Secondary Structures of MERS-CoV, SARS-CoV, and SARS-CoV-2 Spike Proteins Revealed by Infrared Vibrational Spectroscopy

Annalisa D'Arco; Marta Di Fabrizio; Tiziana Mancini; Rosanna Mosetti; Salvatore Macis; Giovanna Tranfo; Giancarlo Della Ventura; Augusto Marcelli; Massimo Petrarca; Stefano Lupi

doi:10.3390/ijms24119550

Secondary Structures of MERS-CoV, SARS-CoV, and SARS-CoV-2 Spike Proteins Revealed by Infrared Vibrational Spectroscopy

Int J Mol Sci. 2023 May 31;24(11):9550. doi: 10.3390/ijms24119550.

Authors

Annalisa D'Arco^{1

2}, Marta Di Fabrizio³, Tiziana Mancini², Rosanna Mosetti², Salvatore Macis², Giovanna Tranfo⁴, Giancarlo Della Ventura^{1

5}, Augusto Marcelli^{1

6}, Massimo Petrarca^{7

8}, Stefano Lupi^{2

7}

Affiliations

¹ Laboratori Nazionali Frascati, National Institute for Nuclear Physics (INFN-LNF), Via E. Fermi 54, 00044 Frascati, Italy.
² Department of Physics, University of Rome 'La Sapienza', P.le A. Moro 2, 00185 Rome, Italy.
³ Laboratory of Biological Electron Microscopy, School of Basic Sciences, Institute of Physics, EPFL & Department of Fundamental Microbiology, Faculty of Biology and Medicine, UNIL, 1015 Lausanne, Switzerland.
⁴ Department of Occupational and Environmental Medicine, Epidemiology and Hygiene, INAIL, Monte Porzio Catone, 00078 Rome, Italy.
⁵ Department of Science, University Rome Tre, Largo San Leonardo Murialdo 1, 00146 Rome, Italy.
⁶ Rome International Centre for Materials Science Superstipes, Via dei Sabelli 119A, 00185 Rome, Italy.
⁷ National Institute for Nuclear Physics Section Rome1, P.le A. Moro 2, 00185 Rome, Italy.
⁸ Department of Basic and Applied Sciences for Engineering (SBAI), University of Rome 'La Sapienza', Via Scarpa 16, 00161 Rome, Italy.

Abstract

All coronaviruses are characterized by spike glycoproteins whose S1 subunits contain the receptor binding domain (RBD). The RBD anchors the virus to the host cellular membrane to regulate the virus transmissibility and infectious process. Although the protein/receptor interaction mainly depends on the spike's conformation, particularly on its S1 unit, their secondary structures are poorly known. In this paper, the S1 conformation was investigated for MERS-CoV, SARS-CoV, and SARS-CoV-2 at serological pH by measuring their Amide I infrared absorption bands. The SARS-CoV-2 S1 secondary structure revealed a strong difference compared to those of MERS-CoV and SARS-CoV, with a significant presence of extended β-sheets. Furthermore, the conformation of the SARS-CoV-2 S1 showed a significant change by moving from serological pH to mild acidic and alkaline pH conditions. Both results suggest the capability of infrared spectroscopy to follow the secondary structure adaptation of the SARS-CoV-2 S1 to different environments.

Keywords: ATR-IR spectroscopy; MERS-CoV; SARS-CoV; SARS-CoV-2; conformation; secondary structure; spike glycoproteins.

MeSH terms

COVID-19*
Humans
Middle East Respiratory Syndrome Coronavirus*
SARS-CoV-2 / metabolism
Spectrum Analysis
Spike Glycoprotein, Coronavirus / metabolism

Substances

spike protein, SARS-CoV-2
Spike Glycoprotein, Coronavirus

Grants and funding

This work was funded by the NATO Science for Peace and Security Program under grant No. 5889 “SARS-CoV-2 Multi-Messenger Monitoring for Occupational Health & Safety (SARS 3M)”, by MIUR—Fondo speciale per la Ricerca—FISR 2020 COVID project titled “Multi-Messenger and Machine Learning Monitoring of SARS-CoV-2 for occupational health & safety (4M SARS-CoV-2)”, the LazioInnova “Gruppi di Ricerca 2020” of the POR FESR 2014/2020—A0375-2020-36651 project entitled “DEUPAS -DEterminazione Ultrasensibile di agenti PAtogeni mediante Spettroscopia”, and finally by the “Avvio alla Ricerca Sapienza 2022” grants entitled “Tracking di SARS-CoV-2 aerodisperso nei luoghi di lavoro mediante spettroscopia vibrazionale ultrasensibile” and “Rivelazione ultra sensibile di composti organici volatili in atmosfera attraverso spettroscopia vibrazionale”. Financial support by the Grant to Department of Science, Roma Tre University (MIUR-Italy Dipartimenti di Eccellenza, ARTICOLO 1, COMMI 314-337 LEGGE 232/2016) is gratefully acknowledged.