Timeline of changes in spike conformational dynamics in emergent SARS-CoV-2 variants reveal progressive stabilization of trimer stalk and enhanced NTD dynamics

Abstract

SARS-CoV-2 emergent variants are characterized by increased transmissibility and each show multiple mutations predominantly localized to the spike (S) protein. Here, amide hydrogen/deuterium exchange mass spectrometry has been applied to track correlative changes in S dynamics from multiple SARS-CoV-2 variants. Our results highlight large differences across variants at two loci with impacts on S dynamics and stability. A significant enhancement in stabilization first occurred with the emergence of D614G S followed by smaller, progressive stabilization in Omicron BA.1 S traced through Alpha S and Delta S variants. Stabilization preceded progressive enhancement in dynamics in the N-terminal domain, wherein Omicron BA.1 S showed the largest magnitude increases relative to other preceding variants. Changes in stabilization and dynamics resulting from specific S mutations detail the evolutionary trajectory of S protein in emerging variants. These carry major implications for SARS- CoV-2 viral fitness and offer new insights into variant-specific therapeutic development.

Structural dynamics in the evolution of SARS-CoV-2 spike glycoprotein

“…4 and Supplementary Figs. [34][35][36][37][38][39][40]. This is due to the direct engagement of these regions by ACE2 and is consistent with previous structural studies that described the spike-ACE2 interface as being constituted by the RBM (residues 438-506) and the residue 417 52 .…”

“…However, as dynamic events largely dominate the spike function, cryo-EM structures alone are unable to uncover the structural dynamics underlying spike opening, ACE2 receptor binding and how this primes the exposure of the S2 trimeric core for fusion, in the ancestral spike and in spikes of VOCs. Due to inner challenges associated with the spike size and its conformational heterogeneity, only a handful of studies have probed its structural dynamics to date [35][36][37][38][39][40][41][42] . We thus lack a clear understanding of the perturbation that mutations in VOCs cause on the spike conformational landscape and how they impact spike function and the dynamics of its epitopes 43 .…”

hACE2-Induced Allosteric Activation in SARS-CoV versus SARS-CoV-2 Spike Assemblies Revealed by Structural Dynamics

“…The comparison of SARS-CoV-2 D614 and G614 S assemblies indicated long-range dynamic coupling between RBD in the spike apex and key functional regions in S2 and showed good agreement with two recent studies. 36,37 We next sought to investigate how spike activation from the hACE2− RBD interaction impacts dynamics in the S2 subunit as well as its contribution to viral fusion. In this case, due to the relatively lower stability in SARS-CoV-2 D614 S and difficulty in enriching stable trimer at the desired concentration for further studies, G614 spike was used to investigate how the SARS-CoV-2 S assembly responds to hACE2 activation in comparison with SARS-CoV S. We incubated soluble monomeric hACE2 with the SARS-CoV S trimer, SARS-CoV-2 G614 S trimer, and trimeric tethered SARS-CoV-2 RBD (as an all-RBD-up control) at a molar ratio of 9:1 (3-fold molar excess per protomer), reaching a >99% bound fraction based on their K D values.…”

Peripheral Transcriptomics in Acute and Long-Term Kidney Dysfunction in SARS-CoV2 Infection

“…Third, our current cohort was enrolled in the early pandemic between March-August of 2020. Given the large sample size of our study complicated by SARS-COV2 strain evolution via dynamic positive selection of mutations within the spike protein rather than mutations in the core, 78,79 these results likely generalize across different variants. It would be remiss to not mention the subjective nature of interpretation of peripheral blood RNASeq results as a heterogenous population can be affected by changes in the percentage of cell types.…”