SARS-CoV-2 Variants: A Comparative Investigation Through Spectroscopy and Computational Simulations of S1 protein domains

SARS-CoV-2 virus caused the largest-scale health emergency of the last few centuries [1,2]. It is characterized by spike (S) glycoproteins, which are the first involved in the anchoring of the host receptor angiotensin-converting enzyme 2 (ACE2) through the receptor binding domain (RBD), presents in subunit 1 of the S [1,2,3]. The virus circulation over the years enabled its adaptation to humans, leading to variants emergence which present numerous RNA mutations related to S protein. These influence the protein behaviour, especially in terms of interaction bridges and strength with ACE2, binding affinity, flexibility, accessibility and performance. In this context, the knowledge of the secondary structure of SARS-CoV-2 variant proteins and their differences are of primary importance to understand the connection with the spreading and infectious mechanisms. In our work, we introduce a comparative study of three S1 monomeric subunits of Alpha, Gamma and Omicron SARS-CoV-2 variant, employing both an experimental approach, taking advantage of infrared (IR) and circular dichroism (CD) spectroscopies, well-established experimental methods for a non-invasive analysis of proteins, in combination with the computational approach via Molecular Dynamics (MD) simulations. Our analysis shows the possibility of obtaining information about order and conformational structure of protein domains with high amino acid similarity, through the research of structural changes induced by very few mutated amino acids. The results shed light on various aspects, such as the secondary structure, hydrophobicity, conformational order and functionalities, from each protein domain to complex S1 structure. References [1] A. D’Arco, M. Di Fabrizio, T. Mancini, R. Mosetti, S. Macis, G. Tranfo, G. Della Ventura, A. Marcelli, M.Petrarca, S. Lupi. Secondary Structures of MERS-CoV, SARS-CoV, and SARS-CoV-2 Spike Proteins Revealed by Infrared Vibrational Spectroscopy. Int. J. Mol. Sci. 24 9550 (2023) [2] T. Mancini, S. Macis, R. Mosetti, N. Luchetti, V. Minicozzi, A. Notargiacomo. M. Pea, A. Marcelli, G. Della Ventura, S. Lupi, A. D’Arco. Infrared Spectroscopy of SARS-CoV-2 Viral Protein: from Receptor Binding Domain to Spike Protein. Adv. Sci. 2400823 (2024) [3] B. J. Bosch, R. Van Der Zee, C. A. M. De Haan, P. J. M. Rottier. The coronavirus spike protein is a class I virus fusion protein: structural and functional characterization of the fusion core complex J. Virol. 77 8801-11 (2003)