Conformational Heterogeneity and Redox Switching of the Cysteine Residues in SARS-CoV-2 Main Protease: A Raman Molecular Fingerprint.

The main protease (Mpro/3CLpro) of the SARS-CoV-2 virus activates the viral nonstructural proteins (nsp) into functional units inside the host cells and kickstarts the viral replication-translation machinery, acting as a central molecular switch. Each Mpro monomer possesses 12 cysteine residues, none of them participating in disulfide bridge formation in the active state. However, as a form of protection in response to oxidation, Cys145, a component of the Mpro catalytic dyad, may form a disulfide linkage with Cys117 alongside the formation of the NOS/SONOS bridge involving Cys22, Cys44, and Lys61. These redox-induced thiol group modifications, especially the disulfide cross-linking, impart a transient dormancy on the enzyme's catalytic function, which is restored under reducing conditions. In our study, Raman spectroscopy was used to explore the conformational heterogeneity of Mpro cysteines by analyzing the molecular fingerprint of various thiol cross-link rotamers and free cysteine SH bond vibrations. At ambient pH 7.8, distinct disulfide bond vibration signals were observed at ∼510 cm-1 (GGG) and ∼553 cm-1 (TGT), alongside an S-H stretch at ∼2564 cm-1 in the Raman spectra (ex. 532 nm) of the air-oxidized protein sample. Evidence for NOS(nitroso-sulfenamide)/SONOS bridges emerged in the 650-900 cm-1 region, with the N-O bond stretching vibration mode centered at ∼885 cm-1. The results validated the presence of both oxidized and reduced conformers of the purified wild-type Mpro in vitro at any given time. Furthermore, the Raman molecular fingerprint of the main protease gives a detailed account of the physical states of various side chain residues and the protein secondary structure and stability by depicting a relatively broad amide 1 band at 1660 cm-1, having a full width at half maxima (FWHM) of ∼52 cm-1. Further analysis indicates that about 40% residues are in α-helical (marker band at 1655 cm-1) conformation space, and β-sheet (component band at ∼1670 cm-1) preferring residue was about 25% of the total protein content. Raman spectra and intrinsic fluorescence further systematically mapped the specific microenvironment of tryptophan and tyrosine residues and their critical involvement in hydrogen bond formation that significantly contributes to the overall stability and function of the main protease.