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Metadynamics As a Tool for Mapping the Conformational and Free-Energy Space of Peptides - The Alanine Dipeptide Case Study

SYSNO ASEP	0351148
Document Type	J - Journal Article
R&D Document Type	Journal Article
Subsidiary J	Článek ve WOS
Title	Metadynamics As a Tool for Mapping the Conformational and Free-Energy Space of Peptides - The Alanine Dipeptide Case Study
Author(s)	Vymětal, Jiří (UOCHB-X)_{RID, ORCID} Vondrášek, Jiří (UOCHB-X)_{RID, ORCID}
Number of authors	2
Source Title	Journal of Physical Chemistry B. - : American Chemical Society - ISSN 1520-6106 Roč. 114, č. 16 (2010), s. 5632-5642
Number of pages	11 s.
Language	eng - English
Country	US - United States
Keywords	metadynamics ; alanine dipeptide ; explicit water models
Subject RIV	CF - Physical ; Theoretical Chemistry
R&D Projects	LC512 GA MŠMT - Ministry of Education, Youth and Sports (MEYS)
CEZ	AV0Z40550506 - UOCHB-X (2005-2011)
UT WOS	000276889100050
DOI	10.1021/jp100950w
Annotation	We have utilized metadynamics for the conformational study of the solvated alanine dipeptide molecule, and our results show that the method has proven to be competent as a fast, robust, and reliable method for the conformation free-energy calculations of peptides in an explicit solvent, surpassing traditional methods such as umbrella sampling. We have also addressed the issue of the influence of different water models on the resulting free-energy profile in order to consistently decompose the setting of our simulation. All of the explicit water models for the simulation of biomolecules TIP3P, TIP4P, TIP4P/Ew, TIP5P, and SPCE have exhibited similar effects on the conformational preferences of alanine dipeptide with no significant differences. All of the tested force fields (ff03, ff99SB, opls-aa, and charmm27) appreciably differ in the population of the individual conformers and the barriers between them.
Workplace	Institute of Organic Chemistry and Biochemistry
Contact	asep@uochb.cas.cz ; Kateřina Šperková, Tel.: 232 002 584 ; Viktorie Chládková, Tel.: 232 002 434
Year of Publishing	2011

Number of the records: 1