Energy Landscape of the SARS-CoV-2 Reveals Extensive Conformational Heterogeneity

Abstract

Cryo-electron microscopy (cryo-EM) has produced a number of structural models of the SARS-CoV-2 spike, already prompting biomedical outcomes. However, these reported models and their associated electrostatic potential maps represent an unknown admixture of conformations stemming from the underlying energy landscape of the spike protein. As for any protein, some of the spike's conformational motions are expected to be biophysically relevant, but cannot be interpreted only by static models. Using experimental cryo-EM images, we present the energy landscape of the spike protein conformations, and identify molecular rearrangements along the most-likely conformational path in the vicinity of the open (so called 1RBD-up) state. The resulting global and local atomic refinements reveal larger movements than those expected by comparing the reported 1RBD-up and 1RBD-down cryo-EM models. Here we report greater degrees of "openness" in global conformations of the 1RBD-up state, not revealed in the single-model interpretations of the density maps, together with conformations that overlap with the reported models. We discover how the glycan shield contributes to the stability of these conformations along the minimum free-energy pathway. A local analysis of seven key binding pockets reveals that six out them, including those for engaging ACE2, therapeutic mini-proteins, linoleic acid, two different kinds of antibodies, and protein-glycan interaction sites, switch conformations between their known apo- and holo-conformations, even when the global spike conformation is 1RBD-up. This is reminiscent of a conformational pre-equilibrium. We found only one binding pocket, namely antibody AB-C135 to remain closed along the entire minimum free energy path, suggesting an induced fit mechanism for this enzyme.

The structural role of SARS-CoV-2 genetic background in the emergence and success of spike mutations: The case of the spike A222V mutation

“…Furthermore, we might be close to the limits of what discrete 3D classification can obtain in a system like the one under study [ 20 – 22 ]. Here, a possible improvement could be provided by using new continuous flexibility approaches, whose practical limits still need to be tested [ 21 – 26 ]. Nevertheless, it is important to note that refinement of the cryo-EM structures in 1-up conformation of both the S:D614G and [S:A222V + S:D614G] mutants in their corresponding maps yielded B-factors that were notably different, especially at the RBD, suggesting that this latter domain was more flexible in the [S:A222V + S:D614G] mutant.…”

The structural role of SARS-CoV-2 genetic background in the emergence and success of spike mutations: the case of the spike A222V mutation

“…Furthermore, we might be close to the limits of what discrete 3D classification can obtain in a system like the one under study (Melero et al, 2020; Sorzano and Carazo 2021; Punjani and Fleet, 2021a). Here, a possible improvement could be provided by using new continuous flexibility approaches, whose practical limits still need to be tested (Sorzano and Carazo 2021; Chen and Ludtke 2021; Seitz et al 2021; Punjani and Fleet 2021b; Mashayekhi et al 2021). Nevertheless, it is important to note that refinement of the cryo-EM structures in 1-up conformation of both the S:D614G and [S:A222V + S:D614G] mutants in their corresponding maps yielded B-factors that were notably different, especially at the RBD, suggesting that this latter domain was more flexible in the [S:A222V + S:D614G] mutant.…”