A consistent set of statistical potentials for quantifying local side-chain and backbone interactions

Qiaojun Fang, David Shortle

Research output: Contribution to journalArticle

Abstract

The frequencies of occurrence of atom arrangements in high-resolution protein structures provide some of the most accurate quantitative measures of interaction energies in proteins. In this report we extend our development of a consistent set of statistical potentials for quantifying local interactions between side-chains and the polypeptide backbone, as well as nearby side-chains. Starting with φ/ψ/χ1 propensities that select for optimal interactions of the 20 amino acid side-chains with the 2 flanking peptide bonds, the following 3 new terms are added: (1) a distance-dependent interaction between the side-chain at i and the carbonyl oxygens and amide protons of the peptide units at i ± 2, i ± 3, and i ± 4; (2) a distance-dependent interaction between the side-chain at position i and side-chains at positions i + 1 through i + 4; and (3) an orientation-dependent interaction between the side-chain at position i and side-chains at i + 1 through i + 4. The relative strengths of these 4 pseudo free energy terms are estimated by the average information content of each scoring matrix and by assessing their performance in a simple fragment threading test. They vary from -0.4--0.5 kcal/mole per residue for φ/ψ/χ1 propensities to a range of -0.15--0.6 kcal/mole per residue for each of the other 3 terms. The combined energy function, containing no interactions between atoms more than 4 residues apart, identifies the correct structural fragment for randomly selected 15 mers over 40% of the time, after searching through 232,000 alternative conformations. For 14 out of 20 sets of all-atom Rosetta decoys analyzed, the native structure has a combined score lower than any of the 1700-1900 decoy conformations. The ability of this energy function to detect energetically important details of local structure is demonstrated by its power to distinguish high-resolution crystal structures from NMR solution structures.

Original languageEnglish (US)
Pages (from-to)90-96
Number of pages7
JournalProteins: Structure, Function and Genetics
Volume60
Issue number1
DOIs
StatePublished - Jun 15 2005

Keywords

  • Boltzmann hypothesis
  • Fragment threading
  • Free energy
  • Knowledge-based potentials
  • Side-chain-backbone interaction
  • Side-chain-side-chain interaction

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology

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