Structural insights in cell-type specific evolution of intra-host diversity by SARS-CoV-2

K Gupta, C Toelzer, MK Williamson… - Nature …, 2022 - nature.com
… In our analysis, all BriSΔ particles exhibited the locked conformation of the S trimer we
had described previously 23 . After applying 3-fold symmetry (C3) we obtained a 2.8 Å cryo-EM …

Molecular simulations suggest vitamins, retinoids and steroids as ligands of the free fatty acid pocket of the SARSCoV‐2 Spike protein

DK Shoemark, CK Colenso, C Toelzer… - Angewandte …, 2021 - Wiley Online Library
… BUDE docks linoleate into the locked SARS-CoV-2 spike trimer in a conformation
consistent with cryo-EM structures. A) Cryo-EM structure of the LA − -bound spike trimer in the …

[HTML][HTML] Structural insight into SARS-CoV-2 neutralizing antibodies and modulation of syncytia

D Asarnow, B Wang, WH Lee, Y Hu, CW Huang… - Cell, 2021 - cell.com
… ACE2 binding but also alter the Spike protein conformational cycle triggered by ACE2
binding. We show that stabilization of different Spike conformations leads to modulation of Spike-…

The molecular mechanism of domain swapping of the C-terminal domain of the SARS-Coronavirus Main Protease

VL Terse, S Gosavi - Biophysical Journal, 2021 - cell.com
… pro (M pro C) locks M pro into a hyperactive … conformations by mutations or ligand binding.
Finally, because all residues in the tryptophan loop are identical in SARS-CoV and SARS-CoV

SARSCoV‐2 structural coverage map reveals viral protein assembly, mimicry, and hijacking mechanisms

SI O'Donoghue, A Schafferhans, N Sikta… - Molecular systems …, 2021 - embopress.org
We modeled 3D structures of all SARSCoV‐2 proteins, generating 2,060 models that span
69% of the viral proteome and provide details not available elsewhere. We found that 6% of …

Computational insight into the mechanism of SARS-CoV-2 membrane fusion

S Borkotoky, D Dey, M Banerjee - Journal of Chemical Information …, 2021 - ACS Publications
… Taken together, this shows that of all of the conformations tested, only the trimeric form of
SARS-CoV-2 FP-L is capable of triggering the formation of a fusion bridge between dual …

Serine 477 plays a crucial role in the interaction of the SARS-CoV-2 spike protein with the human receptor ACE2

A Singh, G Steinkellner, K Köchl, K Gruber… - Scientific reports, 2021 - nature.com
… highly dynamic loop in the SARS-CoV-2 spike protein RBM from residue 475 to 485. It is
predicted by induced fit theory 39 that the binding event induces a conformational change at the …

Structural basis of RNA recognition by the SARS-CoV-2 nucleocapsid phosphoprotein

DC Dinesh, D Chalupska, J Silhan, E Koutna… - PLoS …, 2020 - journals.plos.org
… structures it is locked in one place by crystal lattice contacts. … a set of water-refined
conformations for the protein:dsRNA … it was selected as a representative conformation for the …

Impact of SARS-CoV-2 spike stability and RBD exposure on antigenicity and immunogenicity

L Rutten, M Swart, A Koornneef, P Bouchier… - Scientific Reports, 2024 - nature.com
… In addition, further stabilization of the prefusion conformation of spike might improve … (S-locked),
in which the receptor binding domains (RBDs) were locked in a closed conformation and …

Multivalent designed proteins neutralize SARS-CoV-2 variants of concern and confer protection against infection in mice

AC Hunt, JB Case, YJ Park, L Cao, K Wu… - Science translational …, 2022 - science.org
… syndrome coronavirus 2 (SARS-CoV-2) continue to arise and prolong the coronavirus
containing multiple computationally designed miniprotein inhibitors of SARS-CoV-2. We found the …