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Published online before print December 20, 2007, 10.1110/ps.073237508
Protein Science (2008), 17:293-298. Published by Cold Spring Harbor Laboratory Press. Copyright © 2008 The Protein Society
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Buried water molecules in helical transmembrane proteins

Robert Renthal

Department of Biology, University of Texas at San Antonio, San Antonio, Texas 78249, USA
Department of Biochemistry, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA

(RECEIVED September 10, 2007; FINAL REVISION November 5, 2007; ACCEPTED November 6, 2007)

Buried water molecules (having no contact with bulk solvent) in 30 helical transmembrane (TM) protein structures were identified. The average amount of buried water in helical TM proteins is about the same as for all water-soluble (WS) proteins, but it is greater than the average for helical WS proteins. Buried waters in TM proteins make more polar contacts, and are more frequently found contacting helices than in WS proteins. The distribution of the buried water binding sites across the membrane profile shows that the sites to some extent reflect protein function. There is also evidence for asymmetry of the sites, with more in the extracellular half of the membrane. Many of the buried water contact sites are conserved across families of proteins, including family members having different functions. This suggests that at least some buried waters play a role in structural stabilization. Disease-causing mutations, which are known to result in misfolded TM proteins, occur at buried water contact sites at a higher than random frequency, which also supports a stabilizing role for buried water molecules.

Keywords: membrane protein structure; bacteriorhodopsin; aquaporin; cytochrome c oxidase; rhodopsin


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