A simple and realistic model system for studying hydrogen bonds in beta-sheets

Jan Rossmeisl, Berit Hinnemann, Karsten Wedel Jacobsen, Jens Kehlet Nørskov, Ole H. Olsen, Jan T. Pedersen

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Abstract

We investigate the interaction between peptide chains at the level of state-of-the-art ab initio density functional theory. We propose an interacting periodic polypeptide model for studying the interactions in beta-sheets and apply this to glycine and alanine peptide chains in both parallel and antiparallel structures. The calculated structures of alanine are compared to x-ray structures of beta-sheets and the model is found to reproduce the geometry of the hydrogen bonds very well both concerning parallel and antiparallel beta-sheets. We investigate the structures of both the N-H...O=C and the C-alpha-H...O=C hydrogen bonds. The former is thoroughly investigated, whereas the structure of the latter still is the subject of much discussion. We show that the hydrogen bonds between peptide chains are considerably weaker than what is found in studies of smaller models, e.g., the N-methylacetamide molecule. By molecular mechanics calculations we study the effect of twisting, which is not included in our model. We estimate its contribution to the interaction energy to be small.
Original languageEnglish
JournalJournal of Chemical Physics
Volume118
Issue number21
Pages (from-to)9783-9794
ISSN0021-9606
DOIs
Publication statusPublished - 2003

Bibliographical note

Copyright (2003) American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics.

Keywords

  • ALANINE DIPEPTIDE
  • DENSITY-FUNCTIONAL THEORY
  • CONFORMATIONAL BEHAVIOR
  • N-METHYLACETAMIDE
  • PROTEINS
  • POLYGLYCINE
  • CENTER-DOT-O=C
  • ENERGETICS
  • AB-INITIO
  • PERIODIC BOUNDARY-CONDITIONS

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