Highlight

Machine learning reveals the critical interactions for SARS-CoV‑2. Spike Protein Binding to ACE2 SARS-CoV and SARS-CoV-2 bind to the human ACE2 receptor in practically identical conformations, although several residues of the receptor-binding domain (RBD) differ between them. Herein, we have used molecular dynamics (MD) simulations, machine learning (ML), and free-energy perturbation (FEP) calculations to elucidate the differences in binding by the two viruses. Although only subtle differences were observed from the initial MD simulations of the two RBD–ACE2 complexes, ML identified the individual residues with the most distinctive ACE2 interactions, many of which have been highlighted in previous experimental studies. FEP calculations quantified the corresponding differences in binding free energies to ACE2, and examination of MD trajectories provided structural explanations for these differences. Lastly, the energetics of emerging SARS-CoV-2 mutations were studied, showing that the affinity of the RBD for ACE2 is increased by N501Y and E484K mutations but is slightly decreased by K417N. Journal of Physical Chemistry Letters, 2021.

Recent publications


Structural and functional characterization of DdrC, a novel DNA damage-induced nucleoid associated protein involved in DNA compaction
Anne-Sophie Banneville; Claire Bouthier de la Tour; Salvatore De Bonis; Cecilia Hognon; Jacques-Philippe Colletier; Jean-Marie Teulon; Aline Le Roy; Jean-Luc Pellequer; Antonio Monari; Francois Dehez; Fabrice Confalonieri; Pascale Servant; Joanna Timmins;
Nucleic Acids Research (2022) 50 (13): 7680-7696
Biochemical and Structural Characterization of Chi-Class Glutathione Transferases: A Snapshot on the Glutathione Transferase Encoded by sll0067 Gene in the Cyanobacterium Synechocystis sp. Strain PCC 6803
Eva Mocchetti; Laura Morette; Guillermo Mulliert; Sandrine Mathiot; Benoit Guillot; Francois Dehez; Franck Chauvat; Corinne Cassier-Chauvat; Celine Brochier-Armanet; Claude Didierjean; Arnaud Hecker;
Biomolecules (2022) 12 (10): 1466
Galvani Offset Potential and Constant-pH Simulations of Membrane Proteins
Olivier Bignucolo; Christophe Chipot; Stephan Kellenberger; Benoit Roux;
The Journal of Physical Chemistry B (2022) 23 (36): 6868-6877

News

- Renewal of the Laboratoire International Associé CNRS-University of Illinois at Urbana-Champaign on January 2021
- 新的分子动力学讲义 (Dissemination).
- Kudos to Margaret Blazhynska and Emma Goulard Coderc de Lacam on their DrEAM fellowship supporting their training in the Tajkhorshid and Gumbart research groups.
 

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