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Proteins. 2015 Mar;83(3):403-410. doi: 10.1002/prot.24724. Epub 2015 Jan 21.

Frequent side chain methyl carbon-oxygen hydrogen bonding in proteins revealed by computational and stereochemical analysis of neutron structures.

Author information

1
Departments of Biophysics and Molecular, Cellular, University of Michigan, Ann Arbor, MI 48109, USA.
2
Departments of Biochemistry & Physics, Stanford University, Stanford, CA 94305.
3
Department of Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA.
4
Department of Biological Chemistry, Howard Hughes Medical Institute, University of Michigan, Ann Arbor MI 48109 USA.
5
Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.
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Contributed equally

Abstract

The propensity of backbone Cα atoms to engage in carbon-oxygen (CH · · · O) hydrogen bonding is well-appreciated in protein structure, but side chain CH · · · O hydrogen bonding remains largely uncharacterized. The extent to which side chain methyl groups in proteins participate in CH · · · O hydrogen bonding is examined through a survey of neutron crystal structures, quantum chemistry calculations, and molecular dynamics simulations. Using these approaches, methyl groups were observed to form stabilizing CH · · · O hydrogen bonds within protein structure that are maintained through protein dynamics and participate in correlated motion. Collectively, these findings illustrate that side chain methyl CH · · · O hydrogen bonding contributes to the energetics of protein structure and folding.

KEYWORDS:

CH···O; CH···O CH···O; CHO; CH···O; hydrogen bond; molecular dynamics; neutron structure; quantum mechanics

PMID:
25401519
PMCID:
PMC4747036
DOI:
10.1002/prot.24724
[Indexed for MEDLINE]
Free PMC Article

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