An improved hydrogen bond potential: Impact on medium resolution protein structures

Felcy Fabiola, Richard Bertram, Andrei Korostelev, Michael S. Chapman

Research output: Contribution to journalArticle

92 Scopus citations

Abstract

A new semi-empirical force field has been developed to describe hydrogen-bonding interactions with a directional component. The hydrogen bond potential supports two alternative target angles, motivated by the observation that carbonyl hydrogen bond acceptor angles have a bimodal distribution. It has been implemented as a module for a macromolecular refinement package to be combined with other force field terms in the stereochemically restrained refinement of macromolecules. The parameters for the hydrogen bond potential were optimized to best fit crystallographic data from a number of protein structures. Refinement of medium-resolution structures with this additional restraint leads to improved structure, reducing both the free R-factor and over-fitting. However, the improvement is seen only when stringent hydrogen bond selection criteria are used. These findings highlight common misconceptions about hydrogen bonding in proteins, and provide explanations for why the explicit hydrogen bonding terms of some popular force field sets are often best switched off.

Original languageEnglish (US)
Pages (from-to)1415-1423
Number of pages9
JournalProtein Science
Volume11
Issue number6
DOIs
StatePublished - 2002

Keywords

  • Crystallography
  • Force field
  • Hydrogen bond restraint
  • Hydrogen bonds

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

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