On the interactions of the receptor-binding domain of SARS-CoV-1 and SARS-CoV-2 spike proteins with monoclonal antibodies and the receptor ACE2

Carolina Corrêa Giron; Aatto Laaksonen; Fernando L. Barroso da Silva

The EEs are the core idea of the PROCEEDpKa method 27 where pKa shifts are used to identify the key amino acids responsible for a host-pathogen association. It applies the fact that the location of these shifts is a practical mean to probe molecular interactions as before demonstrated. 67 Moreover, this can be easily measured during computer simulations of a proteinprotein complexation. The predictive properties of this powerful tool have been previously i) statistically analyzed for flaviviruses, ii) compared to other bioinformatic tools (that often ignore that pH and ionic strength can drastically affect the complexation process) and iii) discussed in details in a preceding work. 27 The capacity of this method to test EE for specific mAbs makes it even more appealing for the present study where four known mAbs should be investigated. For the sake of convenience, predicted EE for the studied systems were graphically compared at the sequence level. The pairwise sequence alignments were generated by the server EMBOSS Needle 68 with default settings.