A pH-dependent switch mediates conformational masking of SARS-CoV-2 spike

Zhou, Tongqing; Tsybovsky, Yaroslav; Olia, Adam S.; Gorman, Jason; Rapp, Micah A.; Cerutti, Gabriele; Katsamba, Phinikoula S.; Nazzari, Alexandra; Schön, Arne; Wang, Pengfei; Bimela, Jude; Shi, Wei; Teng, I-Ting; Zhang, Baoshan; Boyington, Jeffrey C.; Chuang, Gwo-Yu; Sampson, Jared M.; Sastry, Mallika; Stephens, Tyler; Stuckey, Jonathan; Wang, Shuishu; Friesner, Richard A.; Ho, David D.; Mascola, John R.; Shapiro, Lawrence; Kwong, Peter D.

SARS-CoV-2 has emerged as a global pathogen(1,2), sparking urgent vaccine development efforts with the trimeric spike(3,4). However, the inability of antibodies like CR3022(5), which binds a cryptic spike epitope with nanomolar affinity(6), to neutralize virus, suggests a spike-based means of neutralization escape. Here, we show the SARS-CoV-2 spike to have 10% the unfolding enthalpy of a globular protein at physiological pH, where it is recognized by antibodies like CR3022, and up to 10-times more unfolding enthalpy at endosomal pH, where it sheds such antibodies, suggesting that the spike evades potentially neutralizing antibody through a pH-dependent mechanism of conformational masking. To understand the compatibility of this mechanism with ACE2-receptor interactions, we carried out binding measurements and determined cryo-EM structures of the spike recognizing up to three ACE2 molecules at both physiological and endosomal pH. In the absence of ACE2, cryo-EM analyses indicated lower pH to reduce conformational heterogeneity. Single-receptor binding domain (RBD)-up conformations dominated at pH 5.5, resolving into a locked all-down conformation at lower pH through lowering of RBD and refolding of a pH-dependent switch. Notably, the emerging Asp614Gly strain(7) partially destabilizes the switch that locks RBD down, thereby enhancing functional interactions with ACE2 while reducing evasion by conformational masking.