Rational design of the survivin/CDK4 complex by combining protein-protein docking and molecular dynamics simulations

Journal of Molecular Modeling

Volumn 19, Issue 4, 2013, Pages 1507-1514

  Selent, Jana ^a   Kaczor, Agnieszka A ^a,b   Guixà González, Ramon ^a   Carrió, Pau ^a   Pastor, Manuel ^a   Obiol Pardo, Cristian ^a,c  

^a UNIVERSITAT POMPEU FABRA   (Spain)

^b MEDICAL UNIVERSITY OF LUBLIN   (Poland)

^c Intelligent Pharma   (Spain)

Author keywords

Apoptosis; Cancer; CDK4; Cell cycle; Molecular dynamics; Molecular modeling; Protein protein docking; Protein protein interactions; Survivin

Indexed keywords

CYCLIN DEPENDENT KINASE 4; MULTIPROTEIN COMPLEX; PROTEIN INHIBITOR; SURVIVIN;

ALPHA HELIX; ARTICLE; DRUG DESIGN; FRACTAL ANALYSIS; MOLECULAR DOCKING; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN STRUCTURE; STATIC ELECTRICITY; X RAY ANALYSIS;

BINDING SITES; CELL CYCLE PROTEINS; CRYSTALLOGRAPHY, X-RAY; CYCLIN-DEPENDENT KINASE 4; CYCLIN-DEPENDENT KINASE 6; CYCLIN-DEPENDENT KINASE INHIBITOR P16; HUMANS; INHIBITOR OF APOPTOSIS PROTEINS; MOLECULAR DOCKING SIMULATION; MOLECULAR DYNAMICS SIMULATION; NEOPLASM PROTEINS; PROTEIN BINDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; STATIC ELECTRICITY; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 84876408900     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-012-1705-8     Document Type: Article

References (37)

1. Velculescu VE, Madden SL, Zhang L, Lash AE, Yu J, Rago C, Lal A, Wang CJ, Beaudry GA, Ciriello KM, Cook BP, Dufault MR, Ferguson AT, Gao Y, He TC, Hermeking H, Hiraldo SK, Hwang PM, Lopez MA, Luderer HF, Mathews B, Petroziello JM, Polyak K, Zawel L, Zhang W, Zhang X, Zhou W, Haluska FG, Jen J, Sukumar S, Landes GM, Riggins GJ, Vogelstein B, Kinzler KW (1999) Analysis of human transcriptomes. Nat Genet 23:387-388
2. Altieri DC (2008) Survivin, cancer networks and pathway-directed drug discovery. Nat Rev Cancer 8:61-70
3. Paik S, Shak S, Tang G, Kim C, Baker J, Cronin M, Baehner FL, Walker MG, Watson D, Park T, Hiller W, Fisher ER, Wickerham DL, Bryant J, Wolmark N (2004) A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer. N Engl J Med 351:2817-2826
4. Fesik SW (2005) Promoting apoptosis as a strategy for cancer drug discovery. Nat Rev Cancer 5:876-885
5. Sun C, Nettesheim D, Liu Z, Olejniczak ET (2005) Solution structure of human Survivin and its binding interface with Smac/Diablo. Biochemistry 44:11-17
6. Dohi T, Okada K, Xia F, Wilford CE, Samuel T, Welsh K, Marusawa H, Zou H, Armstrong R, Matsuzawa S, Salvesen GS, Reed JC, Altieri DC (2004) An IAP-IAP complex inhibits apoptosis. J Biol Chem 279:34087-34090
7. Fortugno P, Beltrami E, Plescia J, Fontana J, Pradhan D, Marchisio PC, Sessa WC, Altieri DC (2003) Regulation of survivin function by Hsp90. Proc Natl Acad Sci USA 100:13791-13796
8. Wheatley SP, Henzing AJ, Dodson H, Khaled W, Earnshaw WC (2004) Aurora-B phosphorylation in vitro identifies a residue of survivin that is essential for its localization and binding to inner centromere protein (INCENP) in vivo. J Biol Chem 279:5655-5660
9. Bourhis E, Hymowitz SG, Cochran AG (2007) The mitotic regulator Survivin binds as a monomer to its functional interactor Borealin. J Biol Chem 282:35018-35023
10. INK4a and Cdk2/Cyclin E complex activation. Oncogene 19:3225-3234
11. Suzuki A, Ito T, Kawano H, Hayashida M, Hayasaki Y, Tsutomi Y, Akahane K, Nakano T, Miura M, Shiraki K (2000) Survivin initiates procaspase 3/p21 complex formation as a result of interaction with Cdk4 to resist Fas-mediated cell death. Oncogene 19:1346-1353
12. Ai MD, Li LL, Zhao XR, Wu Y, Gong JP, Cao Y (2005) Regulation of Survivin and CDK4 by Epstein-Barr virus encoded latent membrane protein 1 in nasopharyngeal carcinoma cell lines. Cell Res 15:777-784
13. Zhang L, Liu J, Lin H, Hu Q, Liu A, Hu Y (2006) Expression of survivin, CDK4, Ki-67 and clinical significance in pediatric acute leukemia. J Huazhong Univ Sci Technol 26:552-554
14. Chantalat L, Skoufias DA, Kleman JP, Jung B, Dideberg O, Margolis RL (2000) Crystal structure of human survivin reveals a bow tie-shaped dimer with two unusual alpha-helical extensions. Mol Cell 6:183-189
15. Day PJ, Cleasby A, Tickle IJ, O'Reilly M, Coyle JE, Holding FP, McMenamin RL, Yon J, Chopra R, Lengauer C, Jhoti H (2009) Crystal structure of human CDK4 in complex with a D-type cyclin. Proc Natl Acad Sci USA 106:4166-4170
16. Russo AA, Tong L, Lee JO, Jeffrey PD, Pavletich NP (1998) Structural basis for inhibition of the cyclin-dependent kinase Cdk6 by the tumour suppressor p16INK4a. Nature 395:237-243
17. ALIGN, http://xylian.igh.cnrs.fr/bin/align-guess.cgi
18. Humphrey W, Dalke A, Schulten K (1996) VMD-visual molecular dynamics. J Mol Graph 14:33-38
19. Eswar N, Mari-Renom MA, Webb B, Madhusudhan MS, Eramian D, Shen M, Pieper U, Sali A (2006) Comparative protein structure modeling with MODELLER. Current protocols in Bioinformatics. Supplement 15, Wiley, New York, pp 5.6.1-5.6.30, 200
20. MOE: Molecular Operating Environment; Chemical Computing Group, Inc. http://www.chemcomp.com/
21. Wang J, Cieplak P, Kollman PA (2000) How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J Comput Chem 21:1049-1074
22. Schneidman-Duhovny D, Inbar Y, Nussinov R, Wolfson HJ (2005) PatchDock and SymmDock: servers for rigid and symmetric docking. Nucleic Acids Res 33:W363-W367
23. Gray JJ, Moughan SE, Wang C, Schueler-Furman O, Kuhlman B, Rohl CA, Baker D (2003) Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J Mol Biol 331:281-299
24. Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA (2001) Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci USA 98:10037-10041
25. PyMOL Molecular Graphics System, Version 1.3, Schrödinger, LLC. http://www.pymol.org
26. Renthal R (1999) Transmembrane and water-soluble helix bundles display reverse patterns of surface roughness. Biochem Biophys Res Commun 263:714-717
27. Sanner MF, Olson AJ, Spehner JC (1996) Reduced surface: an efficient way to compute molecular surfaces. Biopolymers 38:305-320
28. Pang YP, Xu K, El Yazla J, Prendergast F (2000) Successful molecular dynamics simulation of the zinc-bound farnesyltransferase using the cationic dummy atom approach. Protein Sci 9:1857-1865
29. Obiol-Pardo C, Rubio-Martínez J (2007) Comparative evaluation of MMPBSA and XSCORE to compute binding free energy in XIAP-peptide complexes. J Chem Inf Model 47:134-142
30. Obiol-Pardo C, Granadino-Roldán JM, Rubio-Martínez J (2008) Protein-protein recognition as a first step towards the inhibition of XIAP and Survivin anti-apoptotic proteins. J Mol Recognit 21:190-204
31. Case DA, Darden TA, Cheatham TE III, Simmerling CL, Wang J, Duke RE, Luo R, Crowley M, Walker RC, Zhang W, Merz KM, Wang B, Hayik S, Roitberg A, Seabra G, Kolossváry I, Wong KF, Paesani F, Vanicek J, Wu X, Brozell SR, Steinbrecher T, Gohlke H, Yang L, Tan C, Mongan J, Hornak V, Cui G, Mathews DH, Seetin MG, Sagui C, Babin V, Kollman PA (2008) AMBER 10. University of California, San Francisco
32. Harvey MJ, Giupponi G, de Fabritiis G (2009) ACEMD: accelerating biomolecular dynamics in the microsecond time scale. J Chem Theory Comput 5:1632-1639
33. Reynolds C, Damerell D, Jones S (2008) ProtorP: a protein - protein interaction analysis server. Bioinformatics 25:413-414
34. Nooren IM, Thornton JM (2003) Structural characterisation and functional significance of transient protein-protein interactions. J Mol Biol 325:991-1018
35. Kaczor AA, Guixà-González R, Carrió P, Obiol-Pardo C, Pastor M, Selent J (2012) Fractal dimension as a measure of surface roughness of G protein-coupled receptors: implications for structure and function. J Mol Model 18:4465-4467
36. Ross NT, Katt WP, Hamilton AD (2010) Synthetic mimetics of protein secondary structure domains. Phil Trans R Soc A 368:989-1008
37. Pavlyukov MS, Antipova NV, Balashova MV, Vinogradova TV, Kopantzev EP, Shakhparanov MI (2011) Survivin monomer plays an essential role in apoptosis regulation. J Biol Chem 286:23296-23307