Missense Mutations in Transmembrane Domains of Proteins: Phenotypic Propensity of Polar Residues for Human Disease

Proteins: Structure, Function and Genetics

Volumn 54, Issue 4, 2004, Pages 648-656

  Partridge, Anthony W ^b   Therien, Alex G ^b,c   Deber, Charles M ^a  

^a HOSPITAL FOR SICK CHILDREN RESEARCH INSTITUTE   (Canada)

^b UNIVERSITY OF TORONTO   (Canada)

^c MERCK FROSST CENTRE FOR THERAPEUTIC RESEARCH   (Canada)

Author keywords

Bilayer; Bioinformatics; Database; Folding; Helix; Hydrophobic; Statistics

Indexed keywords

ARGININE; MEMBRANE PROTEIN; TRANSMEMBRANE CONDUCTANCE REGULATOR;

AMINO ACID SEQUENCE; ARTICLE; BIOINFORMATICS; CYSTIC FIBROSIS; DATA BASE; GENE MUTATION; GENETIC DISORDER; HUMAN; MEMBRANE STABILIZATION; MISSENSE MUTATION; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; PROKARYOTE; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN STRUCTURE; STATISTICAL ANALYSIS;

AMINO ACIDS; BACTERIAL PROTEINS; CELL MEMBRANE; DATABASES, GENETIC; ELECTROSTATICS; GENETIC DISEASES, INBORN; GENETIC PREDISPOSITION TO DISEASE; HUMANS; HYDROPHOBICITY; MEMBRANE PROTEINS; MUTATION, MISSENSE; PHENOTYPE; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; TEMPERATURE; THERMODYNAMICS;

PROKARYOTA;

EID: 1542376209     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10611     Document Type: Article

References (48)

1. Popot JL, Engelman DM. Helical membrane protein folding, stability, and evolution. Annu Rev Biochem 2000;69:881-922.
2. Gennis RB. Biomembranes: molecular structure and function. New York: Springer-Verlag; 1989.
3. Partridge AW, Therien AG, Deber CM. Polar mutations in membrane proteins as a biophysical basis for disease. Biopolymers 2002;66:350-358.
4. Gurrath M. Peptide-binding G protein-coupled receptors: new opportunities for drug design. Curr Med Chem 2001;8:1605-1648.
5. Krawczak M, Cooper DN. The human gene mutation database. Trends Genet 1997;13:121-122.
6. Krawczak M, Ball EV, Cooper DN. Neighboring-nucleotide effects on the rates of germ-line single-base-pair substitution in human genes. Am J Hum Genet 1998;63:474-488.
7. Antonarakis SE, Krawczak M, Cooper DN. Disease-causing mutations in the human genome. Eur J Pediatr 2000;159 Suppl 3:S173-178.
8. Deber CM, Wang C, Liu LP, Prior AS, Agrawal S, Muskat BL, Cuticchia AJ. TM Finder: a prediction program for transmembrane protein segments using a combination of hydrophobicity and nonpolar phase helicity scales. Protein Sci 2001;10:212-219.
9. Woolfson DN, Williams DH. The influence of proline residues on alpha-helical structure. FEBS Lett 1990;277:185-188.
10. Visiers I, Braunheim BB, Weinstein H. Prokink: a protocol for numerical evaluation of helix distortions by proline. Protein Eng 2000;13:603-606.
11. MacArthur MW, Thornton JM. Influence of proline residues on protein conformation. J Mol Biol 1991;218:397-412.
12. Cordes FS, Bright JN, Sansom MS. Proline-induced distortions of transmembrane helices. J Mol Biol 2002;323:951-960.
13. Tieleman DP, Shrivastava IH, Ulmschneider MR, Sansom MS. Proline-induced hinges in transmembrane helices: possible roles in ion channel gating. Proteins 2001;44:63-72.
14. Sansom MS, Weinstein H. Hinges, swivels and switches: the role of prolines in signalling via transmembrane alpha-helices. Trends Pharmacol Sci 2000;21:445-451.
15. Liu LP, Li SC, Goto NK, Deber CM. Threshold hydrophobicity dictates helical conformations of peptides in membrane environments. Biopolymers 1996;39:465-470.
16. Dawson JP, Weinger JS, Engelman DM. Motifs of serine and threonine can drive association of transmembrane helices. J Mol Biol 2002;316:799-805.
17. Choma C, Gratkowski H, Lear JD, DeGrado WF. Asparagine-mediated self-association of a model transmembrane helix. Nat Struct Biol 2000;7:161-166.
18. Gratkowski H, Lear JD, DeGrado WF. Polar side chains drive the association of model transmembrane peptides. Proc Natl Acad Sci USA 2001;98:880-885.
19. Zhou FX, Merianos HJ, Brunger AT, Engelman DM. Polar residues drive association of polyleucine transmembrane helices. Proc Natl Acad Sci USA 2001;98:2250-2255.
20. Zhou FX, Cocco MJ, Russ WP, Brunger AT, Engelman DM. Interhelical hydrogen bonding drives strong interactions in membrane proteins. Nat Struct Biol 2000;7:154-160.
21. Schneider D, Liu Y, Gerstein M, Engelman DM. Thermostability of membrane protein helix-helix interaction elucidated by statistical analysis. FEBS Lett 2002;532:231-236.
22. Zhou Y, Wen J, Bowie JU. A passive transmembrane helix. Nat Struct Biol 1997;4:986-990.
23. Wen J, Chen X, Bowie JU. Exploring the allowed sequence space of a membrane protein. Nat Struct Biol 1996;3:141-148.
24. Frillingos S, Sahin-Toth M, Wu J, Kaback HR. Cys-scanning mutagenesis: a novel approach to structure function relationships in polytopic membrane proteins. FASEB J 1998;12:1281-1299.
25. Heinz DW, Baase WA, Matthews BW. Folding and function of a T4 lysozyme containing 10 consecutive alanines illustrate the redundancy of information in an amino acid sequence. Proc Natl Acad Sci USA 1992;89:3751-3755.
26. Matthews BW. Structural and genetic analysis of the folding and function of T4 lysozyme. FASEB J 1996;10:35-41.
27. Partridge AW, Melnyk RA, Deber CM. Polar residues in membrane domains of proteins: molecular basis for helix-helix association in a mutant CFTR transmembrane segment. Biochemistry 2002;41:3647-3653.
28. Therien AG, Grant FE, Deber CM. Interhelical hydrogen bonds in the CFTR membrane domain. Nat Struct Biol 2001;8:597-601.
29. Adamian L, Liang J. Interhelical hydrogen bonds and spatial motifs in membrane proteins: polar clamps and serine zippers. Proteins 2002;47:209-218.
30. Wimley WC, Gawrisch K, Creamer TP, White SH. Direct measurement of salt-bridge solvation energies using a peptide model system: implications for protein stability. Proc Natl Acad Sci USA 1996;93:2985-2990.
31. Call ME, Pyrdol J, Wiedmann M, Wucherpfennig KW. The organizing principle in the formation of the T cell receptor-CD3 complex. Cell 2002;111:967-979.
32. Kumar S, Nussinov R. Close-range electrostatic interactions in proteins. Chembiochem 2002;3:604-617.
33. Vieille C, Zeikus GJ. Hyperthermophilic enzymes: sources, uses, and molecular mechanisms for thermostability. Microbiol Mol Biol Rev 2001;65:1-43.
34. Ladenstein R, Antranikian G. Proteins from hyperthermophiles: stability and enzymatic catalysis close to the boiling point of water. Adv Biochem Eng Biotechnol 1998;61:37-85.
35. Chakravarty S, Varadarajan R. Elucidation of determinants of protein stability through genome sequence analysis. FEBS Lett 2000;470:65-69.
36. Bogin O, Levin I, Hacham Y, Tel-Or S, Peretz M, Frolow F, Burstein Y. Structural basis for the enhanced thermal stability of alcohol dehydrogenase mutants from the mesophilic bacterium Clostridium beijerinckii: contribution of salt bridging. Protein Sci 2002;11:2561-2574.
37. Cotten JF, Welsh MJ. Cystic fibrosis-associated mutations at arginine 347 alter the pore architecture of CFTR. Evidence for disruption of a salt bridge. J Biol Chem 1999;274:5429-5435.
38. Smith SO, Smith C, Shekar S, Peersen O, Ziliox M, Aimoto S. Transmembrane interactions in the activation of the Neu receptor tyrosine kinase. Biochemistry 2002;41:9321-9332.
39. Smith SO, Smith CS, Bormann BJ. Strong hydrogen bonding interactions involving a buried glutamic acid in the transmembrane sequence of the neu/ erbB-2 receptor. Nat Struct Biol 1996;3:252-258.
40. Deber CM, Liu LP, Wang C. Perspective: peptides as mimics of transmembrane segments in proteins. J Pept Res 1999;54:200-205.
41. Sullivan JM, Scott KM, Falls HF, Richards JE, Sieving PA. A novel rhodopsin mutation at the retinal binding site (Lys-296-Met) in ADRP. Invest Ophthalmol Vis Sci 1993;34(Suppl):1149.
42. Rao VR, Cohen GB, Oprian DD. Rhodopsin mutation G90D and a molecular mechanism for congenital night blindness. Nature 1994;367:639-642.
43. Sieving PA, Richards JE, Naarendorp F, Bingham EL, Scott K, Alpern M. Dark-light: model for nightblindness from the human rhodopsin Gly-90→Asp mutation. Proc Natl Acad Sci USA 1995;92:880-884.
44. Sato M, Mueckler M. A conserved amino acid motif (R-X-G-R-R) in the Glut1 glucose transporter is an important determinant of membrane topology. J Biol Chem 1999;274:24721-24725.
45. Lemmon MA, Flanagan JM, Treutlein HR, Zhang J, Engelman DM. Sequence specificity in the dimerization of transmembrane alpha-helices. Biochemistry 1992;31:12719-12725.
46. Matsumura M, Signor G, Matthews BW. Substantial increase of protein stability by multiple disulphide bonds. Nature 1989;342:291-293.
47. Palczewski K, Kumasaka T, Hori T, Behnke CA, Motoshima H, Fox BA, Le Trong I, Teller DC, Okada T, Stenkamp RE, Yamamoto M, Miyano M. Crystal structure of rhodopsin: A/G protein-coupled receptor. Science 2000;289:739-745.
48. Guex N, Peitsch MC. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis 1997;18:2714-2723.