Key mutation sites in the SARS-CoV-2 spike protein modulate antibody and ACE2 affinity

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An allosteric center or site is one where a molecule other than the substrate to the protein can bind, altering the conformation of the protein. A paper recently uploaded to the preprint server bioRxiv* by researchers at Chapman University in California (Feb 22nd, 2021) utilized computational methods to screen severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mutants for affinity with the angiotensin-converting enzyme 2 (ACE2) receptor and monoclonal antibodies REG10987 and REG10933. The analysis allowed the group to identify allosteric centers that mediate long-range communication in the protein. The group suggests that it is these centers that allow the spike protein of SARS-CoV-2 to act in such a versatile manner, modulating the response to antibodies while conserving ACE2 affinity.

Which mutations alter affinity?

Deep mutational scanning approaches to the receptor-binding domain (RBD) of SARS-CoV-2 identified constraints in the conformation of the protein regarding its ability to interact with ACE2, though also highlighted that many mutations in the RBD are well-tolerated and do not significantly affect binding affinity. In fact, many modifications were found to improve binding with ACE2 either by directly increasing the affinity, as with N501F, N501T, and Q498Y mutations, or enhancing RBD expression was found for V367F and G502D mutations…

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