Publications from

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Tone Bengtsen, Søren Roi Midtgaard, Viktor Lindahl Holm, Lisbeth Ravnkilde Kjølbye, Nicolai Tidemand Johansen, Giulio Tesei, Sandro Bottaro, Birgit Schiøtt, Lise Arleth and Kresten Lindorff-Larsen. (2020) Structure and dynamics of a nanodisc by integrating NMR, SAXS and SANS experiments with molecular dynamics simulations. eLife 9.


Lise Arleth, Nicolai T. Johansen, Tone Bengtsen, Andreas Haahr Larsen, Frederik Tidemand, Thomas Pomorski and Kresten Lindorff-Larsen. (2020) Small-angle Neutron Scattering Shows that the Solution Structures of the Bacterial Mg2+-Channel CorA are Overall Similar with and without Mg2+ Bound Biophysical Journal 118:12A-12A.


Amanda B. Abildgaard, Sarah K. Gersing, Sven Larsen-Ledet, Sofie V. Nielsen, Amelie Stein, Kresten Lindorff-Larsen and Rasmus Hartmann-Petersen. (2020) Co-Chaperones in Targeting and Delivery of Misfolded Proteins to the 26S Proteasome Biomolecules 10(8).


Andreas Haahr Larsen, Yong Wang, Sandro Bottaro, Sergei Grudinin, Lise Arleth and Kresten Lindorff-Larsen. (2020) Combining molecular dynamics simulations with small-angle X-ray and neutron scattering data to study multi-domain proteins in solution P L o S Computational Biology 16(4).


Caroline Kampmeyer, Jens V. Johansen, Christian Holmberg, Magnus Karlson, Sarah K. Gersing, Heloisa N. Bordallo, Birthe B. Kragelund, Mathilde Hauge Lerche, Isabelle Jourdain, Jakob R. Winther and Rasmus&n (2020) Mutations in a Single Signaling Pathway Allow Cell Growth in Heavy Water A C S Synthetic Biology 9(4):733-748.


Helena Gásdal Karstensen, Nanna Dahl Rendtorff, Lone Sandbjerg Hindbæk, Roberto Colombo, Amelie Stein, Niels Holtum Birkebæk, Rasmus Hartmann-Petersen, Kresten Lindorff-Larsen, Allan Thomas Højland, Michael Bjø (2020) Novel HARS2 missense variants identified in individuals with sensorineural hearing impairment and Perrault syndrome European Journal of Medical Genetics 63(3).


James S. Fraser, Kresten Lindorff-Larsen and Massimiliano Bonomi. (2020) What Will Computational Modeling Approaches Have to Say in the Era of Atomistic Cryo-EM Data? Journal of Chemical Information and Modeling 60(5):2410-2412.


Louise Hamborg, Emma Wenzel Horsted, Kristoffer Enøe Johansson, Martin Willemoës, Kresten Lindorff-Larsen and Kaare Teilum. (2020) Global analysis of protein stability by temperature and chemical denaturation Analytical Biochemistry 605.


Mustapha Carab Ahmed, Ramon Crehuet and Kresten Lindorff-Larsen. (2020) Computing, Analyzing, and Comparing the Radius of Gyration and Hydrodynamic Radius in Conformational Ensembles of Intrinsically Disordered Proteins False:429-445.


Sandro Bottaro, Parker J. Nichols, Beat Vögeli, Michele Parrinello and Kresten Lindorff-Larsen. (2020) Integrating NMR and simulations reveals motions in the UUCG tetraloop Nucleic Acids Research 48(11):5839-5848.


Sandro Bottaro, Tone Bengtsen and Kresten Lindorff-Larsen. (2020) Integrating Molecular Simulation and Experimental Data: A Bayesian/Maximum Entropy Reweighting Approach Book chapter in False Zoltán Gáspári. (eds.) Humana Press, p. 219-240.


Simone Orioli, Andreas Haahr Larsen, Sandro Bottaro and Kresten Lindorff-Larsen. (2020) How to learn from inconsistencies: Integrating molecular simulations with experimental data Book chapter in False Birgit Strodel and Bogdan Barz. (eds.) Academic Press, p. 123-176.



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.


Benjamin Bjerre, Jakob Nissen, Mikkel Madsen, Jurate Kamarauskaite, Rasmus K Norrild, Peter C Holm, Mathilde K Nordentoft, Charlotte O'Shea, Martin Willemoës, Kristoffer E Johansson and Jakob R Wi (2019) Improving folding properties of computationally designed proteins Protein Engineering Design and Selection (Print) 32(3):145-151.


Albert Escobedo, Busra Topal, Micha B. A. Kunze, Juan Aranda, Giulio Chiesa, Daniele Mungianu, Ganeko Bernardo-Seisdedos, Bahareh Eftekharzadeh, Margarida Gairí, Roberta Pierattelli, Isabella C. Felli (2019) Side chain to main chain hydrogen bonds stabilize a polyglutamine helix in a transcription factor Nature Communications 10.


Amanda B. Abildgaard, Amelie Stein, Sofie V. Nielsen, Katrine Schultz-Knudsen, Elena Papaleo, Amruta Shrikhande, Eva R Hoffmann, Inge Bernstein, Anne-Marie Gerdes, Masanobu Takahashi, Chikashi Ishioka (2019) Computational and cellular studies reveal structural destabilization and degradation of MLH1 variants in Lynch syndrome eLife 8.


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 44(7):575-588.


Andrea Cesari, Sandro Bottaro, Kresten Lindorff-Larsen, Pavel Banás, Jiri Sponer and Giovanni Bussi. (2019) Fitting Corrections to an RNA Force Field Using Experimental Data Journal of Chemical Theory and Computation 15(6):3425-3431.


Andreas Prestel, Nanna Wichmann, Joao M. Martins, Riccardo Marabini, Noah Kassem, Sebastian S. Broendum, Marit Otterlei, Olaf Nielsen, Martin Willemoës, Michael Ploug, Wouter Boomsma and Birthe B.&nbs (2019) The PCNA interaction motifs revisited: thinking outside the PIP-box Cellular and Molecular Life Sciences 76(24):4923-4943.


Anne Kathrine Nielsen, Ingvar R. Möller, Yong Wang, Søren G. F. Rasmussen, Kresten Lindorff-Larsen, Kasper D. Rand and Claus J. Loland. (2019) Substrate-induced conformational dynamics of the dopamine transporter Nature Communications 10.


Dennis K. Hansen, Jakob R. Winther and Martin Willemoës. (2019) Steady state kinetic analysis of O-linked GalNAc glycan release catalyzed by endo-a-N-acetylgalactosaminidase Carbohydrate Research 480:54-60.


Dennis V. Pedersen, Trine Amalie Fogh Gadeberg, Caroline Thomas, Yong Wang, Nicolas Joram, Rasmus Kjeldsen Jensen, Sofia M. M. Mazarakis, Margot Revel, Carine El Sissy, Steen V. Petersen, Kresten Lind (2019) Structural Basis for Properdin Oligomerization and Convertase Stimulation in the Human Complement System Frontiers in Immunology 10.


Kresten Lindorff-Larsen. (2019) Dissecting the statistical properties of the linear extrapolation method of determining protein stability Protein engineering, design & selection : PEDS 32(10):471-479.


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 Book chapter in False Rossen Donev. (eds.) Academic Press, p. 61-83.


Martin Cramer Pedersen, Yong Wang, Frederik Grønbæk Tidemand, A. Martel, Kresten Lindorff-Larsen and Lise Arleth. (2019) PSX, Protein-Solvent Exchange: software for calculation of deuterium-exchange effects in small-angle neutron scattering measurements from protein coordinates Journal of Applied Crystallography 52(6):1427-1436.


Massimiliano Bonomi, Giovanni Bussi, Carlo Camilloni, Gareth A. Tribello, Pavel Banas, Alessandro Barducci, Mattia Bernetti, Peter G. Bolhuis, Sandro Bottaro, Davide Branduardi, Riccardo Capelli, Paol (2019) Promoting transparency and reproducibility in enhanced molecular simulations Nature Methods 16(8):670-673.


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 Nu (2019) Pulmonary effects of nanofibrillated celluloses in mice suggest that carboxylation lowers the inflammatory and acute phase responses Environmental Toxicology and Pharmacology 66:116-125.


Noureldin Saleh, Yong Wang, Poul Nissen and Kresten Lindorff-Larsen. (2019) Allosteric modulation of the sarcoplasmic reticulum Ca2+ ATPase by thapsigargin via decoupling of functional motions Physical Chemistry Chemical Physics 21(39):21991-21995.


Ramon Crehuet, Pedro J. Buigues, Xavier Salvatella and Kresten Lindorff-Larsen. (2019) Bayesian-Maximum-Entropy Reweighting of IDP Ensembles Based on NMR Chemical Shifts Entropy 21(9).


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.


Sandro Bottaro, Giovanni Bussi, Giovanni Pinamonti, Sabine Reisser, Wouter Boomsma and Kresten Lindorff-Larsen. (2019) Barnaba: software for analysis of nucleic acid structures and trajectories RNA 25(2):219-231.


Yong Wang, Noureldin Saleh, Xiakun Chu and Kresten Lindorff-Larsen. (2019) A Multi-State Coarse-Grained Simulation Model Captures Conformational Cycling in P-Type ATPases Biophysical Journal 116:300a.



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.


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


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 6:1-24.


Ganesan Senthil Kumar, Michael W. Clarkson, Micha Ben Achim Kunze, Daniele Granata, A. Joshua Wand, Kresten Lindorff-Larsen, Rebecca Page and Wolfgang Peti. (2018) Dynamic activation and regulation of the mitogen-activated protein kinase p38 Proceedings of the National Academy of Sciences of the United States of America 115(18):4655-4660.


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 (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, (2018) Structural Basis of Membrane Protein Chaperoning through the Mitochondrial Intermembrane Space Cell 175(5):1365-1379, e25.


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


Kristoffer Enøe Johansson and Kresten Lindorff-Larsen. (2018) Structural heterogeneity and dynamics in protein evolution and design Current Opinion in Structural Biology 48:157-163.


Lotte Emilie Boyhus, Mia Danielsen, Nina Smidt Bengtson, Micha Ben Achim Kunze, Xavier Kubiak, Tjerk J. Sminia, Jacob Hartvig Løper, Phuong Thu Tran, Kresten Lindorff-Larsen, Søren G.F. Rasmussen, Jesper M (2018) Gs protein peptidomimetics as allosteric modulators of the ß2-adrenergic receptor RSC Advances 8(4):2219-2228.


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.


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  (2018) Nanofibrillated cellulose causes acute pulmonary inflammation that subsides within a month Nanotoxicology 12(7):729-746.


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.


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&n (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.


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:iv-v.


Sandro Bottaro and Kresten Lindorff-Larsen. (2018) Biophysical experiments and biomolecular simulations: a perfect match? 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).


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 48:74-82.


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.



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.


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 37:40-51.


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


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.


Lasse Staby, Charlotte O'Shea, Martin Willemoës, Frederik Theisen, Birthe Brandt Kragelund and Karen Skriver. (2017) Eukaryotic transcription factors: paradigms of protein intrinsic disorder 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.


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-Peters (2017) Predicting the impact of Lynch syndrome-causing missense mutations from structural calculations PLoS Genetics 13(4).


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


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 Dan (2017) Diversity-oriented peptide stapling: a third generation copper-catalysed azide–alkyne cycloaddition stapling and functionalisation strategy 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).


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.


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.


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.


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 (2017) Genotoxic and inflammatory effects of nanofibrillated cellulose in murine lungs Mutagenesis 32(1):23-31.


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



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 FEBS Journal 283(24):4424-4451.


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.


Elena Papaleo, Giorgio Saladino, Matteo Lambrughi, Kresten Lindorff-Larsen, Francesco Luigi Gervasio and Ruth Nussinov. (2016) The role of protein loops and linkers in conformational dynamics and allostery Chemical Reviews 116(11):6391-6423.


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.


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 W (2016) Computational redesign of thioredoxin is hypersensitive towards minor conformational changes in the backbone template Journal of Molecular Biology 428(21):4361-4377.


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.


Matteo Lambrughi, Luca De Gioia, Francesco Luigi Gervasio, Kresten Lindorff-Larsen, Ruth Nussinov, Chiara Urani, Maurizio Bruschi and Elena Papaleo. (2016) DNA-binding protects p53 from interactions with cofactors involved in transcription-independent functions Nucleic Acids Research 44(19):9096-9109.


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).


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.


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.


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



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: transcriptional activation by ANAC013 and ANAC046 and their interactions with RCD1 Biochemical Journal 465(2):281-294.


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.


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.


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).


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, Har (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.


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: Software for Quantitative Ensemble Comparison PloS Computational Biology 11(10).


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.


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  (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.



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.


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).


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).


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.


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 542:28-38.


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.


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.


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).


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.



Marie S. Møller, Darrell Cockburn, Jonas W. Nielsen, Johanne M. Jensen, Malene B. Vester-christensen, Morten M. Nielsen, Joakim M. Andersen, Casper Wilkens, Julie Rannes, Per Hägglund, Anette Henrikse (2013) Surface Binding Sites (SBSs), Mechanism and Regulation of Enzymes Degrading Amylopectin and a-Limit Dextrins Journal of Applied Glycoscience 60(2):101-109.


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).


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: a black hole for oxidized glutathione Nature Chemical Biology 9(2):69-70.


Jakob R. Winther, Helen Webb and John Kay. (2013) Saccharopepsin Book chapter in False Neil D. Rawlings and Guy Salvesen. (eds.) Academic Press, p. 128-133.


Jens Munk, Lea Thøgersen, Lars Erik Uggerhøj, Reinhard Wimmer, Niels Frimodt-Møller, Kresten Lindorff-Larsen and Paul Robert Hansen. (2013) The Structure of the Central Side Chain is Crucial for Anoplin Hemolytic Activity Book chapter in False Michal Lebl. (eds.) American Peptide Society.


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.


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.


Stefano Piana, Kresten Lindorff-Larsen and David E. Shaw. (2013) Atomic-level description of ubiquitin folding Proceedings of the National Academy of Sciences of the United States of America 110(15):5915-5920.


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.


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 Ant (2013) PHAISTOS: a framework for Markov chain Monte Carlo simulation and inference of protein structure Journal of Computational Chemistry 34(19):1697-1705.



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


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).


Jonas Willum Nielsen, Birte Kramhøft, Sophie Bozonnet, Maher Abou Hachem, Susan Louise Svane Stipp, Birte Svensson and Martin Willemoës. (2012) Degradation of the starch components amylopectin and amylose by barley a-amylase 1: role of surface binding site 2 Archives of Biochemistry and Biophysics 528(1):1-6.


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: the influence of composition and branching 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).


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.


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).



Jan Martinussen, Martin Willemoës and Mogens Kilstrup. (2011) The Biochemical Basis | Nucleotide Metabolism Book chapter in False Murray Moo-Young, Michael Butler, Colin Webb, Antonio Moreira, Bernard Grodzinski, Z. F. Cui and Spiros Agathos. (eds.) Elsevier, p. 91-107.


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.


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.


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.


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.


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


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.



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.


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.


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.


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.


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.



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 (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. Eastwoo (2009) Millisecond-scale molecular dynamics simulations on Anton Book chapter in False Association for Computing Machinery.


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.


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


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.


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.


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.



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.


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.


Kaj Frank Jensen, Gert Dandanell, Bjarne Hove-Jensen and Martin Willemoës. (2008) Nucleotides, Nucleosides, and Nucleobases Book chapter in False A. Böck, R. Curtis III, J. B. Kaper, P. D. Karp, F. C. Neidhardt, T. Nyström, J. M. Slauch and C. L. Squires. (eds.) ASM International.


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.


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 (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.



Christian D Geierhaas, Adrian A Nickson, Kresten Lindorff-Larsen, Jane Clarke and Michele Vendruscolo. (2007) BPPred: a Web-based computational tool for predicting biophysical parameters of proteins 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.


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) Redox characteristics of the eukaryotic cytosol. BBA General Subjects.


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, 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.


Kjell O Håkansson and Jakob R Winther. (2007) Structure of glutaredoxin Grx1p C30S mutant from yeast. Acta Crystallographica. Section D: Biological Crystallography 63:288-94.


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.


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.


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.


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 274:5055-5067.


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.



Maher Abou Hachem, Sophie Bozonnet, Martin Willemoës, Birgit C. Bønsager, Morten Munch Nielsen, Kenji Fukuda, Birte Kramhøft, Kenji Maeda, Bent W. Sigurskjold, Per Hägglund, Christine Finnie, Haruhide (2006) Interactions between Barley .ALPHA.-Amylases, Substrates, Inhibitors and Regulatory Proteins Journal of Applied Glycoscience 53(2):163-169.


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.


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.


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.


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. 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, Har (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.


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): a novel mode of calmodulin-target recognition Journal of Molecular Biology 357(2):400-10.



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.


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.


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.


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.


Martin Willemoës, Anne Mølgaard, Eva Helena Johansson and Jan Martinussen. (2005) Lid L11 of the glutamine amidotransferase domain of CTP synthase mediates allosteric GTP activation of glutaminase activity FEBS Journal 272(3):856-864.


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. Kristjansdottir, Kresten Lindorff-Larsen, W. Fieber, Christopher M. Dobson, Michele Vendruscolo and Flemming M. Poulsen. (2005) Formation of Native and Non-native Interactions in Ensembles of Denatured ACBP Molecules from Paramagnetic Relaxation Enhancement Studies Journal of Molecular Biology 347(5):1053-1062.


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 T (2005) Binding of carbohydrates and protein inhibitors to the surfaceof a-amylases Biologia 60(16):27-36.



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 43:6020-6029.


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.


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. 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.


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 424:105-111.


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.



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.


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 413:17-22.


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.


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.



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 269:4772-4779.


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.



H Ostergaard, A Henriksen, F G Hansen and Jakob R. Winther. (2001) Shedding light on disulfide bond formation: engineering a redox switch in green fluorescent protein E M B O Journal 20(21):5853-62.


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.


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.


L H Phylip, W E Lees, B G Brownsey, D Bur, B M Dunn, Jakob R. Winther, A Gustchina, M Li, T Copeland, A Wlodawer and J Kay. (2001) The potency and specificity of the interaction between the IA3 inhibitor and its target aspartic proteinase from Saccharomyces cerevisiae Journal of Biological Chemistry 276(3):2023-30.


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.


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.


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 276:38002-38009.



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


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 45:35408-35412.



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.


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.



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.


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.


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: possible implications for compartmentalized activation in vivo Biochemical Journal:339-44.


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.


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.


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.


H B Van Den Hazel, Morten Kielland-Brandt and Jakob R. Winther. (1996) Review: biosynthesis and function of yeast vacuolar proteases 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.


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.



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.


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.



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.


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.


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.



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.


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.



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.



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.



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.






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.



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.



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