Pseudodihedrals: simplified protein backbone representation with knowledge-based energy.
Pairwise contact energies do not explicitly take protein secondary structure into account, and so provide an incomplete description of conformational energy. In order to construct a Hamiltonian that specifically relates to protein backbone conformations, a simplified backbone angle is used. The pseudodihedral angle (the torsion angle between planes defined by 4 consecutive alpha-carbon atoms) provides a simplified backbone representation and continues to manifest information about secondary-structure elements: the pseudo-Ramachandran plot contains helical and sheetlike regions. The distribution of pseudodihedral angles is highly sensitive to the identity of the central pair of amino acids. Therefore, a sequence-dependent, knowledge-based potential energy was found according to a quasichemical approximation. These functions form complementary additions to the contact potentials currently in use. This pseudodihedral potential greatly enhances the ability to design sequences that are specific to a given conformation and also improves the ability to discriminate a native conformation from many other conformations.
DeWitte
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Department of Chemistry, Harvard University, Cambridge, Massachusetts 02138.
Shakhnovich
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D000596:Amino Acids / Q000737:chemistry; D016208:Databases, Factual; D006026:Glycoside Hydrolases / Q000037:antagonists & inhibitors; D007535:Isomerases / Q000737:chemistry; D008956:Models, Chemical; D009211:Myoglobin / Q000737:chemistry; D017433:Protein Structure, Secondary; D013816:Thermodynamics
D000596:Amino Acids; D009211:Myoglobin; D006026:Glycoside Hydrolases; D007535:Isomerases