Spike protein of SARS2

A.Carbone and F.Oteri work on the Spike protein of SARS2 in collaboration with the group of F.L.Cosset at CIRI in Lyon, expert in non-replicative retroviral pseudoparticles. Based on coevolution analysis of patient sequences and sequences from bats and other species, they aim at identifying key residues in the Spike protein involved in the entry mechanism of the virus in human cells. In the past, the two groups successfully combined their computational and experimental methods to unravel critical features of the original HCV fusion mechanism.

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Statistical Genomics and Biological Physics

The team "Statistical Genomics and Biological Physics" has obtained financial support by the Faculty of Sciences and Engineering of Sorbonne Université, to develop sequence-data driven models of evolutionary landscapes and selective constraints acting in the Covid-19 causing virus SARS-CoV-2. The projects aims at finding signatures of selection in the rapidly increasing number of available genomes, and to interpret them in terms of protein structure, function and protein-protein interactions inside coronaviruses and with the host (e.g. the famous interaction of the viral spike protein with the human ACE2 receptor). 

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Nonribosomal peptide synthetases

Nonribosomal peptide synthetases (NRPSs) are microbial megaenzymes that make a wide variety of small-molecule products, including many that are clinically used as antitumors, antibiotics, or immunosuppressants. Peptide synthesis proceeds with assembly-line logic, where each station on the NRPS assembly line is a multidomain unit called a module. While the function of single modules is well studied, much less is known how they work together. Researchers from the Schmeing lab at McGill University have resolved several dimodular NRPS structures, which show coordinated interactions between modules, and large conformational changes between catalytically relevant states. Martin Weigt from the “Statstical Genomics and Biological Physics” team has performed complementary coevolutionary analyses using the direct coupling analysis (DCA), which confirm the biological relevance and evolutionary conservation of the observed inter-modular interactions. DCA analysis has also allowed to suggest mutations in a module-swapped chimeric NRPS protein, which significantly increased the activity of the protein, a result of direct…

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GEMME

GEMME is a fast, scalable and simple method to predict mutational landscapes from natural sequences. It demonstrates how deleterious effects of a protein mutation are identified by looking at the closest known sequence accepting the mutation in the evolutionary tree of sequences and at its epistatic changes.  The article just appeared in Molecular Biology and Evolution.Link to the articleLink to the webserver

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interacting region

We propose the concept of "interacting region" and the dynJET2 method toward deciphering the complexity underlying protein surface usage and deformability. Interacting regions account for the multiple usage of a protein's surface residues by several partners and for the variability of protein interfaces coming from molecular flexibility. dynJET2 predicts interacting patches by crossing evolutionary, physico‐chemical and geometrical properties of the protein surface with information coming from complete cross‐docking (CC‐D) simulations. Link to the Article

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