Intrinsic torsional potential parameters for conformational analysis of peptides and proteins

Young Kee Kang, Kyoung Tai No, Harold A. Scheraga

Research output: Contribution to journalArticle

23 Citations (Scopus)

Abstract

New sets of intrinsic torsional parameters, obtained by fitting to experimental and/or theoretical values of torsional barriers and relative conformational energies of various uncharged model organic compounds, are presented. They are intended for use in conformational energy computations on peptides and proteins. A three-term Fourier series expansion is used to represent the intrinsic torsional energy. Each set of intrinsic torsional parameters, obtained from a single model compound, reproduces experimental torsional barriers, relative conformational energies, and torsion angles of related molecules not used for the parametrization. The sets of parameters of a new potential function, including electrostatic interactions based on partial atomic charges, and nonbonded, hydrogen-bond, and intrinsic torsional energies, are tested in conformational energy calculations on a model peptide N-acetyl-N′-methylalanineamide. The electrostatic energy component plays a significant role in the total conformational energy and leads to a high relative energy of the αR (A) c onformation compared to the C7 eq (C) conformation, although the latter is still the global minimum. These results differ from those with ECEPP/3, CHARMM, and AMBER, but are reasonably consistent with those from recent ab initio studies.

Original languageEnglish
Pages (from-to)15588-15598
Number of pages11
JournalJournal of physical chemistry
Volume100
Issue number38
DOIs
Publication statusPublished - 1996 Sep 19

All Science Journal Classification (ASJC) codes

  • Engineering(all)
  • Physical and Theoretical Chemistry

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