Robertson AJ, Courtney JM, Shen Y, Ying J, Bax A. Concordance of X-ray and AlphaFold2 Models of SARS-CoV-2 Main Protease with Residual Dipolar Couplings Measured in Solution.
J Am Chem Soc 2021;
143:19306-19310. [PMID:
34757725 PMCID:
PMC8592127 DOI:
10.1021/jacs.1c10588]
[Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
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The
68-kDa homodimeric 3C-like protease of SARS-CoV-2, Mpro (3CLpro/Nsp5), is a promising antiviral drug target. We evaluate
the concordance of models generated by the newly introduced AlphaFold2
structure prediction program with residual dipolar couplings (RDCs)
measured in solution for 15N–1HN and 13C′–1HN atom
pairs. The latter were measured using a new, highly precise TROSY-AntiTROSY
Encoded RDC (TATER) experiment. Three sets of AlphaFold2 models were
evaluated: (1) MproAF, generated using the standard
AlphaFold2 input structural database; (2) MproAFD, where the AlphaFold2 implementation was modified to exclude all
candidate template X-ray structures deposited after Jan 1, 2020; and
(3) MproAFS, which excluded all structures homologous
to coronaviral Mpro. Close agreement between all three
sets of AlphaFold models and experimental RDC data is found for most
of the protein. For residues in well-defined secondary structure,
the agreement decreases somewhat upon Amber relaxation. For these
regions, MproAF agreement exceeds that of most
high-resolution X-ray structures. Residues from domain 2 that comprise
elements of both the active site and the homo-dimerization interface
fit less well across all structures. These results indicate novel
opportunities for combining experimentation with molecular dynamics
simulations, where solution RDCs provide highly precise input for
QM/MM simulations of substrate binding/reaction trajectories.
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