TY - JOUR
AU - Fatafta, Hebah
AU - Samantray, Suman
AU - Sayyed-Ahmad, Abdallah
AU - Coskuner-Weber, Orkid
AU - Strodel, Birgit
TI - Chapter Five - Molecular simulations of IDPs: From ensemble generation to IDP interactions leading to disorder-to-order transitions
JO - Progress in molecular biology and translational science
VL - 183
SN - 1877-1173
CY - Amsterdam [u.a.]
PB - Elsevier
M1 - FZJ-2022-00942
SP - 135-185
PY - 2021
AB - Intrinsically disordered proteins (IDPs) lack a well-defined three-dimensional structure but do exhibit some dynamical and structural ordering. The structural plasticity of IDPs indicates that entropy-driven motions are crucial for their function. Many IDPs undergo function-related disorder-to-order transitions upon by their interaction with specific binding partners. Approaches that are based on both experimental and theoretical tools enable the biophysical characterization of IDPs. Molecular simulations provide insights into IDP structural ensembles and disorder-to-order transition mechanisms. However, such studies depend strongly on the chosen force field parameters and simulation techniques. In this chapter, we provide an overview of IDP characteristics, review all-atom force fields recently developed for IDPs, and present molecular dynamics-based simulation methods that allow IDP ensemble generation as well as the characterization of disorder-to-order transitions. In particular, we introduce metadynamics, replica exchange molecular dynamics simulations, and also kinetic models resulting from Markov State modeling, and provide various examples for the successful application of these simulation methods to IDPs.
LB - PUB:(DE-HGF)16
C6 - 34656328
UR - <Go to ISI:>//WOS:000748722300006
DO - DOI:10.1016/bs.pmbts.2021.06.003
UR - https://juser.fz-juelich.de/record/905717
ER -
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