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

0351148 - ÚOCHB 2011 RIV US eng J - Journal Article
Vymětal, Jiří - Vondrášek, Jiří
Metadynamics As a Tool for Mapping the Conformational and Free-Energy Space of Peptides - The Alanine Dipeptide Case Study.
Journal of Physical Chemistry B. Roč. 114, č. 16 (2010), s. 5632-5642. ISSN 1520-6106. E-ISSN 1520-5207
R&D Projects: GA MŠMT LC512
Institutional research plan: CEZ:AV0Z40550506
Keywords : metadynamics * alanine dipeptide * explicit water models
Subject RIV: CF - Physical ; Theoretical Chemistry
Impact factor: 3.603, year: 2010

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.
Permanent Link: http://hdl.handle.net/11104/0006157