Folding and thermodynamic studies of Trp-cage based on polarized force field

Two replica exchange molecular dynamics (REMD) simulations were carried out to study the thermodynamics of a 20-residue Trp-cage folding based on a newly developed polarized protein-specific charge (PPC). Starting from a fully extended conformation, Trp-cage native conformation was successfully samp...

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Bibliographic Details
Published in:Theoretical chemistry accounts 2012-03, Vol.131 (3), Article 1168
Main Authors: Mei, Ye, Wei, Caiyi, Yip, Yew Mun, Ho, Chun Ying, Zhang, John Z. H., Zhang, Dawei
Format: Article
Language:English
Subjects:
Atomic/Molecular Structure and Spectra
Chemistry
Chemistry and Materials Science
Inorganic Chemistry
Letter
Organic Chemistry
Physical Chemistry
Theoretical and Computational Chemistry
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Summary:Two replica exchange molecular dynamics (REMD) simulations were carried out to study the thermodynamics of a 20-residue Trp-cage folding based on a newly developed polarized protein-specific charge (PPC). Starting from a fully extended conformation, Trp-cage native conformation was successfully sampled using REMD based on a 3-step PPC update. Next, the obtained Trp-cage folded conformation was then used to calculate the PPC in which another REMD was performed to explore the thermodynamic stability of Trp-cage. The theoretical melting temperature T m of ≈325 K was found to be in close agreement with experimental melting temperature, T m of 315 K. This indicates that the PPC was correctly predicting the temperature dependence. The current study provides a direct proof of how electrostatic polarization affects protein folding.
ISSN:1432-881X
1432-2234
DOI:10.1007/s00214-012-1168-0