Tertiary structure prediction and identification of druggable pocket in the cancer biomarker - Osteopontin-c

Journal of Diabetes and Metabolic Disorders

Volumn 13, Issue 1, 2014, Pages

  Sivakumar, Subramaniam ^a,b   Niranjali Devaraj, Sivasitambaram ^b  

^a SRI SANKARA ARTS AND SCIENCE COLLEGE   (India)

^b UNIVERSITY OF MADRAS   (India)

Author keywords

[No Author keywords available]

Indexed keywords

FIBRONECTIN; HERMES ANTIGEN; OSTEOPONTIN; OSTEOPONTIN C; TUMOR MARKER; UNCLASSIFIED DRUG;

AB INITIO CALCULATION; ARTICLE; BINDING SITE; BREAST CANCER; COMPUTER PREDICTION; INFORMATION SERVICE; MOLECULAR DOCKING; MOLECULAR DYNAMICS; NUCLEOTIDE SEQUENCE; PROTEIN EXPRESSION; PROTEIN TERTIARY STRUCTURE; SEQUENCE ANALYSIS;

EID: 84908114976     PISSN: None     EISSN: 22516581     Source Type: Journal    
DOI: 10.1186/2251-6581-13-13     Document Type: Article

References (72)

1. Berns EM, Foekens JA, van Putten WL, van Staveren IL, Portengen H, De Koning WC, Klijn JG. Prognostic factors in human primary breast cancer: comparison of c-myc and HER2/neu amplification. J Steroid Biochem Mol Biol 1992, 43(1-3):13-19.
2. Rangaswami H, Bulbule A, Kundu GC. Osteopontin: role in cell signaling and cancer progression. TRENDS Cell Biol 2006, 16(2):79-87. 10.1016/j.tcb.2005.12.005, 16406521.
3. Gupta GP, Massague J. Cancer metastatsis: building a framework. Cell 2006, 127:679-695. 10.1016/j.cell.2006.11.001, 17110329.
4. Woodhouse EC, Chuaqui RF, Liotta LA. General mechanisms of metastasis. Cancer 1997, 80:1529-1537. 10.1002/(SICI)1097-0142(19971015)80:8+<1529::AID-CNCR2>3.0.CO;2-F, 9362419.
5. Rodrigues LR, Teixeira JA, Schmitt FL, Paulsson M, Lindmark-Mansson H. The role of osteopontin in tumor progression and metastasis in breast cancer. Cancer Epidemiol Biomarkers Prev 2007, 16(6):1087-1097. 10.1158/1055-9965.EPI-06-1008, 17548669.
6. Wai PY, Kuo PC. Osteopontin: regulation in tumor metastasis. Cancer Metastasis Rev 2008, 27:103-118. 10.1007/s10555-007-9104-9, 18049863.
7. Song G, Cai QF, Mao YB, Ming YL, Bao SD, Ouyang GL. Osteopontin promotes ovarian cancer progression and cell survival and increases HIF-1alpha expression through the PI3-K/Akt pathway. Cancer Sci 2008, 99(10):1901-1907.
8. Song G, Ouyang G, Mao Y, Ming Y, Bao S, Hu T. Osteopontin promotes gastric cancer metastasis by augmenting cell survival and invasion through Akt-mediated HIF-1alpha up-regulation and MMP9 activation. J Cell Mol Med 2009, 13:1706-1718. 10.1111/j.1582-4934.2008.00540.x, 19602039.
9. Courter D, Cao H, Kwok S, Kong C, Banh A, Kuo P, Bouley DM, Vice C, Brustugun OT, Denko NC, Koong AC, Giaccia A, Le Q-T. The RGD domain of human osteopontin promotes tumor growth and metastasis through activation of survival pathways. PLoS One 2010, 5:e9633. 10.1371/journal.pone.0009633, 2835762, 20224789.
10. Beausoleil MS, Schulze EB, Goodale D, Postenka CO, Allan AL. Deletion of the thrombin cleavage domain of osteopontin mediates breast cancer cell adhesion, proteolytic activity, tumorgenicity, and metastasis. BMC Cancer 2011, 11:25. 10.1186/1471-2407-11-25, 3034707, 21247495.
11. Chakraborty G, Jain S, Behera R, Ahmed M, Sharma P, Kumar V, Kundu GC. The multifaceted roles of osteopontin in cell signaling, tumor progression and angiogenesis. Curr Mol Me 2006, 6(8):819-830.
12. Young MF, Kerr JM, Termine JD, Wewer UM, Wang MG, McBride OW, Fisher LW. cDNA cloning, mRNA distribution and heterogeneity, chromosomal location, and RFLP analysis of human osteopontin (OPN). Genomics 1990, 7:491-502. 10.1016/0888-7543(90)90191-V, 1974876.
13. Mirza M, Shaughnessy E, Hurley JK, Vanpatten KA, Pestano GA, He B, Weber GF. Osteopontin-c is a selective marker of breast cancer. Int J Cancer 2008, 122(4):889-897. 10.1002/ijc.23204, 17960616.
14. He B, Mirza M, Weber GF. An osteopontin splice variant induces anchorage independence in human breast cancer cells. Oncogene 2006, 25(15):2192-2202. 10.1038/sj.onc.1209248, 16288209.
15. Weber GF. Molecular mechanisms of metastasis. Cancer Lett 2008, 270:181-190. 10.1016/j.canlet.2008.04.030, 18522865.
16. Gasteiger E, Gattiker A, Hoogland C, Ivanyi I, Appel RD, Bairoch A. ExPASy: the proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res 2003, 31(13):3784-3788. 10.1093/nar/gkg563, 168970, 12824418.
17. Bendtsen JD, Nielsen H, von Heijne G, Brunak S. Improved prediction of signal peptides: signalP 3.0. J Mol Biol 2004, 340:783-795. 10.1016/j.jmb.2004.05.028, 15223320.
18. Nielsen H, Engelbrecht J, Brunak S, von Heijne G. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng 1997, 10:1-6.
19. Vijayaraj N, Elasri MO. Structure and function predictions of Msa protein in staphylococcus aureus. BMC Bioinforma 2007, 8(suppl 7):S5.
20. Wu S, Skolnick J, Zhang Y. Ab-initio modeling of small proteins by iterative TASSER simulations. BMC Biol 2007, 5:17. 10.1186/1741-7007-5-17, 1878469, 17488521.
21. Laskoswki RA, MacArthur MW, Moss DS, Thorton JM. PROCHECK: a program to check the stereo-chemical quality of protein structures. J Appl Cryst 1993, 26:283-291.
22. Hooft RWW, Vriend G, Sander C, Abola EE. Errors in protein structures. Nature 1996, 381:272-272.
23. Luthy R, Bowie JU, Eisenberg D. Assessment of protein models with three-dimensional profiles. Nature 1992, 356:83-85. 10.1038/356083a0, 1538787.
24. Colovos C, Yeates TO. Verification of protein structures: patterns of nonbonded atomic interactions. Protein Sci 1993, 2:1511-1519. 10.1002/pro.5560020916, 2142462, 8401235.
25. Pontius J, Richelle J, Wodak SJ. Deviations from standard atomic volumes as a quality measure for protein crystal structures. J Mol Biol 1996, 264:121-136. 10.1006/jmbi.1996.0628, 8950272.
26. Summa CM, Levitt M. Near native structure refinement using in vacuo energy minimization. Proc Natl Acad Sci USA 2007, 104(9):3177-3182. 10.1073/pnas.0611593104, 1802011, 17360625.
27. Van Der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJC. GROMACS: fast, flexible, and free. J Comput Chem 2005, 26:1701-1718. 10.1002/jcc.20291, 16211538.
28. 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.
29. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG. ClustalW and ClustalX version 2. Bioinformatics 2007, 23(21):2947-2948. 10.1093/bioinformatics/btm404, 17846036.
30. Comeau SR, Gatchell DW, Vajda S, Camacho CJ. ClusPro: an automated docking and discrimination method for the prediction of protein complexes. Bioinformatics 2004, 20(1):45-50. 10.1093/bioinformatics/btg371, 14693807.
31. Alasdair TR, Jackson L, Jackson RM. Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites. Bioinformatics 2005, 21(9):1908-1916. 10.1093/bioinformatics/bti315, 15701681.
32. Hendlich M, Rippmann F, Barnickel G. LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins. J Mol Graph Model 1997, 15(6):359-363. 10.1016/S1093-3263(98)00002-3, 9704298.
33. Volkamer A, Griewel A, Grombacher T, Rarey M. Analyzing the topology of active sites: on the prediction of pockets and subpockets. J Chem Inf Model 2010, 50(11):2041-2052. 10.1021/ci100241y, 20945875.
34. Volkamer A, Kuhn D, Grombacher T, Rippmann F, Rarey M. Combining global and local measures for structure-based druggability predictions. J Chem Inf Model 2012, 52(2):360-372. 10.1021/ci200454v, 22148551.
35. Schmidtke P, Barril X. Understanding and predicting druggability. A high-throughput method for detection of drug binding sites. J Med Chem 2010, 53(15):5858-5867. 10.1021/jm100574m, 20684613.
36. Columbus L, Peti W, Etezady-Esfarjani T, Herrmann T, Wuthrich K. NMR structure determination of the conserved hypothetical protein TM1816 from Thermotoga maritima. Proteins 2005, 60(3):552-557. 10.1002/prot.20465, 15937903.
37. Pettersson E, Luning B, Mickos H, Heinegard D. Synthesis, NMR and function of an O-phosphorylated peptide, comprising the RGD-adhesion sequence of osteopontin. Acta Chem Scand 1991, 45(6):604-608.
38. Zhang Y. I-TASSER server for protein 3D structure prediction. BMC Bioinforma 2008, 9:40.
39. Wuttke M, Muller S, Nitsche DP, Paulsson M, Hanisch FG, Maurer P. Structural characterization of human recombinant and bone-derived bone sialoprotein. J Biol Chem 2001, 276(39):36839-36848. 10.1074/jbc.M105689200, 11459848.
40. Bellahcene A, Castronovo V, Ogbureke KU, Fisher LW, Fedarko NS. Small integrin-binding ligand N-linked glycoproteins (SIBLINGs): multifunctional proteins in cancer. Nat Rev Cancer 2008, 8(3):212-226. 10.1038/nrc2345, 2484121, 18292776.
41. Fisher LW, Torchia DA, Fohr B, Young MF, Fedarko NS. Flexible structures of SIBLING proteins, bone sialoprotein, and osteopontin. Biochem Biophys Res Commun 2001, 280(2):460-465. 10.1006/bbrc.2000.4146, 11162539.
42. Ganss B, Kim RH, Sodek J. Bone sialoprotein. Crit Rev Oral Biol Med 1999, 10:79-98. 10.1177/10454411990100010401, 10759428.
43. Sharma A, Askari JA, Humphries MJ, Jones EY, Stuart DI. Crystal structure of a heparin- and integrin-binding segment of human fibronectin. EMBO J 1999, 18(6):1468-1479. 10.1093/emboj/18.6.1468, 1171236, 10075919.
44. Zhong S, Chen X, Zhu X, Dziegielewska B, Bachman KE, Ellenberger T, Ballin JD, Wilson GM, Tomkinson AE, MacKerell AD. Identification and validation of human DNA ligase inhibitors using computer-aided drug design. J Med Chem 2008, 51(15):4553-4562. 10.1021/jm8001668, 2788817, 18630893.
45. Dibrov A, Myal Y, Leygue E. Computational modelling of protein interactions: energy minimization for the refinement and scoring of association decoys. Acta Biotheor 2009, 57(4):419-428. 10.1007/s10441-009-9085-x, 19774465.
46. Gyimesi G, Ramachandran S, Kota P, Dokholyan NV, Sarkadi B, Hegedus T. ATP hydrolysis at one of the two sites in ABC transporters initiates transport related conformational transitions. Biochimica et Biophysica Acta (BBA) - Biomembranes 2011, 1808(12):2954-2964.
47. Dai J, Peng L, Fan K, Wang H, Wei R, Ji G, Cai J, Lu B, Li B, Zhang D, Kang Y, Tan M, Qian W, Guo Y. Osteopontin induces angiogenesis through activation of PI3K/AKT and ERK1/2 in endothelial cells. Oncogene 2009, 28(38):3412-3422. 10.1038/onc.2009.189, 19597469.
48. Grassinger J, Haylock DN, Storan MJ, Haines GO, Williams B, Whitty GA, Vinson AR, Be CL, Li S, Sorensen ES, Tam PP, Denhardt DT, Sheppard D, Choong PF, Nilsson SK. Thrombin-cleaved osteopontin regulates hemopoietic stem and progenitor cell functions through interactions with alpha9beta1 and alpha4beta1 integrins. Blood 2009, 114(1):49-59. 10.1182/blood-2009-01-197988, 19417209.
49. Hirata A, Sugahara T, Nakamura H. Localization of runx2, osterix, and osteopontin in tooth root formation in rat molars. J Histochem Cytochem 2009, 57(4):397-403. 2664981, 19124839.
50. Nasu K, Ishida T, Setoguchi M, Higuchi Y, Akizuki S, Yamamoto S. Expression of wild-type and mutated rabbit osteopontin in Escherichia coli, and their effects on adhesion and migration of P388D1 cells. Biochem J 1995, 307(PT1):257-265. 1136771, 7717985.
51. Tantia MS, Mishra B, Bharani Kumar ST, Mishra BP, Kataria RS, Mukesh M, Vijh RK. Characterization of osteopontin gene of Bubalus bubalis. Animal 2008, 2:987-990.
52. Yamniuk AP, Burling H, Vogel HJ. Thermodynamic characterization of the interactions between the immunoregulatory proteins osteopontin and lactoferrin. Mol Immunol 2009, 46(11-12):2395-2402.
53. Sodek J, Ganss B, Mckee MD. Osteopontin. Crit Rev Oral Biol Med 2000, 11(3):279-303. 10.1177/10454411000110030101, 11021631.
54. Thayer JM, Schoenwolf GC. Early expression of osteopontin in the chick is restricted to rhombomeres 5 and 6 and to a subpopulation of neural crest cells that arise from these segments. Anat Rec 1998, 250:199-209. 10.1002/(SICI)1097-0185(199802)250:2<199::AID-AR10>3.0.CO;2-J, 9489781.
55. Bautista DS, Jian-wu XS, Charulata HS, Chambers FA, Harrisson JF. Inhibition of Arg-Gly-Asp (RGD)-mediated cell adhesion to osteopontin by a monoclonal antibody against osteopontin. J Biol Chem 1994, 269(37):23280-23285.
56. Schulze EB, Hedley BD, Goodale D, Postenka CO, Al-Katib W, Tuck AB, Chambers AF, Allan AL. The thrombin inhibitor Argatroban reduces breast cancer malignancy and metastasis via osteopontin-dependent and osteopontin-independent mechanisms. Breast Cancer Res Treat 2008, 112:243-254. 10.1007/s10549-007-9865-4, 18097747.
57. Senger DR, Perruzzi CA, Papadopoulos-Sergiou A, Van De Water L. Adhesive properties of osteopontin: regulation by a naturally occurring thrombin-cleavage in close proximity to the GRGDS cell-binding domain. Mol Biol Cell 1994, 5:565-574. 10.1091/mbc.5.5.565, 301068, 7522656.
58. Senger DR, Perruzzi CA, Papadopoulos A. Elevated expression of secreted phosphoprotein I (osteopontin, 2ar) as a consequence of neoplastic transformation. Anticancer Res 1989, 9(5):1291-1300.
59. Senger DR, Perruzzi CA, Papadopoulos A, Tenen DG. Purification of a human milk protein closely similar to tumor-secreted phosphoproteins and osteopontin. Biochim Biophys Acta 1989, 996(1-2):43-48.
60. Denhardt DT, Noda M, O'Regan AW, Pavlin D, Berman JS. Osteopontin as a means to cope with environmental insults: regulation of inflammation, tissue remodeling, and cell survival. J Clin Invest 2001, 107:1055-1061. 10.1172/JCI12980, 209291, 11342566.
61. Xuan JW, Hota C, Chambers AF. Recombinant GSThuman osteopontin fusion protein is functional in RGDdependent cell adhesion. J Cell Biochern 1994, 64:247-255.
62. Senger RD, Perruzzi AC. Cell migration promoted by a potent GRGDS-containing thrombin-cleavage fragment of osteopontin. Biochim Biophys Acta 1996, 1314:13-24. 10.1016/S0167-4889(96)00067-5, 8972713.
63. Yokosaki Y, Matsuura N, Sasaki T, Murakami I, Schneider H, Higashiyama S, Saitoht Y, Yamakido M, Taooka Y, Sheppard D. The integrin alpha9beta1 binds to a novel recognition sequence (SVVYGLR) in the thrombin-cleaved amino-terminal fragment of osteopontin. J Biol Chem 1999, 274:36328-36334. 10.1074/jbc.274.51.36328, 10593924.
64. Shigeyuki K, Yasuyuki Y, Mmasahiro M, Tatsuya S, Yuko H, Hiroe T, Rashid MM, Morimoto J, Inobe M, Shijubo N, Chambers AF, Uede T. Mapping of functional epitopes of osteopontin by monoclonal antibodies raised against defined internal sequences. J Cell Biochem 2002, 84:420-432. 10.1002/jcb.10039, 11787071.
65. Mi Z, Oliver T, Guo H, Gao C, Kuo PC. Thrombin-cleaved COOH-terminal osteopontin peptide binds with cyclophilin C to CD147 in murine breast cancer cells. Cancer Res 2007, 67(9):4088-4097. 10.1158/0008-5472.CAN-06-4066, 17483319.
66. Yurchenko V, Constant S, Bukrinsky M. Dealing with the family: CD147 interactions with cyclophilins. Immunology 2006, 117:301-309. 10.1111/j.1365-2567.2005.02316.x, 1782239, 16476049.
67. Sorensen ES, Rasmussen LK, Moller L, Jensen PH, Hojrup P, Petersen TE. Localization of transglutaminase-reactive glutamine residues in bovine osteopontin. Biochem J 1994, 304(Pt 1):13-16. 1137443, 7998923.
68. Smith LL, Greenfield BW, Aruffo A, Giachelli CM. CD44 Is Not an adhesive receptor for osteopontin. J Cell Biochem 1999, 73:20-30. 10.1002/(SICI)1097-4644(19990401)73:1<20::AID-JCB3>3.0.CO;2-3, 10088720.
69. Brian C, Nielsen MS, Haselmann KF, Petersen TE, Sorensen ES. Post-translationally modified residues of native human osteopontin are located in clusters: identification of 36 phosphorylation and five O-glycosylation sites and their biological implications. Biochem J 2005, 390:285-292. 10.1042/BJ20050341, 1184582, 15869464.
70. Cherezov V, Liu W, Derrick JP, Luan B, Aksimentiev A, Katritch V, Caffrey M. In meso crystal structure and docking simulations suggest an alternative proteoglycan binding site in the OpcA outer membrane adhesin. Proteins 2008, 71:24-34. 10.1002/prot.21841, 18076035.
71. Fuller JC, Burgoyne NJ, Jackson RM. Predicting druggable binding sites at the protein-protein interface. Drug Discov Today 2009, 14(3-4):155-161.
72. Ahmed M, Behera R, Chakraborty G, Jain S, Kumar V, Sharma P, Bulbule A, Kale S, Kumar S, Mishra R, Raja R, Saraswati S, Kaur R, Soundararajan G, Kumar D, Thorat D, Sanyal M, Ramdasi A, Ghosh P, Kundu GC. Osteopontin: a potentially important therapeutic target in cancer. Expert Opin Ther Targets 2011, 15:1113-1126. 10.1517/14728222.2011.594438, 21718227.