메뉴 건너뛰기




Volumn 354, Issue 1, 2005, Pages 25-40

pH-dependent conformational flexibility of the SARS-CoV main proteinase (Mpro) dimer: Molecular dynamics simulations and multiple X-ray structure analyses

Author keywords

Conformational flexibility; Molecular dynamics simulation; Multiple X ray structures; New crystal forms; SARS CoV Mpro

Indexed keywords

DIMER; HISTIDINE; MONOMER; PROTEINASE; VIRUS ENZYME;

EID: 27344443434     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2005.09.012     Document Type: Article
Times cited : (158)

References (42)
  • 1
    • 0038362701 scopus 로고    scopus 로고
    • Clinical progression and viral load in a community outbreak of coronavirus-associated SARS pneumonia: A prospective study
    • J.S. Peiris, C.M. Chu, V.C. Cheng, K.S. Chan, I.F. Hung, and L.L. Poon Clinical progression and viral load in a community outbreak of coronavirus-associated SARS pneumonia: a prospective study Lancet 361 2003 1767 1772
    • (2003) Lancet , vol.361 , pp. 1767-1772
    • Peiris, J.S.1    Chu, C.M.2    Cheng, V.C.3    Chan, K.S.4    Hung, I.F.5    Poon, L.L.6
  • 2
  • 4
    • 21744441372 scopus 로고    scopus 로고
    • Molecular mechanisms of severe acute respiratory syndrome (SARS)
    • D.A. Groneberg, R. Hilgenfeld, and P. Zabel Molecular mechanisms of severe acute respiratory syndrome (SARS) Respir. Res. 6 2005 8 23
    • (2005) Respir. Res. , vol.6 , pp. 8-23
    • Groneberg, D.A.1    Hilgenfeld, R.2    Zabel, P.3
  • 6
    • 0037061621 scopus 로고    scopus 로고
    • Structure-based design, synthesis, and biological evaluation of irreversible human rhinovirus 3C protease inhibitors. 6. Structure-activity studies of orally bioavailable, 2-pyridone-containing peptidomimetics
    • P.S. Dragovich, T.J. Prins, R. Zhou, E.L. Brown, F.C. Maldonado, and S.A. Fuhrman Structure-based design, synthesis, and biological evaluation of irreversible human rhinovirus 3C protease inhibitors. 6. Structure-activity studies of orally bioavailable, 2-pyridone-containing peptidomimetics J. Med. Chem. 45 2002 1607 1623
    • (2002) J. Med. Chem. , vol.45 , pp. 1607-1623
    • Dragovich, P.S.1    Prins, T.J.2    Zhou, R.3    Brown, E.L.4    Maldonado, F.C.5    Fuhrman, S.A.6
  • 7
    • 0028235532 scopus 로고
    • Structure of human rhinovirus 3C protease reveals a trypsin-like polypeptide fold, RNA-binding site, and means for cleaving precursor polyprotein
    • D.A. Matthews, W.W. Smith, R.A. Ferre, B. Condon, G. Budahazi, and W. Sisson Structure of human rhinovirus 3C protease reveals a trypsin-like polypeptide fold, RNA-binding site, and means for cleaving precursor polyprotein Cell 77 1994 761 771
    • (1994) Cell , vol.77 , pp. 761-771
    • Matthews, D.A.1    Smith, W.W.2    Ferre, R.A.3    Condon, B.4    Budahazi, G.5    Sisson, W.6
  • 9
    • 12444278968 scopus 로고    scopus 로고
    • A 3D model of SARS_CoV 3CL proteinase and its inhibitors design by virtual screening
    • B. Xiong, C.-S. Gui, X.-Y. Xu, C. Luo, J. Chen, and H.-B. Luo A 3D model of SARS_CoV 3CL proteinase and its inhibitors design by virtual screening Acta Pharmacol. Sin. 24 2003 497 504
    • (2003) Acta Pharmacol. Sin. , vol.24 , pp. 497-504
    • Xiong, B.1    Gui, C.-S.2    Xu, X.-Y.3    Luo, C.4    Chen, J.5    Luo, H.-B.6
  • 11
    • 26444498493 scopus 로고    scopus 로고
    • Design of wide-spectrum inhibitors targeting coronavirus main proteinases
    • H. Yang, W. Xie, X. Xue, K. Yang, J. Ma, and W. Liang Design of wide-spectrum inhibitors targeting coronavirus main proteinases PLoS Biol 3 2005 e324
    • (2005) PLoS Biol , vol.3
    • Yang, H.1    Xie, W.2    Xue, X.3    Yang, K.4    Ma, J.5    Liang, W.6
  • 12
    • 0036646055 scopus 로고    scopus 로고
    • Structure of coronavirus main proteinase reveals combination of a chymotrypsin fold with an α-extra helical domain
    • K. Anand, G.J. Palm, J.R. Mesters, S.G. Siddell, J. Ziebuhr, and R. Hilgenfeld Structure of coronavirus main proteinase reveals combination of a chymotrypsin fold with an α-extra helical domain EMBO J. 21 2002 3213 3224
    • (2002) EMBO J. , vol.21 , pp. 3213-3224
    • Anand, K.1    Palm, G.J.2    Mesters, J.R.3    Siddell, S.G.4    Ziebuhr, J.5    Hilgenfeld, R.6
  • 13
    • 0345255626 scopus 로고    scopus 로고
    • The crystal structures of severe acute respiratory syndrome virus main protease and its complex with an inhibitor
    • H. Yang, M. Yang, Y. Ding, Y. Liu, Z. Lou, and Z. Zhou The crystal structures of severe acute respiratory syndrome virus main protease and its complex with an inhibitor Proc. Natl Acad. Sci. USA 100 2003 13190 13195
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 13190-13195
    • Yang, H.1    Yang, M.2    Ding, Y.3    Liu, Y.4    Lou, Z.5    Zhou, Z.6
  • 15
    • 0030970783 scopus 로고    scopus 로고
    • Biosynthesis, purification, and characterization of the human coronavirus 229E 3C-like proteinase
    • J. Ziebuhr, G. Heusipp, and S.G. Siddell Biosynthesis, purification, and characterization of the human coronavirus 229E 3C-like proteinase J. Virol. 71 1997 3992 3997
    • (1997) J. Virol. , vol.71 , pp. 3992-3997
    • Ziebuhr, J.1    Heusipp, G.2    Siddell, S.G.3
  • 16
    • 2642545063 scopus 로고    scopus 로고
    • 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. Shi, Z. Wei, and J. Song 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. 279 2004 24765 24773
    • (2004) J. Biol. Chem. , vol.279 , pp. 24765-24773
    • Shi, J.1    Wei, Z.2    Song, J.3
  • 17
    • 12844272193 scopus 로고    scopus 로고
    • Severe acute respiratory syndrome coronavirus 3C-like proteinase N terminus is indispensable for proteolytic activity but not for enzyme dimerization: Biochemical and thermodynamic investigation in conjunction with molecular dynamics simulations
    • S. Chen, L. Chen, J. Tan, J. Chen, L. Du, and T. Sun Severe acute respiratory syndrome coronavirus 3C-like proteinase 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. 280 2005 164 173
    • (2005) J. Biol. Chem. , vol.280 , pp. 164-173
    • Chen, S.1    Chen, L.2    Tan, J.3    Chen, J.4    Du, L.5    Sun, T.6
  • 18
    • 9144268403 scopus 로고    scopus 로고
    • Biosynthesis, purification, and substrate specificity of severe acute respiratory syndrome coronavirus 3C-like proteinase
    • K. Fan, P. Wei, Q. Feng, S. Chen, C. Huang, and L. Ma Biosynthesis, purification, and substrate specificity of severe acute respiratory syndrome coronavirus 3C-like proteinase J. Biol. Chem. 279 2004 1637 1642
    • (2004) J. Biol. Chem. , vol.279 , pp. 1637-1642
    • Fan, K.1    Wei, P.2    Feng, Q.3    Chen, S.4    Huang, C.5    Ma, L.6
  • 19
    • 0016115206 scopus 로고
    • Mercaptide-imidazolium ion-pair: The reactive nucleophile in papain catalysis
    • L. Polgar Mercaptide-imidazolium ion-pair: the reactive nucleophile in papain catalysis FEBS Letters 47 1974 15 18
    • (1974) FEBS Letters , vol.47 , pp. 15-18
    • Polgar, L.1
  • 20
    • 0342409311 scopus 로고    scopus 로고
    • Characterization of the active site thiol group of rhinovirus 2A proteinase
    • L. Polgar Characterization of the active site thiol group of rhinovirus 2A proteinase FEBS Letters 481 2000 289 292
    • (2000) FEBS Letters , vol.481 , pp. 289-292
    • Polgar, L.1
  • 21
    • 3142613358 scopus 로고    scopus 로고
    • 3C-like proteinase from SARS coronavirus catalyzes substrate hydrolysis by a general-base mechanism
    • C. Huang, P. Wei, K. Fan, Y. Liu, and L. Lai 3C-like proteinase from SARS coronavirus catalyzes substrate hydrolysis by a general-base mechanism Biochemistry 43 2004 4568 4574
    • (2004) Biochemistry , vol.43 , pp. 4568-4574
    • Huang, C.1    Wei, P.2    Fan, K.3    Liu, Y.4    Lai, L.5
  • 22
    • 10344222619 scopus 로고    scopus 로고
    • Three-dimensional model of a substrate-bound SARS chymotrypsin-like cysteine proteinase predicted by multiple molecular dynamics simulations: Catalytic efficiency regulated by substrate binding
    • Y.P. Pang 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: Struct. Funct. Bioinformat. 57 2004 747 757
    • (2004) Proteins: Struct. Funct. Bioinformat. , vol.57 , pp. 747-757
    • Pang, Y.P.1
  • 23
    • 0031019498 scopus 로고    scopus 로고
    • Stabilization of ion selectivity filter by pore loop ion pairs in an inwardly rectifying potassium channel
    • J. Yang, M. Yu, Y.N. Jan, and L.Y. Jan Stabilization of ion selectivity filter by pore loop ion pairs in an inwardly rectifying potassium channel Proc. Natl Acad. Sci. USA 94 1997 1568 1572
    • (1997) Proc. Natl Acad. Sci. USA , vol.94 , pp. 1568-1572
    • Yang, J.1    Yu, M.2    Jan, Y.N.3    Jan, L.Y.4
  • 24
    • 0031059866 scopus 로고    scopus 로고
    • Processing of X-ray diffraction data collected in oscillation mode
    • Z. Otwinowski, and W. Minor Processing of X-ray diffraction data collected in oscillation mode Methods Enzymol. 276 1997 307 326
    • (1997) Methods Enzymol. , vol.276 , pp. 307-326
    • Otwinowski, Z.1    Minor, W.2
  • 26
    • 0030924992 scopus 로고    scopus 로고
    • Refinement of macromolecular structures by the maximum-likelihood method
    • G.N. Murshudov, A.A. Vagin, and E.J. Dodson Refinement of macromolecular structures by the maximum-likelihood method Acta Crystallog. sect. D 53 1997 240 255
    • (1997) Acta Crystallog. Sect. D , vol.53 , pp. 240-255
    • Murshudov, G.N.1    Vagin, A.A.2    Dodson, E.J.3
  • 27
    • 84889120137 scopus 로고
    • Improved methods for building protein models in electron density maps and the location of errors in these models
    • T.A. Jones, J.Y. Zou, M. Kjeldgaard, and S.W. Cowan Improved methods for building protein models in electron density maps and the location of errors in these models Acta Crystallog. sect. A 47 1991 110 119
    • (1991) Acta Crystallog. Sect. a , vol.47 , pp. 110-119
    • Jones, T.A.1    Zou, J.Y.2    Kjeldgaard, M.3    Cowan, S.W.4
  • 28
    • 0032790081 scopus 로고    scopus 로고
    • XtalView/Xfit-A versatile program for manipulating atomic coordinates and electron density
    • D.E. McRee XtalView/Xfit-A versatile program for manipulating atomic coordinates and electron density J. Struct. Biol. 125 1999 156 165
    • (1999) J. Struct. Biol. , vol.125 , pp. 156-165
    • McRee, D.E.1
  • 31
    • 0035789518 scopus 로고    scopus 로고
    • GROMACS 3.0: A package for molecular simulation and trajectory analysis
    • E. Lindahl, B. Hess, and D. van der Spoel GROMACS 3.0: a package for molecular simulation and trajectory analysis J. Mol. Model. 7 2001 306 317
    • (2001) J. Mol. Model. , vol.7 , pp. 306-317
    • Lindahl, E.1    Hess, B.2    Van Der Spoel, D.3
  • 33
    • 0011746241 scopus 로고
    • A molecular dynamics study of the decane/water interface
    • A.R. Van Buuren, S.J. Marrink, and H.J.C. Berendsen A molecular dynamics study of the decane/water interface J. Phys. Chem. 97 1993 9206 9212
    • (1993) J. Phys. Chem. , vol.97 , pp. 9206-9212
    • Van Buuren, A.R.1    Marrink, S.J.2    Berendsen, H.J.C.3
  • 35
    • 33846823909 scopus 로고
    • Particle mesh Ewald: An Nlog(N) method for Ewald sums in large systems
    • T. Darden, D. York, and L. Pedersen Particle mesh Ewald: an Nlog(N) method for Ewald sums in large systems J. Chem. Phys. 98 1993 10089 10092
    • (1993) J. Chem. Phys. , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 38
    • 0002775934 scopus 로고
    • Interaction models for water in relation to protein hydration
    • B. Pullman D. Reidel Publishing Company Dordrecht, The Netherlands
    • H.J.C. Berendsen, J.P.M. Postma, W.F. van Gunsteren, and J. Hermans Interaction models for water in relation to protein hydration B. Pullman Intermolecular Forces 1981 D. Reidel Publishing Company Dordrecht, The Netherlands 331 342
    • (1981) Intermolecular Forces , pp. 331-342
    • Berendsen, H.J.C.1    Postma, J.P.M.2    Van Gunsteren, W.F.3    Hermans, J.4
  • 39
    • 0028881975 scopus 로고
    • SURFNET: A program for visualizing molecular surfaces, cavities and intermolecular interactions
    • R.A. Laskowski SURFNET: A program for visualizing molecular surfaces, cavities and intermolecular interactions J. Mol. Graph. 13 1995 323 330
    • (1995) J. Mol. Graph. , vol.13 , pp. 323-330
    • Laskowski, R.A.1
  • 40
    • 0026244229 scopus 로고
    • MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures
    • P.J. Kraulis MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures J. Appl. Crystallog. 24 1991 946 950
    • (1991) J. Appl. Crystallog. , vol.24 , pp. 946-950
    • Kraulis, P.J.1
  • 42
    • 9744250871 scopus 로고    scopus 로고
    • Quaternary structure of the severe acute respiratory syndrome (SARS) coronavirus main protease
    • C.-Y. Chou, H.-C. Chang, W.-C. Hsu, T.-Z. Lin, C.-H. Lin, and G.-G. Chang Quaternary structure of the severe acute respiratory syndrome (SARS) coronavirus main protease Biochemistry 43 2004 14958 14970
    • (2004) Biochemistry , vol.43 , pp. 14958-14970
    • Chou, C.-Y.1    Chang, H.-C.2    Hsu, W.-C.3    Lin, T.-Z.4    Lin, C.-H.5    Chang, G.-G.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.