Le ministre de la recherche français a dit sa « préoccupation », mercredi, après cette décision des autorités américaines. Le chercheur du CNRS aurait subi un contrôle aléatoire à son arrivée, avant q...

We introduce NRGSuite-Qt, a PyMOL plugin that provides a comprehensive toolkit for protein modeling, virtual screening, normal mode analysis, and binding-site similarity calculations. Building on the ...

The evolution of SARS-CoV-2, the virus responsible for the COVID-19 pandemic, has produced unprece-dented numbers of structures of the Spike protein. This study presents a comprehensive analysis of 1,...

To best serve the needs of researchers, eLife will provide a partial feed of research to be indexed in the Web of Science Core Collection. eLife will also move from the Scopus Journals Collection to…

The evolution of SARS-CoV-2, the virus responsible for the COVID-19 pandemic, has produced unprecedented numbers of structures of the Spike protein. This study presents a comprehensive analysis of 1,560 published Spike protein structures, capturing most variants that emerged throughout the pandemic and covering diverse heteromerization and interacting complexes. We employ an interaction-energy informed geometric clustering to identify 14 epitopes characterized by their conformational specificity, shared interface with ACE2 binding, and glycosylation patterns. Our per-residue interaction evaluations accurately predict each residue's role in antibody recognition and as well as experimental measurements of immune escape, showing strong correlations with DMS data, thus making it possible to predict the behaviour of future variants. We integrate the structural analysis with a longitudinal analysis of nearly 3 million viral sequences. This broad-ranging structural and longitudinal analysis provides insight into the effect of specific mutations on the energetics of interactions and dynamics of the SARS-CoV-2 Spike protein during the course of the pandemic. Specifically, with the emergence of widespread immunity, we observe an enthalpic trade-off in which mutations in the receptor binding motif (RBM) that promote immune escape also weaken the interaction with ACE2. Additionally, we also observe a second mechanism, that we call entropic trade-off, in which mutations outside of the RBM contribute to decrease the occupancy of the open state of SARS-CoV-2 Spike, thus also contributing to immune escape at the expense of ACE2 binding but without changes on the ACE2 binding interface. This work not only highlights the role of mutations across SARS-CoV-2 Spike variants but also reveals the complex interplay of evolutionary forces shaping the evolution of the SARS-CoV-2 Spike protein over the course of the pandemic. ### Competing Interest Statement The authors have declared no competing interest.

"Dreams are primarily visual precisely because this is the only sense that is disadvantaged by darkness."

Energetic local frustration in proteins may have been positively selected by evolution when related to function such as ligand binding, allostery and other. Here the authors present a methodology to a...

PhD Project - Trashzymes: Mining Municipal solid waste and alkaliphilic species for brilliant cleaning at Procter & Gamble, listed on FindAPhD.com

AbstractMotivation. Mappings of domain-cognate ligand interactions can enhance our understanding of the core concepts of evolution and be used to aid docki