Characteristics of Ramachandran maps of L-alanine diamides as computed by various molecular mechanics, semiempirical and ab initio MO methods. A search for primary standard of peptide conformational stability

Ana M. Rodríguez, Héctor A. Baldoni, Fernando Suvire, Rodolfo Nieto Vázquez, Graciela Zamarbide, Ricardo D. Enriz, Ödön Farkas, András Perczel, Michael A. McAllister, Leslie L. Torday, Julius G. Papp, Imre G. Csizmadia

Research output: Contribution to journalArticle

32 Citations (Scopus)

Abstract

The optimized geometries and relative energies obtained by four force field and two semi-empirical methods were compared with ab initio results computed for formyl-L-alaninamide. Not all methods yielded the same number of minimum energy conformers. Furthermore, while the optimized geometries of the conformers found were comparable, the computed relative energies varied substantially. Also, the force field calculations produced Ramachandran maps that did not even have the appearance of the ab initio Ramachandran map. Correlating the ab initio relative energies (ΔE) or free energy (ΔG) with the log of relative populations, ln(px/pγL), led to linear relationships from which four conformers deviated; two of them (αL and εL) were overly destabilized and two of them (γL and γD) were over-stabilized. It is suggested that, after such deviations are corrected, a primary standard may be obtained that might be useful in further investigations related to force-field parametrization as well as protein folding.

Original languageEnglish
Pages (from-to)275-301
Number of pages27
JournalJournal of Molecular Structure: THEOCHEM
Volume455
Issue number2-3
DOIs
Publication statusPublished - Dec 18 1998

Keywords

  • Alanine diamides
  • Empirical force fields
  • HCONH-CHMe-CONH
  • MeCONH-CHMe-CONHMe
  • Semi-empirical and ab initio MO methods

ASJC Scopus subject areas

  • Biochemistry
  • Condensed Matter Physics
  • Physical and Theoretical Chemistry

Fingerprint Dive into the research topics of 'Characteristics of Ramachandran maps of L-alanine diamides as computed by various molecular mechanics, semiempirical and ab initio MO methods. A search for primary standard of peptide conformational stability'. Together they form a unique fingerprint.

  • Cite this