Interhelical hydrogen bonds and spatial motifs in membrane proteins: Polar clamps and serine zippers

Polar and ionizable amino acid residues are frequently found in the transmembrane (TM) regions of membrane proteins. In this study, we show that they help to form extensive hydrogen bond connections between TM helices. We find that almost all TM helices have interhelical hydrogen bonding. In addition, we find that a pair of contacting TM helices is packed tighter when there are interhelical hydrogen bonds between them. We further describe several spatial motifs in the TM regions, including “Polar Clamp” and “Serine Zipper,” where conserved Ser residues coincide with tightly packed locations in the TM region. With the examples of halorhodopsin, calcium‐transporting ATPase, and bovine cytochrome c oxidase, we discuss the roles of hydrogen bonds in stabilizing helical bundles in polytopic membrane proteins and in protein functions. Proteins 2002;47:209–218. © 2002 Wiley‐Liss, Inc.

[1]  A. Brunger,et al.  Statistical analysis of predicted transmembrane α-helices , 1998 .

[2]  M. Krebs,et al.  Role of helix-helix interactions in assembly of the bacteriorhodopsin lattice. , 1999, Biochemistry.

[3]  Alessandro Senes,et al.  The Cα—H⋅⋅⋅O hydrogen bond: A determinant of stability and specificity in transmembrane helix interactions , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[4]  R. Gennis Cytochrome c Oxidase: One Enzyme, Two Mechanisms? , 1998, Science.

[5]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[6]  M. Gerstein,et al.  Statistical analysis of amino acid patterns in transmembrane helices: the GxxxG motif occurs frequently and in association with beta-branched residues at neighboring positions. , 2000, Journal of molecular biology.

[7]  Manfred Auer,et al.  Structure of fumarate reductase from Wolinella succinogenes at 2.2 Å resolution , 1999, Nature.

[8]  H Luecke,et al.  Structure of bacteriorhodopsin at 1.55 A resolution. , 1999, Journal of molecular biology.

[9]  D. Fu,et al.  Structure of a glycerol-conducting channel and the basis for its selectivity. , 2000, Science.

[10]  D. Herschlag,et al.  The change in hydrogen bond strength accompanying charge rearrangement: implications for enzymatic catalysis. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[11]  N. Green,et al.  The Mechanism of Ca 2 1 Transport by Sarco ( Endo ) plasmic Reticulum Ca 2 1-ATPases * , 1997 .

[12]  B. Chait,et al.  The structure of the potassium channel: molecular basis of K+ conduction and selectivity. , 1998, Science.

[13]  K. Dill Dominant forces in protein folding. , 1990, Biochemistry.

[14]  T. Tomizaki,et al.  Redox-coupled crystal structural changes in bovine heart cytochrome c oxidase. , 1998, Science.

[15]  D. Higgins,et al.  See Blockindiscussions, Blockinstats, Blockinand Blockinauthor Blockinprofiles Blockinfor Blockinthis Blockinpublication Clustal: Blockina Blockinpackage Blockinfor Blockinperforming Multiple Blockinsequence Blockinalignment Blockinon Blockina Minicomputer Article Blockin Blockinin Blockin , 2022 .

[16]  S. White,et al.  Membrane protein folding and stability: physical principles. , 1999, Annual review of biophysics and biomolecular structure.

[17]  T. A. Link,et al.  Complete structure of the 11-subunit bovine mitochondrial cytochrome bc1 complex. , 1998, Science.

[18]  J. Thornton,et al.  Satisfying hydrogen bonding potential in proteins. , 1994, Journal of molecular biology.

[19]  Cori Bargmann,et al.  Multiple independent activations of the neu oncogene by a point mutation altering the transmembrane domain of p185 , 1986, Cell.

[20]  S. O. Smith,et al.  Helix packing in polytopic membrane proteins: role of glycine in transmembrane helix association. , 1999, Biophysical journal.

[21]  Ming-Ming Zhou Phosphothreonine recognition comes into focus , 2000, Nature Structural Biology.

[22]  M. Billeter,et al.  MOLMOL: a program for display and analysis of macromolecular structures. , 1996, Journal of molecular graphics.

[23]  T. D. Schneider,et al.  Sequence logos: a new way to display consensus sequences. , 1990, Nucleic acids research.

[24]  Jie Liang,et al.  Helix-helix packing and interfacial pairwise interactions of residues in membrane proteins. , 2001, Journal of molecular biology.

[25]  D. Rees,et al.  Structure of the Escherichia coli fumarate reductase respiratory complex. , 1999, Science.

[26]  H. Michel,et al.  Structure at 2.7 A resolution of the Paracoccus denitrificans two-subunit cytochrome c oxidase complexed with an antibody FV fragment. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[27]  D. Engelman,et al.  Interhelical hydrogen bonding drives strong interactions in membrane proteins , 2000, Nature Structural Biology.

[28]  N. Green,et al.  The Mechanism of Ca2+ Transport by Sarco(Endo)plasmic Reticulum Ca2+-ATPases* , 1997, The Journal of Biological Chemistry.

[29]  Short and Long Range Functions of Amino Acids in the Transmembrane Region of the Sarcoplasmic Reticulum ATPase , 1996, The Journal of Biological Chemistry.

[30]  R. Huber,et al.  Structure and mechanism of the aberrant ba3‐cytochrome c oxidase from Thermus thermophilus , 2000, The EMBO journal.

[31]  M. Nakasako,et al.  Crystal structure of the calcium pump of sarcoplasmic reticulum at 2.6 Å resolution , 2000, Nature.

[32]  Michael J. Geisow Atlas of protein side chain interactions, vols 1 and 2: by Juswinder Singh and Janet M. Thornton, IRL Press at Oxford University Press, 1992. UK£55.00 (428 + 827 pages) ISBN 0 19 963362 2 , 1994 .

[33]  W. DeGrado,et al.  Polar side chains drive the association of model transmembrane peptides. , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[34]  Herbert Edelsbrunner,et al.  Three-dimensional alpha shapes , 1994, ACM Trans. Graph..

[35]  Michael A. Facello,et al.  Implementation of a randomized algorithm for Delaunay and regular triangulations in three dimensions , 1995, Comput. Aided Geom. Des..

[36]  A. Lupas Coiled coils: new structures and new functions. , 1996, Trends in biochemical sciences.

[37]  William F. DeGrado,et al.  Asparagine-mediated self-association of a model transmembrane helix , 2000, Nature Structural Biology.

[38]  J. Thornton,et al.  Atlas of protein side-chain interactions , 1992 .

[39]  D. Oesterhelt,et al.  Chemical reconstitution of a chloride pump inactivated by a single point mutation. , 1995, The EMBO journal.

[40]  C. Deber,et al.  Interhelical hydrogen bonds in the CFTR membrane domain , 2001, Nature Structural Biology.

[41]  D. Engelman,et al.  The effect of point mutations on the free energy of transmembrane alpha-helix dimerization. , 1997, Journal of molecular biology.

[42]  D. Oesterhelt,et al.  Structure of the light-driven chloride pump halorhodopsin at 1.8 A resolution. , 2000, Science.

[43]  C. Chothia,et al.  The Packing Density in Proteins: Standard Radii and Volumes , 1999 .

[44]  B. Bormann,et al.  Strong hydrogen bonding interactions involving a buried glutamic acid in the transmembrane sequence of the neu/erbB-2 receptor , 1996, Nature Structural Biology.

[45]  James H. Prestegard,et al.  A Transmembrane Helix Dimer: Structure and Implications , 1997, Science.

[46]  T. Marti Refolding of Bacteriorhodopsin from Expressed Polypeptide Fragments* , 1998, The Journal of Biological Chemistry.

[47]  K. Palczewski,et al.  Crystal Structure of Rhodopsin: A G‐Protein‐Coupled Receptor , 2002, Chembiochem : a European journal of chemical biology.