Three-dimensional model of a substrate-bound SARS chymotrypsin-like cysteine proteinase predicted by multiple molecular dynamics simulations: catalytic efficiency regulated by substrate binding

Abstract

Severe acute respiratory syndrome (SARS) is a contagious and deadly disease caused by a new coronavirus. The protein sequence of the chymotrypsin-like cysteine proteinase (CCP) responsible for SARS viral replication has been identified as a target for developing anti-SARS drugs. Here, I report the ATVRLQ(p1)A(p1')-bound CCP 3D model predicted by 420 different molecular dynamics simulations (2.0 ns for each simulation with a 1.0-fs time step). This theoretical model was released at the Protein Data Bank (PDB; code: 1P76) before the release of the first X-ray structure of CCP (PDB code: 1Q2W). In contrast to the catalytic dyad observed in X-ray structures of CCP and other coronavirus cysteine proteinases, a catalytic triad comprising Asp187, His41, and Cys145 is found in the theoretical model of the substrate-bound CCP. The simulations of the CCP complex suggest that substrate binding leads to the displacement of a water molecule entrapped by Asp187 and His41, thus converting the dyad to a more efficient catalytic triad. The CCP complex structure has an expanded active-site pocket that is useful for anti-SARS drug design. In addition, this work demonstrates that multiple molecular dynamics simulations are effective in correcting errors that result from low-sequence-identity homology modeling.

Figure 1

Sequence alignment of transmissible gastroenteritis coronavirus main proteinase (Protein Data Bank [PDB] code: 1LVO) with the chymotrypsin‐like cysteine proteinase (CCP) (PDB code: 1P76) generated by the SWISS‐MODEL program. The most varied sequence region of the active site of the CCP (residues 44–65), the inserted residue of the CCP, and the conserved Asp187 of the CCP are highlighted in yellow, green, and red, respectively.

Figure 2

Overlay of the backbone structures of the truncated chymotrypsin‐like cysteine proteinase (residues 8–45 and 52–197) generated by X‐ray (yellow), SWISS‐MODEL (red) and multiple molecular dynamics simulations (green).

Figure 3

3D model of the substrate‐bound chymotrypsin‐like cysteine proteinase (red: α‐helix; cyan: β‐strand; yellow: substrate in the β‐strand conformation).

Figure 4

Top view of the active site of the chymotrypsin‐like cysteine proteinase showing the catalytic triad.

Figure 5

Different conformations of the catalytic triad in the chymotrypsin‐like cysteine proteinase.

Figure 6

Residues that confer key intermolecular interactions in the multiple‐molecular‐dynamics‐simulations‐refined substrate‐bound chymotrypsin‐like cysteine proteinase (CCP) complex. Substrate is represented with the ball‐and‐stick model. Residues of the CCP are represented with the stick model. The catalytic triad is shown with the thick stick model. Hydrogen atoms are undisplayed except for those consisting of the oxyanion hole. C, O, N, S, and H atoms are shown in white, red, cyan, yellow, and green, respectively.

Figure 7

Overlays of the X‐ray structure of the substrate‐bound chymotrypsin‐like cysteine proteinase (yellow) with the corresponding multiple‐molecular‐dynamics‐simulations model (green) and the corresponding SWISS‐MODEL model (red) (top: residues 183–185; bottom: residues 151–158).

Figure 8

Comparison of the X‐ray structure of the substrate‐bound chymotrypsin‐like cysteine proteinase (middle) with corresponding the multiple‐molecular‐dynamics‐simulations model (left) and the corresponding SWISS‐MODEL model (right) (top: residues 185–192; middle: residues 61–66 and 80; bottom: residues 165–167, 173, and 185–187).

Figure 9

Different side‐chain conformations of Arg289 in the X‐ray structures of acetylcholinesterase in the bound and the unbound states.