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.

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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.

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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.

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