Homology modeling and molecular dynamics study of West Nile virus NS3 protease: A molecular basis for the catalytic activity increased by the NS2B cofactor

Proteins: Structure, Function and Genetics

Volumn 65, Issue 3, 2006, Pages 692-701

  Zhou, Hong ^a   Singh, N Jiten ^a   Kim, Kwang S ^a  

^a Pohang University of Science and Technology (POSTECH)   (South Korea)

Author keywords

Free energy decomposition; Homology modeling; MM GBSA; Molecular dynamics simulation; NS2B cofactor; NS3 protease; West Nile virus

Indexed keywords

NONSTRUCTURAL PROTEIN 3; PROTEIN NS2B; PROTEIN NS4A; SERINE PROTEINASE; UNCLASSIFIED DRUG;

ARTICLE; CRYSTAL STRUCTURE; DENGUE VIRUS; ENZYME ACTIVATION; ENZYME ACTIVITY; ENZYME MECHANISM; ENZYME SUBSTRATE COMPLEX; HEPATITIS C VIRUS; HYDROGEN BOND; MOLECULAR DYNAMICS; MOLECULAR MODEL; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN STABILITY; SIMULATION; TECHNIQUE; VIRION; VIRUS ASSEMBLY; WEST NILE FLAVIVIRUS;

AMINO ACID SEQUENCE; BINDING SITES; CATALYTIC DOMAIN; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION; RNA HELICASES; SEQUENCE ALIGNMENT; SERINE ENDOPEPTIDASES; STRUCTURAL HOMOLOGY, PROTEIN; SUBSTRATE SPECIFICITY; THERMODYNAMICS; VIRAL NONSTRUCTURAL PROTEINS; WEST NILE VIRUS;

DENGUE VIRUS; HEPATITIS C VIRUS; WEST NILE VIRUS;

EID: 33750066620     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21129     Document Type: Article

References (46)

1. CDC. West Nile virus: statistics, surveillance and control. Center for Disease Control, 2004
2. Hall RA, Khromykh AA. West Nile virus vaccines. Expert Opin Biol Ther 2004;4:1295-1305.
3. Pertersen LR, Marfin AA, Gubler DJ. West Nile virus. JAMA 2003;290:524-528.
4. Strauss JH, Strauss EG. Viruses and human disease. San Diego: Academic press; 2002.
5. Lindenbach BD, Rice CM. Molecular biology of flaviviruses. Adv Virus Res 2002;59:23-61.
6. Brinton MA. The molecular biology of West Nile virus: a new invader of the western hemisphere. Annu Rev Microbiol 2002;56: 371-402. Epub 2002 Jan 30 Review.
7. Bartenschlager R, Lohman V, Wilkinson T, Koch JO. Complex formation between the NS3 serine-type proteinase of the hepatitis C virus and NS4A and its importance for polyprotein maturation. J Virol 1995;69:7519-7528.
8. Chambers TJ, Grakoui A, Rice CM. Processing of the yellow fever virus nonstructural polyprotein: a catalytically active NS3 proteinase domain and NS2B are required for cleavages at dibasic sites. J Virol 1991;65:6042-6050.
9. Yusof R, Clum S, Wetzel M, Murthy HM, Padmanabhan R. Purified NS2B/NS3 serine protease of dengue virus type 2 exhibits cofactor NS2B dependence for cleavage of substrates with dibasic amino acids. J Biol Chem 2000;275:9963-9969.
10. Failla C, Tomei L, De Francesco R. Both NS3 and NS4A are required for proteolytic processing of hepatitis C virus nonstructural proteins. J Virol 1994;68:3753-3760.
11. Landro JA, Raybuck SA, Luong YP, O'Malley ET, Harbeson SL, Morgenstern KA, Rao G, Livingston DJ. Mechanistic role of an NS4A peptide cofactor with the truncated NS3 protease of hepatitis C virus: elucidation of the NS4A stimulatory effect via kinetic analysis and inhibitor mapping. Biochemistry 1997;36:9340-9348.
12. Nall TA, Chappell KJ, Stoermer MJ, Fang NX, Tyndall JD, Young PR, Fairlie DP. Enzymatic characterization and homology model of a catalytically active recombinant West Nile virus NS3 protease. J Biol Chem 2004;279:48535-48542.
13. Murthy HM, Clum S, Padmanabhan R. Dengue virus NS3 serine protease: crystal structure and insights into interaction of the active site with substrates by molecular modeling and structural analysis of mutational effects. J Biol Chem 1999;274:5573-5580.
14. Murthy HM, Judge K, DeLucas L, Padmanabhan R. Crystal structure of dengue virus NS3 protease in complex with a Bowman-Birk inhibitor: implications for flaviviral polyprotein processing and drug design. J Mol Biol 2000;301:759-767.
15. Kim JL, Morgenstern KA, Lin C, Fox T, Dwyer MD, Landro JA, Chambers SP, Markland W, Lepre CA, O'Malley ET, Harbeson SL, Rice CM, Murcko MA, Caron PR, Thomson JA. Crystal structure of the hepatitis C virus NS3 protease domain complexed with a synthetic NS4A cofactor peptide. Cell 1996;87:343-355.
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;31:3784-3788. Available at http://kr.expasy.org/.
17. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The protein data bank. Nucleic Acids Res 2002;28:235-242. Available at http://www.rcsb.org/pdb.
18. Sali A, Blundell TL. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 1993;234:779-815.
19. Guex N, Peitsch MC. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis 1997;18:2714-2723.
20. Case DA, Darden TA, Cheatham TE, III, Simmerling CL, Wang J, Duke RE, Luo R, Merz KM, Wang B, Pearlman DA, Crowley M, Brozell S, Tsui V, Gohlke H, Mongan J, Hornak V, Cui G, Beroza P, Schafmeister C, Caldwell JW, Ross WS, and Kollman PA. AMBER8. University of California, San Francisco; 2004.
21. Duan Y, Wu C, Chowdhury S, Lee MC, Xiong G, Zhang W, Yang R, Cieplak P, Luo R, Lee T, Caldwell J, Wang J, Kollman P. A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J Comput Chem 2003;24:1999-2012.
22. Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen LG. A smooth particle mesh Ewald method. J Chem Phys 1995;103:8577-8593.
23. Ding HQ, Karasawa N, Goddard WA. Atomic level simulations on a million particles-the cell multipole method for Coulomb and London nonbond interactions. J Chem Phys 1992;97:4309-4315.
24. Lee SJ, Chung HY, Kim KS. An easy-to-use three-dimensional molecular visualization and analysis program: POSMOL. Bull Korean Chem Soc 2004;25:1061-1064.
25. Massova I, Kollman PA. Combined molecular mechanical and continuum solvent approach (MM-PBSA/GBSA) to predict ligand binding. Perspect Drug Discov 2000;18:113-135.
26. Tsui V, Case DA. Theory and applications of the generalized Born solvation model in macromolecular simulations. Biopolymers 2001;56:275-291.
27. Weiser J, Shenkin PS, Still WC. Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO). J Comput Chem 1999;20:217-230.
28. Yang AS, Honig B. An integrated approach to the analysis and modeling of protein sequences and structures. J Mol Biol 2000;301: 665-711.
29. Lin C, Thomson JA, Rice CM. A central region in the hepatitis C virus NS4A protein allows formation of an active NS3-NS4A serine proteinase complex in vivo and in vitro. J Virol 1995;69: 4373-4380.
30. Aronson HE, Royer WE, Jr, Hendrickson WA. Quantification of tertiary structural conservation despite primary sequence drift in the globin fold. Protein Sci 1994;3:1706-1711.
31. Falgout B, Miller RH, Lai CJ. Deletion analysis of dengue virus type 4 nonstructural protein NS2B: identification of a domain required for NS2B-NS3 protease activity. J Virol 1993;67:2034-2042.
32. Schechter I, Berger A. On the size of the active site in proteases. I. Papain. Biochem Biophys Res Commun 1967;27:157-162.
33. Falgout B, Pethel M, Zhang YM, Lai CJ. Both nonstructural proteins NS2B and NS3 are required for the proteolytic processing of dengue virus nonstructural proteins. J Virol 1991;65: 2467-2475.
34. Alexander CS, Yan X, Pei T. Homology modeling and molecular dynamics simulations of transmembrane domain structure of human neuronal nicotinic acetylcholine receptor. Biophys J 2005;88:1009-1017.
35. McCoy MA, Senior MM, Gesell JJ, Ramanathan L, Wyss DF. Solution structure and dynamics of the single-chain hepatitis C virus NS3 protease NS4A cofactor complex. J Mol Biol 2001; 305:1099-1110.
36. Barbato G, Cicero DO, Cordier F, Narjes F, Gerlach B, Sambucini S, Grzesiek S, Matassa VG, De Francesco R, Bazzo R. Inhibitor binding induces active site stabilization of the HCV NS3 protein serine protease domain. EMBO J 2000;19:1195-1206.
37. Barbato G, Cicero DO, Nardi MC, Steinkuhler C, Cortese R, De Francesco R, Bazzo R. The solution structure of the N-terminal proteinase domain of the hepatitis C virus (HCV) NS3 protein provides new insights into its activation and catalytic mechanism. J Mol Biol 1999;289:371-384.
38. Kim KS, Kim D, Lee JY, Tarakeshwar P, Oh KS. Catalytic mechanism of enzymes: preorganization, short strong hydrogen bond, and charge buffering. Biochemistry 2002;41:5300-5306.
39. Manojkumar TK, Cui C, Kim KS. Theoretical insights into the mechanism of acetylcholinesterase catalyzed acylation of acetylcholine. J Comput Chem 2005;26:606-611.
40. Suh SB, Kim JC, Choi YC, Kim KS. Nature of one-dimensional short hydrogen bonding: bond distances, bond energies, and solvent effects. J Am Chem Soc 2004;126:2186-2193.
41. Kim KS, Oh KS, Lee JY. Catalytic role of enzymes: short strong H-bond induced proton shuttles and electron rearrangements. Proc Natl Acad Sci USA 2000;97:6373-6378.
42. Berg JM, Tymoczko JL, Stryer L. Biochemistry. New York: W. H. Freeman; 2002. 232p.
43. Sotriffer CA, Kramer O, Klebe G, Probing flexibility and "induced-fit" phenomena in aldose reductase by comparative crystal structure analysis and molecular dynamics simulations. Proteins 2004;56:52-66.
44. de Oliveira CA, Guimaraes CR, Barreiro G, de Alencastro RB, Investigation of the induced-fit mechanism and catalytic activity of the human cytomegalovirus protease homodimer via molecular dynamics simulations. Proteins 2003;52:483-491.
45. Massova I, Kollman PA. Computational alanine scanning to probe protein-protein interactions: a novel approach to evaluate binding free energies. J Am Chem Soc 1999;121:8133-8143.
46. Gohlke H, Kiel C, Case DA. Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes. J Mol Biol 2003;330:891-913.