Comparing theoretical and experimental backbone-dependent sidechain conformational preferences for linear, branched, aromatic and polar residues

Emil Marcus, Donald A. Keller, Masayuki Shibata, Rick L. Ornstein, Robert Rein

Research output: Contribution to journalArticlepeer-review

8 Scopus citations

Abstract

An Ecepp-3 conformational study based on a φ-ψ grid search with sidechain minimization was carried out on the N-acetyl N′-methyl amides of four representative amino acids: Met, Phe, Ile, and Ser, and the distribution of χ1 backbone-dependent rotamer preferences was compared with the similar distribution obtained from the backbone-dependent rotamer library for proteins developed by Dunbrack and Karplus (J. Mol. Biol. 230 (1993) 543). The experimental distribution is best reproduced theoretically in the case of the linear sidechain of Met, reasonably well for the bulky sidechains of the aromatic Phe and asymmetrically β-branched Ile, and only partially for the short polar sidechain of Ser. In the case of the Ser dipeptide the difference is accounted for by the missing H bonds.

Original languageEnglish (US)
Pages (from-to)157-171
Number of pages15
JournalChemical Physics
Volume204
Issue number2-3 SPEC. ISS.
DOIs
StatePublished - Apr 1 1996
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • General Physics and Astronomy
  • Physical and Theoretical Chemistry

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