Surface recognition elements of membrane protein oligomerization

Proteins: Structure, Function and Genetics

Volumn 70, Issue 3, 2008, Pages 786-793

  Rath, Arianna ^a,b   Deber, Charles M ^a,b  

^a HOSPITAL FOR SICK CHILDREN RESEARCH INSTITUTE   (Canada)

^b UNIVERSITY OF TORONTO   (Canada)

Author keywords

Folding; Helix helix interactions; Membrane protein; Oligomerization; Prediction

Indexed keywords

LIPID; MEMBRANE PROTEIN; OLIGOMER; POLYPEPTIDE;

ALPHA HELIX; AMINO ACID COMPOSITION; ARTICLE; MOLECULAR RECOGNITION; OLIGOMERIZATION; PREDICTION; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN MOTIF; PROTEIN PROTEIN INTERACTION; PROTEIN QUATERNARY STRUCTURE; PROTEIN STRUCTURE; SURFACE PROPERTY;

AMINO ACID MOTIFS; DATABASES, PROTEIN; DIMERIZATION; MEMBRANE PROTEINS; MODELS, MOLECULAR; PROTEIN FOLDING; PROTEIN STRUCTURE, QUATERNARY; PROTEIN SUBUNITS; SURFACE PROPERTIES;

EID: 38849122877     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21569     Document Type: Article

References (58)

1. Wallin E, von Heijne G. Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms. Protein Sci 1998;7:1029-1038.
2. Liu Y, Gerstein M, Engelman DM. Transmembrane protein domains rarely use covalent domain recombination as an evolutionary mechanism. Proc Natl Acad Sci USA 2004;101:3495-3497.
3. Senes A, Engel DE, DeGrado WF. Folding of helical membrane proteins: the role of polar. Gxxx G-like and proline motifs. Curr Opin Struct Biol 2004;14:465-479.
4. Walters RF, DeGrado WF. Helix-packing motifs in membrane proteins. Proc Natl Acad Sci USA 2006;103:13658-13663.
5. Adamian L, Jackups R, Jr, Binkowski TA, Liang J. Higher-order interhelical spatial interactions in membrane proteins. J Mol Biol 2003;327:251-272.
6. Leonov H, Arkin IT. A periodicity analysis of transmembrane helices. Bioinformatics 2005;21:2604-2610.
7. Dawson JP, Weinger JS, Engelman DM. Motifs of serine and threonine can drive association of transmembrane helices. J Mol Biol 2002;316:799-805.
8. Sal-Man N, Gerber D, Shai Y. The identification of a minimal dimerization motif QXXS that enables homo- and hetero-association of transmembrane helices in vivo. J Biol Chem 2005;280: 27449-27457.
9. North B, Cristian L, Fu Stowell X, Lear JD, Saven JG, Degrado WF. Characterization of a membrane protein folding motif, the ser zipper, using designed peptides. J Mol Biol 2006;359:930-939.
10. Rath A, Deber CM. Patterns of membrane protein assembly reflect selection for non-proliferative structures. FEBS Lett 2007;581:1335-1341.
11. Tusnady GE, Dosztanyi Z, Simon I. PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank. Nucleic Acids Res 2005;33(Database issue):D275-D278.
12. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL
13. Huang Y, Lemieux MJ, Song J, Auer M, Wang DN. Structure and mechanism of the glycerol-3-phosphate transporter from Escherichia coli. Science 2003;301:616-620.
14. Mirza O, Guan L, Verner G, Iwata S, Kaback HR. Structural evidence for induced fit and a mechanism for sugar/H+ symport in LacY. EMBO J 2006;25:1177-1183.
15. Wang Y, Zhang Y, Ha Y. Crystal structure of a rhomboid family intramembrane protease. Nature 2006;444:179-180.
16. MacKenzie KR, Prestegard JH, Engelman DM. A transmembrane helix dimer: structure and implications. Science 1997;276:131-133.
17. Call ME, Schnell JR, Xu C, Lutz RA, Chou JJ, Wucherpfennig KW. The structure of the zetazeta transmembrane dimer reveals features essential for its assembly with the T cell receptor. Cell 2006;127: 355-368.
18. Locher KP, Lee AT, Rees DC. The E. coli BtuCD structure: a framework for ABC transporter architecture and mechanism. Science 2002;296:1091-1098.
19. Dutzler R, Campbell EB, MacKinnon R. Gating the selectivity filter in ClC chloride channels. Science 2003;300:108-112.
20. Dawson RJ, Locher KP. Structure of a bacterial multidrug ABC transporter. Nature 2006;443:180-185.
21. Hollenstein K, Frei DC, Locher KP. Structure of an ABC transporter in complex with its binding protein. Nature 2007;446:213-216.
22. Van den Berg B, Clemons WM, Jr, Collinson I, Modis Y, Hartmann E, Harrison SC, Rapoport TA. X-ray structure of a protein-conducting channel. Nature 2004;427:36-44.
23. Lieberman RL, Rosenzweig AC. Crystal structure of a membrane-bound metalloenzyme that catalyses the biological oxidation of methane. Nature 2005;434:177-182.
24. Andrade SL, Dickmanns A, Ficner R, Einsle O. Crystal structure of the archaeal ammonium transporter Amt-1 from Archaeoglobus fulgidus. Proc Natl Acad Sci USA 2005;102:14994-14999.
25. Seeger MA, Schiefner A, Eicher T, Verrey F, Diederichs K, Pos KM. Structural asymmetry of AcrB trimer suggests a peristaltic pump mechanism. Science 2006;313:1295-1298.
26. Boudker O, Ryan RM, Yernool D, Shimamoto K, Gouaux E. Coupling substrate and ion binding to extracellular gate of a sodium-dependent aspartate transporter. Nature 2007;445:387-393.
27. Fu D, Libson A, Miercke LJ, Weitzman C, Nollert P, Krucinski J, Stroud RM. Structure of a glycerol-conducting channel and the basis for its selectivity. Science 2000;290:481-486.
28. Tornroth-Horsefield S, Wang Y, Hedfalk K, Johanson U, Karlsson M, Tajkhorshid E, Neutze R, Kjellbom P. Structural mechanism of plant aquaporin gating. Nature 2006;439:688-694.
29. Jiang Y, Lee A, Chen J, Cadene M, Chait BT, MacKinnon R. Crystal structure and mechanism of a calcium-gated potassium channel. Nature 2002;417:515-522.
30. Gulbis JM, Kuo A, Smith B, Doyle DA, Edwards A, Arrowsmith C, Sundstrom M. Two intermediate gating state crystal structures of the KirBac3.1 K+ channel. PDB Release 2004;12-07, in press.
31. Long SB, Campbell EB, Mackinnon R. Crystal structure of a mammalian voltage-dependent Shaker family K+ channel. Science 2005;309:897-903.
32. +-conducting channel. Nature 2006;440:570-574.
33. + channel. Nature 2003;423:33-41.
34. Oxenoid K, Chou JJ. The structure of phospholamban pentamer reveals a channel-like architecture in membranes. Proc Natl Acad Sci USA 2005;102:10870-10875.
35. Unwin N. Refined structure of the nicotinic acetylcholine receptor at 4Å resolution. J Mol Biol 2005;346:967-989.
36. Eshaghi S, Niegowski D, Kohl A, Martinez Molina D, Lesley SA, Nordlund P. Crystal structure of a divalent metal ion transporter CorA at 2.9 angstrom resolution. Science 2006;313:354-357.
37. Steinbacher S, Bass RB, Strop P, Rees DC. Structures of the prokaryotic mechanosensitive channels MscL and MscS. Current topics in membranes, Vol. 58. San Diego: Academic Press; 2007.
38. +-ATPase from Enterococcus hirae. Science 2005;308:654-659.
39. +-ATPase from Ilyobacter tartaricus. Science 2005;308:659-662.
40. Hubbard SJ, Thornton, JM. 'NACCESS', Computer Program, Department of Biochemistry and Molecular Biology, University College London. 2.1.1; 1993.
41. Johnson RM, Rath A, Melnyk RA, Deber CM. Lipid solvation effects contribute to the affinity of Gly-xxx-Gly motif-mediated helix-helix interactions. Biochemistry 2006;45:8507-8515.
42. Javadpour MM, Eilers M, Groesbeek M, Smith SO. Helix packing in polytopic membrane proteins: role of glycine in transmembrane helix association. Biophys J 1999;77:1609-1618.
43. Mueckler M, Makepeace C. Identification of an amino acid residue that lies between the exofacial vestibule and exofacial substrate-binding site of the Glut1 sugar permeation pathway. J Biol Chem 1997;272:30141-30146.
44. +-coupled multidrug transporter from Escherichia coli, reveals a hydrophobic pathway for solutes. J Biol Chem 1999;274:19480-19486.
45. Cao W, Matherly LH. Characterization of a cysteine-less human reduced folate carrier: localization of a substrate-binding domain by cysteine-scanning mutagenesis and cysteine accessibility methods. Biochem J 2003;374(Part 1):27-36.
46. + antiporter NhaA faces a water-filled channel required for ion transport. J Biol Chem 2004;279:40567-40575.
47. Hubbard TJ, Blundell TL. Comparison of solvent-inaccessible cores of homologous proteins: definitions useful for protein modelling. Protein Eng 1987;1:159-171.
48. Bajaj K, Chakrabarti P, Varadarajan R. Mutagenesis-based definitions and probes of residue burial in proteins. Proc Natl Acad Sci USA 2005;102:16221-16226.
49. Eilers M, Patel AB, Liu W, Smith SO. Comparison of helix interactions in membrane and soluble alpha-bundle proteins. Biophys J 2002;82:2720-2736.
50. Stevens TJ, Mizuguchi K, Arkin IT. Distinct protein interfaces in transmembrane domains suggest an in vivo folding model. Protein Sci 2004;13:3028-3037.
51. Adamian L, Nanda V, DeGrado WF, Liang J. Empirical lipid propensities of amino acid residues in multispan α helical membrane proteins. Proteins 2005;59:496-509.
52. Johnson RM, Rath A, Deber CM. The position of the Gly-xxx-Gly motif in transmembrane segments modulates dimer affinity. Biochem Cell Biol 2006;84:1006-1012.
53. Hildebrand PW, Lorenzen S, Goede A, Preissner R. Analysis and prediction of helix-helix interactions in membrane channels and transporters. Proteins 2006;64:253-262.
54. Gray TM, Matthews BW. Intrahelical hydrogen bonding of serine, threonine and cysteine residues within α-helices and its relevance to membrane-bound proteins. J Mol Biol 1984;175:75-81.
55. Bogan AA, Thorn KS. Anatomy of hot spots in protein interfaces. J Mol Biol 1998;280:1-9.
56. Schneider D, Engelman DM. Motifs of two small residues can assist but are not sufficient to mediate transmembrane helix interactions. J Mol Biol 2004;343:799-804.
57. Melnyk RA, Kim S, Curran AR, Engelman DM, Bowie JU, Deber CM. The affinity of GXXXG motifs in transmembrane helix-helix interactions is modulated by long-range communication. J Biol Chem 2004;279:16591-16597.
58. Bowie JU. Solving the membrane protein folding problem. Nature 2005;438:581-589.