Cancer-associated mutations are preferentially distributed in protein kinase functional sites

Proteins: Structure, Function and Bioinformatics

Volumn 77, Issue 4, 2009, Pages 892-903

  Izarzugaza, Jose M G ^a   Redfern, Oliver C ^b   Orengo, Christine A ^b   Valencia, Alfonso ^a  

^a Centro Nacional de Investigaciones Oncológicas   (Spain)

^b UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

Cancer; Driver mutation; Functional; Kinase; Kinome; Passenger mutation; Point mutation; Polymorphism; Single nucleotide polymorphism; SNP; Somatic mutation

Indexed keywords

PROTEIN KINASE;

AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; CANCER GENETICS; CONTROLLED STUDY; DISEASE ASSOCIATION; ENZYME ANALYSIS; ENZYME BINDING; ENZYME CONFORMATION; ENZYME STABILITY; ENZYME STRUCTURE; ENZYME SUBSTRATE; GENE MUTATION; GENE SEQUENCE; PATHOGENICITY; POINT MUTATION; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN LOCALIZATION; SINGLE NUCLEOTIDE POLYMORPHISM; SOMATIC MUTATION; TUMOR GROWTH;

CATALYTIC DOMAIN; CONSERVED SEQUENCE; HUMANS; MODELS, MOLECULAR; MUTATION; NEOPLASMS; POINT MUTATION; POLYMORPHISM, SINGLE NUCLEOTIDE; PROTEIN CONFORMATION; PROTEIN KINASES;

EID: 70449923872     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22512     Document Type: Article

References (60)

1. Collins FS, Brooks LD, Chakravarti A. A DNA polymorphism discovery resource for research on human genetic variation. Genome Res 1998;8:1229-1231. (Pubitemid 29039095)
2. Taillon-Miller P, Gu Z, Li Q, Hillier L, Kwok PY. Overlapping genomic sequences: a treasure trove of single-nucleotide polymorphisms. Genome Res 1998;8:748-754. (Pubitemid 28403175)
3. Schattner P, Diekhans M. Regions of extreme synonymous codon selection in mammalian genes. Nucleic Acids Res 2006;34:1700-1710.
4. Sauna ZE, Kimchi-Sarfaty C, Ambudkar SV, Gottesman MM. Silent polymorphisms speak: how they affect pharmacogenomics and the treatment of cancer. Cancer Res 2007;67:9609-9612. (Pubitemid 47621204)
5. Torkamani A, Schork NJ. Distribution analysis of nonsynonymous polymorphisms within the human kinase gene family. Genomics 2007;90:49-58. (Pubitemid 46900997)
6. Greenman C, Stephens P, Smith R, et al. Patterns of somatic mutation in human cancer genomes. Nature 2007;446:153-158. (Pubitemid 46398669)
7. Wood LD, Williams Parsons D, Jones S, Lin J, Sjöblom T, Leary RJ, Shen D, Boca SM, Barber T, Ptak J, Silliman N, Szabo S, Dezso Z, Ustyanksky V, Nikolskaya T, Nikolsky Y, Karchin R, Wilson PA, Kaminker JS, Zhang Z, Croshaw R, Willis J, Dawson D, Shipitsin M, Willson JKV, Sukumar S, Polyak K, Park BH, Pethiyagoda CL, Pant PVK, Ballinger DG, Sparks AB, Hartigan J, Smith DR, Suh E, Papadopoulos N, Buckhaults P, Markowitz SD, Parmigiani G, Kinzler KW, Velculescu VE, Vogelstein B. The genomic landscapes of human breast and colorectal cancers. Science 2007;318:1108-1113. (Pubitemid 350134889)
8. Futreal PA, Coin L, Marshall M, Down T, Hubbard T, Wooster R, Rahman N, Stratton MR. A census of human cancer genes. Nat Rev Cancer 2004;4:177-183.
9. Garber K. The second wave in kinase cancer drugs. Nat Biotechnol 2006;312:1175-1178.
10. Manning G, Whyte DB, Martinez R, Hunter T, Sudarsanam S. The protein kinase complement of the human genome. Science 2001;298:1912-1914.
11. Ubersax JA, Woodbury EL, Quang PN, Paraz M, Blethrow JD, et al. Targets of the cyclin-dependet kinase Cdk1. Nature 2003;425:859-864.
12. Ptacek J, Devgan G, Michaud G, Zhu H, Zhu X, et al. Global analysis of protein phosphorylation in yeast. Nature 2005;438:679-684. (Pubitemid 41740579)
13. Wang Z, Moult J. SNPs, protein structure, and disease. Hum Mutat 2001;17:263-270.
14. Ferrer-Costa C, Orozco M, De La Cruz X. Characterization of disease-associated single amino acid polymorphisms in terms of sequence and structure properties. J Mol Biol 2002;315:771-786. (Pubitemid 34729325)
15. Wang Z, Moult J. Three-dimensional structural location and molecular functional effects of missense SNPs in the T cell receptor Vbeta domain. Proteins 2003;53:748-757. (Pubitemid 37352187)
16. Ng PC, Henikoff S. SIFT: predicting amino acid changes that affect protein function. Nucleic Acids Res 2003;31:3812-3814. (Pubitemid 37442253)
17. Ferrer-Costa C, Orozco M, De La Cruz X. Sequence-based prediction of pathological mutations. Proteins 2004;57:811-819.
18. Ferrer-Costa C, Gelpí JL, Zamakola L, Parraga I, De La Cruz X, Orozco M. PMUT: a web-based tool for the annotation of pathological mutations on proteins. Bioinformatics 2005;21:3176-3178. (Pubitemid 41418475)
19. Yue P, Moult J. Identification and analysis of deleterious human SNPs. J Mol Biol 2006;356:1263-1274. (Pubitemid 43199928)
20. Torkamani A, Schork NJ. Accurate prediction of deleterious protein kinase polymorphisms. Bioinformatics 2007;23:2918-2925. (Pubitemid 350162899)
21. Fraser H, Plotkin J. Using protein complexes to predict phenotypic effects of gene mutation. Genome Biol 2007;8:R252. (Pubitemid 351917497)
22. Bromberg Y, Yachdav G, Rost B. SNAP predicts effect of mutations on protein function. Bioinformatics 2008;24:2397-2398.
23. Mort M, Ivanov D, Cooper DN, Chuzhanova NA. A meta-analysis of nonsense mutations causing human genetic disease. Hum Mutat 2008;29:1037-1047.
24. Liu J, Zhang Y, Lei X, Zhang Z. Natural selection of protein structural and functional properties: a single nucleotide polymorphism perspective. Genome Biol 2008;9:R69. (Pubitemid 351974308)
25. Pazos F, Helmer-Citterich M, Ausiello G, Valencia A. Correlated mutations contain information about protein-protein interaction. J Mol Biol 1997;271:511-523. (Pubitemid 27373087)
26. Graña O, Baker D, Maccallum RM, Meiler J, Punta M, Rost B, Tress ML, Valencia A. CASP6 assessment of contact prediction. Proteins 2005;61(Suppl 7):214-224.
27. Izarzugaza JMG, Graña O, Tress ML, Valencia A, Clarke ND. Assessment of intramolecular contact predictions for CASP7. Proteins 2007;69(Suppl 8):152-158. (Pubitemid 350210122)
28. Pei J, Grishin NV. AL2CO: calculation of positional conservation in a protein sequence alignment. Bioinformatics 2001;17:700-712. (Pubitemid 32851378)
29. Knight JD, Qian B, Baker D, Kothary R. Conservation, variability and the modeling of active protein kinases. PLoS 2007;2:e982.
30. Ló pez G, Valencia A, Tress ML. FireDB - a database of functionally important residues from proteins of known structure. Nucleic Acids Res 2007;35:D219-D223.
31. Casari G, Sander C, Valencia A. A method to predict functional residues in proteins. Nat Struct Biol 1995;2:171-178. (Pubitemid 26040653)
32. Pazos F, Rausell A, Valencia A. Phylogeny-independent detection of functional residues. Bioinformatics 2006;22:1440-1448.
33. Dhillon AS, Hagan S, Rath O, Kolch W. MAP kinase signaling pathways in cancer. Oncogene 2007;26:3279-3290. (Pubitemid 46763021)
34. Kahn CR, Flier JS, Bar RS, Archer JA, Gorden P, Martin MM, Roth J. The syndromes of insulin resistance and acanthosis nigricans: insulin receptor disorders in man. N Engl J Med 1976;294:739-745.
35. Grigorescu F, Flier JS, Kahn CR. Defect in insulin receptor phosphorylation in erythrocytes and fibroblasts associated with severe insulin resistance. J Biol Chem 1984;259:15003-15006. (Pubitemid 15191290)
36. Grunberger G, Comi RJ, Taylor SI, Gorden P. Tyrosine kinase activity of the insulin receptor of patients with type A extreme insulin resistance: studies with circulating mononuclear cells and cultured lymphocytes. J Clin Endocrinol Metab 1984;59:1152-1158. (Pubitemid 15223352)
37. Prince MJ, Smith FE, Peters EJ, Stuart CA. Functional characteristics of decreased insulin receptors on fibroblasts obtained from a subject with severe insulin resistance and acanthosis nigricans. Diabetes 1986;35:148-154.
38. Bromberg Y, Rost B. Comprehensive in silico mutagenesis highlights functionally important residues in proteins. Bioinformatics 2008;24:i207-i212.
39. Caceres M, Teran CG, Rodriguez S, Medina M. Prevalence of insulin resistance and its association with metabolic syndrome criteria among Bolivian children and adolescents with obesity. BMC Pediatr 2008;8:31.
40. Bonaventure J, El Ghouzzi V. Molecular and cellular bases of syndromic craniosynostoses. Expert Rev Mol Med 2003;5:1-17.
41. Leroy JG, Nuytinck L, Lambert J, Naeyaert JM, Mortier GR. Acanthosis nigricans in a child with mild osteochondrodysplasia and K650Q mutation in the FGFR3 gene. Am JMed Genet A 2007;143:3144-3149. (Pubitemid 350274830)
42. Zankl A, Elakis G, Susman RD, Inglis G, Gardener G, Buckley MF, Roscioli T. Prenatal and postnatal presentation of severe achondroplasia with developmental delay and acanthosis nigricans (SADDAN) due to the FGFR3 Lys650Met mutation. Am J Med Genet A 2008;146:212-218.
43. Fonseca R, Costa-Lima MA, Cosentino V, Orioli IM. Second case of Beare-Stevenson syndrome with an FGFR2 Ser372Cys mutation. Am J Med Genet A 2008;146:658-660.
44. Davies H, Bignell GR, Cox C, Stephens P, Edkins S, Clegg S, Teague J, Woffendin H, Garnett MJ, Bottomley W, Davis N, Dicks E, Ewing R, Floyd Y, Gray K, Hall S, Hawes R, Hughes J, Kosmidou V, Menzies A, Mould C, Parker A, Stevens C, Watt S, Hooper S, Wilson R, Jayatilake H, Gusterson BA, Cooper C, Shipley J, Hargrave D, Pritchard-Jones K, Maitland N, Chenevix-Trench G, Riggins GJ, Bigner DD, Palmieri G, Cossu A, Flanagan A, Nicholson A, Ho JW, Leung SY, Yuen ST, Weber BL, Seigler HF, Darrow TL, Paterson H, Marais R, Marshall CJ, Wooster R, Stratton MR, Futreal PA. Mutations of the BRAF gene in human cancer. Nature 2002;417:949-954. (Pubitemid 34716871)
45. Lee JW, Yoo NJ, Soung YH, Kim HS, Park WS, Kim SY, Lee JH, Park JY, Cho YG, Kim CJ, Ko YH, Kim SH, Nam SW, Lee JY, Lee SH. BRAF mutations in non-Hodgkin's lymphoma. Br J Cancer 2003;89:1958-1960.
46. Hurst JM, McMillan LEM, Porter CT, Allen J, Fakorede A, Martin ACR. The SAAPdb web resource: A large-scale structural analysis of mutant proteins. Hum Mutat 2009;30:616-624.
47. Sjöblom T, Jones S, Wood LD, Parsons DW, Lin J, Barber TD, Mandelker D, Leary RJ, Ptak J, Silliman N, Szabo S, Buckhaults P, Farrell C, Meeh P, Markowitz SD, Willis J, Dawson D, Willson JK, Gazdar AF, Hartigan J, Wu L, Liu C, Parmigiani G, Park BH, Bachman KE, Papadopoulos N, Vogelstein B, Kinzler KW, Velculescu VE. The consensus coding sequences of human breast and colorectal cancers. Science 2006;314:268-274. (Pubitemid 44571966)
48. Torkamani A, Kannan N, Taylor SS, Schork NJ. Congenital disease SNPs target lineage specific structural elements in protein kinases. Proc Natl Acad Sci USA 2008;105:9011-9016.
49. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997;25:3389-3402. (Pubitemid 27359211)
50. Edgar RC. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 2004;5:113.
51. Fiser A, Sali A. Modeller: generation and refinement of homology-based protein structure models. Methods Enzymol 2003;374:461-491. (Pubitemid 37531821)
52. Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res 2001;29:308-311. (Pubitemid 32054478)
53. Hubbard TJ, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G, Cunningham F, Cutts T, Down T, Dyer SC, Fitzgerald S, Fernandez-Banet J, Graf S, Haider S, Hammond M, Herrero J, Holland R, Howe K, Johnson N, Kahari A, Keefe D, Kokocinski F, Kulesha E, Lawson D, Longden I, Melsopp C, Megy K, Meidl P, Ouverdin B, Parker A, Prlic A, Rice S, Rios D, Schuster M, Sealy I, Severin J, Slater G, Smedley D, Spudich G, Trevanion S, Vilella A, Vogel J, White S, Wood M, Cox T, Curwen V, Durbin R, Fernandez-Suarez XM, Flicek P, Kasprzyk A, Proctor G, Searle S, Smith J, Ureta-Vidal A, Birney E. Ensembl 2007. Nucl Acids Res 2007;35:D610-D617.
54. Berman HM, Westbrock J, Feng Z, Gillilan G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The protein data bank. Nucleic Acids Res 2000;28:235-242.
55. Prlić A, Down TA, Hubbard TJP. Adding some SPICE to DAS. Bioinformatics 2005;21(Suppl 2):ii40-ii41.
56. Shannon CE. A mathematical theory of communication. Bell Syts Tech J 1948.
57. Orengo CA. CORA - topological fingerprints for protein structural families. Protein Sci 1999;8:699-715.
58. Glaser F, Rosenberg Y, Kessel A, Pupko T, Ben-Tal N. The ConSurf-HSSP database: the mapping of evolutionary conservation among homologs onto PDB structures. Proteins 2005;58:610-617. (Pubitemid 40176033)
59. Porter CT, Bartlett GJ, Thornton JM. The catalytic site atlas: a resource of catalytic sites and residues identified in enzymes using structural data. Nucleic Acids Res 2004;32:D129-D133.
60. Greenacre MJ. Theory and application of correspondence analysis. London: Academic Press; 1984.