Improving Martini 3 for Disordered and Multidomain Proteins
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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.
I: Journal of Chemical Theory and Computation, Bind 18, Nr. 4, 2022, s. 2033-2041.Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt
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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
N1 - Publisher Copyright: © 2022 American Chemical Society. All rights reserved.
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