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Molecular simulations of IDPs: From ensemble generation to IDP interactions leading to disorder-to-order transitions by Hebah Fatafta; Suman Samantray; Abdallah Sayyed-Ahmad; Orkid Coskuner-Weber; Birgit Strodel is a book available to read on EtoBox.

What is Molecular simulations of IDPs: From ensemble generation to IDP interactions leading to disorder-to-order transitions about?

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

Author

Hebah Fatafta; Suman Samantray; Abdallah Sayyed-Ahmad; Orkid Coskuner-Weber; Birgit Strodel

Publisher

Elsevier Science & Technology

Published

2021

Language

EN

ISBN

9780323853002

Subjects

Science, Chemistry, Medical