Molecular dynamics simulations and functional characterization of the interactions of the PAR2 ectodomain with factor VIIa

Proteins: Structure, Function and Bioinformatics

Volumn 77, Issue 3, 2009, Pages 559-569

  Zhang, Qing ^a   Petersen, Helle H ^a   Ostergaard, Henrik ^a   Ruf, Wolfram ^a   Olson, Arthur J ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

Molecular dynamics simulation; PAR2 cleavage; Serine protease; TF FVIIa signaling

Indexed keywords

BLOOD CLOTTING FACTOR 7A; PROTEIN ANTIBODY; PROTEINASE ACTIVATED RECEPTOR 2;

ARTICLE; CONTROLLED STUDY; ELECTROCHEMISTRY; ENZYME ACTIVE SITE; EPITOPE MAPPING; HUMAN; HUMAN CELL; HYDROGEN BOND; MOLECULAR DOCKING; MOLECULAR DYNAMICS; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN CLEAVAGE; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN PROTEIN INTERACTION; SIGNAL TRANSDUCTION; STRUCTURE ANALYSIS;

CATALYTIC DOMAIN; COMPUTER SIMULATION; ENDOTHELIAL CELLS; EPITOPES; FACTOR VIIA; GLYCOSYLATION; HUMANS; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY; RECEPTOR, PAR-2; SIGNAL TRANSDUCTION; SOLVENTS; UMBILICAL VEINS;

EID: 70349310267     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22468     Document Type: Article

References (34)

1. Morrissey JH, Gregory SA, Mackman N, Edgington TS. Tissue factor regulation and gene organization. Oxf Surv Eukaryot Genes 1989;6:67-84.
2. Edgington TS, Mackman N, Brand K, Ruf W. The structural biology of expression and function of tissue factor. Thromb Haemost 1991;66:67-79.
3. Edgington TS, Ruf W, Rehemtulla A, Mackman N. The molecular biology of initiation of coagulation by tissue factor. Curr Stud Hematol Blood Transfus 1991;(58):15-21.
4. Monroe DM, Key NS. The tissue factor-factor VIIa complex: procoagulant activity, regulation, and multitasking. J Thromb Haemost 2007;5:1097-1105. (Pubitemid 46902106)
5. Versteeg HH, Ruf W. Emerging insights in tissue factor-dependent signaling events. Semin Thromb Hemost 2006;32:24-32. (Pubitemid 43297433)
6. Macfarlane SR, Seatter MJ, Kanke T, Hunter GD, Plevin R. Proteinase-activated receptors. Pharmacol Rev 2001;53:245-282.
7. Ruf W, Mueller BM. Thrombin generation and the pathogenesis of cancer. Semin Thromb Hemost 2006;32 Suppl 1:61-68.
8. al-Ani B, Saifeddine M, Hollenberg MD. Detection of functional receptors for the proteinase-activated-receptor-2-activating polypeptide. SLIGRL-NH2, in rat vascular and gastric smooth muscle. Can J Physiol Pharmacol 1995;73:1203-1207.
9. Banner DW, D'Arcy A, Chene C, Winkler FK, Guha A, Konigsberg WH, Nemerson Y, Kirchhofer D. The crystal structure of the complex of blood coagulation factor VIIa with soluble tissue factor. Nature 1996;380:41-46. (Pubitemid 26076234)
10. Nystedt S, Emilsson K, Larsson AK, Strombeck B, Sundelin J. Molecular cloning and functional expression of the gene encoding the human proteinase-activated receptor 2. Eur J Biochem 1995;232:84-89.
11. Bohm SK, Kong W, Bromme D, Smeekens SP, Anderson DC, Connolly A, Kahn M, Nelken NA, Coughlin SR, Payan DG, Bunnett NW. Molecular cloning, expression and potential functions of the human proteinase-activated receptor-2. Biochem J 1996;314 (Part 3):1009-1016. (Pubitemid 26097768)
12. Voet D, Voet JG, Pratt CW. Fundamentals of biochemistry. New York, Wiley; 1999.
13. Eigenbrot C. Structure, function, and activation of coagulation factor VII. Curr Protein Pept Sci 2002;3:287-299. (Pubitemid 34594308)
14. Wildgoose P, Foster D, Schiodt J, Wiberg FC, Birktoft JJ, Petersen LC. Identification of a calcium binding site in the protease domain of human blood coagulation factor VII: evidence for its role in factor VII-tissue factor interaction. Biochemistry 1993;32:114-119. (Pubitemid 23033327)
15. Compton SJ, Sandhu S, Wijesuriya SJ, Hollenberg MD. Glycosylation of human proteinase-activated receptor-2 (hPAR2): role in cell surface expression and signalling. Biochem J 2002;368 (Part 2):495-505. (Pubitemid 35454527)
16. Oganesyan V, Oganesyan N, Terzyan S, Qu D, Dauter Z, Esmon NL, Esmon CT. The crystal structure of the endothelial protein C receptor and a bound phospholipid. J Biol Chem 2002;277:24851-24854. (Pubitemid 34951783)
17. Case DA, Darden TA, Cheatham TE,III Simmerling CL, Wang J, Duke RE, Luo R, Merz KM, Pearlman DA, Crowley M, Walker RC, Zhang W, Wang B, Hayik S, Roitberg A, Seabra G, Wong KF, Paesani F, Wu X, Brozell S, Tsui V, Gohlke H, Yang L, Tan C, Mongan J, Hornak V, Cui G, Beroza P, Mathews DH, Schafmeister C, Ross WS, Kollman PA. AMBER 9. San Francisco: University of California; 2006.
18. Wang J, Cieplak P, Kollman PA. How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J Comput Chem 2000;21:1049-1074.
19. Cieplak P, Cornell WD, Bayly CI, Kollman PA. Application of the multimolecule and multiconformational RESP methodology to biopolymers: charge derivation for DNA. RNA, and proteins. J Comput Chem 1995;16:1357-1377.
20. Pigache A, Cieplak P, Dupradeau F-Y. Automatic and highly reproducible RESP and ESP charge derivation: application to the development of programs RED and X RED. 27th annual ACS meeting, Anaheim, CA; 2004.
21. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Montgomery JA, Jr, Vreven T, Kudin KN, Burant JC, Millam JM, Iyengar SS, Tomasi J, Barone V, Mennucci B, Cossi M, Scalmani G, Rega N, Petersson GA, Nakatsuji H, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Klene M, Li X, Knox JE, Hratchian HP, Cross JB, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Ayala PY, Morokuma K, Voth GA, Salvador P, Dannenberg JJ, Zakrzewski VG, Dapprich S, Daniels AD, Strain MC, Farkas O, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Ortiz JV, Cui Q, Baboul AG, Clifford S, Cioslowski J, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Martin RL, Fox DJ, Keith T, Al- Laham MA, Peng CY, Nanayakkara A, Challacombe M, Gill PMW, Johnson B, Chen W, Wong MW, Gonzalez C, Pople JA. Gaussian 03, Revision B. 04. Pittsburgh, PA: Gaussian Inc.; 2003.
22. Onufriev A, Bashford D, Case DA. Exploring protein native states and large-scale conformational changes with a modified generalized born model. Proteins 2004;55:383-394. (Pubitemid 38437495)
23. Ryckaert J-P, Ciccotti G, Berendsen HJC. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys 1977;23:327-341.
24. Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A, Haak JR. Molecular dynamics with coupling to an external bath. J Chem Phys 1984;81:3684-3690.
25. Weiser J, Shenkin PS, Still WC. Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO). J Comput Chem 1999;20:217-230. (Pubitemid 129653030)
26. Jorgensen WL, Chandreskhar J, Madura JD, Imprey RW, Klein ML. Comparison of simple potential functions for simulating liquid water. J Chem Phys 1983;79:926-935.
27. Aqvist J. Ion-water interaction potentials derived from free energy perturbation simulations. J Phys Chem 1990;94:8021-8024.
28. Marchand S, Roux B. Molecular dynamics study of calbindin D9k in the apo and singly and doubly calcium-loaded states. Proteins 1998;33:265-284. (Pubitemid 28457978)
29. Jorgensen WL, Tirado-Rives J. The OPLS potential functions for proteins. Energy minimizations for crystals of cyclic peptides and crambin. J Am Chem Soc 1988;110:1657-1666.
30. Ahamed J, Belting M, Ruf W. Regulation of tissue factor-induced signaling by endogenous and recombinant tissue factor pathway inhibitor 1. Blood 2005;105:2384-2391. (Pubitemid 40387035)
31. Dickinson CD, Shobe J, Ruf W. Influence of cofactor binding and active site occupancy on the conformation of the macromolecular substrate exosite of factor VIIa. J Mol Biol 1998;277:959-971. (Pubitemid 28195993)
32. Hedstrom L. Serine protease mechanism and specificity. Chem Rev 2002;102:4501-4524.
33. Sanner MF, Olson AJ, Spehner J-C. Reduced surface: An efficient way to compute molecular surfaces. Biopolymers 1996;38:305-320. (Pubitemid 2626536)
34. McCallum CD, Su B, Neuenschwander PF, Morrissey JH, Johnson AE. Tissue factor positions and maintains the factor VIIa active site far above the membrane surface even in the absence of the factor VIIa Gla domain. A fluorescence resonance energy transfer study. J Biol Chem 1997;272:30160-30166. (Pubitemid 27512216)