Multiscale enhanced sampling of intrinsically disordered protein conformations

Bibliographische Detailangaben
Veröffentlicht in:	Journal of computational chemistry. - 1984. - 37(2016), 6 vom: 05. März, Seite 550-7
1. Verfasser:	Lee, Kuo Hao (VerfasserIn)
Weitere Verfasser:	Chen, Jianhan
Format:	Online-Aufsatz
Sprache:	English
Veröffentlicht:	2016
Zugriff auf das übergeordnete Werk:	Journal of computational chemistry
Schlagworte:	Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. intrinsically disordered proteins molecular dynamics protein structure replica exchange Intrinsically Disordered Proteins Peptides

Beschreibung
Zusammenfassung:	© 2015 Wiley Periodicals, Inc. In a recently developed multiscale enhanced sampling (MSES) technique, topology-based coarse-grained (CG) models are coupled to atomistic force fields to enhance the sampling of atomistic protein conformations. Here, the MSES protocol is refined by designing more sophisticated Hamiltonian/temperature replica exchange schemes that involve additional parameters in the MSES coupling restraint potential, to more carefully control how conformations are coupled between the atomistic and CG models. A specific focus is to derive an optimal MSES protocol for simulating conformational ensembles of intrinsically disordered proteins (IDPs). The efficacy of the refined protocols, referred to as MSES-soft asymptote (SA), was evaluated using two model peptides with various levels of residual helicities. The results show that MSES-SA generates more reversible helix-coil transitions and leads to improved convergence on various ensemble conformational properties. This study further suggests that more detailed CG models are likely necessary for more effective sampling of local conformational transition of IDPs. © 2015 Wiley Periodicals, Inc
Beschreibung:	Date Completed 25.10.2016 Date Revised 30.12.2016 published: Print-Electronic Citation Status MEDLINE
ISSN:	1096-987X
DOI:	10.1002/jcc.23957