Conformational study of dipeptides: A sensitivity analysis approach

Roberta Susnow, Clarence Schutt, Herschel Rabitz, Shankar Subramaniam

Research output: Contribution to journalArticle

11 Scopus citations

Abstract

This article studies the backbone influence on the side chains of N‐methyl N′‐acetyl amides (dipeptides) of alanine, valine, phenylalanine, leucine, isoleucine, glutamine, and lysine. Several local minima corresponding to protein ϕ, ψ, and χ values for each dipeptide are determined through optimization in the MM2 force field. These local minima are located in various regions on the Ramachandran map related to particular protein secondary structures. The dipeptide backbone influence on the side chain is explored via the sensitivity of the side chain torsion angles χ with respect to the backbone ϕ and ψ angles. Sensitivity coefficients are calculated, describing the χ response to an externally imposed change in ϕ or ψ. The χ response, which depends on the backbone conformation in a particular region, is induced primarily by the van der Waals and dipole interactions between the backbone and the side chain, which change with a deviation in ϕ or ψ. Various sensitivity trends are observed in the particular Ramachandran regions, revealing the subtle relationships between the dipeptide backbone and the side chain. © 1994 by John Wiley & Sons, Inc.

Original languageEnglish (US)
Pages (from-to)947-962
Number of pages16
JournalJournal of Computational Chemistry
Volume15
Issue number9
DOIs
StatePublished - Sep 1994

All Science Journal Classification (ASJC) codes

  • Chemistry(all)
  • Computational Mathematics

Fingerprint Dive into the research topics of 'Conformational study of dipeptides: A sensitivity analysis approach'. Together they form a unique fingerprint.

  • Cite this