My research
Co-evolution of blocks of residues in proteins and their specialization along phylogenetic trees. It has been demonstrated that evolutionarily conserved networks of residues mediate allosteric communication in proteins involved in cellular signaling, the process by which signals originating at one site in a protein propagate reliably to affect distant functional sites. The general principles of protein structure that underlie this process remain unknown. In a seminal paper Ranganathan described a sequence-based statistical method for quantitatively mapping the global network of amino acid interactions in a protein.
The method reveals a surprisingly simple architecture for amino acid interactions in each protein family: a small subset of residues forms physically connected networks that link distant functional sites in the tertiary structure. The evolutionarily conserved sparse networks of amino acid interactions are proposed as representative structural motifs for allosteric communication in proteins.
To investigate further Ranganathan approach, Baussand developed a new method, based on a fine combinatorial analysis of phyogenetic trees associated to a protein family to reconstruct networks of co-evolved residues from sequence analysis. The approach was used to detect motifs of co-evolved residues which will be used to detect distantly related protein pairs. Our new aim is first to undertand the differences between the statistcal methodologies and the combinatorial one. Second we will define blocks of residues that co-evolve.