A directed essential dynamics simulation of peptide folding.

Changjun Chen; Yi Xiao; Linsen Zhang

doi:10.1529/biophysj.104.046904

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A directed essential dynamics simulation of peptide folding.

Changjun Chen·Yi Xiao·Linsen Zhang

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Abstract

We present a directed essential dynamics (DED) method for peptide and protein folding. DED is a molecular dynamics method based on the essential dynamics sampling and the principal component analysis. The main idea of DED is to use principal component analysis to determine the direction of the most active collective motion of peptides at short intervals of time (20 fs) during the folding process and then add an additional force along it to adjust the folding direction. This method can make the peptides avoid being trapped in the local minima for a long time and enhance the sampling efficiency in conformational space during the simulation. An S-peptide with 15 amino acids is used to demonstrate the DED method. The results show that DED can lead the S-peptide to fold quickly into the native state, whereas traditional molecular dynamics needs more time to do this.

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Biophysics Computer Simulation Hydrogen Bonding Models, Molecular Models, Statistical Models, Theoretical Peptides Principal Component Analysis Protein Conformation Protein Folding Temperature Thermodynamics Time Factors Journal Article Research Support, Non-U.S. Gov't

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Changjun Chen, Yi Xiao, Linsen Zhang. 2005-02-24. A directed essential dynamics simulation of peptide folding.. https://doi.org/10.1529/biophysj.104.046904

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