[Modeling of the SARS coronavirus main proteinase and conformational flexibility of the active site].
SARS coronavirus 3CL proteinase is the key enzyme for virus replication which may serve as the target for drug discovery against SARS. A 3D structure model has been built for SARS coronavirus 3CL proteinase by comparative protein modeling. A homodimer model of the proteinase was also built. Analysis of the dimeric interface suggests the 3CL proteinase may have dimer form in solution. The conformational flexibility of the active site has been simulated by molecular dynamics combined with multi-canonical sampling. The active site loops have two typical conformations which may be related to the conformational movement associated with the enzymatic reaction.
Liu
Shiyong
S
State Key Laboratory of Structural Chemistry of Stable and Unstable Species, College of Chemistry and Molecular Engineering & Center for Theoretical Biology, Peking University, Beijing 100871, China.
Pei
Jianfeng
J
Chen
Hao
H
Zhu
Xiaolei
X
Liu
Zhenming
Z
Ma
Wenzhe
W
He
Fenglei
F
Lai
Luhua
L
D000595:Amino Acid Sequence; D001665:Binding Sites; D000086782:Coronavirus 3C Proteases; D003546:Cysteine Endopeptidases / Q000737:chemistry*; D019281:Dimerization; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D045473:Severe acute respiratory syndrome-related coronavirus / Q000201:enzymology*
D003546:Cysteine Endopeptidases; D000086782:Coronavirus 3C Proteases