Concordance of X-ray and AlphaFold2 Models of SARS-CoV-2 Main Protease with Residual Dipolar Couplings Measured in Solution.

ABSTRACT: The 68-kDa homodimeric 3C-like protease of SARS-CoV-2, M^pro (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-¹H^N and ¹³C'-¹H^N 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) M^pro_AF, generated using the standard AlphaFold2 input structural database; (2) M^pro_AFD, where the AlphaFold2 implementation was modified to exclude all candidate template X-ray structures deposited after

SUBMITTER: Robertson AJ 

PROVIDER: S-EPMC8592127 | biostudies-literature | 2021 Nov

REPOSITORIES: biostudies-literature