PEPTIDE MECHANICS - A FORCE-FIELD FOR PEPTIDES AND PROTEINS WORKING WITH ENTIRE RESIDUES AS SMALLEST UNITS

The central ingredient of any structure modeling tool is a molecular model or force field that accounts for proper geometry and energy calculation. For protein and peptide modeling based on entire amino acids as building blocks, we describe a peptide force field in which each amino acid is represented by a single point in space, taken at the position of the alpha-carbon atom. Apart from the positional coordinates, these units carry the two torsional angles phi and psi as additional degrees of freedom to account for the orientations of the peptide links. While some of the energy terms are analogous to expressions in atomic force fields, the presence of the angular variables leads to fundamental differences with new features and additional terms with no atomic counterparts. The force field reproduces secondary structure elements with very good accuracy. Globular parts of tertiary packing stay near the experimental structures with a rms deviation in C-alpha positions of 0.1-0.3 nm and about 25-degrees in phi and psi, depending on the size of the structure. A tendency for larger discrepancies is observed in exposed loops or terminal segments the conformations of which may be strongly influenced by neighboring domains. Finally, a scope of possible applications is presented. They range from modeling activities, such as model building by homology, to coarse scanning of conformation space in conformation analysis and structure determination. An extension to a dynamics model would offer the possibility to eliminate the less interesting high-frequency modes that in all-atom force-field dynamics absorb most of the computational effort.