Pseudodihedrals: simplified protein backbone representation with knowledge-based energy.

R S DeWitte; E I Shakhnovich

doi:10.1002/pro.5560030922

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Pseudodihedrals: simplified protein backbone representation with knowledge-based energy.

R S DeWitte·E I Shakhnovich

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Abstract

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.

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Amino Acids Databases, Factual Glycoside Hydrolases Isomerases Models, Chemical Myoglobin Protein Structure, Secondary Thermodynamics Comparative Study Journal Article Research Support, Non-U.S. Gov't

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R S DeWitte, E I Shakhnovich. 1994. Pseudodihedrals: simplified protein backbone representation with knowledge-based energy.. https://doi.org/10.1002/pro.5560030922

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