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Review

Advanced Sampling Methods for Multiscale Simulation of Disordered Proteins and Dynamic Interactions

by 1,†, 1,† and 1,2,*
1
Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA
2
Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
*
Author to whom correspondence should be addressed.
These authors contributed equally to this paper.
Academic Editors: Thomas R. Caulfield and Alexander T. Baker
Biomolecules 2021, 11(10), 1416; https://doi.org/10.3390/biom11101416
Received: 31 August 2021 / Revised: 22 September 2021 / Accepted: 24 September 2021 / Published: 28 September 2021
Intrinsically disordered proteins (IDPs) are highly prevalent and play important roles in biology and human diseases. It is now also recognized that many IDPs remain dynamic even in specific complexes and functional assemblies. Computer simulations are essential for deriving a molecular description of the disordered protein ensembles and dynamic interactions for a mechanistic understanding of IDPs in biology, diseases, and therapeutics. Here, we provide an in-depth review of recent advances in the multi-scale simulation of disordered protein states, with a particular emphasis on the development and application of advanced sampling techniques for studying IDPs. These techniques are critical for adequate sampling of the manifold functionally relevant conformational spaces of IDPs. Together with dramatically improved protein force fields, these advanced simulation approaches have achieved substantial success and demonstrated significant promise towards the quantitative and predictive modeling of IDPs and their dynamic interactions. We will also discuss important challenges remaining in the atomistic simulation of larger systems and how various coarse-grained approaches may help to bridge the remaining gaps in the accessible time- and length-scales of IDP simulations. View Full-Text
Keywords: conformational ensemble; enhanced sampling; generalized Born; Gō-model; implicit solvent; liquid-liquid phase transition; replica exchange; protein force fields conformational ensemble; enhanced sampling; generalized Born; Gō-model; implicit solvent; liquid-liquid phase transition; replica exchange; protein force fields
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MDPI and ACS Style

Gong, X.; Zhang, Y.; Chen, J. Advanced Sampling Methods for Multiscale Simulation of Disordered Proteins and Dynamic Interactions. Biomolecules 2021, 11, 1416. https://doi.org/10.3390/biom11101416

AMA Style

Gong X, Zhang Y, Chen J. Advanced Sampling Methods for Multiscale Simulation of Disordered Proteins and Dynamic Interactions. Biomolecules. 2021; 11(10):1416. https://doi.org/10.3390/biom11101416

Chicago/Turabian Style

Gong, Xiping, Yumeng Zhang, and Jianhan Chen. 2021. "Advanced Sampling Methods for Multiscale Simulation of Disordered Proteins and Dynamic Interactions" Biomolecules 11, no. 10: 1416. https://doi.org/10.3390/biom11101416

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