Insight into the activity of SARS main protease: Molecular dynamics study of dimeric and monomeric form of enzyme

Proteins: Structure, Function and Genetics

Volumn 66, Issue 2, 2007, Pages 467-479

  Zheng, Kewen ^a,b,c   Ma, Guozheng ^b   Zhou, Jinming ^c   Zen, Min ^b   Zhao, Wenna ^b   Jiang, Yongjun ^b   Yu, Qingsen ^b   Feng, Jialiang ^a  

^a SHANGHAI UNIVERSITY   (China)

^b ZHEJIANG UNIVERSITY   (China)

^c SHANGHAI INSTITUTE OF ORGANIC CHEMISTRY   (China)

Author keywords

Dimer; Intermolecular interaction; Main protease; Molecular dynamics; Monomer; SARS coronavirus

Indexed keywords

CYSTEINE; DIMER; GLUTAMINE; HISTIDINE; MONOMER; PROTEINASE;

ARTICLE; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; ENZYME ACTIVITY; ENZYME BINDING; ENZYME CONFORMATION; ENZYME SPECIFICITY; ENZYME STABILITY; ENZYME STRUCTURE; HYDROGEN BOND; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; NONHUMAN; PRIORITY JOURNAL; SARS CORONAVIRUS; SIMULATION; X RAY CRYSTALLOGRAPHY;

CATALYTIC DOMAIN; COMPUTER SIMULATION; CYSTEINE ENDOPEPTIDASES; DIMERIZATION; HYDROGEN BONDING; HYDROLYSIS; MODELS, CHEMICAL; MODELS, MOLECULAR; PROTEASE INHIBITORS; PROTEIN CONFORMATION; PROTEIN INTERACTION MAPPING; SARS VIRUS; STRUCTURE-ACTIVITY RELATIONSHIP; SUBSTRATE SPECIFICITY; VIRAL PROTEINS; WATER;

SARS CORONAVIRUS;

EID: 33846028793     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21160     Document Type: Article

References (32)

1. Leng Q, Bentwich Z. A novel coronavirus and SARS. N Engl J Med 2003;49:709.
2. Kuiken T, Fouchier RA, Schutten M, Rimmelzwaan GF, van Amerongen G, van Riel D, Laman JD, de Jong T, van Doornum G, Lim W, Ling AE, Chan PK, Tam JS, Zambon MC, Gopal R, Drosten C, van der Werf S, Escriou N, Manuguerra JC, Stohr K, Peiris JS, Osterhaus AD. Newly discovered coronavirus as the primary cause of severe acute respiratory syndrome. Lancet 2003;362:263-270.
3. Rota PA, Oberste MS, Monroe SS, Nix WA, Campagnoli R, Icenogle JP, Penaranda S, Bankamp B, Maher K, Chen MH, Tong S, Tamin A, Lowe L, Frace M, DeRisi JL, Chen Q, Wang D, Erdman DD, Peret TC, Burns C, Ksiazek TG, Rollin PE, Sanchez A, Liffick S, Holloway B, Limor J, McCaustland K, Olsen-Rasmussen M, Fouchier R, Gunther S, Osterhaus AD, Drosten C, Pallansch MA, Anderson LJ, Bellini WJ. Characterization of a novel coronavirus associated with severe acute respiratory syndrome. Science 2003;300:1394-1399.
4. Marra MA, Jones SJM, Astell CR, Holt RA, Brooks-Wilson A, Butterfield YSN, Khattra J, Asano JK, Barber SA, Chan SY, Cloutier A, Coughlin SM, Freeman D, Girn N, Griffith OL, Leach SR, Mayo M, McDonald H, Montgomery SB, Pandoh PK, Petrescu AS, Robertson AG, Schein JE, Siddiqui A, Smailus DE, Stott JM, Yang GS, Plummer F, Andonov A, Artsob H, Bastien N, Bernard K, Booth TF, Bowness D, Czub M, Drebot M, Fernando L, Flick R, Garbutt M, Gray M, Grolla A, Jones S, Feldmann H, Meyers A, Kabani A, Li Y, Normand S, Stroher U, Tipples GA, Tyler S, Vogrig R, Ward D, Watson B, Brunham RC, Krajden M, Petric M, Skowronski DM, Upton C, Roper RL. The Genome sequence of the SARS-associated coronavirus. Science 2003;300:1399-1404.
5. Ziebuhr J, Snijder EJ, Gorbalenya AE. Virus-encoded proteinases and proteolytic processing in the Nidovirales. J Gen Virol 2000;81:853-879.
6. Kiemer L, Lund O, Brunak S, Blom N. Coronavirus 3CLpro proteinase cleavage sites: possible relevance to SARS virus pathology. BMC Bioinformatics 2004;5:72-81.
7. John TA, Kuo CJ, Hsieh HP, Wang YC, Huang KK, Lin CPC, Huang PF, Chen X, Liang PH. Evaluation of metal-conjugated compounds as inhibitors of 3CL protease of SARS-CoV. FEBS Lett 2004;574:116-120.
8. Zhang XW, Ya YL. Exploring the binding mechanism of the main proteinase in SARS-associated coronavirus and its implication to anti-SARS drug design. Bioorg Med Chem 2004;12:2219-2223.
9. Bacha U, Jennifer B, Adrian VC, Stephanie AL, Ernesto F. Identification of novel inhibitors of the SARS coronavirus main protease 3Clpro. Biochemistry 2004;43:4906-4912.
10. Chung YW, Jan JT, Ma SH, Kuo CJ, Juan HF, Cheng YSE, Hsu HH, Huang HC, Wu D, Brik A, Liang FS, Liu RS, Fang JM, Chen ST, Liang PH, Wong CH. Small molecules targeting severe acute respiratory syndrome human coronavirus. Proc Natl Acad Sci USA 2004;101:10012-10017.
11. Sirois S, Wei DQ, Du Q, Chou KC. Virtual screening for SARS-CoV protease based on KZ7088 pharmacophore points. J Chem Inf Comput Sci 2004;44:1111-1122.
12. Jain RP, Pettersson HI, Zhang J, Aull KD, Fortin PD, Huitema C, Eltis LD, Parrish JC, James MNG, John DS, Vederas C. Synthesis and evaluation of keto-glutamine analogues as potent inhibitors of severe acute respiratory syndrome 3Clpro. J Med Chem 2004;47:6113-6116.
13. Zheng K, Yu Q, Wang Y, Zhang B, Hu G. Electrostatic and hydrophobic interactions in SARS coronarirus main proteinase dimer. Act Chim Sin 2004;62:542-549.
14. Anand K, Palm GJ, Mesters JR, Siddell SG, Ziebuhr J, Hilgenfeld R. Structure of coronavirus main proteinase reveals combination of a chymotrypsin fold with an extra alphahelical domain. EMBO J 2002;21:3213-3224.
15. Fan K, Wei P, Feng Q, Chen S, Huang C, Ma L, Lai B, Pei J, Liu Y, Chen J, Lai L. Biosynthesis, purification, and substrate specificity of severe acute respiratory syndrome coronavirus 3C-like proteinase. J Biol Chem 2004;279:1637-1642.
16. Shi J, Wei Z, Song J. Dissection study on the severe acute respiratory syndrome 3C-like protease reveals the critical role of the extra domain in dimerization of the enzyme: defining the extra domain as a new target for design of highly specific protease inhibitors. J Biol Chem 2004;279:24765-24773.
17. Yang HT, Yang M, Ding Y, Liu Y, Lou Z, Zhou Z, Sun L, Mo L, Ye S, Pang H, Gao GF, Anand K, Bartlam M, Hilgenfeld R, Rao Z. The crystal structures of severe acute respiratory syndrome virus main protease and its complex with an inhibitor. Proc Natl Acad Sci USA 2003;100:13190-13195.
18. pro) structure: basis for design of anti-SARS drugs. Science 2003;300:1763-1767.
19. Chou CY, Chang HC, Hsu WC, Lin TZ, Lin CH, Chang GG. Quaternary structure of the severe acute respiratory syndrome (SARS) coronavirus main protease. Biochemistry 2004;43:14958-14970.
20. Lee VS, Wittayanarakul K, Remsungnen T, Parasuk V, Sompornpisut P, Chantratita W, Sangma C, Vannarat S, Srichaikul P, Hannongbua S, Saparpakorn P, Treesuman W, Aruksakulwong O, Pasomsub E, Promsri S, Chuakheaw D, Hannaghua S. Structure and dynamics of SARS coronavirus proteinase: the primary key to the designing and screening for anti-SARS drugs. Sci Asia 2003;29:181-188.
21. Liu HL, Lin JC, Ho Y, Hsieh WC, Chen CW, Su YC. Molecular dynamics simulations of various coronavirus main proteinases. J Biomol Struct Dyn 2004;221:65-77.
22. Pang YP. Three-dimensional model of a substrate-bound SARS chymotrypsin-like cysteine proteinase predicted by multiple molecular dynamics simulations: catalytic efficiency regulated by substrate binding. Proteins 2004;57:747-757.
23. Huang C, Wei P, Fan K, Liu Y, Lai L. 3C-like proteinase from SARS coronavirus catalyzes substrate hydrolysis by a general-base mechanism. Biochemistry 2004;43:4568-4574.
24. Simmerling C, Darden T, Merz KM, Stanton RV, Chen A, Vincent AJJ, Crowley M, Tsui V, Radmer R, Duan Y, Pitera J, Massova I, Seibel GL, Singh UC, Weiner P, Kollman PA. AMBER 7. San Francisco: University of California; 2002.
25. Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc 1995;117:5179-5197.
26. Ryckaert JP, Ciccitti G, Berendsen HJC. Numerical integration of the Cartesian equations of motion of a system with constrains: Molecular dynamics of n-alkanes. J Comput Phys 1977;23:327-341.
27. Hockney RW, Eastwood JW. Computer simulations using particles. New York: McGraw Hill; 1981.
28. 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.
29. Berendsen HC, Postma JPM, Gunsteren WF, DiNola A, Haak JR. Molecular dynamics with coupling to an external bath. J Comput Phys 1984;81:3684-3690.
30. Ziebuhr J, Heusipp G, Siddell SG. Biosynthesis, purification, and characterization of the human coronavirus 229E 3C-like proteinase. J Virol 1997;71:3992-3997.
31. Hegyi A, Friebe A, Gorbalenya AE, Ziebuhr J. Mutational analysis of the active centre of coronavirus 3C-like proteases. J Gen Virol 2002;83:581-593.
32. Chen S, Chen L, Tan J, Chen J, Du L, Sun T, Shen J, Chen K, Jiang H, Shen X. SARS coronavirus 3CLpro N-terminus is indispensable for proteolytic activity but not for enzyme dimerization: biochemical and thermodynamic investigation in conjunction with molecular dynamics simulations. J Biol Chem 2005;280:164-173.