Conformational-analysis of the Backbone-dependent Rotamer Preferences of Protein Side-chains

RL Dunbrack; M Karplus

doi:10.1038/nsb0594-334

Conformational-analysis of the Backbone-dependent Rotamer Preferences of Protein Side-chains

RL Dunbrack, M Karplus

Cancer Signaling and Microenvironment (CSM)

Research output: Contribution to journal › Article › peer-review

301 Scopus citations

Abstract

Amino acids have sidechain rotamer preferences dependent on the backbone dihedral angles phi and psi. These preferences provide a method for rapid structure prediction which is a significant improvement over backbone-independent rotamer libraries. We demonstrate here that simple arguments based on conformational analysis can account for many of the features of the observed backbone dependence of the sidechain rotamers. Steric repulsions corresponding to the 'butane' and 'syn-pentane' effects make certain conformers rare, as has been observed experimentally.

Original language	American English
Pages (from-to)	334-340
Number of pages	7
Journal	Nature Structural Biology
Volume	1
Issue number	5
DOIs	https://doi.org/10.1038/nsb0594-334
State	Published - May 1994

Keywords

Amino Acids/chemistry
Hydrocarbons/chemistry
Models, Molecular
Molecular Conformation
Protein Conformation
Rotation

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10.1038/nsb0594-334

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AB - Amino acids have sidechain rotamer preferences dependent on the backbone dihedral angles phi and psi. These preferences provide a method for rapid structure prediction which is a significant improvement over backbone-independent rotamer libraries. We demonstrate here that simple arguments based on conformational analysis can account for many of the features of the observed backbone dependence of the sidechain rotamers. Steric repulsions corresponding to the 'butane' and 'syn-pentane' effects make certain conformers rare, as has been observed experimentally.

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KW - Hydrocarbons/chemistry

KW - Models, Molecular

KW - Molecular Conformation

KW - Protein Conformation

KW - Rotation

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Conformational-analysis of the Backbone-dependent Rotamer Preferences of Protein Side-chains

Abstract

Keywords

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