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Hydrogen-Bonding and Packing Features of Membrane Proteins: Functional Implications

Peter Werner Hildebrand ^*, Stefan Günther ^*, Andrean Goede ^*, Lucy Forrest , Cornelius Frömmel  and Robert Preissner ^*

^* Institute of Molecular Biology and Bioinformatics, Charité University Medicine, Berlin, Germany; Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biology and Center for Computational Biology and Bioinformatics, Columbia University, New York, New York 10032 USA; and Medical Faculty, Georg-August-Universität Göttingen, Göttingen, Germany

Correspondence: Address reprint requests to Dr. Peter Werner Hildebrand, University Medicine Berlin, Institute of Biochemistry Charité, Monbijoustr. 1a, Berlin D-10117, Germany. E-mail: peter.hildebrand{at}charite.de.

The recent structural elucidation of about one dozen channels (in which we include transporters) has provided further evidence that these membrane proteins typically undergo large movements during their function. However, it is still not well understood how these proteins achieve the necessary trade-off between stability and mobility. To identify specific structural properties of channels, we compared the helix-packing and hydrogen-bonding patterns of channels with those of membrane coils; the latter is a class of membrane proteins whose structures are expected to be more rigid. We describe in detail how in channels, helix pairs are usually arranged in packing motifs with large crossing angles (|| 40°), where the (small) side chains point away from the packing core and the backbones of the two helices are in close contact. We found that this contributes to a significant enrichment of C–H···O bonds and to a packing geometry where right-handed parallel ( = –40° ± 10°) and antiparallel ( = +140° ± 25°) arrangements are equally preferred. By sharp contrast, the interdigitation and hydrogen bonding of side chains in helix pairs of membrane coils results in narrowly distributed left-handed antiparallel arrangements with crossing angles = –160° ± 10° (|| 20°). In addition, we show that these different helix-packing modes of the two types of membrane proteins correspond to specific hydrogen-bonding patterns. In particular, in channels, three times as many of the hydrogen-bonded helix pairs are found in parallel right-handed motifs than are non-hydrogen-bonded helix pairs. Finally, we discuss how the presence of weak hydrogen bonds, water-containing cavities, and right-handed crossing angles may facilitate the required conformational flexibility between helix pairs of channels while maintaining sufficient structural stability.