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

Access

info:eu-repo/semantics/closedAccess

Date

2021

Author

Fatafta, Hebah
Samantray, Suman
Sayyed-Ahmad, Abdallah
Weber, Orkide Coşkuner
Strodel, Birgit

Metadata

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Citation

Fatafta, H., Samantray, S., Sayyed-Ahmad, A., Coskuner-Weber, O., & Strodel, B. (2021). Molecular simulations of IDPs: From ensemble generation to IDP interactions leading to disorder-to-order transitions. Progress in Molecular Biology and Translational Science, 183, 135-185.

Abstract

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 meta-dynamics, 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.

Source

Dancing Protein Clouds: Intrinsically Disordered Proteins In The Norm And Pathology, Pt C

Volume

183

URI

https://hdl.handle.net/20.500.12846/651

Collections

  • WoS İndeksli Yayınlar Koleksiyonu [315]



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