Local amide I mode frequencies and coupling constants in polypeptides

Jun Ho Choi, Sihyun Ham, Minhaeng Cho

Research output: Contribution to journalArticle

130 Citations (Scopus)

Abstract

Ab initio calculations of the amide I modes of right-handed α-helical, 310-helical, left-handed α-helical, π-helical, parallel β-sheet, antiparallel β-sheet, and fully extended β-sheet polypeptide conformations with two to five peptide bonds were performed to investigate the site dependencies of the local amide I mode frequencies and vibrational coupling constants between neighboring peptides. A Hessian matrix reconstruction method is used to obtain these quantities from the ab initio-calculated amide I normal modes. The local amide I mode frequencies of the peptides in the inner region of a given helical polypeptide are significantly larger than those of terminal peptides, whereas the local amide I mode frequencies of β-sheet polypeptides are not site-dependent. The amide I vibrational coupling constants are not sensitive to the length of the polypeptide, but they are found to be strongly dependent on the three-dimensional conformation of the polypeptides. An empirical model for predicting diagonal amide I mode frequency shift is used to theoretically describe the site dependence of the local amide I mode frequency.

Original languageEnglish
Pages (from-to)9132-9138
Number of pages7
JournalJournal of Physical Chemistry B
Volume107
Issue number34
Publication statusPublished - 2003 Aug 28

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ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Surfaces, Coatings and Films
  • Materials Chemistry

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