):13854-9.



Willy Wriggers, Kate A. Stafford, Yibing Shan, Stefano Piana, Paul Maragakis, Kresten Lindorff-Larsen, Patrick J. Miller, Justin Gullingsrud, Charles A. Rendleman, Michael P. Eastwood, Ron O. Dror and David E. Shaw. (2009) Automated Event Detection and Activity Monitoring in Long Molecular Dynamics Simulations Journal of Chemical Theory and Computation 5(10):2595-2605.


David E. Shaw, Ron O. Dror, John K. Salmon, J. P. Grossman, Kenneth M. Mackenzie, Joseph A. Bank, Cliff Young, Martin M. Deneroff, Brannon Batson, Kevin J. Bowers, Edmond Chow, Michael P. Eastwood, Doug Ierardi, John L. Klepeis, Jeffrey Kuskin, Richard H. Larson, Kresten Lindorff-Larsen, Paul Maragakis, Mark A. Moraes, Stefano Piana, Yibing Shan and Brian Towles. (2009) Millisecond-scale molecular dynamics simulations on Anton Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis 5(10):2595-2605.


Jan Riemer, Christian Appenzeller-Herzog, Linda Johansson, Bernd Bodenmiller, Rasmus Hartmann-Petersen and Lars Ellgaard. (2009) A luminal flavoprotein in endoplasmic reticulum-associated degradation Proceedings of the National Academy of Science of the United States of America 106(35):14831-6.


Johan G Olsen, Robert Dagil, Louise Meinert Niclasen, Ole E Sørensen and Birthe B Kragelund. (2009) Structure of the Mature Streptococcal Cysteine Protease Exotoxin mSpeB in Its Active Dimeric Form Journal of Molecular Biology 393(3):693-703.


John L Klepeis, Kresten Lindorff-Larsen, Ron O Dror and David E Shaw. (2009) Long-timescale molecular dynamics simulations of protein structure and function Current Opinion in Structural Biology 19(2):120-7.


Julie H B Siggaard, Eva Johansson, Tina Reinholdt Vognsen, Signe Smedegaard Helt, Pernille Harris, Sine Larsen and Martin Willemoës. (2009) Concerted bifunctionality of the dCTP deaminase-dUTPase from Methanocaldococcus jannaschii: a structural and pre-steady state kinetic analysis Archives of Biochemistry and Biophysics 490(1):42-9.


Katrine M Andersen, Louise Kjær Klausen, Søren Prag, Anders H Johnsen, Colin A Semple, Klavs B Hendil and Rasmus Hartmann-Petersen. (2009) Thioredoxin Txnl1/TRP32 Is a Redox-active Cofactor of the 26 S Proteasome Journal of Biological Chemistry 284(22):15246-15254.


Klaus Aksel Bjørner Hendil, Franziska Kriegenburg, Keiji Tanaka, Shigeo Murata, Anne-Marie B Lauridsen, Anders H Johnsen and Rasmus Hartmann-Petersen. (2009) The 20S proteasome as an assembly platform for the 19S regulatory complex Journal of Molecular Biology 394(2):320-328.


Kresten Lindorff-Larsen and Jesper Ferkinghoff-Borg. (2009) Similarity measures for protein ensembles PLoS ONE 4(1):2595-2605.


Kristine Steen Jensen, Rosa Erritzøe Hansen and Jakob R Winther. (2009) Kinetic and Thermodynamic Aspects of Cellular Thiol-Disulfide Redox Regulation Antioxidants & Redox Signaling 11(5):1047-1058.


Kaare Teilum, Johan G Olsen and Birthe B Kragelund. (2009) Functional aspects of protein flexibility Cellular and Molecular Life Sciences 66(14):2231-47.


Kaare Teilum, Melanie H Smith, Eike Schulz, Lea C Christensen, Gleb Solomentsev, Mikael Oliveberg and Mikael Akke. (2009) Transient structural distortion of metal-free Cu/Zn superoxide dismutase triggers aberrant oligomerization Proceedings of the National Academy of Science of the United States of America 106(43):18273-8.


Louise Madsen, Michael Seeger, Colin A Semple and Rasmus Hartmann-Petersen. (2009) New ATPase regulators-p97 goes to the PUB International Journal of Biochemistry & Cell Biology 41(12):2380-8.


Mikael Borg, Wouter Krogh Boomsma, J. Ferkinghoff-Borg, Jes Frellsen, Tim Philipp Harder, K.V. Mardia, P. Røgen, Kasper Stovgaard and Thomas Wim Hamelryck. (2009) A probabilistic approach to protein structureprediction: PHAISTOS in CASP8 School of Mathematics 5(11):65-70.


Mikael Borg, Wouter Krogh Boomsma, Jesper Ferkinghoff-Borg, Jes Frellsen, Tim Philipp Harder, Kanti Mardia, P. Røgen, Kasper Stovgaard and Thomas Wim Hamelryck. (2009) A probabilistic approach to protein structure prediction LASR 2009 — Statistical Tools for Challenges in Bioinformatics. Proceedings 5(11):65-70.


Nicole Dennhart, Linda M M Weigang, Maho Fujiwara, Tamo Fukamizo, Karen Skriver and Thomas Letzel. (2009) 26kDa endochitinase from barley seeds: real-time monitoring of the enzymatic reaction and substrate binding experiments using electrospray ionization mass spectrometry Journal of Biotechnology 143(4):274-83.


Nora Badawi, Stig Rønhede, Stefan Olsson, Birthe Brandt Kragelund, Anders Holten Johnsen, Ole Stig Jacobsen and Jens Aamand. (2009) Metabolites of the phenylurea herbicides chlorotoluron, diuron, isoproturonand linuron produced by the soil fungus Mortierella sp. Environmental Pollution 157(10):2806-2812.


Rosa E Hansen and Jakob R Winther. (2009) An introduction to methods for analyzing thiols and disulfides: Reactions, reagents, and practical considerations Analytical Biochemistry 394(2):147-58.


Rosa E Hansen, Doris Roth and Jakob R Winther. (2009) Quantifying the global cellular thiol-disulfide status Proceedings of the National Academy of Science of the United States of America 106(2):422-427.


Sine L Svenningsen, Kimberly C Tu and Bonnie L Bassler. (2009) Gene dosage compensation calibrates four regulatory RNAs to control Vibrio cholerae quorum sensing EMBO Journal 28(4):429-39.


Stig Christoffersen, Anders Kadziola, Eva Johansson, Michael Rasmussen, Martin Willemoës and Kaj Frank Jensen. (2009) Structural and kinetic studies of the allosteric transition in Sulfolobus solfataricus uracil phosphoribosyltransferase: Permanent activation by engineering of the C-terminus Journal of Molecular Biology 393(2):464-477.


Tamo Fukamizo, Ryoh Miyake, Atsushi Tamura, Tasayuki Ohnuma, Karen Skriver, Niko Pursiainen and Andre Juffer. (2009) A flexible loop controlling the enzymatic activity and specificity in a glycosyl hydrolase family 19 endochitinase from barley seeds Biochimica et Biophysica Acta - Proteins and Proteomics 1794(8):1159-1167.



Sine L. Svenningsen. (2008) Small RNA control of cell-to-cell communication in Vibrio harveyi and Vibrio cholerae small RNA control of quorum sensing Evolution from Cellular to Social Scales 28(4):429-39.


Anders B. Nørgaard, Jesper Ferkinghoff-Borg and Kresten Lindorff-Larsen. (2008) Experimental parameterization of an energy function for the simulation of unfolded proteins Biophysical Journal 94(1):182-192.


Christian Appenzeller-Herzog and Lars Ellgaard. (2008) In vivo reduction-oxidation state of protein disulfide isomerase: the two active sites independently occur in the reduced and oxidized forms Antioxidants & Redox Signaling 10(1):55-64.


Christian Appenzeller-Herzog, Jan Riemer, Brian Christensen, Esben B. Sørensen and Lars Ellgaard. (2008) A novel disulphide switch mechanism in Ero1 balances ER oxidation in human cells EMBO Journal 27(35):2977–2987.


Franziska Kriegenburg, Michael Seeger, Yasushi Saeki, Keiji Tanaka, Anne-Marie B Lauridsen, Rasmus Hartmann-Petersen and Klavs B Hendil. (2008) Mammalian 26S proteasomes remain intact during protein degradation Cell 135(2):355-65.


Giuseppe Maulucci, Valentina Labate, Marina Mele, Emiliano Panieri, Giuseppe Arcovito, Tommaso Galeotti, Henrik Østergaard, Jakob R Winther, Marco De Spirito and Giovambattista Pani. (2008) High-resolution imaging of redox signaling in live cells through an oxidation-sensitive yellow fluorescent protein Science signaling 1(43):pl3 1-15.


H Reynaldo López-Mirabal, Jakob R Winther and Morten C Kielland-Brandt. (2008) Oxidant resistance in a yeast mutant deficient in the Sit4 phosphatase Current Genetics 53(5):275-86.


H Reynaldo López-Mirabal, Jakob R Winther, Michael Thorsen and Morten C Kielland-Brandt. (2008) Mutations in the RAM network confer resistance to the thiol oxidant 4,4'-dipyridyl disulfide Molecular Genetics and Genomics 279(6):629-42.


Jais R Bjelke, Ole H Olsen, Michel Fodje, L Anders Svensson, Susanne Bang, Gert Bolt, Birthe B Kragelund and Egon Persson. (2008) Mechanism of the Ca2+-induced enhancement of the intrinsic factor VIIa activity Journal of Biological Chemistry 283(38):25863-70.


Jakob Wiborg, Charlotte O'Shea and Karen Skriver. (2008) Biochemical function of typical and variant Arabidopsis thaliana U-box E3 ubiquitin-protein ligases Biochemical Journal 413(3):447-457.


Jens Danielsson, Leena Liljedahl, Elsa Ba´ra´ny-Wallje, Pernille Sønderby, Line Hyltoft Kristensen, Maria A Martinez-Yamout, H Jane Dyson, Peter E Wright, Flemming M Poulsen, Lena Ma¨ler, Astrid Gra¨slund and Birthe B Kragelund. (2008) The intrinsically disordered RNR inhibitor Sml1 is a dynamic dimer Biochemistry 47(50):13428-13437.


Jesper S Hansen, Nils J Færgeman, Birthe B Kragelund and Jens Knudsen. (2008) Acyl-CoA-binding protein (ACBP) localizes to the endoplasmic reticulum and Golgi in a ligand-dependent manner in mammalian cells. Biochemical Journal 410(3):463-472.


Kaj Frank Jensen, Gert Dandanell, Bjarne Hove-Jensen and Martin Willemoës. (2008) Nucleotides, Nucleosides, and Nucleobases EcoSal. Escherichia coli and Salmonella: cellular and molecular biology 490(1):42-9.


Kasper Munch Terkelsen, Wouter Krogh Boomsma, Eske Willerslev and Rasmus Nielsen. (2008) Fast phylogenetic DNA barcoding Philosophical Transactions of the Royal Society of London. Biological Sciences 363(1512):3997-4002.


Kasper Munch Terkelsen, Wouter Krogh Boomsma, John P. Huelsenbeck, Eske Willerslev and Rasmus Nielsen. (2008) Statistical assignment of DNA sequences using Bayesian phylogenetics Systematic Biology 57(5):750-757.


Kimberly C. Tu, Christopher M. Waters, Sine L. Svenningsen and Bonnie L. Bassler. (2008) A small-RNA-mediated negative feedback loop controls quorum-sensing dynamics in Vibrio harveyi Molecular Microbiology 70(4):896-907.


Line Hyltoft Kristensen, Peter E. Nielsen, Christian Isak Jørgensen, Birthe B Kragelund and Niels Erik Møllegaard. (2008) Phosphate Selective Uranyl Photo-Affinity Cleavage of Proteins. Determination of Phosphorylation Sites. ChemBioChem 9(15):2377-81.


Louise Madsen, Katrine M Andersen, Søren Prag, Torben Moos, Colin A Semple, Michael Seeger and Rasmus Hartmann-Petersen. (2008) Ubxd1 is a novel co-factor of the human p97 ATPase. International Journal of Biochemistry & Cell Biology 40(12):2927-42.


M. M. Nielsen, E. S. Seo, A. Dilokpimol, J. Andersen, M. Abou Hachem, H. Naested, Martin Willemoës, S. Bozonnet, L. Kandra, G. Gymnt, R. Haser, N. Aghajari and B. Svensson. (2008) Roles of multiple surface sites, long substrate binding clefts, and carbohydrate binding modules in the action of amylolytic enzymes on polysaccharide substrates Biocatalysis and Biotransformation 26:59-67.


Nadine Anders, Michael M. Nielsen, Jutta Keicher, York-Dieter Stierhof, Masahiko Furutani, Gerd Jürgens, Masao Tasaka and Karen Skriver. (2008) Membrane association of the Arabidopsis ARF exchange factor GNOM involves interaction of conserved domains Plant Cell 20(1):142-51.


Namiko Mitarai, Kim Sneppen and Steen Pedersen. (2008) Ribosome collisions and Translation efficiency: Optimization by codon usage and mRNA destabilization Journal of Molecular Biology 382(1):236-245.


Paul Maragakis, Kresten Lindorff-Larsen, Michael P Eastwood, Ron O Dror, John L Klepeis, Isaiah T Arkin, Morten ؠJensen, Huafeng Xu, Nikola Trbovic, Richard A Friesner, Arthur G Palmer Iii and David E Shaw. (2008) Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces & Biophysical 112(19):6155-6158.


Signe Smedegaard Helt, Majbritt Thymark, Pernille Harris, Claus Aagaard, Jes Dietrich, Sine Larsen and Martin Willemoes. (2008) Mechanism of dTTP inhibition of the bifunctional dCTP deaminase:dUTPase encoded by Mycobacterium tuberculosis Journal of Molecular Biology 376(2):554-69.


Sine Lo Svenningsen. (2008) A negative feedback loop involving small RNAs accelerates Vibrio cholerae'stransition out of quorum-sensing mode Genes & Development 22(2):226-38.


Sine Lo Svenningsen. (2008) A small-RNA-mediated negative feedback loop controls quorum-sensing dynamics inVibrio harveyi Molecular Microbiology 70(4):896-907.


Wouter Krogh Boomsma, Kanti V. Mardia, Charles C. Taylor, Jesper Ferkinghoff-Borg, Anders Krogh and Thomas Hamelryck. (2008) A generative, probabilistic model of local protein structure Proceedings of the National Academy of Science of the United States of America 105(26):8932-8937.



Caspar Elo Christensen, Birthe Brandt Kragelund, Penny Von Wettstein-Knowles and Anette Henriksen. (2007) Structure of the human beta-ketoacyl [ACP] synthase from the mitochondrial type II fatty acid synthase Protein Science 16(2):261-272.


Caspar Elo Christensen, Birthe B Kragelund, Penny von Wettstein-Knowles and Anette Henriksen. (2007) Structure of the human beta-ketoacyl [ACP] synthase from the mitochondrial type II fatty acid synthase. Protein Science 16(2):261-72.


Christian D Geierhaas, Adrian A Nickson, Kresten Lindorff-Larsen, Jane Clarke and Michele Vendruscolo. (2007) BPPred Protein Science 16(1):125-34.


Christian Appenzeller-Herzog and Lars Ellgaard. (2007) The human PDI family: Versatility packed into a single fold. BBA General Subjects 280(46):33859-33867.


Eske Willerslev, Enrico Cappellini, Wouter Krogh Boomsma, Rasmus Nielsen, Martin Bay Hebsgaard, Tina Blumensaadt Brand, Michael Hofreiter, Michael Bunce, Hendrik N. Poinar, Dorthe Dahl-Jensen, Sigfus Johann Johnsen, Jørgen Peder Steffensen, Ole Bennike, Jean-Luc Schwenninger, Roger Nathan, Simon Armitage, Cees-Jan de Hoog, Vasily Alfimov, Marcus Christl, Juerg Beer, Raimund Muscheler, Joel Barker, Martin Sharp, Kirsty E. H. Penkman, James Haile, Pierre Taberlet, M. Thomas. P. Gilbert, Antonella Casoli, Elisa Campani and Matthew J. Collins. (2007) Ancient biomolecules from deep ice cores reveal a forested southern Greenland. Science 317(5834):111-114.


Eva Johansson, Majbritt Thymark, Julie H Bynck, Mathias Fanø, Sine Larsen and Martin Willemoës. (2007) Regulation of dCTP deaminase from Escherichia coli by nonallosteric dTTP binding to an inactive form of the enzyme FEBS Journal 274(16):4188-4198.


H Reynaldo López-Mirabal and Jakob R Winther. (2007) The thiol oxidant dipyridyl disulfide can supply the PDI-Ero1p pathway with additional oxidative equivalents. Antonie van Leeuwenhoek. International Journal of General and Molecular Microbiology 92(4):463-72.


H Reynaldo López-Mirabal and Jakob R Winther. (2007) Redox characteristics of the eukaryotic cytosol. BBA General Subjects 7(3):391-403.


H Reynaldo López-Mirabal, Jakob R Winther and Morten C Kielland-Brandt. (2007) Genetic interaction between the ero1-1 and leu2 mutations in Saccharomyces cerevisiae. Bioscience, Biotechnology, and Biochemistry 71(12):2934-42.


H Reynaldo López-Mirabal, Michael Thorsen, Morten C Kielland-Brandt, Michel B Toledano and Jakob R Winther. (2007) Cytoplasmic glutathione redox status determines survival upon exposure to the thiol-oxidant 4,4'-dipyridyl disulfide. FEMS Yeast Research 7(3):391-403.


Jean-Baptiste Jomain, Estelle Tallet, Isabelle Broutin, Sylviane Hoos, Jan van Agthoven, Arnaud Ducruix, Paul A Kelly, Birthe B Kragelund, Patrick England and Vincent Goffin. (2007) Structural and thermodynamic bases for the design of pure prolactin receptor antagonists: X-ray structure of Del1-9-G129R-hPRL. Journal of Biological Chemistry 282(45):33118-31.


Johannes Haugstetter, Maurer Michael, Thomas Blicher, Martin Pagac, Gerhard Wider and Lars Ellgaard. (2007) Structure-function analysis of the ER oxidoreductase TMX3 reveals interdomain stabilization of the N-terminal redox-active domain Journal of Biological Chemistry 280(46):33859-33867.


Katrine M Andersen, Colin A Semple and Rasmus Hartmann-Petersen. (2007) Characterisation of the nascent polypeptide-associated complex in fission yeast. Molecular Biology Reports 34(4):275-81.


Katrine S Larsen, Henrik Østergaard, Jais R Bjelke, Ole H Olsen, Hanne B Rasmussen, Leif Christensen, Birthe B Kragelund and Henning R Stennicke. (2007) Engineering the substrate and inhibitor specificities of human coagulation Factor VIIa. Biochemical Journal 405(3):429-38.


Kristofer Modig, Vibeke W. Jürgensen, Kresten Lindorff-Larsen, Wolfgang Fieber, Henrik G Bohr and Flemming Martin Poulsen. (2007) Detection of initiation sites in protein folding of the four helix bundle ACBP by chemical shift analysis. FEBS Letters 581(25):4965-4971.


Louise Kjær Klausen, Andrea Schulze, Michael Seeger and Rasmus Hartmann-Petersen. (2007) Ubiquitin domain proteins in disease Biochemistry 8(1):1.


Majbritt Thymark, Eva Johansson, Sine Larsen and Martin Willemoës. (2007) Mutational analysis of the nucleotide binding site of Escherichia coli dCTP deaminase Archives of Biochemistry and Biophysics 470(1):20-6.


Mario Schelhaas, Johan Malmström, Lucas Pelkmans, Johannes Haugstetter, Lars Ellgaard, Kay Grünewald and Ari Helenius. (2007) Simian Virus 40 depends on ER protein folding and quality control factors for entry into host cells. Cell 131(3):516-29.


Morten Ejby, Michael A Sørensen and Steen Pedersen. (2007) Pseudouridylation of helix 69 of 23S rRNA is necessary for an effective translation termination. Proceedings of the National Academy of Science of the United States of America 104(49):19410-5.


Patrik Lundström, Kaare Teilum, Tommy Carstensen, Irina Bezsonova, Silke Wiesner, D Flemming Hansen, Tomasz L Religa, Mikael Akke and Lewis E Kay. (2007) Fractional 13C enrichment of isolated carbons using [1-13C]- or [2- 13C]-glucose facilitates the accurate measurement of dynamics at backbone Calpha and side-chain methyl positions in proteins Journal of Biomolecular NMR 38(3):199-212.


Penny von Wettstein-Knowles. (2007) Analyses of barley spike mutant waxes identify alkenes, cyclopropanes and internally branched alkanes with dominating isomers at carbon 9 The Plant Journal 49(2):250-264.


Rosa E Hansen, Henrik Østergaard, Per Nørgaard and Jakob R Winther. (2007) Quantification of protein thiols and dithiols in the picomolar range using sodium borohydride and 4,4'-dithiodipyridine. Analytical Biochemistry 363(1):77-82.


Sandra Lerche Søndergaard, Niels Frimodt-Møller, Birthe Brandt Kragelund and Paul Robert Hansen. (2007) Structure-activity study of the antibacterial peptide fallaxin Protein Science 16(9):1969-1976.


Sophie Bozonnet, Morten Tovborg Jensen, Morten Munch Nielsen, Nushin Aghajari, Malene H. Jensen, Birte Kramhøft, Martin Willemoës, Samuel Tanier, Richard Haser and Birte Svensson. (2007) The pair of sugar tongs site on the non-catalytic domain C of barley a-amylase participates in substrate binding and activity FEBS Journal 274(1):5055-5067.


Thomas Møller Hansen, S Nader S Reihani, Lene B Oddershede and Michael A Sørensen. (2007) Correlation between mechanical strength of messenger RNA pseudoknots and ribosomal frameshifting. Proceedings of the National Academy of Science of the United States of America 104(14):5830-5.


Wenzhong Wang, Jakob R Winther and Colin Thorpe. (2007) Erv2p: characterization of the redox behavior of a yeast sulfhydryl oxidase. Biochemistry 46(11):3246-54.



C. J. Francis, Kresten Lindorff-Larsen, R. B. Best and M. Bendruscolo. (2006) Characterization of the residual structure in the unfolded state of the Delta 131 Delta fragment of staphylococcal nuclease Proteins - Structure Function and Bioinformatics 65(1):145-52.


Gitte A Jensen, Olav M Andersen, Alexandre M J J Bonvin, Ida Bjerrum-Bohr, Michael Etzerodt, Hans C Thøgersen, Charlotte O'Shea, Flemming M Poulsen and Birthe B Kragelund. (2006) Binding site structure of one LRP-RAP complex: implications for a common ligand-receptor binding motif. Journal of Molecular Biology 362(4):700-16.


Heidi Asschenfeldt Ernst, Leila Lo Leggio, M. Willemoes, G. A. Leonard, P. Blum and Sine Larsen. (2006) Structure of the Sulfolobus solfataricus alpha-glucosidase: Implications for domain conservation and substrate recognition in GH31 Journal of Molecular Biology 358(4):1106-24.


Houman Ghasriani, Kaare Teilum, Ylva Johnsson, Per Fernlund and Torbjörn Drakenberg. (2006) Solution structures of human and porcine beta-microseminoprotein Journal of Molecular Biology 362(3):502-15.


Jais R Bjelke, Egon Persson, Hanne B Rasmussen, Birthe B Kragelund and Ole H Olsen. (2006) A loop of coagulation factor VIIa influencing macromolecular substrate specificity. FEBS Letters 581(1):71-6.


Jakob Ploug Jørgensen, Anne-Marie Lauridsen, Poul Kristensen, Karen Dissing, Anders H Johnsen, Klavs B Hendil and Rasmus Hartmann-Petersen. (2006) Adrm1, a putative cell adhesion regulating protein, is a novel proteasome-associated factor. Journal of Molecular Biology 360(5):1043-52.


Kjell Ove Håkansson, Henrik Østergaard and Jakob R. Winther. (2006) Crystallization of mutant forms of glutaredoxin Grx1p from yeast Acta Crystallographica. Section F : Structural Biology and Crystallization Communications 62(9):920-922.


Kaare Teilum, Flemming M Poulsen and Mikael Akke. (2006) The inverted chevron plot measured by NMR relaxation reveals a native-like unfolding intermediate in acyl-CoA binding protein Proceedings of the National Academy of Science of the United States of America 103(18):6877-82.


Kaare Teilum, Ulrika Brath, Patrik Lundström and Mikael Akke. (2006) Biosynthetic 13C labeling of aromatic side chains in proteins for NMR relaxation measurements Journal of the American Chemical Society 128(8):2506-7.


M. ABou Hachem, S. Bozonnet, M. Willemoes, B. Kramhøft, K. Fukuda, Birgit C. Bønsager, M. T. Jensen, J. Nøhr, N. Tranier, N.. Juge, x. Robert, Richard Haser, N. Aghajari and B. Svensson. (2006) Interactions of barley alpha-amylase isozymes with Ca2+, substrates and proteinaceous inhibitors Biocatalysis and Biotransformation 24:83-93.


M. S. Kulp, E. M. Frickel, Lars Ellgaard and J. S. Weismann. (2006) Domain architecture of protein-disulfide isomerase facilitates its dual role as an oxidase and an isomerase in Ero1p-mediated disulfide formation. Journal of Biological Chemistry 281(2):876-84..


M. Louhivuori, R. Otten, Kresten Lindorff-Larsen and A. Annila. (2006) Conformational fluctuations affect protein alignment in dilute liquid crystal media. Journal of the American Chemical Society 128(13):4371-4376.


Maher Abou Hachem, Sophie Bozonnet, Martin Willemoës, Birgit C. Bønsager, Morten Munch Nielsen, Kenji Fukuda, Birte Kramhøft, Kenji Maeda, Bent Walther Sigurskjold, Per Hägglund, Christine Finnie, Haruhide Mori, Xavier Robert, Malene H. Jensen, Samuel Tranier, Nushin Aghajari, Richard Haser and Birte Svensson. (2006) Interactions between Barley a-Amylases, Substrates, Inhibitors and Regulatory Proteins Journal of Applied Glycoscience 53(2):163-169.


Marianne Paulsen, Connie Lund, Zarqa Akram, Jakob R Winther, Nina Horn and Lisbeth Birk Møller. (2006) Evidence that translation reinitiation leads to a partially functional Menkes protein containing two copper-binding sites American Journal of Human Genetics 79(2):214-29.


Michael Riis Hansen, Jesper Tranekjær Jørgensen and Gert Dandanell. (2006) Xanthosine utilization in Salmonella enterica serovar Typhimurium is recovered by a single aspartate-to-glycine substitution in xanthosine phosphorylase. Journal of Bacteriology 188(11):4153-7.


Michael Nielsen, Jacob Albrethsen, Flemming Hofmann Larsen and K. Skriver. (2006) The Arabidopsis ADP-ribosylation factor (ARF) and ARF-like (ARL) system and its regulation by BIG2, a large ARF-GEF Plant Science 171(6):707-717.


Olof Björnberg, Henrik Ostergaard and Jakob R Winther. (2006) Measuring intracellular redox conditions using GFP-based sensors Antioxidants & Redox Signaling 8:354-61.


Olof Björnberg, Henrik Østergaard and Jakob R Winther. (2006) Mechanistic insight provided by glutaredoxin within a fusion to redox-sensitive yellow fluorescent protein Biochemistry 45(7):2362-71.


R. B. Best, Kresten Lindorff-Larsen, M. A. DePristo and M. VEndruscolo. (2006) Relation between native ensembles and experimental structures of proteins. Proceedings of the National Academy of Science of the United States of America 103(29):10901-6.


Vidya Chandran, Elliott J Stollar, Kresten Lindorff-Larsen, Jeffrey F Harper, Walter J Chazin, Christopher M Dobson, Ben F Luisi and John Christodoulou. (2006) Structure of the regulatory apparatus of a calcium-dependent protein kinase (CDPK) Journal of Molecular Biology 357(2):400-10.


Wouter Boomsma, John T. Kent, Kanti V. Mardia, Charles C. Taylor and Thomas Hamelryck. (2006) Graphical models and directional statistics capture protein structure Interdisciplinary Statistics and Bioinformatics 317(5834):111-114.



Addie Nina Olsen, Heidi Asschenfeldt Ernst, Leila Lo Leggio and Karen Skriver. (2005) DNA-binding specificity and molecular functions of NAC transcription factors Plant Science 169(4):785-797.


Emanuele Paci, K. Lindorff-Larsen, Christopher M. Dobson, Martin Karplus and Michele Vendruscolo. (2005) Transition State Contact Orders Correlate with Protein Folding Rates Journal of Molecular Biology 352(3):495-500.


Eva Johansson, Mathias Fanø, Julie H Bynck, Jan Neuhard, Sine Larsen, Bent W Sigurskjold, Ulla Christensen and Martin Willemoës. (2005) Structures of dCTP deaminase from Escherichia coli with bound substrate and product: reaction mechanism and determinants of mono- and bifunctionality for a family of enzymes Journal of Biological Chemistry 280(4):3051-9.


Gert Dandanell, R.H. Szczepanowski, B. Kierdaszuk, D. Shugar and M. Bochtler. (2005) Escherichia coli Purine Nucleoside Phosphorylase II, the Product of the xapA Gene Journal of Molecular Biology 348(1):113-25.


Heidi Asschenfeldt Ernst, Martin Willemoës, Leila Lo Leggio, Gordon Leonard, Paul Blum and Sine Larsen. (2005) Characterization of different crystal forms of the a-glucosidase MalA from Sulfolobus solfataricus Acta Crystallographica Section F 61:1039-1042.


Heidi Asschenfeldt Ernst, Martin Willemoës, Leila Lo Leggio, Gordon Leonard, Paul Blum and Sine Larsen. (2005) Characterization of different crystal forms of the alpha-glucosidase MalA from Sulfolobus solfataricus Acta Crystallographica. Section F : Structural Biology and Crystallization Communications 61:1039-42.


K. A. Dittmar, Michael Askvad Sørensen, J. Elf, M. Ehrenberg and Tao Pan. (2005) Selective charging of tRNA isoacceptors induced by amino-acid starvation EMBO Reports 6(2):151–157.


Karen L. Maxwell, D. Wildes, A. Zarrine-Afsar, Miguel A. De Los Rios Rivos, Andrew G. Brown, Claire T. Friel, Linda Hedberg, Jia-Cherng Horng, Diana Bona, Erik J. Miller, Alexis Vallée-Bélisle, Ewan R. G. Main, Francesco Bemporad, Linlin Qiu, Kaare Teilum, Ngoc-Diep Vu, Aled M. Edwards, Ingo Ruczinski, Flemming M. Poulsen, Birthe Brandt Kragelund, Stephen W. Michnick, Fabrizio Chiti, Yawen Bai, Stephen J. Hagen, Luis Serrano, Mikael Oliveberg, Daniel P. Raleigh, Pernilla Wittung Stafshede, Sheena E. Radford, Sophie e. Jackson, Tobin R. Sosnick, Susan Margusee, Alan R. Davidson and Kevin W. Plaxco. (2005) Protein folding: Defining a standard set of experimental conditions and a preliminary kinetic data set of two-state proteins Protein Science 14(3):602-616.


Katrine M Andersen, Kay Hofmann and Rasmus Hartmann-Petersen. (2005) Ubiquitin-binding proteins: similar, but different. Essays in Biochemistry 41(5):49-67.


Kresten Lindorff-Larsen, Robert B. Best and Michele Vendruscolo. (2005) Interpreting Dynamically-Averaged Scalar Couplings in Proteins Journal of Biomolecular NMR 32(4):273-280.


Kresten Lindorff-Larsen, Robert B. Best, M. A. DePristo, C. M. Dobson and Michele Vendruscolo. (2005) Simultaneous determination of protein structure and dynamics Nature 433(7022):128-132.


Kaare Teilum, Birthe Brandt Kragelund and Flemming Martin Poulsen. (2005) Application of Hydrogen Exchange Kinetics to Studies of Protein Folding Protein Folding Handbook 103(18):6877-82.


Kaare Teilum, Jeffrey C Hoch, Vincent Goffin, Sandrina Kinet, Joseph A Martial and Birthe B Kragelund. (2005) Solution structure of human prolactin Journal of Molecular Biology 351(4):810-23.


Kaare Teilum, Thorsten Thormann, Nigel R. Caterer, Heidi I. Poulsen, Peter H. Jensen, Jens Knudsen, Birthe Brandt Kragelund and Flemming M. Poulsen. (2005) Different secondary structure elements as scaffolds for protein folding transition states of two homologous four-helix bundles Proteins - Structure Function and Bioinformatics 59(1):80-90.


M. M. Dedmon, K. Lindorff-Larsen, J. Christodoulou, Michele Vendruscolo and C. M. Dobson. (2005) Mapping Long-Range Interactions in a-Synuclein using Spin-Label NMR and Ensemble Molecular Dynamics Simulations Journal of the American Chemical Society 127(2):476-477.


Martin Willemoes and M. Kilstrup. (2005) Nucleoside triphosphate synthesis catalysed by adenylate kinase is ADP dependent Archives of Biochemistry and Biophysics 444(2):195-199.


Michael Askvad Sørensen, J. Elf, E. Bouakaz, T. Tenson, S. Sanyal, G. R. Björk and M. Ehrenberg. (2005) Over Expression of a tRNALeu Isoacceptor Changes Charging Pattern of Leucine tRNAs and Reveals New Codon Reading Journal of Molecular Biology 354(1):16-24.


Michael Riis Hansen and Gert Dandanell. (2005) Purification and characterization of RihC, a xanthosine-inosine-uridine-adenosine-preferring hydrolase from Salmonella enterica serovar Typhimurium Biochimica et Biophysica Acta - General Subjects 1723:55-62.


Rasmus Hartmann-Petersen and Colin Gordon. (2005) Quantifying protein-protein interactions in the ubiquitin pathway by surface plasmon resonance. Methods in Enzymology 399(5):164-77.


Rosa E Hansen, Henrik Østergaard and Jakob R Winther. (2005) Increasing the reactivity of an artificial dithiol-disulfide pair through modification of the electrostatic milieu Biochemistry 44(15):5899-906.


S. Rønhede, Bo Jensen, Søren Rosendahl, Birthe Brandt Kragelund, Rene K. Juhler and J. Aamand. (2005) Hydroxylation of the Herbicide Isoproturon by Fungi Isolated from Agricultural soil Applied and Environmental Microbiology 71(12):7927-7932.


Sine Lo Svenningsen, Nina Constantino, Donald L Court and Sankar Adhya. (2005) On the role of Cro in lambda prophage induction Proceedings of the National Academy of Science of the United States of America 102(12):4465-4469.


Sophie Bozonnet, Birgit C. Bønsager, Birte Kramhøft, Haruhide Mori, Maher Abou Hachem, Martin Willemoës, Morten T. Jensen, Kenji Fukuda, Peter K. Nielsen, Nathalie Juge, Nushin Aghajari, Samuel Tranier, Xavier Robert, Richard Haser and Birte Svensson. (2005) Binding of carbohydrates and protein inhibitors to the surfaceof a-amylases Biologia 60(16):27-36.


Tsuneo Ohnishi, André H Juffer, Masahiro Tamoi, Karen Skriver and Tamo Fukamizo. (2005) 26 kDa endochitinase from barley seeds: an interaction of the ionizable side chains essential for catalysis Journal of Biochemistry 138(5):553-62.


Wolfgang Fieber, Birthe Brandt Kragelund, Morten Peter Meldal and Flemming M. Poulsen. (2005) Reversible Dimerization of Acid-Denatured ACBP Controlled by Helix A4 Biochemistry 44(5):1375-1384.


Wouter Boomsma and Thomas Hamelryck. (2005) Full cyclic coordinate descent BMC bioinformatics 6(5834):111-114.



Jakob R. Winther, Lowri H. Phylip and John Kay. (2004) Saccharopepsin Aspartic and Metallo Peptidases 44(15):5899-906.


Addie Nina Olsen, Heidi Asschenfeldt Ernst, Leila Lo Leggio, Eva Helena Johansson, Sine Larsen and Karen Skriver. (2004) Preliminary crystallographic analysis of the NAC domain of ANAC, a member of the plant-specific NAC transcription factor family Acta Crystallographica. Section D: Biological Crystallography 60(6):112-115.


Camilla Christiansen, Phaedria M St Hilaire and Jakob R. Winther. (2004) Fluorometric polyethyleneglycol-peptide hybrid substrates for quantitative assay of protein disulfide isomerase Analytical Biochemistry 333(1):148-55.


Emanuele Paci, Claire T Friel, Kresten Lindorff-Larsen, Sheena E Radford, Martin Karplus and Michele Vendruscolo. (2004) Comparison of the transition state ensembles for folding of Im7 and Im9 determined using all-atom molecular dynamics simulations with phi value restraints Proteins: Structure, Function, and Bioinformatics 54(3):513-25.


Eva Helena Johansson, Jan Neuhard, Martin Willemoes and Sine Larsen. (2004) Structural, Kinetic, and Mutational Studies of the Zinc Ion Environment in Tetramic Cytidine Deaminase Biochemistry 43(16):6020-6029.


Eva Johansson, Jan Neuhard, Martin Willemoës and Sine Larsen. (2004) Structural, kinetic, and mutational studies of the zinc ion environment in tetrameric cytidine deaminase Biochemistry 43(20):6020-9.


Heidi Asschenfeldt Ernst, Addie Nina Olsen, Karen Skriver, Sine Larsen and Leila Lo Leggio. (2004) Structure of the conserved domain of ANAC, a member of the NAC family of transcription factors EMBO Reports 5(4):297-303.


Henrik Østergaard, Christine Tachibana and Jakob R. Winther. (2004) Monitoring disulfide bond formation in the eukaryotic cytosol Journal of Cell Biology 166(3):337-45.


J. G. Olsen, A. Rasmussen, Penny von Wettstein-Knowles and H. Wada. (2004) Structure of the mitochondrial Beta-ketoacyl -(acyl carrier protein) synthase from Arabidopsis and its role in fatty acid synthesis FEBS Letters 16:170-74.


J. Nielsen, M. A. Kristensen, Martin Willemoes, F. C. Nielsen and Jan Christiansen. (2004) Sequential dimerization of human zipcode-binding protein IMP1 on RNA: a cooperative mechanism providing RNP stability Nucleic Acids Research 32(14):4368-4376.


Klavs B Hendil and Rasmus Hartmann-Petersen. (2004) Proteasomes: a complex story. Current Protein and Peptide Science 5(3):135-51.


Kresten Lindorff-Larsen, Michele Vendruscolo, Emanuele Paci and Christopher M Dobson. (2004) Transition states for protein folding have native topologies despite high structural variability Nature Structural and Molecular Biology 11(5):443-9.


Kresten Lindorff-Larsen, Sigridur Kristjansdottir, Kaare Teilum, Wolfgang Fieber, Christopher M Dobson, Flemming Martin Poulsen and Michele Vendruscolo. (2004) Determination of an ensemble of structures representing the denatured state of the bovine acyl-coenzyme a binding protein Journal of the American Chemical Society 126(10):3291-3219.


Martin Willemoes. (2004) Competition between ammonia derived from internal glutamine hydrolysis and hydroxylamine present in the solution for incorporation into UTP as catalysed by Lactococcus lactis CTP synthase Archives of Biochemistry and Biophysics 424(16):105-111.


Miranda Stone, Rasmus Hartmann-Petersen, Michael Seeger, Dawadschargal Bech-Otschir, Mairi Wallace and Colin Gordon. (2004) Uch2/Uch37 is the major deubiquitinating enzyme associated with the 26S proteasome in fission yeast. Journal of Molecular Biology 344(3):697-706.


Pernille Andersen, Birthe B Kragelund, Addie N Olsen, Flemming H Larsen, Nam-Hai Chua, Flemming M Poulsen and Karen Skriver. (2004) Structure and biochemical function of a prototypical Arabidopsis U-box domain Journal of Biological Chemistry 279(38):40053-40061.


Rasmus Hartmann-Petersen and Colin Gordon. (2004) Protein degradation: recognition of ubiquitinylated substrates. Current Biology 14(18):R754-6.


Rasmus Hartmann-Petersen and Colin Gordon. (2004) Integral UBL domain proteins: a family of proteasome interacting proteins. Seminars in Cell and Developmental Biology 15(2):247-59.


Rasmus Hartmann-Petersen, Mairi Wallace, Kay Hofmann, Grete Koch, Anders H Johnsen, Klavs B Hendil and Colin Gordon. (2004) The Ubx2 and Ubx3 cofactors direct Cdc48 activity to proteolytic and nonproteolytic ubiquitin-dependent processes. Current Biology 14(9):824-8.


Rasmus Hartmann-Petersen. (2004) Meeting report: The ubiqitin family gathers The Biochemist 14(26):34-36.


René Thomsen and Wouter Boomsma. (2004) Multiple sequence alignment using SAGA Applications of Evolutionary Computing 6(5834):111-114.


Ruoyu Xiao, Bonney Wilkinson, Anton Solovyov, Jakob R. Winther, Arne Holmgren, Johanna Lundström-Ljung and Hiram F Gilbert. (2004) The contributions of protein disulfide isomerase and its homologues to oxidative protein folding in the yeast endoplasmic reticulum Journal of Biological Chemistry 279(48):49780-6.


Tanja la Cour, Lars Kiemer, Anne Mølgaard, Ramneek Gupta, Karen Skriver and Søren Brunak. (2004) Analysis and prediction of leucine-rich nuclear export signals. Protein Engineering Design and Selection (Print Edition) 17(6):527-36.


Wouter Boomsma. (2004) A comparison of adaptive operator scheduling methods on the traveling salesman problem Evolutionary Computation in Combinatorial Optimization 6(5834):111-114.



A.M. Sanden, I. Prytz, I. Tubelekas, C. Forsberg, H. Le, A. Hektor, P. Neubauer, Z. Pragai, C. Harwood, A. Ward, A. Picon, J.T. de Mattos, P. Postma, A. Farewell, T. Nystrøm, S. Reeh, Steen Pedersen and G. Larsson. (2003) Limiting factors in Escherichia colifed-batch production of recombinant proteins Biotechnology and Bioengineering (Print) 104:158-166.


Addie Nina Olsen and K. Skriver. (2003) Ligand mimicry? Plant-parasitic nematode polypeptide with similarity to CLAVATA3 Trends in Plant Science 279(8):55-57.


Caroline F Wright, Kresten Lindorff-Larsen, Lucy G Randles and Jane Clarke. (2003) Parallel protein-unfolding pathways revealed and mapped Nature Structural and Molecular Biology 10(8):658-62.


Kresten Lindorff-Larsen, Emanuele Paci, Luis Serrano, Christopher M Dobson and Michele Vendruscolo. (2003) Calculation of mutational free energy changes in transition states for protein folding Biophysical Journal 85(2):1207-14.


Krestine Greve, Tanja La Cour Bravo Munoz, Michael Krogh Jensen, Flemming Martin Poulsen and K. Skriver. (2003) Interactions between plant RING-H2 and plant-specific NAC (NAM/ATAF1/2/CUC2) proteins: RING-H2 molecular specificity and cellular localization. Biochemical Journal 279(371):97-108.


Kristoffer Torbjørn Bæk, Sine Lo Svenningsen, Harvey Eisen, Kim Sneppen and Stanley Brown. (2003) Single-cell Analysis of Lambda Immunity Regulation Journal of Molecular Biology 334(3):363-372.


Martin Willemoes and Sine Larsen. (2003) Substrate inhibition of Lactococcus lactis cytidine 5'-triphosphate synthase by ammonium chloride is enhanced by salt-dependent tetramer dissociation Archives of Biochemistry and Biophysics 413(11):17-22.


Martin Willemoes. (2003) Thr-431 and Arg-433 Are Part of a Conserved Sequence Motif of the Glutamine Amidotransferase Domain of CTP Synthases and Are Involved in GTP Activation of the Lactococcus lactis Enzyme Journal of Biological Chemistry 278(11):9407-9411.


Mette Christensen, Tudor Borza, Gert Dandanell, Anne-Marie Gilles, Octavian Barzu, Rod A. Kelln and Jan Neuhard. (2003) Regulation of Expression of the 2-Deoxy-D-Ribose Utilization Regulon, deoQKPX, from Salmonella enterica serovar Typhimurium Journal of Bacteriology 185(20):6042-6050.


Michael Seeger, Rasmus Hartmann-Petersen, Caroline R M Wilkinson, Mairi Wallace, Itaru Samejima, Martin S Taylor and Colin Gordon. (2003) Interaction of the anaphase-promoting complex/cyclosome and proteasome protein complexes with multiubiquitin chain-binding proteins. Journal of Biological Chemistry 278(19):16791-6.


Per Nørgaard, Christine Tachibana, Anette W Bruun and Jakob R. Winther. (2003) Gene regulation in response to protein disulphide isomerase deficiency Yeast (Chichester, England) 20(7):645-52.


Rasmus Hartmann-Petersen, Colin A M Semple, Chris P Ponting, Klavs B Hendil and Colin Gordon. (2003) UBA domain containing proteins in fission yeast. International Journal of Biochemistry & Cell Biology 35(5):629-36.


Rasmus Hartmann-Petersen, Klavs B Hendil and Colin Gordon. (2003) Ubiquitin binding proteins protect ubiquitin conjugates from disassembly. FEBS Letters 535:77-81.


Rasmus Hartmann-Petersen, Michael Seeger and Colin Gordon. (2003) Transferring substrates to the 26S proteasome. TIBS -Trends in Biochemical Sciences. Regular ed. 28(1):26-31.


Tanja La Cour Bravo Munoz, R. Gupta, K. Rapacki, K. Skriver, Flemming Martin Poulsen and S. Brunak. (2003) NESbase version 1.0: a database of nuclear export signals. Nucleic Acids Research 279(31):1393-1396.


Wouter Boomsma. (2003) Using adaptive operator scheduling on problem domains with an operator manifold The 2003 Congress on Evolutionary Computation, 2003. CEC'03 6(5834):111-114.



A.S. Carlsson, S.T. LaBrie, A.J. Kinney, Penny von Wettstein-Knowles and J. Browse. (2002) A KAS2 cDNA complements the phenotypes of the Arabidopsis fab1 mutant that differs in a single residue bordering the substrate binding pocket Plant Journal 29(6):761-770.


Addie Nina Olsen, John Mundy and Karen Skriver. (2002) Peptomics, identification of novel cationic Arabidopsis peptides with conserved sequence motifs. In Silico Biology 2(4):441-51.


Esben Selmer Buhl, Niels Jessen, Rasmus Pold, Thomas Ledet, Allan Flyvbjerg, Steen B Pedersen, Oluf Pedersen, Ole Schmitz and Sten Lund. (2002) Long-term AICAR administration reduces metabolic disturbances and lowers blood pressure in rats displaying features of the insulin resistance syndrome Diabetes 51(7):2199-206.


Jens K Thomsen, Birthe B Kragelund, Kaare Teilum, Jens Knudsen and Flemming M Poulsen. (2002) Transient intermediary states with high and low folding probabilities in the apparent two-state folding equilibrium of ACBP at low pH Journal of Molecular Biology 318(3):805-14.


Klavs B Hendil, Rasmus Hartmann-Petersen and Keiji Tanaka. (2002) 26 S proteasomes function as stable entities. Journal of Molecular Biology 315(4):627-36.


Kaare Teilum, Birthe B Kragelund and Flemming M Poulsen. (2002) Transient structure formation in unfolded acyl-coenzyme A-binding protein observed by site-directed spin labelling Journal of Molecular Biology 324(2):349-57.


Kaare Teilum, K. Maki, Birthe Brandt Kragelund, Flemming Martin Poulsen and H. Roder. (2002) Early kinetic intermediate in the folding of acyl-coenzyme A binding protein detected by fluorescence labelling and rapid mixing Proceedings of the National Academy of Sciences U.S.A. 365(99):9807-9812.


Kaare Teilum, Kosuke Maki, Birthe B Kragelund, Flemming M Poulsen and Heinrich Roder. (2002) Early kinetic intermediate in the folding of acyl-CoA binding protein detected by fluorescence labeling and ultrarapid mixing Proceedings of the National Academy of Science of the United States of America 99(15):9807-12.


M.C. Wadum, J.K. Villadsen, S. Feddersen, R.S. Moller, T.B. Neergaard, Birthe Brandt Kragelund, P. Hojrup, N.J. Faergeman and J. Knudsen. (2002) Fluorescently labelled bovine acyl-CoA-binding protein acting as an acyl-CoA sensor: interaction with CoA and acyl-CoA esters and its use in measuring free acyl-CoA esters and non-esterified fatty acids Biochemical Journal 365(15):165-172.


Martin Willemoes and Bent Walther Sigurskjold. (2002) Steady-state kinetics of the glutaminase reaction of CTP synthase from Lactococcus lactis. The role of the allosteric activator GTP in coupling between glutamine hydrolysis and CTP synthesis FEBS Journal 269(11):4772-4779.


Martin Willemoës, Mogens Kilstrup, Peter Roepstorff and Karin Hammer. (2002) Proteome analysis of a Lactococcus lactis strain overexpressing gapA suggests that the gene product is an auxiliary glyceraldehyde 3-phosphate dehydrogenase Proteomics 2(8):1041-1046.


P. G. Sørensen and Gert Dandanell. (2002) A new type of didhydroorotate dehydrogenase, type 1S, from the thermoacidophilic archaeon Sulfolobus solfataricus Extremopiles 6(3):245-251.


Søren Prag, Eugene A Lepekhin, Kateryna Kolkova, Rasmus Hartmann-Petersen, Anna Kawa, Peter S Walmod, Vadym Belman, Helen C Gallagher, Vladimir Berezin, Elisabeth Bock and Nina Pedersen. (2002) NCAM regulates cell motility. Journal of Cell Science 115:283-92.



A Henriksen, O Mirza, C Indiani, K Teilum, G Smulevich, K G Welinder and M Gajhede. (2001) Structure of soybean seed coat peroxidase: a plant peroxidase with unusual stability and haem-apoprotein interactions Protein Science 10(1):108-15.


C R Wilkinson, M Seeger, R Hartmann-Petersen, M Stone, M Wallace, C Semple and C Gordon. (2001) Proteins containing the UBA domain are able to bind to multi-ubiquitin chains. Nature Cell Biology 3(10):939-43.


K Møller, L D Tidemand, Jakob R. Winther, Lisbeth Olsson, Jure Piskur and J Nielsen. (2001) Production of a heterologous proteinase A by Saccharomyces kluyveri Applied Microbiology and Biotechnology 57:216-9.


Kirsten Arnvig McGuire, Mads Siggaard-Andersen, M. Gita Bangera, Johan Gotthardt Olsen and Penny von Wettstein-Knowles. (2001) Β-Ketoacyl - (Acyl Carrier Protein) Synthase I of Escherichia coli: Aspects of the Condensation Mechanism Revealed by Analyses of Mutations in the Active Site Pocket Biochemistry 29:9836-9845.


Kresten Lindorff-Larsen and J R Winther. (2001) Surprisingly high stability of barley lipid transfer protein, LTP1, towards denaturant, heat and proteases F E B S Letters 488(3):145-8.


Kresten Lindorff-Larsen, Mathilde H. Lerche, Flemming Martin Poulsen, Peter Roepstorff and Jakob R. Winther. (2001) Barley lipid transfer protein, LTP1, contains a new type of lipid-like post-translational modification Journal of Biological Chemistry 276(36):33547-53.


M.A. Sørensen. (2001) Charging Levels of Four tRNA Species in Escherichia coli Rel+ and REL- Strains during Amino Acid Starvation: A Simple Model for the Effect of ppGpp on Translational Accuracy Journal of Molecular Biology 307(3):785-798.


Morten Helge Hauberg Nørholm and Gert Dandanell. (2001) Specificity and Topology of the Escherichia coli Xanthosine Permease, a Representative of the NHS Subfamily of the Major Facilitator Superfamily Journal of Bacteriology 6(183):4900-4909.


P S Walmod, R Hartmann-Petersen, A Berezin, S Prag, V V Kiselyov, V Berezin and E Bock. (2001) Evaluation of individual-cell motility. Methods in Molecular Biology 161:59-83.


P Nørgaard, V Westphal, C Tachibana, L Alsøe, B Holst and Jakob R. Winther. (2001) Functional differences in yeast protein disulfide isomerases Journal of Cell Biology 152(3):553-62.


Penny von Wettstein-Knowles, Johan Gotthardt Olsen, Kirsten Arnvig McGuire and Sine Larsen. (2001) Fatty Acid Biosynthesis: Fatty Acid Synthase. Molecular aspects of β-ketoacyl synthase (KAS) catalysis. Biochemical Society 29(28):601-607.


Per Nørgaard and Jakob R. Winther. (2001) Mutation of yeast Eug1p CXXS active sites to CXXC results in a dramatic increase in protein disulphide isomerase activity Biochemical Journal 358(1):269-274.


R Hartmann-Petersen, K Tanaka and K B Hendil. (2001) Quaternary structure of the ATPase complex of human 26S proteasomes determined by chemical cross-linking. Archives of Biochemistry and Biophysics 386(1):89-94.


Rikke B. Jensen, Tanja la Cour, Jacob Albrethsen, Michael Marinus Nielsen and Karen Skriver. (2001) FYVE zinc-finger proteins in the plant model Arabidopsis thaliana: idenfication of Ptdins3P-binding residues by comparison of classic and variant FYVE dominans. Biochemical Journal 2(359):165-173.


Steen L.L. Wadskov-Hansen, Martin Willemoes, Jan Martinussen, Karin Hammer, Jan Neuhard and Sine Larsen. (2001) Cloning and Verification of the Lactococcus lactis pyrG Gene and Characterization of th Gene Product, CTP Synthase Journal of Biological Chemistry 276(8):38002-38009.



B B Kragelund, A Hauenschild, G Carlström, O Pongs and B E Finn. (2000) 1H, 13C, and 15N assignments of un-myristoylated Ca2+-frequenin, a synaptic efficacy modulator Journal of Biomolecular N M R 16(1):85-6.


K Teilum, B B Kragelund, J Knudsen and F M Poulsen. (2000) Formation of hydrogen bonds precedes the rate-limiting formation of persistent structure in the folding of ACBP Journal of Molecular Biology 301(5):1307-14.


Kirsten Arnvig McGuire, J.N. McGuire and Penny von Wettstein-Knowles. (2000) Acyl carrier protein (ACP) inhibition and other differences between b-ketoacyl synthase (KAS) I and II Biochemical Society Transactions(28):607-610.


Kresten Lindorff-Larsen and Jakob R. Winther. (2000) Thiol alkylation below neutral pH Analytical Biochemistry 286(2):308-10.


L Ostergaard, K Teilum, O Mirza, O Mattsson, M Petersen, K G Welinder, J Mundy, M Gajhede and A. Henriksen. (2000) Arabidopsis ATP A2 peroxidase. Expression and high-resolution structure of a plant peroxidase with implications for lignification. Plant Molecular Biology 44(2):231-43.


M Li, L H Phylip, W E Lees, Jakob R. Winther, B M Dunn, A Wlodawer, J Kay and A Gustchina. (2000) The aspartic proteinase from Saccharomyces cerevisiae folds its own inhibitor into a helix Nature Structural and Molecular Biology 7(2):113-7.


Martin Willemoes, Bjarne Hove-Jensen and Sine Larsen. (2000) Steady State Kinetic Model for the Binding of Substrates and Allosteric Effectors to Escherichia coli Phosphoribosyl-diphosphate Synthase. Journal of Biological Chemistry 45(8):35408-35412.


Penny von Wettstein-Knowles, J.G. Olsen, Kirsten Arnvig Mcguire and Sine Larsen. (2000) Molecular aspects of beta-ketoacyl synthase (KAS) catalysis Biochem. Soc. Trans. 29(28):601-607.


R B Jensen, K Lykke-Andersen, G I Frandsen, J Haseloff, H M Jespersen, J Mundy and K Skriver. (2000) Promiscuous and specific phospholipid binding by domains in ZAC, a membrane-associated Arabidopsis protein with an ARF GAP zinc finger and a C2 domain. Plant Molecular Biology 44(6):799-814.


R Hartmann-Petersen, P S Walmod, A Berezin, V Berezin and E Bock. (2000) Individual cell motility studied by time-lapse video recording: influence of experimental conditions. Cytometry. Part B: Clinical Cytometry 40(4):260-70.


R.W. King and Penny von Wettstein-Knowles. (2000) Epicuticular waxes and regulation of ear wetting and pre-harvest sprouting in barley and wheat Euphytica(112):157-166.


Steen Pedersen. (2000) Thermodynamics of heat-shock response. Physical Review Letters 51(7):Phys Rev Lett; 84: 3005-8..



B B Kragelund, J Knudsen and F M Poulsen. (1999) Acyl-coenzyme A binding protein (ACBP) B B A - Reviews on Cancer 1441:150-61.


Birthe Brandt Kragelund, J. Knudsen and Flemming Poulsen. (1999) Acyl-coenzyme A binding protein, ACBP BBA General Subjects 1441:150-161.


Birthe Brandt Kragelund, Peter Osmark, Thomas B. Neergaard, Jacob Schiødt, Karsten Kristiansen, Jens Knudsen and Flemming Poulsen. (1999) The formation of a native-like structure containing eight conserved hydrophobic residues is rate limiting in two-state protein folding of ACBP Nature Structural and Molecular Biology 6(6):594-601.


Casper Jørgensen and Gert Dandanell. (1999) Isolation and characterization of mutations in the Escherichia coli regulatory protein XapR Journal of Bacteriology 6:4397-4403.


K Teilum, L Ostergaard and K G Welinder. (1999) Disulfide bond formation and folding of plant peroxidases expressed as inclusion body protein in Escherichia coli thioredoxin reductase negative strains Protein Expression and Purification 15(1):77-82.


M U Jørgensen, S D Emr and Jakob R. Winther. (1999) Ligand recognition and domain structure of Vps10p, a vacuolar protein sorting receptor in Saccharomyces cerevisiae European Journal of Biochemistry 260(2):461-9.


Rikke Jensen, Karen Skriver and Hans Jespersen. (1999) PMZ, a cDNA from Arabidopsis thaliana encoding a putative novel zinc finger motif with homologs in vertabrates and mammals Plant Molecular Biology 40(6):745.


V Westphal, N J Darby and Jakob R. Winther. (1999) Functional properties of the two redox-active sites in yeast protein disulphide isomerase in vitro and in vivo Journal of Molecular Biology 286(4):1229-39.



B B Kragelund, M Jönsson, G Bifulco, W J Chazin, H Nilsson, B E Finn and S Linse. (1998) Hydrophobic core substitutions in calbindin D9k Biochemistry 37(25):8926-37.


A W Bruun, I Svendsen, S O Sørensen, Morten Kielland-Brandt and Jakob R. Winther. (1998) A high-affinity inhibitor of yeast carboxypeptidase Y is encoded by TFS1 and shows homology to a family of lipid binding proteins Biochemistry 37(10):3351-7.


Birthe Brandt Kragelund, B. Heinemann, J. Knudsen and Flemming Poulsen. (1998) Mapping the lifetimes of local opening events in a native state protein Protein Sci. 37(7):2237-2248.


Birthe Brandt Kragelund, M. Jönsson, G. Bifulco, W.J. Chazin, H. Nilsson, B.E. Finn and S. Linse. (1998) Hydrophobic core substitutions in calbindin D9k: Effects on Ca2+ binding and dissociation Biochemistry 37(37):8926-8937.


Dora Raventos Segura, K. Skriver, M. Schlein, K. Karnahl, S. Rogers, J.C. Rogers and John Williams Mundy. (1998) HRT, a novel transcriptional repressor from plants Journal of Biological Chemistry 40(273):23313-20.


J C Spetzler, V Westphal, Jakob R. Winther and M Meldal. (1998) Preparation of fluorescence quenched libraries containing interchain disulphide bonds for studies of protein disulphide isomerases Journal of Peptide Science 4(2):128-37.


M.A. Sørensen, J. Fricke and Steen Pedersen. (1998) Ribosomal Protein S1 required for translation of most, if not all, natural mRNAs in Escherichia coli in vivo Journal of Molecular Biology 51(280):561-569.


Malene Kappen Krüger and M.A. Sørensen. (1998) Aminoacylation of hypomodified tRNAGlu in vivo Journal of Molecular Biology 284(3):609-620.


Malene Kappen Krüger, Steen Pedersen, T.G. Hagervall and M.A. Sørensen. (1998) The modification of the wobble base of tRNAGlu modulates the translation rate of glutamic acid codons in vivo J. Mol. Biol. 51(284):609-620.


T E Maar, Trine Meldgaard Lund, G Gegelashvili, R Hartmann-Petersen, Michael J. Moran, H Pasantes-Morales, V Berezin, E Bock and A Schousboe. (1998) Effects of taurine depletion on cell migration and NCAM expression in cultures of dissociated mouse cerebellum and N2A cells Amino Acids 15(1):77-88.


V Westphal, J C Spetzler, M Meldal, U Christensen and Jakob R. Winther. (1998) Kinetic analysis of the mechanism and specificity of protein-disulfide isomerase using fluorescence-quenched peptides Journal of Biological Chemistry 273(39):24992-9.



Bjørn Holst, Christine Tachibana and Jakob R. Winther. (1997) Active site mutations in yeast protein disulfide isomerase cause dithiothreitol sensitivity and a reduced rate of protein folding in the endoplasmic reticulum Journal of Cell Biology 138(6):1229-1238.


H Van Den Hazel, A M Wolff, Morten Kielland-Brandt and Jakob R. Winther. (1997) Mechanism and ion-dependence of in vitro autoactivation of yeast proteinase A Biochemical Journal(39):339-44.


Iben Schildt Sørensen and Gert Dandanell. (1997) Identification and sequence analysis of Sulfolobus solfataricus purE and purK genes FEMS Microbiology Letters 154(2):173-180.


M.H. Lerche, Birthe Brandt Kragelund, L. Bech and Flemming Poulsen. (1997) Structure of lipid-transfer protein complexed with palmitoyl-CoA. A hydrophobic binding site expandable to fit both large and small lipid-like ligands Structure 37(5):291-306.


Martin Willemoës and Bjarne Hove-Jensen. (1997) Binding of Divalent Magnesium by Escherichia coli Phosphoribosyl Diphosphate Synthetase Biochemistry 36(16):5078-5083.



B Holst, A W Bruun, Morten Kielland-Brandt and Jakob R. Winther. (1996) Competition between folding and glycosylation in the endoplasmic reticulum E M B O Journal 15(14):3538-46.


Birthe Brandt Kragelund, P. Højrup, M.S. Jensen, C.K. Schjerling, E. Juul, J. Knudsen and Flemming Poulsen. (1996) Fast and one-step folding of closely and distantly related homologous proteins of a four-helix bundle family J. Mol. Biol. 37(256):187-200.


C Ramos and Jakob R. Winther. (1996) Exchange of regions of the carboxypeptidase Y propeptide. Sequence specificity and function in folding in vivo European Journal of Biochemistry 242(1):29-35.


C.R. Robinson, E.W. Chung, Birthe Brandt Kragelund, J. Knudsen, R.T. Aplin, Flemming Poulsen and C.M. Dobson. (1996) Probing the nature of non-covalent interactions by mass spectrometry. A study of protein-CoA ligand interactions and assembly J. Amer. Chem. 37(118):8646-8653.


F van Voorst, Morten Kielland-Brandt and Jakob R. Winther. (1996) Mutational analysis of the vacuolar sorting signal of procarboxypeptidase Y in yeast shows a low requirement for sequence conservation Journal of Biological Chemistry 271(2):841-6.


Gitte Frandsen, Frieder Muller-Uri, Michael Nielsen, John Mundy and Karen Skriver. (1996) Novel plant Ca2+-binding protein expressed in response to abscisic acid and osmotic stress The Journal of Biological Chemistry 271(273):343-348.


H B Van Den Hazel, Morten Kielland-Brandt and Jakob R. Winther. (1996) Review Yeast (Chichester, England) 12(1):1-16.


Martin Willemoës, Dan Nilsson and Bjarne Hove-Jensen. (1996) Effects of mutagenesis of aspartic acid residues in the putative phosphoribosyl diphosphate binding site of Escherichia coli phosphoribosyl diphosphate synthetase on metal ion specificity and ribose-5-phosphate binding Biochemistry 35(25):8181-8186.


Nils J. Færgeman, B.W. Sigurskjold, Birthe Brandt Kragelund, K.V. Andersen and J. Knudsen. (1996) Thermodynamics of ligand binding to acyl-coenzyme, A binding protein studied by titration calometry Biochemistry 37(35):14118-14126.


V Westphal, E G Marcusson, Jakob R. Winther, S D Emr and H B van den Hazel. (1996) Multiple pathways for vacuolar sorting of yeast proteinase A Journal of Biological Chemistry 271(20):11865-70.



Birthe Brandt Kragelund, C.R. Robinson, J. Knudsen, C.M. Dobson and Flemming Poulsen. (1995) Folding of a four-helix bundle. Studies of acyl-coenzyme A binding protein Biochemistry 37(34):7217-7224.


Birthe Brandt Kragelund, J. Knudsen and Flemming Poulsen. (1995) Local perturbations by ligand binding on hydrogen exchange kinetics in a four-helix bundle protein, acyl-coenzyme A binding protein (ACBP) J. Mol. Biol. 37(250):695-706.


Corina Seeger, Claus Poulsen and Gert Dandanell. (1995) Identification and Characterization of Genes (xapA, xapB, and xapR) involved in Xanthosine Catabolism in Eschericia coli Journal of Bacteriology 154:5506-5516.


H B van den Hazel, Morten Kielland-Brandt and Jakob R. Winther. (1995) Random substitution of large parts of the propeptide of yeast proteinase A Journal of Biological Chemistry 270(15):8602-9.


Henrik Pedersen, Jens Dall, Gert Dandanell and Poul Valentin-Hansen. (1995) Gene-regulatory modules in Eschericia coli: nucleoprotein complexes formed by cAMP-CRP and CytR at the nupG promotor Molecular Microbiology 154:843-853.


U Grauschopf, Jakob R. Winther, P Korber, T Zander, P Dallinger and J C Bardwell. (1995) Why is DsbA such an oxidizing disulfide catalyst? Cell 83(6):947-55.



Bushra Chaudhry, Frieder Müller-Uri, Verena Cameron-Mills, Simon Gough, David Simpson, K. Skriver and John Williams Mundy. (1994) The barley 60 kDa jasmonate-induced protein (JIP60) is a novel ribosome-inactivating protein Plant Journal 271:815-824.


C Ramos, Jakob R. Winther and Morten Kielland-Brandt. (1994) Requirement of the propeptide for in vivo formation of active yeast carboxypeptidase Y Journal of Biological Chemistry 269(9):7006-12.


C.G. Jensen, S. Brown and Steen Pedersen. (1994) Effect of 4.5S RNA Depletion on Escherichia coli Protein Synthesis and Secretion Journal of Bacteriology 236:2502-2506.


Jakob R. Winther, P Sørensen and Morten Kielland-Brandt. (1994) Refolding of a carboxypeptidase Y folding intermediate in vitro by low-affinity binding of the proregion Journal of Biological Chemistry 269(35):22007-13.


M.A. Sørensen, K.F. Jensen and Steen Pedersen. (1994) High Concentrations of ppGpp Decrease the RNA Chain Growth Rate. Implications for Protein Synthesis and Translation Fidelity During Amino Acid Starvation in Escherichia coli Journal of Molecular Biology 51:441-454.


Michael Askvad Sørensen, Kaj Frank Jensen and Steen Pedersen. (1994) High concentrations of ppGpp decrease the RNA chain growth rate: implications for protein synthesis and translational fidelity during amino acid starvation in Escherichia coli Journal of Molecular Biology 236:441-454.


Robert Leah, K. Skriver, Søren Knudsen, Jan Ruud-Hansen, Natasha V. Raikhei and John Williams Mundy. (1994) Identification of an enhancer/silencer sequence directing the aleurone-specific expression of a barley chitinase gene Plant Journal 271:579-589.


S O Sørensen and Jakob R. Winther. (1994) Active-site residues of procarboxypeptidase Y are accessible to chemical modification BBA General Subjects 1205(2):289-93.


S O Sørensen, H B van den Hazel, Morten Kielland-Brandt and Jakob R. Winther. (1994) pH-dependent processing of yeast procarboxypeptidase Y by proteinase A in vivo and in vitro European Journal of Biochemistry 220(1):19-27.



Birthe Brandt Kragelund, K.V. Andersen, J.C. Madsen, J. Knudsen and Flemming Poulsen. (1993) Threedimensional structure of the complex acyl-coenzyme, A binding protein and palmitoyl-coenzyme A J. Mol. Biol. 37(230):1260-1277.


H B van den Hazel, Morten Kielland-Brandt and Jakob R. Winther. (1993) The propeptide is required for in vivo formation of stable active yeast proteinase A and can function even when not covalently linked to the mature region Journal of Biological Chemistry 268(24):18002-7.


J. Vind, M.A. Sørensen, M.D. Rasmussen and Steen Pedersen. (1993) Synthesis of proteins in Escherichia coli is limited by the concentration of free ribosomes Journal of Molecular Biology 240:678-688.


Karin Hammer, Lisbeth Bech, Palle Hobolth and Gert Dandanell. (1993) DNA specificity of Escherichia coli deoP1 operator-DeoR repressor recognition Mol. Gen. Genet. 237:129-133.


M.D. Rasmussen, M.A. Sørensen and Steen Pedersen. (1993) Isolation and characterization of mutants with impaired regulation of rpsA, the gene encoding ribosomal protein S1 of Escherichia coli Molecular Genetics and Genomics 240:23-28.


P Sørensen, Jakob R. Winther, N C Kaarsholm and F M Poulsen. (1993) The pro region required for folding of carboxypeptidase Y is a partially folded domain with little regular structural core Biochemistry 32(45):12160-6.



Gert Dandanell. (1992) DeoR repression at-a-distance only weakly responds to changes in interoperator separation and DNA topology Nucleic Acids Research 20(20):5407-5412.


H B van den Hazel, Morten Kielland-Brandt and Jakob R. Winther. (1992) Autoactivation of proteinase A initiates activation of yeast vacuolar zymogens European Journal of Biochemistry 207(1):277-83.


U. Vogel, M.A. Sørensen, Steen Pedersen, Kaj Frank Jensen and M. Kilstrup. (1992) Decreasing transcription elongation rate in Escherichia coli exposed to amino acid starvation Molecular Microbiology 6(15):2191-2200.



Gert Dandanell and K. Hammer. (1991) DeoP1 promoter and operator mutants in Escherichia coli: Isolation and characterization Molecular Microbiology 20(5):2371-2376.


Gert Dandanell, Kjeld Norris and Karin Hammer. (1991) Long-distance deoR regulation of gene expression in Escherichia coli Recombiant DNA Technology I. Annals of the New York Academy of Sciences 20(646):19-30.


Jakob R. Winther and P Sørensen. (1991) Propeptide of carboxypeptidase Y provides a chaperone-like function as well as inhibition of the enzymatic activity Proceedings of the National Academy of Sciences of the United States of America 88(20):9330-4.


Jakob R. Winther, T H Stevens and Morten Kielland-Brandt. (1991) Yeast carboxypeptidase Y requires glycosylation for efficient intracellular transport, but not for vacuolar sorting, in vivo stability, or activity European Journal of Biochemistry 197(3):681-9.


M.A. Sørensen and Steen Pedersen. (1991) Cysteine, Even in Low Concentrations, Induces Transient Amino Acid Starvation in Escherichia coli J. Bacteriol. 6:5244-46.


M.A. Sørensen and Steen Pedersen. (1991) Absolute in vivo translation rates of individual codons in Escherichia coli: The two glutamic acid codons GAA and GAG are translated with a threefold difference in rate Journal of Molecular Biology 222(2):265-280.


Ulla Vogel, Steen Pedersen and Kaj Frank Jensen. (1991) An unusual correlation between ppGpp pool size and rate of ribosome synthesis during partial pyrimidine starvation of Escherichia coli Journal of Bacteriology 173(3):1168-1174.



Gert Dandanell and Karin Hammer. (1990) In vivo CRP-cAMP regulation of the deoP1 and deoP2 promoter of E. coli K12 Molecular Genetics (Life Sci Adv) 9(646):41-45.


L A Valls, Jakob R. Winther and T H Stevens. (1990) Yeast carboxypeptidase Y vacuolar targeting signal is defined by four propeptide amino acids Journal of Cell Biology 111(2):361-8.



Lisbeth Mortensen, Gert Dandanell and Karin Hammer. (1989) Purification and characterization of the deoR repressor of Escherichia coli EMBO Journal 8(1):325-331.


Michael Askvad Sørensen, C G Kurland and Steen Pedersen. (1989) Codon usage determines translation rate in Escherichia coli Journal of Molecular Biology 207(2):365-77.



Gert Dandanell, Poul Valentin-Hansen, Jens Erik Løve Larsen and Karin Hammer. (1987) Long-Range cooperativity between gene regulatory sequences in a prokaryote Nature 325(6107):823-826.





Lene M. Bech, John Nielsen, Jakob R. Winther, Morten C. Kielland-Brandt and Klaus Breddam. (1986) Mutational replacement of methionine by arginine in the S'1 substrate binding site of yeast carboxypeptidase Carlsberg Research Communications 51(6):459-465.


Gert Dandanell, Donald L. Court and Karin Hammer. (1986) A single-copy galK promoter cloning vector suitable for cloning strong promoters Gene Analysis Techniques 3(6):102-111.



Jakob R. Winther, Morten C. Kielland-Brandt and Klaus Breddam. (1985) Increased hydrophobicity of the S'1 binding site in carboxypeptidase Y obtained by site-directed mutagenesis Carlsberg Research Communications 50(5):273-284.


Gert Dandanell and Karin Hammer. (1985) Two operator sites separated by 599 base pairs are required for deoR repression of the deo operon of Escherichia coli EMBO Journal 4(12):3333-3338.



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