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

A new high-coordination lattice model of polypeptide chains has been designed and tested. The model employs a single united atom representation of amino acid residues. These atoms are centered on protein side groups. Characteristic short-range distance correlations have been built into the model, thereby providing a rather accurate description of proteinlike conformational stiffness. Sequence-specific interaction schemes have been derived from sequence similarity and sequence-structure compatibility criteria. The conformations of the model chain observed in isothermal Monte Carlo simulations reproduce protein secondary structure with high fidelity. Implications for structural studies of protein systems are briefly discussed.