Next Article in Journal
Cationic Antimicrobial Polymers and Their Assemblies
Next Article in Special Issue
The Role of Short-Chain Conjugated Poly-(R)-3-Hydroxybutyrate (cPHB) in Protein Folding
Previous Article in Journal
Rab27 GTPases Distribute Extracellular Nanomaps for Invasive Growth and Metastasis: Implications for Prognosis and Treatment
Previous Article in Special Issue
Recurrent Structural Motifs in Non-Homologous Protein Structures
Int. J. Mol. Sci. 2013, 14(5), 9893-9905; doi:10.3390/ijms14059893
Article

Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics

,
,
,
*  and *
Faculty of Chemistry, University of Warsaw, L. Pasteura 1, Warsaw 02-093, Poland
* Authors to whom correspondence should be addressed.
Received: 7 March 2013 / Revised: 9 April 2013 / Accepted: 24 April 2013 / Published: 10 May 2013
(This article belongs to the collection Protein Folding)
View Full-Text   |   Download PDF [407 KB, 19 June 2014; original version 19 June 2014]   |   Browse Figures
SciFeed

Abstract

We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combination accelerates system convergence several times in comparison with all-atom simulations starting from the extended chain conformation, demonstrated by the analysis of melting curves, the number of native-like conformations as a function of time and secondary structure propagation. The results strongly suggest that the proposed multiscale method could be an efficient and accurate tool for high-resolution studies of protein folding dynamics in larger systems.
Keywords: CABS; replica-exchange molecular dynamics; multiscale modeling; protein folding CABS; replica-exchange molecular dynamics; multiscale modeling; protein folding
This is an open access article distributed under the Creative Commons Attribution License (CC BY 3.0).

Share & Cite This Article

Further Mendeley | CiteULike
Export to BibTeX |
EndNote |
RIS
MDPI and ACS Style

Wabik, J.; Kmiecik, S.; Gront, D.; Kouza, M.; Koliński, A. Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics. Int. J. Mol. Sci. 2013, 14, 9893-9905.

View more citation formats

Related Articles

Article Metrics

For more information on the journal, click here

Comments

[Return to top]
Int. J. Mol. Sci. EISSN 1422-0067 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert