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Protein Phosphatase 1D (PPM1D) Structure Prediction Using Homology Modeling
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  • Journal title : Journal of the Chosun Natural Science
  • Volume 9, Issue 1,  2016, pp.35-40
  • Publisher : The Research Institute of Chosun Natural Science
  • DOI : 10.13160/ricns.2016.9.1.35
 Title & Authors
Protein Phosphatase 1D (PPM1D) Structure Prediction Using Homology Modeling
Nagarajan, Santhosh Kumar; Madhavan, Thirumurthy;
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Protein phosphatase manganese dependent 1D (PPM1D) is one of the Ser/Thr protein phosphatases belongs to the PP2C family. They play an important role in cancer tumorigenesis of various tumors including neuroblastoma, pancreatic adenocarcinoma, medulloblastoma, breast cancer, prostate cancer and ovarian cancer. Even though PPM1D is involved in the pathophysiology of various tumors, the three dimensional protein structure is still unknown. Hence in the present study, homology modelling of PPM1D was performed. 20 different models were modelled using single- and multiple-template based homology modelling and validated using different techniques. Best models were selected based on the validation. Three models were selected and found to have similar structures. The predicted models may be useful as a tool in studying the pathophysiological role of PPM1D.
PPM1D;WIP1;PP2C;Homology Modelling;
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조선자연과학논문집, 2016. vol.9. 4, pp.234-240 crossref(new window)
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X. Lu, T. A. Nguyen, S. H. Moon, Y. Darlington, M. Sommer, and L. A. Donehower, "The type 2C phosphatase Wip1: an oncogenic regulator of tumor suppressor and DNA damage response pathways", Cancer Metast. Rev., Vol. 27, pp. 123-135, 2008. crossref(new window)

H. Yang, X. Y. Gao, P. Li, and T. S. Jiang, "PPM1D overexpression predicts poor prognosis in non-small cell lung cancer", Tumor Biol., Vol. 36, pp. 2179-2184, 2015. crossref(new window)

F. Saito-Ohara, I. Imoto, J. Inoue, H. Hosoi, A. Nakagawara, T. Sugimoto, J. Inazawa, "PPM1D is a potential target for 17q gain in neuroblastoma", Cancer Res., Vol. 63, pp. 1876-1883, 2003.

P. Loukopoulos, T. Shibata, H. Katoh, A. Kokubu, M. Sakamoto, K. Yamazaki, T. Kosuge, Y. Kanai, F. Hosoda, I. Imoto, M. Ohki, J. Inazawa, and S. Hirohashi, "Genome-wide array-based comparative genomic hybridization analysis of pancreatic adenocarcinoma: identification of genetic indicators that predict patient outcome", Cancer Sci., vol. 98, pp. 392-400, 2007. crossref(new window)

R. C. Castellino, M. D. Bortoli, X. Lu, S. H. Moon, T. A. Nguyen, M. A. Shepard, P. H. Rao, L. A. Donehower, and J. Y. Kim, "Medulloblastomas overexpress the p53-inactivating oncogene WIP1/PPM1D", J. Neuro-oncol., Vol. 86, pp. 245-256, 2008. crossref(new window)

M. B. Lambros, R. Natrajan, F. C. Geyer, M. A. Lopez-Garcia, K. J. Dedes, K. Savage, M. Lacroix-Triki, R. L. Jones, C. J. Lord, S. Linardopoulos, A. Ashworth, and J. S. Reis-Filho, "PPM1D gene amplification and overexpression in breast cancer: a qRT-PCR and chromogenic in situ hybridization study", Modern Pathol., Vol. 23, pp. 1334-1345, 2010. crossref(new window)

J. Parssinen, E. L. Alarmo, S. Khan, R. Karhu, M. Vihinen, and A. Kallioniemi, "Identification of differentially expressed genes after PPM1D silencing in breast cancer", Cancer Lett., Vol. 259, pp. 61-70, 2008. crossref(new window)

S. Shreeram, O. N. Demidov, W. K. Hee, H. Yamaguchi, N. Onishi, C. Kek, O. N. Timofeev, C. Dudgeon, A. J. Fornace, C. W. Anderson, Y. Minami, E. Appella, and D. V. Bulavin, "Wip1 phosphatase modulates ATM-dependent signaling pathways", Mol. Cell, Vol. 23, pp. 757-764, 2006. crossref(new window)

L. Jiao, D. Shen, G. Liu, J. Jia, J. Geng, H. Wang, and Y. Sun, "PPM1D as a novel biomarker for prostate cancer after radical prostatectomy", Anticancer Res., Vol. 34, No. 2919-2925, 2014.

G. C. Baker, J. J. Smith, and D. A. Cowan. "Review and re-analysis of domain-specific 16S primers", J. Microbiol. Meth., Vol. 55, pp. 541-555, 2003. crossref(new window)

S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, "Basic local alignment search tool", J. Mol. Biol., Vol. 215, pp. 403-410, 1990. crossref(new window)

H. M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, and P. E. Bourne, "The protein data bank", Nucleic Acids Res., Vol. 28, pp. 235-242, 2000. crossref(new window)

M. Shalini and T. Madhavan, "Homology modeling of CCR 4: Novel therapeutic target and preferential maker for Th2 cells", J. Chosun Natural Sci., Vol. 7, pp. 234-240, 2014. crossref(new window)

B. Sathya and T. Madhavan, "Homology modeling of cysteinyl leukotriene1 receptor", J. Chosun Natural Sci., Vol. 8, pp. 13-18, 2015. crossref(new window)

S. K. Nagarajan, and T. Madhavan, "3D structure prediction of thromboxane A2 receptor by homology modeling", J. Chosun Natural Sci., Vol. 8, pp. 75-79, 2015. crossref(new window)

B. K Kuntal, P. Aparoy, and P. Reddanna, "Easy-Modeller: A graphical interface to MODELLER", BMC Research Notes, Vol. 3, pp. 226, 2010. crossref(new window)

N. Eswar, M. A. Marti-Renom, B. Webb, M. S. Madhusudhan, D. Eramian, M. Shen, U. Pieper, and A. Sali, "Comparative protein structure modeling With MODELLER", Current Protocols in Bioinformatics, New York: John Wiley & Sons, Inc., pp. 5.6.1-5.6.30, 2006.

S. C. Lovell, I. W. Davis, W. B. Arendall III, P. I. W. de Bakker, J. M. Word, M. G. Prisant, J. S. Richardson, and D. C. Richardson, "Structure validation by $C{\alpha}$ geometry: ${\phi}$, ${\psi}$ and $C{\beta}$ deviation", Proteins., Vol. 50, pp. 437-450, 2002.

J. U. Bowie, R. Luthy, D. Eisenberg, "A method to identify protein sequences that fold into a known three-dimensional structure", Science, Vol. 253, pp. 164-170, 1991. crossref(new window)

J. D. Thompson, D. G. Higgins, and T. J. Gibson, "CLUSTAL W: improving the sensitivity of progressive equence weighting, position-specific gap penalties and weight matrix choice", Nucleic Acids Res., Vol. 22, pp. 4673-4680, 1994. crossref(new window)