Conformational ensembles of noncoding elements in the SARS-CoV-2 genome from molecular dynamics simulations

S Bottaro, G Bussi… - Journal of the American …, 2021 - ACS Publications
… studies using locked nucleic acids … conformational heterogeneity of five stem-loop elements,
ranging in size between 17 and 44 nucleotides, located at the 5′-UTR in the SARS-CoV-2 …

Conformational dynamics of SARS-CoV-2 trimeric spike glycoprotein in complex with receptor ACE2 revealed by cryo-EM

C Xu, Y Wang, C Liu, C Zhang, W Han, X Hong… - Science …, 2021 - science.org
… of SARS-CoV-2 RBD by ACE2. Our findings depict the mechanism of ACE2-induced S trimer
conformational … , facilitating development of anti–SARS-CoV-2 vaccines and therapeutics. …

Double lock of a potent human therapeutic monoclonal antibody against SARS-CoV-2

L Zhu, YQ Deng, RR Zhang, Z Cui… - National Science …, 2021 - academic.oup.com
… Cryo-EM studies on complex of SARS-CoV-2 trimeric S with HB27 Fab … SARS-CoV-2 from
binding to the ACE2 receptor. Binding of the antibody also restrains any further conformational

[HTML][HTML] Predicted pH-dependent stability of SARS-CoV-2 spike protein trimer from interfacial acidic groups

VR Lobo, J Warwicker - Computational and structural biotechnology journal, 2021 - Elsevier
… in a locked conformation. According to this model, their replacement (perhaps with asparagine)
would remove the pH-dependent destabilisation of locked spike trimer conformations, …

[PDF][PDF] A new inactive conformation of SARS-CoV-2 main protease

E Fornasier, ML Macchia, G Giachin… - … Section D: Structural …, 2022 - journals.iucr.org
… incompetent conformation and that many of the key interactions of the active conformation
of … This novel conformation is relevant both for comprehension of the mechanism of action of …

Distinct conformational states of SARS-CoV-2 spike protein

Y Cai, J Zhang, T Xiao, H Peng, SM Sterling… - Science, 2020 - science.org
… The overall architecture of the SARS-CoV-2 S2 in the postfusion conformation is nearly …
-S2' fragment makes up three helical regions locked by two disulfide bonds that pack against the …

SARS-COV-2 Mpro conformational changes induced by covalently bound ligands

GM Ferreira, T Kronenberger, AK Tonduru… - Journal of …, 2022 - Taylor & Francis
… We hypothesize that the Phe140-His163 π-π interaction (with an average distance of ∼4.1
Å, Figure 5I ) would be relevant to lock His163 in a hydrogen bond prone conformation. …

Proton-coupled conformational activation of SARS coronavirus main proteases and opportunity for designing small-molecule broad-spectrum targeted covalent …

N Verma, JA Henderson, J Shen - Journal of the American …, 2020 - ACS Publications
… However, when His172 is charged, it forms a salt bridge with Glu166, which locks Glu166 in
SARS-CoV Mpro, our data provides a detailed molecular mechanism of the conformational

Energy landscape of the SARS-CoV-2 reveals extensive conformational heterogeneity

G Mashayekhi, J Vant, A Polavarapu… - Current Research in …, 2022 - Elsevier
… the SARS-CoV-2 Spike Protein spanned by two conformational coordinates. In this study,
each continuous conformational … A conformational coordinate consists of a space of 50 binned …

… protein stability analysis and network modeling of multiple conformational states of the SARS-CoV-2 Spike D614G mutant: conformational plasticity and frustration …

GM Verkhivker, S Agajanian, R Kassab… - Journal of Chemical …, 2022 - ACS Publications
… -CoV-2 spike protein … the conformational flexibility and energetic frustration at the interprotomer
interfaces may serve as an efficient mechanism for allosteric regulation of the SARS-CoV-…