A New Insight into Structural and Functional Impact of Single-Nucleotide Polymorphisms in PTEN Gene

Cell Biochemistry and Biophysics

Volumn 66, Issue 2, 2013, Pages 249-263

  George Priya Doss, C ^a   Rajith, B ^a  

^a VIT UNIVERSITY   (India)

Author keywords

Molecular dynamics simulation; Post translational modification; PTEN; SNPs

Indexed keywords

PHOSPHATIDYLINOSITOL 3,4,5 TRISPHOSPHATE 3 PHOSPHATASE;

AMINO ACID SEQUENCE; ARTICLE; CHEMISTRY; FACTUAL DATABASE; GENETICS; HUMAN; HYDROGEN BOND; METABOLISM; MOLECULAR DYNAMICS; MOLECULAR GENETICS; PRINCIPAL COMPONENT ANALYSIS; PROTEIN PROTEIN INTERACTION; SINGLE NUCLEOTIDE POLYMORPHISM; THERMODYNAMICS;

AMINO ACID SEQUENCE; DATABASES, FACTUAL; HUMANS; HYDROGEN BONDING; MOLECULAR DYNAMICS SIMULATION; MOLECULAR SEQUENCE DATA; POLYMORPHISM, SINGLE NUCLEOTIDE; PRINCIPAL COMPONENT ANALYSIS; PROTEIN INTERACTION MAPS; PTEN PHOSPHOHYDROLASE; THERMODYNAMICS;

EID: 84878111284     PISSN: 10859195     EISSN: None     Source Type: Journal    
DOI: 10.1007/s12013-012-9472-9     Document Type: Article

References (65)

1. Keniry, M., & Parsons, R. (2008). The role of PTEN signaling perturbations in cancer and in targeted therapy. Oncogene, 27, 5477-5485.
2. Nakamura, N., Ramaswamy, S., Vazquez, F., Signoretti, S., Loda, M., et al. (2000). Forkhead transcription factors are critical effectors of cell death and cell cycle arrest downstream of PTEN. Molecular and Cellular Biology, 20, 8969-8982.
3. Stokoe, D. (2001). PTEN. Current Biology, 11, R502.
4. Yamada, K. M., & Araki, M. (2001). Tumor suppressor PTEN: Modulator of cell signaling, growth, migration and apoptosis. Journal of Cell Science, 114, 2375-2382.
5. Zaghloul, N. A., & Katsanis, N. (2010). Functional modules, mutational load and human genetic disease. Trends in Genetics, 26, 168-176.
6. Rabbani, B., Mahdieh, N., Ashtiani, M. T., Setoodeh, A., & Rabbani, A. (2012). In silico structural, functional and pathogenicity evaluation of a novel mutation: An overview of HSD3B2 gene mutations. Gene, 503, 215-221.
7. Lino, C. C. L., Renault, N., Farce, A., Cauffiez, C., Allorge, D., et al. (2011). Genetic polymorphism of CYP4A11 and CYP4A22 genes and in silico insights from comparative 3D modelling in a French population. Gene, 487, 10-20.
8. Ng, P. C., & Henikoff, S. (2003). SIFT: Predicting amino acid changes that affect protein function. Nucleic Acids, 31, 3812-3814.
9. Adzhubei, I. A., Schmidt, S., Peshkin, L., Ramensky, V. E., Gerasimova, A., et al. (2010). A method and server for predicting damaging missense mutations. Nature Methods, 7, 248-249.
10. Capriotti, E., Fariselli, P., Rossi, I., & Casadio, R. (2008). A three-state prediction of single point mutations on protein stability changes. BMC Bioinformatics, 9(Suppl 2), S6.
11. Capriotti, E., Calabrese, R., & Casadio, R. (2006). Predicting the insurgence of human genetic diseases associated to single point protein mutations with support vector machines and evolutionary information. Bioinformatics, 22, 2729-2734.
12. Calabrese, R., Capriotti, E., Fariselli, P., Martelli, P. L., & Casadio, R. (2009). Functional annotations improve the predictive score of human disease-related mutations in proteins. Human Mutation, 30, 1237-1244.
13. Yuan, H. Y., Chiou, J. J., Tseng, W. H., Liu, C. H., Liu, C. K., et al. (2006). FASTSNP: An always up-to-date and extendable service for SNP function analysis and prioritization. Nucleic Acids Research, 34, W635-W641.
14. Lee, P. H., & Shatkay, H. (2008). F-SNP: Computationally predicted functional SNPs for disease association studies. Nucleic Acids Research, 36, D820-D824.
15. Zhou, F., Xue, Y., Yao, X., & Xu, Y. (2006). A general user interface for prediction servers of proteins' post-translational modification sites. Nature Protocols, 1, 1318-1321.
16. Grasbon, F. E., Lorenz, H., Mann, U., Nitsch, R. M., Windl, O., et al. (2004). Loss of glycosylation associated with the T183A mutation in human prion disease. Acta Neuropathologica, 108, 476-484.
17. Thomas, M., Dadgar, N., Aphale, A., Harrell, J. M., Kunkel, R., et al. (2004). Androgen receptor acetylation site mutations cause trafficking defects, misfolding, and aggregation similar to expanded glutamine tracts. Journal of Biological Chemistry, 279, 8389-8395.
18. Vazquez, F. (2000). Phosphorylation of the PTEN tail regulates protein stability and function. Molecular and Cellular Biology, 20, 5010-5018.
19. Tolkacheva, T., Boddapati, M., Sanfiz, A., Tsuchida, K., Kimmelman, A. C., et al. (2001). Regulation of PTEN binding to MAGI-2 by two putative phosphorylation sites at threonine 382 and 383. Cancer Research, 61, 4985-4989.
20. Amberger, J., Bocchini, C. A., Scott, A. F., & Hamosh, A. (2009). Online Mendelian inheritance in man (OMIM). Nucleic Acids Research, 37, D793-D796.
21. Sherry, S. T., Ward, M., & Sirotkin, K. (2001). dbSNP: The NCBI database of genetic variation. Nucleic Acids Research, 29, 308-311.
22. Amos, B., & Rolf, A. (1996). The SWISS-PROT protein sequence data bank and its new supplement TREMBL. Nucleic Acids Research, 24, 21-25.
23. Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., et al. (2000). The protein data bank. Nucleic Acids Research, 28, 235-242.
24. Petersen, B., Petersen, T. N., Andersen, P., Nielsen, M., & Lundegaard, C. (2009). A generic method for assignment of reliability scores applied to solvent accessibility predictions. BMC Structural Biology, 31, 9-51.
25. Venselaar, H., Te Beek, T. A., Kuipers, R. K., Hekkelman, M. L., & Vriend, G. (2010). Protein structure analysis of mutations causing inheritable diseases. An e-Science approach with life scientist friendly interfaces. BMC Bioinformatics, 8, 11-548.
26. Szklarczyk, D., Franceschini, A., Kuhn, M., Simonovic, M., Roth, A., et al. (2011). The STRING database in 2011: Functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Research, 39, D561-D568.
27. Lee, J. O., Yang, H., Georgescu, M. M., Di Cristofano, A., Maehama, T., et al. (1999). Crystal structure of the PTEN tumor suppressor: Implications for its phosphoinositide phosphatase activity and membrane association. Cell, 99, 323-334.
28. Hess, B., Kutzner, D., & Spoel, D. (2008). GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. Journal of Chemical Theory and Computation, 4, 435-447.
29. Jorgensen, W. L. (1983). Comparison of simple potential functions for simulating liquid water. Journal of Chemical Physics, 79, 926.
30. Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., et al. (1995). A smooth particle meshes Ewald method. Journal of Chemical Physics, 103, 8577-8593.
31. Amadei, A., Linssen, A. B. M., & Berendsen, H. J. C. (1993). Essential dynamics of proteins. Proteins, 17, 412-425.
32. George, P. D. C., & Rajith, B. (2012). Computational refinement of functional single nucleotide polymorphisms associated with ATM gene. PLoS ONE, 7(4), e34573.
33. Rajith, B., & George, P. D. C. (2011). Path to facilitate the prediction of functional amino acid substitutions in red blood cell disorders-A computational approach. PLoS ONE, 6(9), e24607.
34. Thusberg, J., & Vihinen, M. (2009). Pathogenic or not? And if so, then how? Studying the effects of missense mutations using bioinformatics methods. Human Mutation, 30, 703-714.
35. Hicks, S., Wheeler, D. A., Plon, S. E., & Kimmel, M. (2011). Prediction of missense mutation functionality depends on both the algorithm and sequence alignment employed. Human Mutation, 6, 661-668.
36. Khan, S., & Vihinen, M. (2010). Performance of protein stability predictors. Human Mutation, 31, 675-678.
37. Han, S. Y., Kato, H., Kato, S., Suzuki, T., Shibata, H., et al. (2000). Functional evaluation of PTEN missense mutations using in vitro phosphoinositide phosphatase assay. Cancer Research, 60, 3147-3151.
38. Steck, P. A., Pershouse, M. A., Jasser, S. A., Yung, W. K., Lin, H., et al. (1997). Identification of a candidate tumour suppressor gene, MMAC1, at chromosome 10q23. 3 that is mutated in multiple advanced cancers. Nature Genetics, 15, 356-362.
39. Celebi, J. T., Shendrik, I., Silversm, D. N., & Peacocke, M. (2000). Identification of PTEN mutations in metastatic melanoma specimens. Journal of Medical Genetics, 37, 653-657.
40. Marsh, D. J., Kum, J. B., Lunetta, K. L., Bennett, M. J., Gorlin, R. J., et al. (1999). PTEN mutation spectrum and genotype-phenotype correlations in Bannayan-Riley-Ruvalcaba syndrome suggest a single entity with Cowden syndrome. Human Molecular Genetics, 8, 1461-1472.
41. Olschwang, S., Serova, S. O. M., Lenoir, G. M., & Thomas, G. (1998). PTEN germ-line mutations in juvenile polyposis coli. Nature Genetics, 18, 12-14.
42. Maxwell, G. L., Risinger, J. I., Gumbs, C., Shaw, H., Bentley, R., et al. (1998). Mutation of the PTEN tumor suppressor gene in endometrial hyperplasias. Cancer Research, 58, 2500-2503.
43. Marsh, D. J., Theodosopoulos, G., Howell, V., Richardson, A. L., Benn, D. E., et al. (2001). Rapid mutation scanning of genes associated with familial cancer syndromes using denaturing high-performance liquid chromatography. Neoplasia, 3, 236-244.
44. Reardon, W., Zhou, X. P., & Eng, C. (2001). A novel germline mutation of the PTEN gene in a patient with macrocephaly, ventricular dilatation, and features of VATER association. Journal of Medical Genetics, 38, 820-823.
45. Marsh, D. J., Dahia, P. L., Caron, S., Kum, J. B., Frayling, I. M., et al. (1998). Germline PTEN mutations in Cowden syndrome-like families. Journal of Medical Genetics, 35, 881-885.
46. Butler, M. G., Dasouki, M. J., Zhou, X. P., Talebizadeh, Z., Brown, M., et al. (2005). Subset of individuals with autism spectrum disorders and extreme macrocephaly associated with germline PTEN tumour suppressor gene mutations. Journal of Medical Genetics, 42, 318-321.
47. De Vivo, I., Gertig, D. M., Nagase, S., Hankinson, S. E., O'Brien, R., et al. (2000). Novel germline mutations in the PTEN tumour suppressor gene found in women with multiple cancers. Journal of Medical Genetics, 37, 336-341.
48. Poetsch, M., Lorenz, G., & Kleist, B. (2002). Detection of new PTEN/MMAC1 mutations in head and neck squamous cell carcinomas with loss of chromosome 10. Cancer Genetics and Cytogenetics, 132, 20-24.
49. Nelen, M. R., van Peeters, S. W. C., Hassel, M. B., Gorlin, R. J., et al. (1997). Germline mutations in the PTEN/MMAC1 gene in patients with Cowden disease. Human Molecular Genetics, 6, 1383-1387.
50. Myers, M. P., Stolarov, J. P., Eng, C., Li, J., Wang, S. I., et al. (1997). P-TEN, the tumor suppressor from human chromosome 10q23, is a dual-specificity phosphatase. Proceedings of the National Academy of Science of the United State of America, 94, 9052-9057.
51. Tekin, M., Hişmi, B. O., Fitoz, S., Yalçinkaya, F., & Ekim, M. (2006). A germline PTEN mutation with manifestations of prenatal onset and verrucous epidermal nevus. American Journal of Medical Genetics Part A, 140, 1472-1475.
52. Tsou, H. C., Teng, D. H., Ping, X. L., Brancolini, V., Davis, T., et al. (1997). The role of MMAC1 mutations in early-onset breast cancer: Causative in association with Cowden syndrome and excluded in BRCA1-negative cases. American Journal of Human Genetics, 1997(61), 1036-1043.
53. Nelen, M. R., Kremer, H., Konings, I. B., Schoute, F., van, E. A. J., et al. (1999). Novel PTEN mutations in patients with Cowden disease: Absence of clear genotype-phenotype correlations. European Journal of Human Genetics, 7, 267-273.
54. Staal, F. J., van Luijt, R. B., Baert, M. R., van Drunen, J., van Bakel, H., et al. (2002). A novel germline mutation of PTEN associated with brain tumours of multiple lineages. British Journal of Cancer, 86, 1586-1591.
55. Wang, Q., Wei, Y., Mottamal, M., Roberts, M. F., & Krilov, G. (2010). Understanding the stereospecific interactions of 3-deoxyphosphatidylinositol derivatives with the PTEN phosphatase domain. Journal of Molecular Graphics and Modelling, 29, 102-114.
56. Doniger, S. W., Kim, H. S., Swain, D., Corcuera, D., & Williams, M. (2008). Catalog of neutral and deleterious polymorphism in yeast. PLoS Genetics, 29(4), e1000183.
57. Aly, T. A., Eller, E., Ide, A., Gowan, K., Babu, S. R., et al. (2006). Multi-SNP analysis of MHC region: Remarkable conservation of HLA-A1-B8-DR3 haplotype. Diabetes, 55, 1265-1269.
58. Sandberg, R., Neilson, J. R., Sarma, A., Sharp, P. A., & Burge, C. B. (2008). Proliferating cells express mrnas with shortened 39 untranslated regions and fewer microRNA target sites. Science, 320, 1643-1647.
59. Wang, G., Guo, X., & Floros, J. (2005). Differences in the translation efficiency and mRNA stability mediated by 59-UTR splice variants of human SP-A1 and SPA2 genes. AJP - Lung Physiol., 289, L497-L508.
60. Andrés-Pons, A., Rodríguez-Escudero, I., Gil, A., Blanco, A., & Vega, A. (2007). In vivo functional analysis of the counterbalance of hyperactive phosphatidylinositol 3-kinase p110 catalytic oncoproteins by the tumor suppressor PTEN. Cancer Research, 20, 9731-9739.
61. Li, Z., Dong, X., Wang, Z., Liu, W., & Deng, N. (2005). Regulation of PTEN by Rho small GTPases. Nature Cell Biology, 7, 399-404.
62. Koul, D., Jasser, S. A., Lu, Y., Davies, M. A., & Shen, R. (2002). Motif analysis of the tumor suppressor gene MMAC/PTEN identifies tyrosines critical for tumor suppression and lipid phosphatase activity. Oncogene, 21, 2357-2364.
63. Miller, S. J., Lou, D. Y., Seldin, D. C., Lane, W. S., & Neel, B. G. (2002). Direct identification of PTEN phosphorylation sites. FEBS Letters, 528, 145-153.
64. Birle, D., Bottini, N., Williams, S., Huynh, H., deBelle, I., et al. (2002). Negative feedback regulation of the tumor suppressor PTEN by phosphoinositide-induced serine phosphorylation. Journal of Immunology, 169, 286-291.
65. Torres, J., & Pulido, R. (2001). The tumor suppressor PTEN is phosphorylated by the protein kinase CK2 at its C terminus. Implications for PTEN stability to proteasome-mediated degradation. Journal of Biological Chemistry, 276, 993-998.