Relative stability of major types of β-turns as a function of amino acid composition: A study based on ab initio energetic and natural abundance data

András Perczel, Imre Jákli, Michael A. McAllister, Imre G. Csizmadia

Research output: Contribution to journalArticle

21 Citations (Scopus)

Abstract

Folding properties of small globular proteins are determined by their amino acid sequence (primary structure). This holds both for local (secondary structure) and for global conformational features of linear polypeptides and proteins composed from natural amino acid derivatives. It thus provides the rational basis of structure prediction algorithms. The shortest secondary structure element, the β-turn, most typically adopts either a type I or a type II form, depending on the amino acid composition. Herein we investigate the sequence-dependent folding stability of both major types of β-turns using simple dipeptide models (-Xxx-Yyy-). Gas-phase ab initio properties of 16 carefully selected and suitably protected dipeptide models (for example Val-Ser, Ala-Gly, Ser-Ser) were studied. For each backbone fold most probable side-chain conformers were considered. Fully optimized 3-21G RHF molecular structures were employed in medium level [B3LYP/6-311++G(d,p)//RHF/3-21G] energy calculations to estimate relative populations of the different backbone conformers. Our results show that the preference for β-turn forms as calculated by quantum mechanics and observed in X-ray determined proteins correlates significantly.

Original languageEnglish
Pages (from-to)2551-2566
Number of pages16
JournalChemistry - A European Journal
Volume9
Issue number11
DOIs
Publication statusPublished - Jun 6 2003

Keywords

  • Ab initio calculations
  • Conformation analysis
  • Protein folding
  • Protein models
  • β-turns

ASJC Scopus subject areas

  • Catalysis
  • Organic Chemistry

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