Quantum mechanical study of secondary structure formation in protected dipeptides

Phys Chem Chem Phys. 2010 May 14;12(18):4678-85. doi: 10.1039/b923041f. Epub 2010 Mar 16.

Abstract

An extensive computational study of the conformational preferences of three capped dipeptides: Ac-Xxx-Phe-NH(2), Xxx = Gly, Ala, Val is reported. On the basis of local second-order Møller-Plesset perturbation theory (LMP2) and DFT computations we were able to identify the experimentally observed conformers as gamma(L)-gamma(L)(g-) and beta-turn I(g+) in Ac-Gly-Phe-NH(2), and Ac-Ala-Phe-NH(2), and as the closely related gamma(L)(g+)-gamma(L)(g-) and beta-turn I(a,g+) in Ac-Val-Phe-NH(2). In contrast to the experimental observation that peptides with bulky side chain have a propensity for beta-turns, we show that in Ac-Val-Phe-NH(2) the minimum energy structure corresponds to the experimentally non detected beta-strand.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Dipeptides / chemistry*
  • Electrons
  • Molecular Dynamics Simulation
  • Protein Structure, Secondary
  • Quantum Theory*
  • Spectrophotometry, Infrared

Substances

  • Dipeptides