Computational investigation of pathogenic nsSNPs in CEP63 protein

Gene

Volumn 503, Issue 1, 2012, Pages 75-82

  Kumar, Ambuj ^a   Purohit, Rituraj ^a  

^a VIT UNIVERSITY   (India)

Author keywords

Aneuploidy; Cancer; CEP63; Molecular dynamics simulation; Single nucleotide polymorphism

Indexed keywords

CEP63 PROTEIN; CYTOPLASM PROTEIN; HYDROGEN; PROLINE; UNCLASSIFIED DRUG;

ALLELE; ANEUPLOIDY; ARTICLE; CENTROSOME; DISEASE ASSOCIATION; GENETIC CODE; HYDROGEN BOND; MATHEMATICAL ANALYSIS; MOLECULAR DYNAMICS; MOLECULAR MODEL; MUTANT; NONSYNONYMOUS SINGLE NUCLEOTIDE POLYMORPHISM; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM;

AMINO ACID SEQUENCE; ANEUPLOIDY; CENTROSOME; COMPUTER SIMULATION; DATABASES, GENETIC; GENETIC PREDISPOSITION TO DISEASE; HUMANS; MOLECULAR SEQUENCE DATA; NEOPLASM PROTEINS; POLYMORPHISM, SINGLE NUCLEOTIDE; PROTEIN CONFORMATION;

EID: 84861790146     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2012.04.032     Document Type: Article

References (64)

1. Altschul S.F., et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25:3389-3402.
2. Amadei A., Linssen A.B., Berendsen H.J. Essential dynamics of proteins. Proteins 1993, 17:412-425.
3. Becchis M., et al. The additionally glycosylated variant of human sex hormone-binding globulin (SHBG) is linked to estrogen-dependence of breast cancer. Breast Cancer Res. Treat. 1999, 54:101-107.
4. Berendsen H.J.C., Postma J.P.M., van Gunsteren W.F., Dinola A., Haak J.R. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 1984, 8:3684-3690.
5. Berman, et al. The Protein Data Bank. Acta. Crystallogr. D. Biol. Crystallogr. 2002, 58:899-907.
6. Bettencourt-Dias M., Glover D.M. Centrosome biogenesis and function: centrosomics brings new understanding. Nat. Rev. Mol. Cell Biol. 2007, 8:451-463.
7. Bourke E., et al. DNA damage induces Chk1-dependent centrosome amplification. EMBO Rep. 2007, 8:603-609.
8. Buim M.E., Soares F.A., Sarkis A.S., Nagai M.A. The transcripts of SFRP1, CEP63 and EIF4G2 genes are frequently downregulated in transitional cell carcinomas of the bladder. Oncology 2005, 69:445-454.
9. Calabrese R., Capriotti E., Fariselli P., Martelli P.L., Casadio R. Functional annotations improve the predictive score of human disease-related mutations in proteins. Hum. Mutat. 2009, 30:1237-1244.
10. Capriotti E., Calabrese R., Casadio R. Predicting the insurgence of human genetic diseases associated to single point protein mutations with support vector machines and evolutionary information. Bioinformatics 2006, 22:2729-2734.
11. Carvalho M.A., et al. Determination of cancer risk associated with germ line BRCA1 missense variants by functional analysis. Cancer Res. 2007, 67:1494-1501.
12. Carvalho M., et al. Analysis of a set of missense, frameshift, and in-frame deletion variants of BRCA1. Mutat. Res. 2009, 660:1-11.
13. Cheatham T.E., Miller J.L., Fox T., Darden T.A., Kollman P.A. Molecular dynamics simulations on solvated biomolecular systems: the particle mesh Ewald method leads to stable trajectories of DNA, RNA, and proteins. J. Am. Chem. Soc. 1995, 14:4193-4194.
14. Chen S., et al. Cyclin-dependent kinases regulate epigenetic gene silencing through phosphorylation of EZH2. Nat. Cell Biol. 2010, 12:1108-1114.
15. Dai W., Cogswell J.P. Polo-like kinases and the microtubule organization center: targets for cancer therapies. Prog. Cell. Cycle. Res. 2003, 5:327-334.
16. Darden T., York D., Pedersen L. Particle mesh Ewald: an N·log(N) method for Ewald sums in large systems. J. Chem. Phys. 1993, 12:10089-10092.
17. Dodson H., Bourke E., Jeffers L.J., Vagnarelli P., Sonoda E., Takeda S., et al. Centrosome amplification induced by DNA damage occurs during a prolonged G2 phase and involves ATM. EMBO J. 2004, 23:3864-3873.
18. Doxsey S., Zimmerman W., Mikule K. Centrosome control of the cell cycle. Trends. Cell Biol. 2005, 15:303-311.
19. Duensing A., Liu Y., Tseng M., Malumbres M., Barbacid M., Duensing S. Cyclin-dependent kinase 2 is dispensable for normal centrosome duplication but required for oncogene-induced centrosome overduplication. Oncogene 2006, 25:2943-2949.
20. Ganem N.J., Godinho S.A., Pellman D. A mechanism linking extra centrosomes to chromosomal instability. Nature 2009, 460:278-282.
21. Goldgar D.E., Easton D.F., Deffenbaugh A.M., Monteiro A.N., Tavtigian S.V., Couch F.J. Integrated evaluation of DNA sequence variants of unknown clinical significance: application to BRCA1 and BRCA2. Am. J. Hum. Genet. 2004, 75:535-544.
22. Hess B., Bekker H., Berendsen H.J.C., Fraaije J.G.E.M. LINCS: a linear constraint solver for molecular simulations. J. Comput. Chem. 1997, 12:1463-1472.
23. Hess B., Kutzner C., van der Spoel D., Lindahl E. GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J. Chem. Theory Comput. 2008, 4:435-447.
24. Hu X., Moscinski L.C. Cdc2: a monopotent or pluripotent CDK?. Cell Prolif. 2011, 44:205-211.
25. Jackman M., Lindon C., Nigg E.A., Pines J. Active cyclin B1-Cdk1 first appears on centrosomes in prophase. Nat. Cell Biol. 2003, 5:143-148.
26. Kaplan W., Littlejohn T.G. Swiss-PDB viewer (Deep View). Brief. Bioinform. 2001, 2:195-197.
27. Karchin R. Next generation tools for the annotation of human SNPs. Brief. Bioinform. 2009, 10:35-52.
28. 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.
29. Laskowski R.A., MacArthur M.W., Moss D.S., Thornton J.M. PROCHECK-a program to check the stereochemical quality of protein structures. J. Appl. Cryst. 1993, 26:283-291.
30. Leber B., Maier B., Fuchs F., Chi J., Riffel P., Anderhub S., et al. Proteins required for centrosome clustering in cancer cells. Sci. Transl. Med. 2010, 2:33ra88.
31. Leonardi E., Martella M., Tosatto S.C., Murgia A. Identification and in silico analysis of novel von Hippel-Lindau (VHL) gene variants from a large population. Ann. Hum. Genet. 2011, 75:483-496.
32. Li B., Krishnan V.G., Mort M.E., Xin F., Kamati K.K., Cooper D.N., Mooney S.D., Radivojac P. Automated inference of molecular mechanisms of disease from amino acid substitutions. Bioinformatics 2009, 25:2744-2750.
33. Löffler H., Lukas J., Bartek J., Krämer A. Structure meets function centrosomes, genome maintenance and the DNA damage response. Exp. Cell Res. 2006, 312:2633-2640.
34. Löffler H., et al. Cep63 recruits Cdk1 to the centrosome: implications for regulation of mitotic entry, centrosome amplification, and genome maintenance. Cancer Res. 2011, 71:2129-2139.
35. Lupas A., Van Dyke M., Stock J. Predicting coiled coils from protein sequences. Science 1991, 252:1162-1164.
36. Marti-Renom M.A., Stuart A.C., Fiser A., Sánchez R., Melo F., Sali A. Comparative protein structure modeling of genes and genomes. Annu. Rev. Biophys. Biomol. Struct. 2000, 29:291-325.
37. Matthess Y., Raab M., Sanhaji M., Lavrik I.N., Strebhardt K. Cdk1/cyclin B1 controls Fas-mediated apoptosis by regulating caspase-8 activity. Mol. Cell. Biol. 2010, 30:5726-5740.
38. Meraldi P., Honda R., Nigg E.A. Aurora-A overexpression reveals tetraploidization as a major route to centrosome amplification in p53À/À cells. EMBO J. 2002, 21:483-492.
39. Mooney S. Bioinformatics approaches and resources for single nucleotide polymorphism functional analysis. Brief. Bioinform. 2005, 6:44-56.
40. Nakamura A., Naito M., Arai H., Fujita N. Mitotic phosphorylation of Aki1 at Ser208 by cyclin B1-Cdk1 complex. Biochem. Biophys. Res. Commun. 2010, 393:872-876.
41. Ng P.C., Henikoff S. Predicting the effects of amino acid substitutions on protein function. Annu. Rev. Genomics Hum. Genet. 2006, 7:61-80.
42. Parrinello M., Rahman A. Crystal structure and pair potentials: a molecular-dynamics study. Phys. Rev. Lett. 1980, 45:1196-1199.
43. 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.
44. Purohit R., Rajasekaran R., Sudandiradoss C., George Priya Doss C., Ramanathan K., Sethumadhavan R. Studies on flexibility and binding affinity of Asp25 of HIV-1 protease mutants. Int. J. Biol. Macromol. 2008, 42:386-391.
45. 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.
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. Quintyne N.J., Reing J.E., Hoffelder D.R., Gollin S.M., Saunders W.S. Spindle multipolarity is prevented by centrosomal clustering. Science 2005, 307:127-129.
48. 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 2011, 10.1007/s00726-011-1108-7.
49. Ramensky V., Bork P., Sunyaev S. Human non-synonymous SNPs: server and survey. Nucleic Acids Res. 2002, 30:3894-3900.
50. Savas S., Ahmad M.F., Shariff M., Kim D.Y., Ozcelik H. Candidate nsSNPs that can affect the functions and interactions of cell cycle proteins. Proteins 2005, 58:697-705.
51. Sharma A., et al. Genetic association, post-translational modification, and protein-protein interactions in Type 2 diabetes mellitus. Mol. Cell. Proteomics 2005, 4:1029-1037.
52. Shen J., Deininger P.L., Zhao H. Applications of computational algorithm tools to identify functional SNPs in cytokine genes. Cytokine 2006, 35:62-66.
53. Sherry S.T., et al. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001, 29:308-311.
54. Sir J.H., Barr A.R., Nicholas A.K. A primary microcephaly protein complex forms a ring around parental centrioles. Nat. Genet. 2011, 43:1147-1153.
55. Smith E., Dejsuphong D., Balestrini A. An ATM- and ATR-dependent checkpoint inactivates spindle assembly by targeting CEP63. Nat. Cell Biol. 2009, 11:278-285.
56. Steward R.E., MacArthur M.W., Laskowski R.A., Thornton J.M. Molecular basis of inherited diseases: a structural perspective. Trends Genet. 2003, 19:505-513.
57. Takada S., Kelkar A., Theurkauf W.E. Drosophila checkpoint kinase 2 couples centrosome function and spindle assembly to genomic integrity. Cell 2003, 113:87-99.
58. Terrano Upreti M., Chambers T.C. Cyclin-dependent kinase 1-mediated Bcl-xL/Bcl-2 phosphorylation acts as a functional link coupling mitotic arrest and apoptosis. Mol. Cell. Biol. 2010, 30:640-656.
59. Tsukahara T., Tanno Y., Watanabe Y. Phosphorylation of the CPC by Cdk1 promotes chromosome bi-orientation. Nature 2010, 467:719-723.
60. Vogt G., Chapgier A., Yang K. Gains of glycosylation comprise an unexpectedly large group of pathogenic mutations. Nat. Genet. 2005, 37:692-700.
61. Waite A., De Rosa M.C., Brancaccio A., Blake D.J. A gain-of-glycosylation mutation associated with myoclonus-dystonia syndrome affects trafficking and processing of mouse ε-sarcoglycan in the late secretory pathway. Hum. Mutat. 2011, 32:1246-1258.
62. 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:W407-W410.
63. Zhang X., Chen Q., Feng J. Sequential phosphorylation of Nedd1 by Cdk1 and Plk1 is required for targeting of the gammaTuRC to the centrosome. J. Cell Sci. 2009, 122:2240-2251.
64. Zyss D., Gergely F. Centrosome function in cancer: guilty or innocent?. Trends Cell Biol. 2009, 19:334-346.