Conformational flexibility and structural variability of SARS-CoV2 S protein

• Published in: Structure (London) 2021-08, Vol.29 (8), p.834-845.e5
• Main Authors: Pramanick, Ishika, Sengupta, Nayanika, Mishra, Suman, Pandey, Suman, Girish, Nidhi, Das, Alakta, Dutta, Somnath
• Format: Article
• Language: English
• Subjects: 3D reconstruction; cryo-EM; Cryoelectron Microscopy; Humans; Hydrogen-Ion Concentration; Models, Molecular; negative staining; pH-dependent; Protein Binding; Protein Conformation; Protein Domains; S-head; SARS-CoV-2 - chemistry; SARS-CoV-2 - metabolism; Single Molecule Imaging; single particle; solvent accessibility; Spike Glycoprotein, Coronavirus - chemistry; Spike Glycoprotein, Coronavirus - metabolism; spike homotrimer; stalk domain; TEM
• ISSN: 0969-2126; 1878-4186
• DOI: 10.1016/j.str.2021.04.006

Spike (S) glycoprotein of SARS-CoV2 exists chiefly in two conformations, open and closed. Most previous structural studies on S protein have been conducted at pH 8.0, but knowledge of the conformational propensities under both physiological and endosomal pH conditions is important to inform vaccine development. Our current study employed single-particle cryoelectron microscopy to visualize multiple states of open and closed conformations of S protein at physiological pH 7.4 and near-physiological pH 6.5 and pH 8.0. Propensities of open and closed conformations were found to differ with pH changes, whereby around 68% of S protein exists in open conformation at pH 7.4. Furthermore, we noticed a continuous movement in the N-terminal domain, receptor-binding domain (RBD), S2 domain, and stalk domain of S protein conformations at various pH values. Several key residues involving RBD-neutralizing epitopes are differentially exposed in each conformation. This study will assist in developing novel therapeutic measures against SARS-CoV2. [Display omitted] •Structural flexibility and variability of S protein at (near) physiological pH•Predominance of 1-RBD up conformation at pH 7.4•Differential surface exposure of amino acid residues that bind neutralizing antibody•Diverse length and orientation of stalk domain of S2 subunit In this study, Pramanick et al. demonstrate inherent structural flexibility of NTD, RBD, and stalk domain of SARS-CoV2 Spike glycoprotein. Eleven high-resolution cryo-EM structures obtained over a range of near-physiological pH values indicate a trend of increasing open conformational state of S protein at physiological pH 7.4.