Structural and functional restraints on the occurrence of single amino acid variations in human proteins

PLoS ONE

Volumn 5, Issue 2, 2010, Pages

  Gong, Sungsam ^a   Blundell, Tom L ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; PROTEIN;

AMINO ACID SUBSTITUTION; ARTICLE; GENE STRUCTURE; GENETIC POLYMORPHISM; GENETIC VARIABILITY; HUMAN; HYDROGEN BOND; PROTEIN INTERACTION; PROTEIN SECONDARY STRUCTURE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; GENETIC PREDISPOSITION; GENETICS; METABOLISM; MUTATION; PROTEIN BINDING; PROTEIN DATABASE; PROTEIN TERTIARY STRUCTURE; STRUCTURE ACTIVITY RELATION;

AMINO ACID SUBSTITUTION; BINDING SITES; DATABASES, PROTEIN; GENETIC PREDISPOSITION TO DISEASE; GENETIC VARIATION; HUMANS; HYDROGEN BONDING; MODELS, MOLECULAR; MUTATION; POLYMORPHISM, GENETIC; PROTEIN BINDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; PROTEINS; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 77949465285     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0009186     Document Type: Article

References (57)

1. Gong S, Worth CL, Bickerton GR, Lee S, Tanramluk D, et al. (2009) Structural and functional restraints in the evolution of protein families and superfamilies. Biochem Soc Trans 37: 727-733.
2. Kimura M (1968) Evolutionary rate at the molecular level. Nature 217: 624-626.
3. Ohta T (1973) Slightly deleterious mutant substitutions in evolution. Nature 246: 96-98.
4. Worth CL, Gong S, Blundell TL (2009) Structural and functional constraints in the evolution of protein families. Nat Rev Mol Cell Biol 10: 709-720.
5. Hubbard TJ, Blundell TL (1987) Comparison of solvent-inaccessible cores of homologous proteins: definitions useful for protein modelling. Protein Eng 1: 159-171.
6. Worth CL, Blundell TL (2009) Satisfaction of hydrogen-bonding potential influences the conservation of polar sidechains. Proteins 75: 413-429.
7. Ahn SM, Kim TH, Lee S, Kim D, Ghang H, et al. (2009) The first Korean genome sequence and analysis: Full genome sequencing for a socio-ethnic group. Genome Res 19: 1622-1629.
8. Levy S, Sutton G, Ng PC, Feuk L, Halpern AL, et al. (2007) The diploid genome sequence of an individual human. PLoS Biol 5: e254.
9. Wang J, Wang W, Li R, Li Y, Tian G, et al. (2008) The diploid genome sequence of an Asian individual. Nature 456: 60-65.
10. Wheeler DA, Srinivasan M, Egholm M, Shen Y, Chen L, et al. (2008) The complete genome of an individual by massively parallel DNA sequencing. Nature 452: 872-876.
11. Ng PC, Levy S, Huang J, Stockwell TB, Walenz BP, et al. (2008) Genetic variation in an individual human exome. PLoS Genet 4: e1000160.
12. Cargill M, Altshuler D, Ireland J, Sklar P, Ardlie K, et al. (1999) Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nat Genet 22: 231-238.
13. Sunyaev S, Hanke J, Aydin A, Wirkner U, Zastrow I, et al. (1999) Prediction of nonsynonymous single nucleotide polymorphisms in human disease-associated genes. J Mol Med 77: 754-760.
14. Sunyaev S, Ramensky V, Bork P (2000) Towards a structural basis of human non-synonymous single nucleotide polymorphisms. Trends Genet 16: 198-200.
15. Wang Z, Moult J (2001) SNPs, protein structure, and disease. Hum Mutat 17: 263-270.
16. Botstein D, Risch N (2003) Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease. Nat Genet 33 Suppl: 228-237.
17. Yue P, Li Z, Moult J (2005) Loss of protein structure stability as a major causative factor in monogenic disease. J Mol Biol 353: 459-473.
18. Ferrer-Costa C, Orozco M, de la Cruz X (2002) Characterization of disease-associated single amino acid polymorphisms in terms of sequence and structure properties. Journal of Molecular Biology 315: 771-786.
19. Steward RE, MacArthur MW, Laskowski RA, Thornton JM (2003) Molecular basis of inherited diseases: a structural perspective. Trends Genet 19: 505-513.
20. Worth CL, Bickerton GR, Schreyer A, Forman JR, Cheng TM, et al. (2007) A structural bioinformatics approach to the analysis of nonsynonymous single nucleotide polymorphisms (nsSNPs) and their relation to disease. J Bioinform Comput Biol 5: 1297-1318.
21. Bao L, Cui Y (2006) Functional impacts of non-synonymous single nucleotide polymorphisms: selective constraint and structural environments. FEBS Lett 580: 1231-1234.
22. Ng PC, Henikoff S (2003) SIFT: Predicting amino acid changes that affect protein function. Nucleic Acids Res 31: 3812-3814.
23. Yip YL, Famiglietti M, Gos A, Duek PD, David FP, et al. (2008) Annotating single amino acid polymorphisms in the UniProt/Swiss-Prot knowledgebase. Hum Mutat 29: 361-366.
24. Hubbard TJ, Aken BL, Ayling S, Ballester B, Beal K, et al. (2009) Ensembl 2009. Nucleic Acids Res 37: D690-697.
25. Forbes SA, Bhamra G, Bamford S, Dawson E, Kok C, et al. (2008) The Catalogue of Somatic Mutations in Cancer (COSMIC). Curr Protoc Hum Genet Chapter 10: Unit 10 11.
26. (2009) The Universal Protein Resource (UniProt) 2009. Nucleic Acids Res 37: D169-174.
27. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, et al. (2000) The Protein Data Bank. Nucleic Acids Res 28: 235-242.
28. Overington J, Donnelly D, Johnson MS, Sali A, Blundell TL (1992) Environment-specific amino acid substitution tables: tertiary templates and prediction of protein folds. Protein Sci 1: 216-226.
29. Overington J, Johnson MS, Sali A, Blundell TL (1990) Tertiary structural constraints on protein evolutionary diversity: templates, key residues and structure prediction. Proc Biol Sci 241: 132-145.
30. Murzin AG, Brenner SE, Hubbard T, Chothia C (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 247: 536-540.
31. Dayhoff MO, Eck RV (1968) Atlas of Protein Sequence and Structure. Natl Biomed Res Found 3: 33.
32. Henikoff S, Henikoff JG (1992) Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci U S A 89: 10915-10919.
33. Deane CM, Allen FH, Taylor R, Blundell TL (1999) Carbonyl-carbonyl interactions stabilize the partially allowed Ramachandran conformations of asparagine and aspartic acid. Protein Eng 12: 1025-1028.
34. Talavera D, Taylor MS, Thornton JM (2009) The (non)malignancy of cancerous amino acidic substitutions. Proteins.
35. Jansen GA, Hogenhout EM, Ferdinandusse S, Waterham HR, Ofman R, et al. (2000) Human phytanoyl-CoA hydroxylase: resolution of the gene structure and the molecular basis of Refsum's disease. Hum Mol Genet 9: 1195-1200.
36. Jansen GA, Ofman R, Ferdinandusse S, Ijlst L, Muijsers AO, et al. (1997) Refsum disease is caused by mutations in the phytanoyl-CoA hydroxylase gene. Nat Genet 17: 190-193.
37. Mihalik SJ, Morrell JC, Kim D, Sacksteder KA, Watkins PA, et al. (1997) Identification of PAHX, a Refsum disease gene. Nat Genet 17: 185-189.
38. Jansen GA, Ferdinandusse S, Hogenhout EM, Verhoeven NM, Jakobs C, et al. (1999) Phytanoyl-CoA hydroxylase deficiency. Enzymological and molecular basis of classical Refsum disease. Adv Exp Med Biol 466: 371-376.
39. Capriotti E, Fariselli P, Casadio R (2005) I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure. Nucleic Acids Res 33: W306-310.
40. Cheng J, Randall A, Baldi P (2006) Prediction of protein stability changes for single-site mutations using support vector machines. Proteins 62: 1125-1132.
41. Dehouck Y, Grosfils A, Folch B, Gilis D, Bogaerts P, et al. (2009) Fast and accurate predictions of protein stability changes upon mutations using statistical potentials and neural networks: PoPMuSiC-2.0. Bioinformatics.
42. Guerois R, Nielsen JE, Serrano L (2002) Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J Mol Biol 320: 369-387.
43. Masso M, Vaisman II (2008) Accurate prediction of stability changes in protein mutants by combining machine learning with structure based computational mutagenesis. Bioinformatics 24: 2002-2009.
44. Greenman C, Stephens P, Smith R, Dalgliesh GL, Hunter C, et al. (2007) Patterns of somatic mutation in human cancer genomes. Nature 446: 153-158.
45. Goldberg AL (2003) Protein degradation and protection against misfolded or damaged proteins. Nature 426: 895-899.
46. Ferrer-Costa C, Orozco M, de la Cruz X (2007) Characterization of compensated mutations in terms of structural and physico-chemical properties. J Mol Biol 365: 249-256.
47. Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, et al. (2001) dbSNP: the NCBI database of genetic variation. Nucleic Acids Res 29: 308-311.
48. Frazer KA, Ballinger DG, Cox DR, Hinds DA, Stuve LL, et al. (2007) A second generation human haplotype map of over 3.1 million SNPs. Nature 449: 851-861.
49. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
50. Li W, Godzik A (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22: 1658-1659.
51. Gong S, Blundell TL (2008) Discarding functional residues from the substitution table improves predictions of active sites within three-dimensional structures. PLoS Comput Biol 4: e1000179.
52. Mizuguchi K, Deane CM, Blundell TL, Johnson MS, Overington JP (1998) JOY: protein sequence-structure representation and analysis. Bioinformatics 14: 617-623.
53. Lee S, Blundell TL (2009) Ulla: a program for calculating environment-specific amino acid substitution tables. Bioinformatics 25: 1976-1977.
54. Ihaka R, Gentleman R (1996) R: A Language for Data Analysis and Graphics. Journal of Computational and Graphical Statistics 5: 299-314.
55. Shenkin PS, Erman B, Mastrandrea LD (1991) Information-theoretical entropy as a measure of sequence variability. Proteins 11: 297-313.
56. DeLano WL (2002) The PyMOL Molecular Graphics System. Palo Alto, CA, USA: DeLano Scientific.
57. Waterhouse AM, Procter JB, Martin DM, Clamp M, Barton GJ (2009) Jalview Version 2-a multiple sequence alignment editor and analysis workbench. Bioinformatics 25: 1189-1191.