From receptor binding domain to Spike glycoprotein: infrared spectroscopic investigation of SARS-CoV-2 protein domain

Coronaviruses are characterized by spike (S) glycoproteins, which are the largest structural membrane proteins and the first involved in the anchoring of the host receptor angiotensin-converting enzyme 2 (ACE2) through the receptor binding domain (RBD). It is composed by two subunits: S1, responsible for recognition/anchoring to the host receptor ACE2 and containing the RBD; S2, responsible for the membrane fusion [1,2]. Their secondary structures are of great interest for shedding light on various aspects, from functionality to pathogenesis, finally to spectral fingerprint for the design of optical biosensors. Motivated by this, our work aims of the characterization of the whole monomeric SARS-CoV-2 S protein, its constituting components, namely RBD, S1 and S2 regions, at serological pH (7.4) and the S1 alterations induced to chemical/physical environmental modifications. The secondary structure of SARS-CoV-2 S protein and its constituting components are investigated by measuring their amide I absorption bands through Attenuated Total Reflectance Infrared spectroscopy (ATR-IR), one of the main techniques used in the secondary structure analysis of proteins [3,4,5]. The spectroscopic results are analysed observing how the different proteins features change as long as the amino acids sequence grows up or after an environmental. Experimental data in combination with MultiFOLD predictions, Define Secondary Structure of Proteins (DSSP) web server and Gravy value calculations, provide a comprehensive understanding of RBD, S1, S2, and S proteins in terms of their secondary structure content, conformational order, and interaction with the solvent.