Structural basis for substrate specificity of alphavirus nsP2 proteases

Journal of Molecular Graphics and Modelling

Volumn 29, Issue 1, 2010, Pages 46-53

  Russo, Andrew T ^a   Malmstrom, Robert D ^a   White, Mark A ^a   Watowich, Stanley J ^a  

^a University of Texas Medical Branch School of Medicine   (United States)

Author keywords

Alphavirus; NsP2 protease; Protease specificity

Indexed keywords

ALPHAVIRUS; ALPHAVIRUSES; BINDING SURFACE; CATALYTIC MECHANISMS; CATALYTIC SITES; CLEAVAGE SITES; CYSTEINE PROTEASE; HOMOLOGY MODELLING; IMIDAZOLIUM; ION PAIRS; MOLECULAR DYNAMICS SIMULATIONS; NSP2 PROTEASE; PROTEASE SPECIFICITY; STRUCTURAL BASIS; STRUCTURAL STUDIES; SUBSITES; SUBSTRATE BINDING; SUBSTRATE RECOGNITION; SUBSTRATE SPECIFICITY; THIOLATES; VIRAL GENOME;

BINDING ENERGY; VIRUSES;

MOLECULAR DYNAMICS;

CYSTEINE PROTEINASE; HISTIDINE; LYSINE; NSP2 PROTEASE; PAPAIN; SERINE; UNCLASSIFIED DRUG; VIRUS PROTEIN;

ALPHA VIRUS; ARTICLE; ENZYME ACTIVE SITE; ENZYME MECHANISM; ENZYME SPECIFICITY; ENZYME STRUCTURE; MOLECULAR DYNAMICS; MOLECULAR RECOGNITION; MOLECULAR STABILITY; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SIMULATION; VENEZUELAN EQUINE ENCEPHALOMYELITIS ALPHAVIRUS; VIRUS GENOME; VIRUS REPLICATION; VIRUS STRAIN;

ALPHAVIRUS; AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; BINDING SITES; BIOCATALYSIS; CYSTEINE ENDOPEPTIDASES; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; STRUCTURE-ACTIVITY RELATIONSHIP; SUBSTRATE SPECIFICITY;

ALPHAVIRUS; VENEZUELAN EQUINE ENCEPHALITIS VIRUS;

EID: 77955773469     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmgm.2010.04.005     Document Type: Article

References (21)

1. Strauss J.H., Strauss E.G. The alphaviruses: gene expression, replication, and evolution. Microbiol. Rev. 1994, 58:491-562.
2. Lahariya C., Pradhan S.K. Emergence of chikungunya virus in Indian subcontinent after 32 years: a review. J. Vector Borne Dis. 2006, 43:151-160.
3. N/A Outbreak news. Chikungunya. India. Wkly. Epidemiol. Rec. 2006, 81:409-410.
4. Aguilar P.V., Paessler S., Carrara A.S., Baron S., Poast J., Wang E., Moncayo A.C., Anishchenko M., Watts D., Tesh R.B., Weaver S.C. Variation in interferon sensitivity and induction among strains of eastern equine encephalitis virus. J. Virol. 2005, 79:11300-11310.
5. Lulla A., Lulla V., Tints K., Ahola T., Merits A. Molecular determinants of substrate specificity for Semliki Forest virus nonstructural protease. J. Virol. 2006, 80:5413-5422.
6. Vasiljeva L., Merits A., Golubtsov A., Sizemskaja V., Kaariainen L., Ahola T. Regulation of the sequential processing of Semliki Forest virus replicase polyprotein. J. Biol. Chem. 2003, 278:41636-41645.
7. Vasiljeva L., Valmu L., Kaariainen L., Merits A. Site-specific protease activity of the carboxyl-terminal domain of Semliki Forest virus replicase protein nsP2. J. Biol. Chem. 2001, 276:30786-30793.
8. Schechter I., Berger A. On the size of the active site in proteases. I. Papain. Biochem. Biophys. Res. Commun. 1967, 27:157-162.
9. Russo A.T., White M.A., Watowich S.J. The crystal structure of the Venezuelan equine encephalitis alphavirus nsP2 protease. Structure 2006, 14:1449-1458.
10. Mossessova E., Lima C.D. Ulp1-SUMO crystal structure and genetic analysis reveal conserved interactions and a regulatory element essential for cell growth in yeast. Mol. Cell. 2000, 5:865-876.
11. Brooks B.R., Brooks C.L., Mackerell A.D., Nilsson L., Petrella R.J., Roux B., Won Y., Archontis G., Bartels C., Boresch S., Caflisch A., Caves L., Cui Q., Dinner A.R., Feig M., Fischer S., Gao J., Hodoscek M., Im W., Kuczera K., Lazaridis T., Ma J., Ovchinnikov V., Paci E., Pastor R.W., Post C.B., Pu J.Z., Schaefer M., Tidor B., Venable R.M., Woodcock H.L., Wu X., Yang W., York D.M., Karplus M. CHARMM: the biomolecular simulation program. J. Comput. Chem. 2009, 30:1545-1614.
12. Brunger A.T., Karplus M. Polar hydrogen positions in proteins: empirical energy placement and neutron diffraction comparison. Proteins 1988, 4:148-156.
13. MacKerell A.D., Bashford D., Bellott, Dunbrack R.L., Evanseck J.D., Field M.J., Fischer S., Gao J., Guo H., Ha S., Joseph-McCarthy D., Kuchnir L., Kuczera K., Lau F.T.K., Mattos C., Michnick S., Ngo T., Nguyen D.T., Prodhom B., Reiher W.E., Roux B., Schlenkrich M., Smith J.C., Stote R., Straub J., Watanabe M., Wiorkiewicz-Kuczera J., Yin D., Karplus M. All-atom empirical potential for molecular modeling and dynamics studies of proteins, Ć. J. Phys. Chem. B 1998, 102:3586-3616.
14. Wallace A.C., Laskowski R.A., Thornton J.M. LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Eng. 1995, 8:127-134.
15. Sobolev V., Sorokine A., Prilusky J., Abola E.E., Edelman M. Automated analysis of interatomic contacts in proteins. Bioinformatics 1999, 15:327-332.
16. a values. Proteins 2005, 61:704-721.
17. Beveridge A.J. A theoretical study of the active sites of papain and S195C rat trypsin: implications for the low reactivity of mutant serine proteinases. Protein Sci. 1996, 5:1355-1365.
18. Polgar L. Mercaptide-imidazolium ion-pair: the reactive nucleophile in papain catalysis. FEBS Lett. 1974, 47:15-18.
19. Lewis S.D., Johnson F.A., Shafer J.A. Potentiometric determination of ionizations at the active site of papain. Biochemistry 1976, 15:5009-5017.
20. Dawson R.M.C., Elliot D.C., Elliot W.H., Jones K.M. Data for Biochemical Research 1989, Clarendon Press, Oxford. 3rd ed.
21. Golubtsov A., Kaariainen L., Caldentey J. Characterization of the cysteine protease domain of Semliki Forest virus replicase protein nsP2 by in vitro mutagenesis. FEBS Lett. 2006, 580:1502-1508.