Understanding the specificity of serpin-protease complexes through interface analysis

Journal of Biomolecular Structure and Dynamics

Volumn 33, Issue 6, 2015, Pages 1352-1362

  Rashid, Qudsia ^a   Kapil, Charu ^a   Singh, Poonam ^a   Kumari, Vineeta ^a   Jairajpuri, Mohamad Aman ^a  

^a JAMIA MILLIA ISLAMIA CENTRAL UNIVERSITY   (India)

Author keywords

exosite; interface; patch; serine protease; serpins

Indexed keywords

PROTEINASE; SERPIN PROTEASE COMPLEX; UNCLASSIFIED DRUG; AMINO ACID; PROTEIN BINDING; SERINE PROTEINASE INHIBITOR;

ARTICLE; COMPLEX FORMATION; CONTROLLED STUDY; ENZYME ACTIVITY; ENZYME ASSAY; ENZYME MECHANISM; ENZYME MODIFICATION; ENZYME SPECIFICITY; ENZYME STRUCTURE; GENETIC CONSERVATION; HUMAN; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; PRIORITY JOURNAL; RESIDUE ANALYSIS; AMINO ACID SEQUENCE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; CLASSIFICATION; GENETIC DATABASE; GENETICS; INFORMATION PROCESSING; METABOLISM; MOLECULAR GENETICS; PHYLOGENY; POSITION WEIGHT MATRIX; PROTEIN CONFORMATION; SEQUENCE ALIGNMENT;

AMINO ACID SEQUENCE; AMINO ACIDS; BINDING SITES; DATABASES, GENETIC; DATASETS AS TOPIC; ENDOPEPTIDASES; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PHYLOGENY; POSITION-SPECIFIC SCORING MATRICES; PROTEIN BINDING; PROTEIN CONFORMATION; SEQUENCE ALIGNMENT; SERPINS;

EID: 84925745524     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.2014.947525     Document Type: Article

References (37)

1. Acland, A. (2013). Database resources of the National Center for Biotechnology Information. Nucleic Acids Research, 41, D8-D20.
2. Bots, M., Medema, J. P. (2008). Serpins in T cell immunity. Journal of Leukocyte Biology, 84, 1238-1247.
3. Chandrasekaran, V., Lee, C. J., Lin, P., Duke, R. E., Pedersen, L. G. (2009). A computational modeling and molecular dynamics study of the Michaelis complex of human protein Z-dependent protease inhibitor (ZPI) and factor Xa (FXa). Journal of Molecular Modeling, 15, 897-911.
4. Chen, L., Manithody, C., Yang, L., Rezaie, A. R. (2004). Zymogenic and enzymatic properties of the 70-80 loop mutants of factor X/Xa. Protein Science, 13, 431-442.
5. Chuang, Y. J., Swanson, R., Raja, S. M., Bock, S. C., Olson, S. T. (2001). The antithrombin P1 residue is important for target proteinase specificity but not for heparin activation of the serpin. Characterization of P1 antithrombin variants with altered proteinase specificity but normal heparin activation. Biochemistry, 40, 6670-6679.
6. Crooks, G. E., Hon, G., Chandonia, J. M., Brenner, S. E. (2004). WebLogo: A sequence logo generator. Genome Research, 14, 1188-1190.
7. Dementiev, A., Dobo, J., Gettins, P. G. (2006). Active site distortion is sufficient for proteinase inhibition by serpins: Structure of the covalent complex of alpha1-proteinase inhibitor with porcine pancreatic elastase. Journal of Biological Chemistry, 281, 3452-3457.
8. Gettins, P. G. (2002). Serpin structure, mechanism, and function. Chemical Reviews, 102, 4751-4804.
9. Gettins, P. G., Olson, S. T. (2009). Exosite determinants of serpin specificity. Journal of Biological Chemistry, 284, 20441-20445.
10. Guex, N., Peitsch, M. C. (1997). SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling. Electrophoresis, 18, 2714-2723.
11. Guharoy, M., Pal, A., Dasgupta, M., Chakrabarti, P. (2011). PRICE (PRotein Interface Conservation and Energetics): A server for the analysis of protein-protein interfaces. Journal of Structural and Functional Genomics, 12, 33-41.
12. Huang, X., Swanson, R., Broze Jr., G. J., Olson, S. T. (2008). Kinetic characterization of the protein Z-dependent protease inhibitor reaction with blood coagulation factor Xa. Journal of Biological Chemistry, 283, 29770-29783.
13. Hubbard, S. J., Thornton, J. M. (1993). NACCESS-Computer program. London: Department of Biochemistry and Molecular Biology, University College London.
14. Huntington, J. A. (2006). Shape-shifting serpins-Advantages of a mobile mechanism. Trends in Biochemical Sciences, 31, 427-435.
15. Huntington, J. A., Read, R. J., Carrell, R. W. (2000). Structure of a serpin-protease complex shows inhibition by deformation. Nature, 407, 923-926.
16. Izaguirre, G., Olson, S. T. (2006). Residues Tyr253 and Glu255 in strand 3 of beta-sheet C of antithrombin are key determinants of an exosite made accessible by heparin activation to promote rapid inhibition of factors Xa and IXa. Journal of Biological Chemistry, 281, 13424-13432.
17. Izaguirre, G., Zhang, W., Swanson, R., Bedsted, T., Olson, S. T. (2003). Localization of an antithrombin exosite that promotes rapid inhibition of factors Xa and IXa dependent on heparin activation of the serpin. Journal of Biological Chemistry, 278, 51433-51440.
18. Jones, S., Thornton, J. M. (1996). Principles of protein-protein interactions. Proceedings of the National Academy of Sciences, 93, 13-20.
19. Knauer, D. J., Majumdar, D., Fong, P. C., Knauer, M. F. (2000). SERPIN regulation of factor XIa. The novel observation that protease nexin 1 in the presence of heparin is a more potent inhibitor of factor XIa than C1 inhibitor. Journal of Biological Chemistry, 275, 37340-37346.
20. Li, W., Adams, T. E., Kjellberg, M., Stenflo, J., Huntington, J. A. (2007). Structure of native protein C inhibitor provides insight into its multiple functions. Journal of Biological Chemistry, 282, 13759-13768.
21. Li, W., Adams, T. E., Nangalia, J., Esmon, C. T., Huntington, J. A. (2008). Molecular basis of thrombin recognition by protein C inhibitor revealed by the 1.6-A structure of the heparin-bridged complex. Proceedings of the National Academy of Sciences, 105, 4661-4666.
22. Lijnen, H. R. (2005). Pleiotropic functions of plasminogen activator inhibitor-1. Journal of Thrombosis and Haemostasis, 3, 35-45.
23. Manithody, C., Yang, L., Rezaie, A. R. (2002). Role of basic residues of the autolysis loop in the catalytic function of factor Xa. Biochemistry, 41, 6780-6788.
24. McDonald, I. K., Thornton, J. M. (1994). Satisfying hydrogen bonding potential in proteins. Journal of Molecular Biology, 238, 777-793.
25. Olson, S. T., Bjork, I., Sheffer, R., Craig, P. A., Shore, J. D., Choay, J. (1992). Role of the antithrombin-binding pentasaccharide in heparin acceleration of antithrombin-proteinase reactions. Resolution of the antithrombin conformational change contribution to heparin rate enhancement. Journal of Biological Chemistry, 267, 12528-12538.
26. Olson, S. T., Richard, B., Izaguirre, G., Schedin-Weiss, S., Gettins, P. G. (2010). Molecular mechanisms of antithrombin-heparin regulation of blood clotting proteinases. A paradigm for understanding proteinase regulation by serpin family protein proteinase inhibitors. Biochimie, 92, 1587-1596.
27. Patston, P. A., Church, F. C., Olson, S. T. (2004). Serpin-ligand interactions. Methods, 32, 93-109.
28. Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., Ferrin, T. E. (2004). UCSF Chimera-A visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25, 1605-1612.
29. Potempa, J., Korzus, E., Travis, J. (1994). The serpin superfamily of proteinase inhibitors: structure, function, and regulation. Journal of Biological Chemistry, 269, 15957-15960.
30. Rezaie, A. R., Bae, J. S., Manithody, C., Qureshi, S. H., Yang, L. (2008). Protein Z-dependent protease inhibitor binds to the C-terminal domain of protein Z. Journal of Biological Chemistry, 283, 19922-19926.
31. Saha, R. P., Bahadur, R. P., Pal, A., Mandal, S., Chakrabarti, P. (2006). ProFace: A server for the analysis of the physicochemical features of protein-protein interfaces. BMC Structural Biology, 6, 11.
32. Swapna, L. S., Bhaskara, R. M., Sharma, J., Srinivasan, N. (2012). Roles of residues in the interface of transient protein-protein complexes before complexation. Scientific Reports, 2, 334.
33. Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., Kumar, S. (2011). MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution, 28, 2731-2739.
34. Vangone, A., Spinelli, R., Scarano, V., Cavallo, L., Oliva, R. (2011). COCOMAPS: A web application to analyze and visualize contacts at the interface of biomolecular complexes. Bioinformatics, 27, 2915-2916.
35. Whisstock, J. C., Silverman, G. A., Bird, P. I., Bottomley, S. P., Kaiserman, D., Luke, C. J.,., Huntington, J. A. (2010). Serpins flex their muscle: II. Structural insights into target peptidase recognition, polymerization, and transport functions. Journal of Biological Chemistry, 285, 24307-24312.
36. Yang, L., Manithody, C., Olson, S. T., Rezaie, A. R. (2003). Contribution of basic residues of the autolysis loop to the substrate and inhibitor specificity of factor IXa. Journal of Biological Chemistry, 278, 25032-25038.
37. Yang, L., Manithody, C., Qureshi, S. H., Rezaie, A. R. (2010). Role of the residues of the 39-loop in determining the substrate and inhibitor specificity of factor IXa. Journal of Biological Chemistry, 285, 28488-28495.