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Originally published as Biophys J. BioFAST on August 31, 2004.
doi:10.1529/biophysj.104.044024
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Biophysical Journal 87:3460-3469 (2004)
© 2004 The Biophysical Society

Analysis of Side-Chain Rotamers in Transmembrane Proteins

Aaron K. Chamberlain and James U. Bowie

Department of Chemistry and Biochemistry, UCLA-DOE Center for Genomics and Proteomics, Molecular Biology Institute, University of California, Los Angeles, California 90095-1570

Correspondence: Address reprint requests to James U. Bowie, E-mail: bowie{at}mbi.ucla.edu.

We measured the frequency of side-chain rotamers in 14 {alpha}-helical and 16 ß-barrel membrane protein structures and found that the membrane environment considerably perturbs the rotamer frequencies compared to soluble proteins. Although there are limited experimental data, we found statistically significant changes in rotamer preferences depending on the residue environment. Rotamer distributions were influenced by whether the residues were lipid or protein facing, and whether the residues were found near the N- or C-terminus. Hydrogen-bonding interactions with the helical backbone perturbs the rotamer populations of Ser and His. Trp and Tyr favor side-chain conformations that allow their side chains to extend their polar atoms out of the membrane core, thereby aligning the side-chain polarity gradient with the polarity gradient of the membrane. Our results demonstrate how the membrane environment influences protein structures, providing information that will be useful in the structure prediction and design of transmembrane proteins.




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