Molecular docking and molecular dynamics study on the effect of ERCC1 deleterious polymorphisms in ERCC1-XPF heterodimer

Applied Biochemistry and Biotechnology

Volumn 172, Issue 3, 2014, Pages 1265-1281

  George Priya Doss, C ^a   Nagasundaram, N ^a  

^a VIT UNIVERSITY   (India)

Author keywords

ERCC1 XPF; Molecular dynamics; Protein protein interaction; SNPs

Indexed keywords

BIOMOLECULES; CHEMOTHERAPY; COMPUTER SIMULATION; DISEASES; GENES; HYDROGEN BONDS; MOLECULAR MODELING; PLATINUM COMPOUNDS; PROTEINS;

COMPLEX STABILITY; DYNAMIC APPROACHES; ERCC1-XPF; MOLECULAR DOCKING; MOLECULAR DYNAMICS SIMULATIONS; NUCLEOTIDE EXCISION REPAIR; PROTEIN-PROTEIN INTERACTIONS; SNPS;

MOLECULAR DYNAMICS;

CISPLATIN; EXCISION REPAIR CROSS COMPLEMENTING PROTEIN 1; PROTEIN; UNCLASSIFIED DRUG; XPF PROTEIN; DNA BINDING PROTEIN; ENDONUCLEASE; ERCC1 PROTEIN, HUMAN;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; BIOTECHNOLOGY; CANCER PATIENT; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; DNA DAMAGE; DNA REPAIR; DNA SEQUENCE; EXCISION REPAIR; GENE IDENTIFICATION; GENETIC STABILITY; GENETIC VARIABILITY; HUMAN; HYDROGEN BOND; MISSENSE MUTATION; MOLECULAR DOCKING; MOLECULAR DYNAMICS; PREDICTION; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN PROTEIN INTERACTION; PROTEIN STABILITY; PROTEIN STRUCTURE; SEQUENCE ALIGNMENT; SINGLE NUCLEOTIDE POLYMORPHISM; STATIC ELECTRICITY; ANIMAL; CHEMISTRY; CHO CELL LINE; CRICETULUS; GENE DELETION; GENETIC POLYMORPHISM; GENETICS; HAMSTER; NEOPLASMS; STRUCTURE ACTIVITY RELATION;

ANIMALS; CHO CELLS; CISPLATIN; CRICETINAE; CRICETULUS; DNA DAMAGE; DNA REPAIR; DNA-BINDING PROTEINS; ENDONUCLEASES; HUMANS; MOLECULAR DOCKING SIMULATION; MOLECULAR DYNAMICS SIMULATION; NEOPLASMS; POLYMORPHISM, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE DELETION; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 84896317901     PISSN: 02732289     EISSN: 15590291     Source Type: Journal    
DOI: 10.1007/s12010-013-0592-5     Document Type: Article

References (70)

1. De Laat, W. L., Appeldoorn, E., Jaspers, N. G., & Hoeijmakers, J. H. (1998). The Journal of Biological Chemistry, 273, 7835-7842.
2. Volker, M., Mone, M. J., Karmakar, P., van Hoffen, A., Schul, W., Vermeulen, W., et al. (2001). Molecular Cell, 8, 213-224.
3. De Boer, J., & Hoeijmakers, J. H. (2000). Carcinogenesis, 21, 453-460.
4. Jaspers, N. G., Raams, A., Silengo, M. C., Wijgers, N., Niedernhofer, L. J., Robinson, A. R., et al. (2007). American Journal of Human Genetics, 80, 457-466.
5. Chen, P., Wiencke, J., Aldape, K., Kesler Diaz, A., Miiker, R., Kelsey, K., et al. (2000). Cancer Epidemiology, Biomarkers & Prevention, 9, 843-847.
6. Yu, J. J., Lee, K. B., Mu, C., Li, Q., Abernathy, T. V., et al. (2000). International Journal of Oncology, 16, 555-560.
7. Bradbury, P. A., Kulke, M. H., Heist, R. S., Zhou, W., Ma, C., Xu, W., et al. (2009). Pharmacogenetics and Genomics, 19(8), 613-625.
8. Sunyaev, S., Hanke, J., Aydin, A., Wirkner, U., Zastrow, I., Reich, J., et al. (1999). Journal of Molecular Medicine, 77, 754-760.
9. Cargill, M., Altshuler, D., Ireland, J., Sklar, P., Ardlie, K., Patil, N., et al. (1999). Nature Genetics, 22, 231-238.
10. Chasman, D., & Adams, R. M. (2001). Journal of Molecular Biology, 307, 683-706.
11. Ng, P. C., & Henikoff, S. (2001). Genome Research, 11, 863-874.
12. Wang, Z., & Moult, J. (2001). Human Mutation, 17, 263-270.
13. Ng, P. C., & Henikoff, S. (2006). Annual Review of Genomics and Human Genetics, 7, 61-80.
14. Mooney, S. (2005). Briefings in Bioinformatics, 6, 44-56.
15. Steward, R. E., MacArthur, M. W., Laskowski, R. A., & Thornton, J. M. (2003). TrendsGenetics, 19, 505-513.
16. Laskowski, R. A., & Thornton, J. M. (2008). Nature Reviews Genetics, 9, 141-151.
17. Pruitt, K. D., Tatusova, T., & Maglott, D. R. (2007). Nucleic Acids Research, 35, 61-65.
18. Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., et al. (2000). Nucleic Acids Research, 28, 235-242.
19. Amos, B., & Rolf, A. (1996). Nucleic Acids Research, 24, 21-25.
20. Tsodikov, O. V., Enzlin, J. H., Scharer, O. D., & Ellenberger, T. (2005). Proceedings of the National Academy of Sciences of the United States of America, 102, 11236-11241.
21. Kaplan, W., & Littlejohn, T. G. (2001). Briefings in Bioinformatics, 2, 195-197.
22. Kumar, P., Henikoff, S., & Ng, P. C. (2009). Nature Protocols, 4, 1073-1081.
23. Mi, H., Guo, N., Kejariwal, A., & Thomas, P. D. (2007). Nucleic Acids Research, 35, 247-252.
24. Capriotti, E., Fariselli, P., Rossi, I., & Casadio, R. (2008). BMC Bioinformatics, 9(Suppl 2):S6
25. Ramensky, V., Bork, P., & Sunyaev, S. (2002). Nucleic Acids Research, 30, 3894-3900.
26. Ng, P. C., & Henikoff, S. (2003). Nucleic Acids Research, 13, 3812-3814.
27. Dominguez, C., Boelens, R., & Bonvin, A. M. (2003). Journal of the American Chemical Society, 125, 1731-1737.
28. de Vries, S. J., van Dijk, M., & Bonvin, A. M. J. J. (2010). Nature Protocols, 5, 883-897.
29. Nilges, M. (1995). Journal of Molecular Biology, 245, 645-660.
30. Nilges, M., Macias, M. J., O'Donoghue, S. I., & Oschkinat, H. (1997). Journal of Molecular Biology, 269, 408-422.
31. Brunger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., et al. (1998). Acta Crystallographica. Section D, Biological Crystallography, 54, 905-921.
32. Hess, B., Kutzner, C., van der Spoel, D., & Lindahl, E. (2008). Journal of Chemical Theory and Computation, 4, 435-447.
33. Kutzner, C., van der Spoel, D., Fechner, M., Lindahl, E., Schmittn, U. W., de Groot, B. L., et al. (2007). Journal of Compound Chemistry, 28, 2075-2084.
34. Van Gunsteren, W.F., Billeter, S.R., Eising, A.A., Hunenberger, P.H., & Kruger, P. (1996). Zurich, Groningen
35. Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., & Klein, M. L. (1983). The Journal of Chemical Physics, 79, 926.
36. Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., DiNola, A., & Haak, J. R. (1984). The Journal of Chemical Physics, 81, 3684-3690.
37. Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., & Pedersen, L. G. (1995). The Journal of Chemical Physics, 103, 8577-8593.
38. Case, D.A., Pearlman, D.A., Caldwell, J.W., Wang, J., Ross, W.S., Simmerling, T.A., et al. (2002). San Francisco, CA, University of California
39. Baker, E. N., & Hubbard, R. E. (1984). Progress in Biophysics and Molecular Biology, 44, 97-179.
40. Halperin, I., Ma, B., Wolfson, H., & Nussinov, R. (2002). Proteins: Structure, Function, and Genetics, 47, 409-443.
41. Janin, J., Henrick, K., Moult, J., Eyck, L. T., Sternberg, M. J., Vajda, S., et al. (2003). Proteins: Structure, Function, and Genetics, 52, 2-9.
42. Dominguez, C., Boelens, R., & Bonvin, A. M. (2003). Journal of the American Chemical Society, 125, 1731-1737.
43. Teng, S., Madej, T., Panchenko, A., & Alexov, E. (2009). Biophysical Journal, 96(6), 2178-2188.
44. Zhang, Z., Norris, J., Schwartz, C., & Alexov, E. (2011). PLoS One, 6(5), e2037.
45. Garcia, A. E. (1992). Physical Review Letters, 68, 2696-2699.
46. Cui, Q., & Bahar, I. (2006). Chapman & Hall/CRC. FL: Boca Raton.
47. Pimentel, G.C., & McClellan, A.L. (1960). Freeman: San Francisco
48. Desiraju, G., & Steiner, T. (1999). Oxford University Press: Oxford
49. Schuster, P., Zundel, G., & Sandorfy, C. (1976). Elsevier Science Publishing. Amsterdam: North-Holland.
50. Gerlt, J. A., Kreevoy, M. M., Cleland, W. W., & Frey, P. A. (1997). Chemistry and Biology, 4, 259-267.
51. Becker, O., Mackerell, A., Roux, B., Watanabe, M., & Eds. (2001). Computational Biochemistry & Biophysics, Marcel Dekker, New York
52. Eisenberg, D., & McClachlan, A. (1986). Nature, 319, 199-203.
53. Wesson, L., & Eisenberg, D. (1992). Protection Science, 1(2), 227-235.
54. Fraternali, F., & van Gunsteren, W. (1996). Journal of Molecular Biology, 256, 939-948.
55. Ferrara, P., Apostolakis, J., & Caflisch, A. (2002). Proteins, 46, 24-33.
56. Koehl, P., & Delarue, M. (1994). Proteins, 20, 264-278.
57. Bradbury, P. A., Kulke, M. H., Heist, R. S., Zhou, W., Ma, C., Xu, W., et al. (2009). Pharmacogenet Genomics, 19(8), 613-25.
58. Bradbury, P. A., Kulke, M. H., Heist, R. S., Zhou, W., Ma, C., Xu, W., et al. (2009). Pharmacogenetics and Genomics, 19(8), 613-625.
59. Giovannetti, E., Pacetti, P., Reni, M., Leon, L. G., Mambrini, A., Vasile, E., et al. (2011). Pharmacogenomics, 12, 1641-1652.
60. Wang, Z., & Moult, J. (2001). Human Mutation, 17, 263-270.
61. George Priya Doss, C., Sudandiradoss, C., Rajasekaran, R., Purohit, R., Ramanathan, K., & Sethumadhavan, R. (2008). Journal of Biomedical Informatics, 41, 607-612.
62. Nagasundaram, N., & Priya Doss, C. G. (2011). Journal Carcinogenesis, 10, 26.
63. Doss, C. G., & Nagasundaram, N. (2012). PLoS One, 7(2), e31677.
64. Mohamed, A. J., Yu, L., Backesjo, C. M., Vargas, L., & Faryal, R. (2009). Immunological Reviews, 228, 58-73.
65. Muller, C. W., Schlauderer, G. J., Reinstein, J., & Schulz, G. E. (1996). Structure, 4, 147-156.
66. Vihinen, M. (1987). Protein Engineering, 1, 477-480.
67. Bikadi, Z., Demko, L., & Hazai, E. (2007). Archives of Biochemistry and Biophysics, 461, 225-234.
68. Ahmad, S., Gromiha, M. M., & Sarai, A. (2004). Bioinformatics, 20, 477-486.
69. International HapMap Consortium. (2005). Nature, 27,437(7063).
70. Collins, F. S., Guyer, M. S., & Charkravarti, A. (1997). Science, 278, 1580-1581.