Improving Martini 3 for Disordered and Multidomain Proteins

Research output: Contribution to journal › Journal article › Research › peer-review

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Improving Martini 3 for Disordered and Multidomain Proteins. / Thomasen, F. Emil; Pesce, Francesco; Roesgaard, Mette Ahrensback; Tesei, Giulio; Lindorff-Larsen, Kresten.

In: Journal of Chemical Theory and Computation, Vol. 18, No. 4, 2022, p. 2033-2041.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Thomasen, FE, Pesce, F, Roesgaard, MA, Tesei, G & Lindorff-Larsen, K 2022, 'Improving Martini 3 for Disordered and Multidomain Proteins', Journal of Chemical Theory and Computation, vol. 18, no. 4, pp. 2033-2041. https://doi.org/10.1021/acs.jctc.1c01042

APA

Thomasen, F. E., Pesce, F., Roesgaard, M. A., Tesei, G., & Lindorff-Larsen, K. (2022). Improving Martini 3 for Disordered and Multidomain Proteins. Journal of Chemical Theory and Computation, 18(4), 2033-2041. https://doi.org/10.1021/acs.jctc.1c01042

Vancouver

Thomasen FE, Pesce F, Roesgaard MA, Tesei G, Lindorff-Larsen K. Improving Martini 3 for Disordered and Multidomain Proteins. Journal of Chemical Theory and Computation. 2022;18(4):2033-2041. https://doi.org/10.1021/acs.jctc.1c01042

Author

Thomasen, F. Emil ; Pesce, Francesco ; Roesgaard, Mette Ahrensback ; Tesei, Giulio ; Lindorff-Larsen, Kresten. / Improving Martini 3 for Disordered and Multidomain Proteins. In: Journal of Chemical Theory and Computation. 2022 ; Vol. 18, No. 4. pp. 2033-2041.

Bibtex

@article{19c0e66c38e243b89c5d63cf82ed4671,

title = "Improving Martini 3 for Disordered and Multidomain Proteins",

abstract = "Coarse-grained molecular dynamics simulations are a useful tool to determine conformational ensembles of proteins. Here, we show that the coarse-grained force field Martini 3 underestimates the global dimensions of intrinsically disordered proteins (IDPs) and multidomain proteins when compared with small-angle X-ray scattering (SAXS) data and that increasing the strength of protein-water interactions favors more expanded conformations. We find that increasing the strength of interactions between protein and water by ca. 10% results in improved agreement with the SAXS data for IDPs and multidomain proteins. We also show that this correction results in a more accurate description of self-association of IDPs and folded proteins and better agreement with paramagnetic relaxation enhancement data for most IDPs. While simulations with this revised force field still show deviations to experiments for some systems, our results suggest that it is overall a substantial improvement for coarse-grained simulations of soluble proteins.",

author = "Thomasen, {F. Emil} and Francesco Pesce and Roesgaard, {Mette Ahrensback} and Giulio Tesei and Kresten Lindorff-Larsen",

year = "2022",

doi = "10.1021/acs.jctc.1c01042",

language = "English",

volume = "18",

pages = "2033--2041",

journal = "Journal of Chemical Theory and Computation",

issn = "1549-9618",

publisher = "American Chemical Society",

number = "4",

}

RIS

TY - JOUR

T1 - Improving Martini 3 for Disordered and Multidomain Proteins

AU - Thomasen, F. Emil

AU - Pesce, Francesco

AU - Roesgaard, Mette Ahrensback

AU - Tesei, Giulio

AU - Lindorff-Larsen, Kresten

PY - 2022

Y1 - 2022

N2 - Coarse-grained molecular dynamics simulations are a useful tool to determine conformational ensembles of proteins. Here, we show that the coarse-grained force field Martini 3 underestimates the global dimensions of intrinsically disordered proteins (IDPs) and multidomain proteins when compared with small-angle X-ray scattering (SAXS) data and that increasing the strength of protein-water interactions favors more expanded conformations. We find that increasing the strength of interactions between protein and water by ca. 10% results in improved agreement with the SAXS data for IDPs and multidomain proteins. We also show that this correction results in a more accurate description of self-association of IDPs and folded proteins and better agreement with paramagnetic relaxation enhancement data for most IDPs. While simulations with this revised force field still show deviations to experiments for some systems, our results suggest that it is overall a substantial improvement for coarse-grained simulations of soluble proteins.

AB - Coarse-grained molecular dynamics simulations are a useful tool to determine conformational ensembles of proteins. Here, we show that the coarse-grained force field Martini 3 underestimates the global dimensions of intrinsically disordered proteins (IDPs) and multidomain proteins when compared with small-angle X-ray scattering (SAXS) data and that increasing the strength of protein-water interactions favors more expanded conformations. We find that increasing the strength of interactions between protein and water by ca. 10% results in improved agreement with the SAXS data for IDPs and multidomain proteins. We also show that this correction results in a more accurate description of self-association of IDPs and folded proteins and better agreement with paramagnetic relaxation enhancement data for most IDPs. While simulations with this revised force field still show deviations to experiments for some systems, our results suggest that it is overall a substantial improvement for coarse-grained simulations of soluble proteins.

U2 - 10.1021/acs.jctc.1c01042

DO - 10.1021/acs.jctc.1c01042

M3 - Journal article

C2 - 35377637

AN - SCOPUS:85128169386

VL - 18

SP - 2033

EP - 2041

JO - Journal of Chemical Theory and Computation

JF - Journal of Chemical Theory and Computation

SN - 1549-9618

IS - 4

ER -

ID: 305701507

Department of Biology