Mutational analysis of TYR gene and its structural consequences in OCA1A

Gene

Volumn 513, Issue 1, 2013, Pages 184-195

  K, Balu ^a   Purohit, Rituraj ^a  

^a VIT UNIVERSITY   (India)

Author keywords

Deleterious mutation; Flexibility; Hydrogen bonding; OCA1A; Salt bridges

Indexed keywords

MEMBRANE PROTEIN; TYR PROTEIN; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; GENETIC ASSOCIATION; HYDROGEN BOND; MISSENSE MUTATION; MUTATIONAL ANALYSIS; OCULOCUTANEOUS ALBINISM; OCULOCUTANEOUS ALBINISM TYPE 1A; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN FUNCTION; PROTEIN STABILITY; PROTEIN STRUCTURE; QUANTITATIVE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; STRUCTURE ACTIVITY RELATION;

ALBINISM, OCULOCUTANEOUS; DATA MINING; DNA MUTATIONAL ANALYSIS; GENE FREQUENCY; GENETIC VARIATION; HUMANS; MELANINS; MONOPHENOL MONOOXYGENASE; POLYMORPHISM, SINGLE NUCLEOTIDE; PROTEIN CONFORMATION; SEVERITY OF ILLNESS INDEX;

EID: 84872379319     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2012.09.128     Document Type: Article

References (74)

1. Amberger J., Bocchini C.A., Scott A.F., Hamosh A. McKusick's Online Mendelian Inheritance in Man (OMIM). Nucleic Acids Res. 2009, 37:793-796.
2. Amos B., Rolf A. The SWISS-PROT protein sequence data bank and its new supplement TREMBL. Nucleic Acids Res. 1996, 24:21-25.
3. Baran M., Mazerski J. Molecular modelling of membrane sterols with the use of GROMOS 96 force field. Chem. Phys. Lipids 2002, 120:21-31.
4. Breimer L.H., Winder A.F., Jay B., Jay M. Initiation codon mutation of the tyrosinase gene as a cause of human albinism. Clin. Chim. Acta 1994, 227:17-22.
5. Brooks-Wilson A.R., Kaurah P., Suriano G. Germline Ecadherin mutations in hereditary diffuse gastric cancer: assessment of 42 new families and review of genetic screening criteria. J. Med. Genet. 2004, 41:508-517.
6. Camand O., et al. Mutation analysis of the tyrosinase gene in oculocutaneous albinism. Hum. Mutat. 2001, 17:352.
7. Capriotti E., Altman R.B. Improving the prediction of disease-related variants using protein three-dimensional structure. BMC Bioinforma. 2011, 4:S3.
8. Capriotti E., Fariselli P., Casadio R. I-Mutant 2.0: Predicting stability changes upon mutation from the protein sequence or structure. Nucleic Acids Res. 2005, 33:306-310.
9. Cargill M., et al. Characterization of single nucleotide polymorphisms in coding regions of human genes. Nat. Genet. 1999, 22:231-238.
10. Chaki M., Mukhopadhyay A., Ray K. Determination of variants in the 3'-region of the tyrosinase gene requires locus specific amplification. Hum. Mutat. 2005, 26:53-58.
11. Chakravarty S., Varadarajan R. Residue depth: a novel parameter for the analysis of protein structure and stability. Structure 1999, 7:723-732.
12. Chasman D., Adams R.M. Predicting the functional consequences of non-synonymous single nucleotide polymorphisms: structure-based assessment of amino acid variation. J. Mol. Biol. 2001, 307:683-706.
13. Chiche L., Gregoret L.M., Cohen F.E., Kollman P.A. Protein model structure evaluation using the solvation free energy of folding. Proc. Natl. Acad. Sci. U. S. A. 1990, 87:3240-3243.
14. Constantini S., Colonna G., Facchiano A.M. ESBRI: a software for evaluating the salt bridges in proteins. Bioinformation 2008, 3:137-139.
15. Cooksey C.J., et al. Evidence of the indirect formation of the catecholic intermediate substrate responsible for the autoactivation kinetics of tyrosinase. J. Biol. Chem. 1997, 272:26226-26235.
16. Doss C.G.P., et al. Identification and structural comparison of deleterious mutations in nsSNPs of ABL1 gene in chronic myeloid leukemia: a bio-informatics study. J. Biomed. Inform. 2008, 41:607-612.
17. Doss C.G.P., Rajasekaran R., Sudandiradoss C. A novel computational and structural analysis of nsSNPs in CFTR gene. Genomic Med. 2008, 2:23-32.
18. Gershoni-Baruch R., et al. Mutations of the tyrosinase gene in patients with oculocutaneous albinism from various ethnic groups in Israel. Am. J. Hum. Genet. 1994, 54:586-594.
19. Harpaz Y., Gerstein M., Chothia C. Volume changes on protein folding. Structure 1994, 2:641-649.
20. Hess B., Kutzner C., Spoel D., Lindahl E. GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J. Chem. Theory Comput. 2008, 4:435-447.
21. Hollup S.M., Salensminde G., Reuter N. WEBnm@: a web application for normal mode analysis of proteins. BMC Bioinforma. 2005, 6:1-8.
22. Hutton S.M., Spritz R.A. A comprehensive genetic study of autosomal recessive ocular albinism in Caucasian patients. Invest. Ophthalmol. Vis. Sci. 2008, 49:868-872.
23. Jerome N., et al. Assessing protein loop flexibility by hierarchical Monte Carlo sampling. J. Chem. Theory Comput. 2011, 7:1564-1574.
24. Kanetsky P.A., et al. Assessment of polymorphic variants in the melanocortin-1 receptor gene with cutaneous pigmentation using an evolutionary approach. Cancer Epidemiol. Biomarkers Prev. 2004, 13:808-819.
25. King R.A., Mentink M.M., Oetting W.S. Non-random distribution of missense mutations within the human tyrosinase gene in Type 1 (tyrosinase-related) oculocutaneous albinism. Mol. Biol. Med. 1991, 8:19-29.
26. King R.A., et al. Tyrosinase gene mutations in oculocutaneous albinism 1 (OCA1): definition of the phenotype. Hum. Genet. 2003, 113:502-513.
27. Kumar A., Purohit R. Computational investigation of pathogenic nsSNPs in CEP63 protein. Gene 2012, 503:75-82.
28. Kumar A., Purohit R. Computational screening and molecular dynamics simulation of disease associated nsSNPs in CENP-E. Mutat. Res. 2012, 10.1016/j.mrfmmm.2012.08.005.
29. Kumar P., Henikoff S., Ng P.C. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat. Protoc. 2009, 4:1073-1081.
30. Kwon B.S., Haq A.K., Pomerantz S.H., Halaban R. Isolation and sequence of a cDNA clone for human tyrosinase that maps at the mouse c-albino locus. Proc. Natl. Acad. Sci. U. S. A. 1987, 84:7473-7477.
31. Luthy R., Bowie J.U., Eisenberg D. Assessment of protein models with three-dimensional profiles. Nature 1992, 356:83-85.
32. Ng P.C., Henikoff S. Accounting for human polymorphisms predicted to affect protein function. Genome Res. 2002, 12:436-446.
33. Oetting W.S. The tyrosinase gene and oculocutaneous albinism type 1 (OCA1): a model for understanding the molecular biology of melanin formation. Pigment Cell Res. 2000, 13:320-325.
34. Oetting W.S., King R.A. Molecular analysis of type I-A (tyrosinase negative) oculocutaneous albinism. Hum. Genet. 1992, 90:258-262.
35. Oetting W.S., King R.A. Molecular basis of oculocutaneous albinism. J. Invest. Dermatol. 1994, 103:131-136.
36. Oetting W.S., et al. Molecular analysis of an extended family with type IA (tyrosinase negative) oculocutaneous albinism. J. Invest. Dermatol. 1991, 97:15-19.
37. Oetting W.S., Fryer J.P., King R.A. Mutations of the human tyrosinase gene associated with tyrosinase related oculocutaneous albinism (OCA1). Hum. Mutat. 1998, 12:433-434.
38. Opitz S., et al. Detection of 53 novel DNA variations within the tyrosinase gene and accumulation of mutations in 17 patients with albinism. Hum. Mutat. 2004, 23:630-631.
39. Passmore L.A., Kaesmann-Kellner B., Weber B.H.F. Novel and recurrent mutations in the tyrosinase gene and the P gene in the German albino population. Hum. Genet. 1999, 105:200-210.
40. Pedersen T.G., et al. A nuclear magnetic resonance study of the hydrogen-exchange behaviour of lysozyme in crystals and solution. J. Mol. Biol. 1991, 218:413-426.
41. Pintar A., Pongor S. The 'first in-last out' hypothesis on protein folding revisited. Proteins 2005, 60:584-590.
42. Pintar A., Carugo O., Pongor S. Atom depth in protein structure and function. Trends Biochem. Sci. 2003, 28:593-597.
43. Pintar A., Carugo O., Pongor S. Atom depth as a descriptor of the protein interior. Biophys. J. 2003, 84:2553-2561.
44. Purohit R., Sethumadhavan R. Structural basis for the resilience of darunavir (TMC114) resistance major flap mutations of HIV-1 protease. Interdiscip. Sci. 2009, 1:320-328.
45. Purohit R., et al. Studies on flexibility and binding affinity of Asp25 of HIV-1 protease mutants. Int. J. Biol. Macromol. 2008, 42:386-391.
46. Purohit R., Rajendran V., Sethumadhavan R. Studies on adaptability of binding residues and flap region of TMC-114 resistance HIV-1 protease mutants. J. Biomol. Struct. Dyn. 2011, 29:137-152.
47. Purohit R., Rajendran V., Sethumadhavan R. Relationship between mutation of serine residue at 315th position in M. tuberculosis catalase-peroxidase enzyme and Isoniazid susceptibility: an in silico analysis. J. Mol. Model. 2011, 17:869-877.
48. Rajasekaran R., et al. Computational and structural investigation of deleterious functional SNPs in breast cancer BRCA2 gene. Chin. J. Biotechnol. 2008, 5:851-856.
49. Rajasekaran R., et al. Effect of deleterious nsSNP on the HER2 receptor based on stability and binding affinity with herceptin: a computational approach. C. R. Biol. 2008, 331:409-417.
50. Rajendran V., Purohit R., Sethumadhavan R. In-silico investigation of molecular mechanism of laminopathy cause by a point mutation (R482W) in lamin A/C protein. Amino acids 2012, 43:603-615.
51. Sarakatsannis J.N., Duan Y. Statistical characterization of salt bridges in proteins. Proteins 2005, 60:732-739.
52. Sherry S.T., et al. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001, 29:308-311.
53. Spoel D.V.D., et al. GROMACS: fast, flexible, and free. J. Comput. Chem. 2005, 26:1701-1718.
54. Spritz R.A., Strunk K.M., Giebel L.B., King R.A. Detection of mutations in the tyrosinase gene in a patient with type IA oculocutaneous albinism. N. Engl. J. Med. 1990, 332:1724-1728.
55. Spritz R.A., Strunk K.M., Hsieh C.L., Sekhon G.S., Francke U. Homozygous tyrosinase gene mutation in an American black with tyrosinase-negative (type IA) oculocutaneous albinism. Am. J. Hum. Genet. 1991, 48:318-324.
56. Spritz R.A., et al. Novel mutations of the tyrosinase (TYR) gene in type I oculocutaneous albinism (OCA1). Hum. Mutat. 1997, 10:171-174.
57. Stenson P.D., et al. The Human Gene Mutation Database: 2008 update. Genome Med. 2009, 1:13.
58. Suhre K., Sanejouand Y.H. ElNemo: a normal mode web-server for protein movement analysis and the generation of templates for molecular replacement. Nucleic Acids Res. 2004, 32:610-614.
59. Summers C.G., Oetting W.S., King R.A. Diagnosis of oculocutaneous albinism with molecular analysis. Am. J. Ophthalmol. 1996, 121:724-726.
60. Sunyaev S., Ramensky V., Bork P. Towards a structural basis of human non-synonymous single nucleotide polymorphisms. Trends Genet. 2000, 16:198-200.
61. Sunyaev S., et al. Prediction of deleterious human alleles. Hum. Mol. Genet. 2001, 10:591-597.
62. Tan K.P., Varadarajan R., Madhusudhan M.S. DEPTH: a web server to compute depth and predict small-molecule binding cavities in proteins. Nucleic Acids Res. 2011, 39:242-248.
63. Thomas P.D., et al. PANTHER: a library of protein families and subfamilies indexed by function. Genome Res. 2003, 13:2129-2141.
64. Tomita Y., Takeda A., Okinaga S., Tagami H., Shibahara S. Human oculocutaneous albinism caused by single base insertion in the tyrosinase gene. Biochem. Biophys. Res. Commun. 1989, 164:990-996.
65. Toyofuku K., et al. Oculocutaneous albinism types 1 and 3 are ER retention diseases: mutation of tyrosinase or Tyrp1 can affect the processing of both mutant and wild-type proteins. FASEB J. 2001, 15:2149-2161.
66. Tripathi R.A., et al. Mutations of the tyrosinase gene in Indo-Pakistani patients with type I (tyrosinase-deficient) oculocutaneous albinism (OCA). Am. J. Hum. Genet. 1993, 53:1173-1179.
67. Wang Y., Guo X., Li W., Lian S. Four novel mutations of TYR gene in Chinese OCA1 patients. J. Dermatol. Sci. 2009, 53:80-81.
68. Wiederstein M., Sippl M.J. ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res. 2007, 35:407-410.
69. Wilcox D.E., Porras A.G., Hwang Y.T. Substrate analogue binding to the coupled binuclear copper active site in tyrosinase. J. Am. Chem. Soc. 1995, 107:4015-4027.
70. Willard L., et al. VADAR: a web server for quantitative evaluation of protein structure quality. Nucleic Acids Res. 2003, 31:3316-3319.
71. Wu S., Zhang Y. LOMETS: a local meta-threading-server for protein structure Prediction. Nucleic Acids Res. 2007, 35:3375-3382.
72. Yuan H.Y., et al. FASTSNP: an always up-to-date and extendable service for SNP function analysis and prioritization. Nucleic Acids Res. 2006, 34:635-641.
73. Zahed L., Zahreddine H., Noureddine B. Molecular basis of oculocutaneous albinism type 1 in Lebanese patients. J. Hum. Genet. 2005, 50:317-319.
74. Zhang E.Y., Fu D.J., Pak Y.A. Genetic polymorphisms in human proton-dependent dipeptide transporter PEPT1: implications for the functional role of Pro586. J. Pharmacol. Exp. Ther. 2004, 310:437-445.