Description
Title: Multiscale Simulation of Disordered Proteins and Dynamic Interactions Using Advanced Sampling Methods
Abstract: Proteins that are intrinsically disordered (IDPs) are extremely common and play crucial roles in biology and human diseases. The fact that many IDPs continue to be dynamic even in particular complexes and functional assemblies is now also acknowledged. For a mechanistic understanding of IDPs in biology, diseases, and therapeutics, molecular descriptions of disordered protein ensembles and dynamic interactions must be derived through computer simulations. Here, we give a comprehensive overview of recent developments in the multi-scale simulation of disordered protein states, with a focus on the creation and use of cutting-edge sampling methods for researching IDPs. These methods are essential for a sufficient sampling of the diverse conformational spaces of IDPs that are functionally relevant. These cutting-edge simulation techniques, along with significantly enhanced protein force fields, have shown significant promise for the quantitative and predictive modeling of IDPs and their dynamic interactions. We will also go over some of the significant issues that still need to be resolved in the atomistic simulation of larger systems as well as how different coarse-rained strategies might be able to close some of the remaining gaps in the reachable time- and length-scales of IDP simulations.
Keywords: conformational ensemble; enhanced sampling; generalized Born; Go-model; implicit ̄solvent; liquid-liquid phase transition; replica exchange; protein force fields
Paper Quality: SCOPUS / Web of Science Level Research Paper
Subject: Biomolecules
Writer Experience: 20+ Years
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