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PMID: 12021440 Published · ppublish English Journal Article Research Support, U.S. Gov't, Non-P.H.S.

An improved hydrogen bond potential: impact on medium resolution protein structures.

Protein science : a publication of the Protein Society ·Vol. 11 ·No. 6 ·2002-06-00 ·Pages 1415-23

Fabiola F, Bertram R, Korostelev A, Chapman MS

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.

MeSH Terms
Animals Humans Hydrogen Bonding Models, Molecular Molecular Structure Protein Structure, Secondary Proteins/chemistry
Chemicals
Proteins
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Fabiola Felcy
Kasha Laboratory of Biophysics, Florida State University, Tallahassee, Florida 32306-4380, USA.
Bertram Richard
Korostelev Andrei
Chapman Michael S
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Article Info
Journal
Protein science : a publication of the Protein Society
Abbr.
Protein Sci
ISSN
0961-8368
DOI
10.1110/ps.4890102
Published
2002-06-00
Pages
1415-23
Language
English
Region
United States
NLM ID
9211750
PMCID
PMC2373622
Subset
IM
External Links
PubMed source DOI: 10.1110/ps.4890102 PMC Full Text View journal details
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