PSEUDODIHEDRALS - SIMPLIFIED PROTEIN BACKBONE REPRESENTATION WITH KNOWLEDGE-BASED ENERGY

Pairwise contact energies do not explicitly take protein secondary str ucture into account, and so provide an incomplete description of confo rmational energy. In order to construct a Hamiltonian that specificall y relates to protein backbone conformations, a simplified backbone ang le is used. The pseudodihedral angle (the torsion angle between planes defined by 4 consecutive alpha-carbon atoms) provides a simplified ba ckbone representation and continues to manifest information about seco ndary-structure elements: the pseudo-Ramachandran plot contains helica l and sheetlike regions. The distribution of pseudodihedral angles is highly sensitive to the identity of the central pair of amino acids. T herefore, a sequence-dependent, knowledge-based potential energy was f ound according to a quasichemical approximation. These functions form complementary additions to the contact potentials currently in use. Th is pseudodihedral potential greatly enhances the ability to design seq uences that are specific to a given conformation and also improves the ability to discriminate a native conformation from many other conform ations.