Relationship between a point mutation S97C in CK1δ protein and its affect on ATP-binding affinity

Journal of Biomolecular Structure and Dynamics

Volumn 32, Issue 3, 2014, Pages 394-405

  Kumar, Ambuj ^a   Rajendran, Vidya ^a   Sethumadhavan, Rao ^a   Purohit, Rituraj ^a,b  

^a VIT UNIVERSITY   (India)

^b Human Genetics Foundation   (Italy)

Author keywords

Cancer; centrosome; CK1 ; kinesin homology domain; molecular dynamics simulation

Indexed keywords

ADENOSINE TRIPHOSPHATE; CASEIN KINASE IDELTA;

ARTICLE; BINDING AFFINITY; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; ENZYME CONFORMATION; HYDROGEN BOND; MOLECULAR DOCKING; MOLECULAR DYNAMICS; MOLECULAR MECHANICS; POINT MUTATION; PRINCIPAL COMPONENT ANALYSIS; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN PROTEIN INTERACTION; STRUCTURE ANALYSIS;

ADENOSINE TRIPHOSPHATE; BREAST NEOPLASMS; CARCINOMA, DUCTAL, BREAST; CASEIN KINASE IDELTA; COMPUTER SIMULATION; CYSTEINE; FEMALE; HUMANS; MOLECULAR DOCKING SIMULATION; MOLECULAR DYNAMICS SIMULATION; POINT MUTATION; SERINE; SIGNAL TRANSDUCTION;

EID: 84892966839     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.2013.770373     Document Type: Article

References (41)

1. Amadei, A., Linssen, A. B., & Berendsen, H. J. (1993). Essential dynamics of proteins. Proteins, 17, 412-425.
2. Behrend, L., Stöter, M., Kurth, M., Rutter, G., Heukeshoven, J., Deppert, W., & Knippschild, U. (2000). Interaction of casein kinase 1 delta (CK1delta) with post-Golgi structures, microtubules and the spindle apparatus. European Journal of Cell Biology, 79, 240-251.
3. Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., Dinola, A., & Haak, J. R. (1984). Molecular dynamics with coupling to an external bath. Journal of Chemical Physics, 8, 3684-3690.
4. Berman, H. M., Battistuz, T., Bhat, T. N., Bluhm, W. F., Bourne, P. E., Burkhardt, K., Zardecki, C. (2002). The protein data bank. Acta Crystallographica. Section D, Biological Crystallography, 58, 899-907.
5. Brockschmidt, C., Hirner, H., Huber, N., Eismann, T., Hillenbrand, A., Giamas, G., & Knippschild, U. (2008). Anti-apoptotic and growth-stimulatory functions of CK1 delta and epsilon in ductal adenocarcinoma of the pancreas are inhibited by IC261 in vitro and in vivo. Gut, 57, 799-806.
6. Cheatham III, T.E., Miller, J. L., Fox, T., Darden, T. A., & Kollman, P. A. (1995). Molecular dynamics simulations on solvated biomolecular systems: The particle mesh Ewald method leads to stable trajectories of DNA, RNA, and proteins. Journal of the American Chemical Society, 14, 4193-4194.
7. Dundas, J., Ouyang, Z., Tseng, J., Binkowski, A., Turpaz, Y., et al. (2006). CASTp: Computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues. Nucleic Acids Research, 34, W116-W118.
8. Frierson, H. F.Jr., El-Naggar, A. K., Welsh, J. B., Sapinoso, L. M., Su, A. I., et al. (2002). Large scale molecular analysis identifies genes with altered expression in salivary adenoid cystic carcinoma. American Journal of Pathology, 161, 1315-1323.
9. Grueneberg, D. A., Degot, S., Pearlberg, J., Li, W., Davies, J. E., et al. (2008). Kinase requirements in human cells: I. Comparing kinase requirements across various cell types. Proceedings of the National Academy Science USA, 105, 16472-16477.
10. Guex, N., & Peitsch, M. C. (1997). SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling. Electrophoresis, 18, 2714-2723.
11. Hess, B., Kutzner, C., van der Spoel, D., & Lindahl, E. (2008). GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. Journal of Chemical Theory and Computation, 4, 435-447.
12. Hirner, H., Günes, C., Bischof, J., Wolff, S., Grothey, A., Kühl, M., Knippschild, U. (2012). Impaired CK1 delta activity attenuates SV40-induced cellular transformation in vitro and mouse mammary carcinogenesis in vivo. PLoS One, 7, e29709.
13. Kamaraj, B., & Purohit, R. (2013). Mutational analysis of TYR gene and its structural consequences in OCA1A. Gene, 513 (1), 184-195.
14. Knippschild, U., Gocht, A., Wolff, S., Huber, N., Löhler, J., & Stöter, M. (2005a). The casein kinase 1 family: Participation in multiple cellular processes in eukaryotes. Cellular Signalling, 17, 675-689.
15. Knippschild, U., Wolff, S., Giamas, G., Brockschmidt, C., Wittau, M., Würl, P. U., Stöter, M. (2005b). The role of the casein kinase 1 (CK1) family in different signaling pathways linked to cancer development. Onkologie, 28, 508-514.
16. Kumar, A., & Purohit, R. (2012a). Computational investigation of pathogenic nsSNPs in CEP63 protein. Gene, 503, 75-82.
17. Kumar, A., & Purohit, R. (2012b). Computational screening and molecular dynamics simulation of disease associated nsSNPs in CENP-E. Mutation Research, 738-739, 28-37.
18. Kumar, A., & Purohit, R. (2012c). Computational centrosomics: An approach to understand the dynamic behaviour of centrosome. Gene, 511(1), 125-126.
19. Li, D., Herrera, S., Bubula, N., Nikitina, E., Palmer, A. A., et al. (2011). Casein kinase 1 enables nucleus accumbens amphetamine-induced locomotion by regulating AMPA receptor phosphorylation. Journal of Neurochemistry, 118, 237-247.
20. Long, A., Zhao, H., & Huang, X. (2011). Structural basis for the interaction between casein kinase 1 delta and a potent and selective inhibitor. Journal of Medicinal Chemistry, 55, 956-960.
21. Manning, G., Whyte, D. B., Martinez, R., Hunter, T., & Sudarsanam, S. (2002). The protein kinase complement of the human genome. Science, 298, 1912-1934.
22. Mashiach, E., Schneidman-Duhovny, D., Peri, A., Shavit, Y., Nussinov, R., & Wolfson, H. J. (2010). An integrated suite of fast docking algorithms. Proteins, 78, 3197-3204.
23. Milne, D. M., Looby, P., & Meek, D. W. (2001). Catalytic activity of protein kinase CK1 delta (casein kinase 1delta) is essential for its normal subcellular localization. Experimental Cell Research, 263, 43-54.
24. Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., et al. (2009). AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry, 30, 2785-2791.
25. Okamura, A., Iwata, N., Nagata, A., Tamekane, A., Shimoyama, M., et al. (2004). Involvement of casein kinase Iepsilon in cytokine-induced granulocytic differentiation. Blood, 103, 2997-3004.
26. Price, M. A. (2006). CKI, there's more than one: Casein kinase I family members in Wnt and Hedgehog signaling. Genes and Development, 20, 399-410.
27. Purohit, R., Rajasekaran, R., Sudandiradoss, C., George Priya Doss, C., Ramanathan, K., & Sethumadhavan, R. (2008). Studies on flexibility and binding affinity of Asp25 of HIV-1 protease mutants. International Journal of Biological Macromolecules, 42, 386-391.
28. Purohit, R., Rajendran, V., & Sethumadhavan, R. (2011). Relationship between mutation of serineresidue at 315th position in M. tuberculosis catalase-peroxidase enzyme and isoniazidsusceptibility: An in silico analysis. Journal of Molecular Modeling, 17, 869-877.
29. Purohit, R., Rajendran, V., & Sethumadhavan, R. (2011). Studies on adaptability of binding residues and flap region of TMC-114 resistance HIV-1 protease mutants. Journal of Biomolecular Structure & Dynamics, 29, 137-152.
30. Purohit, R., & Sethumadhavan, R. (2009). Structural basis for the resilience of Darunavir (TMC114) resistance major flap mutations of HIV-1 protease. Interdisciplinary Science, 1, 320-328.
31. Rajendran, V., Purohit, R., & Sethumadhavan, R. (2012). In silico investigation of molecular mechanism of laminopathy cause by a point mutation (R482W) in lamin A/C protein. Amino Acids, 43, 603-615.
32. Rajendran, V., & Sethumadhavan, R. (2012). Drug resistance mechanism of PncA in mycobacterium tuberculosis. Journal of Biomolecular Structure & Dynamics. doi:10.1080/07391102.2012.759885
33. Roof, D. M., Meluh, P. B., & Rose, M. D. (1992). Kinesinrelated proteins required for assembly of the mitotic spindle. Journal of Cell Biology, 118, 95-108.
34. Schwab, C., DeMaggio, A. J., Ghoshal, N., Binder, L. I., Kuret, J., & McGeer, P. L. (2000). Casein kinase 1 delta is associated with pathological accumulation of tau in several neurodegenerative diseases. Neurobiology of Aging, 21, 503-510.
35. Sillibourne, J. E., Milne, D. M., Takahashi, M., Ono, Y., & Meek, D. W. (2002). Centrosomal anchoring of the protein kinase CK1delta mediated by attachment to the large, coiled-coil scaffolding protein CG-NAP/AKAP450. Journal of Molecular Biology, 322, 785-797.
36. Sjöblom, T., Jones, S., Wood, L. D., Parsons, D. W., Lin, J., et al. (2006). The consensus coding sequences of human breast and colorectal cancers. Science, 314, 268-274.
37. Stöter, M., Bamberger, A. M., Aslan, B., Kurth, M., Speidel, D., Löning, T., Frank, H. G., Knippschild, U. (2005). Inhibition of casein kinase I delta alters mitotic spindle formation and induces apoptosis in trophoblast cells. Oncogene, 24, 7964-7975.
38. Vielhaber, E., & Virshup, D. M. (2011). Casein kinase I: From obscurity to center stage. IUBMB Life, 51, 73-78.
39. Virshup, D. M., Eide, E. J., Forger, D. B., Gallego, M., & Harnish, E. V. (2007). Reversible protein phosphorylation regulates circadian rhythms. Cold Spring Harbor Symposia on Quantitative Biology, 72, 413-420.
40. Xu, R. M., Carmel, G., Sweet, R. M., Kuret, J., & Cheng, X. (1995). Crystal structure of casein kinase-1, a phosphate-directed protein kinase. EMBO Journal, 14, 1015-1023.
41. Zyss, D., Ebrahimi, H., & Gergely, F. (2011). Casein kinase I delta controls centrosome positioning during T cell activation. Journal of Cell Biology, 195, 781-797.