Binding strength and hydrogen bond numbers between Covid-19 RBD and HVR of antibody (preprint)

ABSTRACT

The global battle against the Covid-19 pandemic relies strongly on the human defence of antibody, which is assumed to bind the Receptor Binding Domain of the antigen with its Hypervariable Region. Due to the similarity to other viruses such as SARS, however, our understanding of the antibody-virus interaction has been limited to the genomic sequencing, which poses serious challenges to the containment, vaccine exploration and rapid serum testing. Based on the physical/chemical nature of the interaction, infrared spectroscopy was employed to reveal the binding disparity, when unusual temperature dependence was discovered from the 1550cm 1 absorption band, attributed to the hydrogen bonds by carboxyl/amino groups, binding the SARS-CoV-2 spike protein and closely resembled SARS-CoV-2 or SARS-CoV-1 antibodies. The infrared absorption intensity, associated with the number of hydrogen bonds, was found to increase sharply between 27C and 31C, with the relative absorbance matches at 37C the hydrogen bonding numbers of the two antibody types (19 vs 12). As a result, the specificity of the SARS-CoV-2 antibody will be more conclusive beyond 31C, instead of at the usual room temperature of 20C - 25C, when the vaccine research and antibody diagnosis would likely be undermined.