An efficient Monte Carlo model of protein chains. Modeling the short-range correlations between side group centers of mass

Article Abstract:

The short-range correlations between side group centers of mass were investigated using an efficient Monte Carlo model of protein chains. The model is a novel high-coordination lattice framework of polypeptide chains that employs a single united atom representation of amino acid residues. Sequence-specific interaction schemes were derived from sequence similarity and sequence-structure compatibility criteria. The conformations of the model chain observed in isothermal Monte Carlo experiments reproduce protein secondary structure with high fidelity.

Usage, Polymerase chain reaction, Polypeptides, Molecules, Monte Carlo method, Monte Carlo methods

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Influence of Go-like interactions on global shapes of energy landscapes in [beta]-barrel forming model proteins: inherent structure analysis and statistical temperature molecular dynamics simulation

Article Abstract:

The properties of Go-like protein models are examined in terms of the potential energy landscape (PEL). The alteration of the PEL has induced a significant change in the folding mechanism and the appearance of multiple van der Waals loops in the statistical temperature of the Go-like model is associated with the development of the intermediate states.

Analysis, Molecular dynamics, Van der Waals forces

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A statistical mechanical model for beta-sheet formation

Article Abstract:

Research is presented demonstrating the use of a statistical mechanical model to measure the forces surrounding the formation of monomeric beta-sheets of peptides in aqueous solution.

Peptides, Biophysics, Mechanical chemistry

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