Molecular basis of receptor-ligand recognition in the Immunological Synapse
Our long-term goal is to understand the principles underlying molecular recognition and selectivity at the immunological synapse through a multi-disciplinary program exploiting complementary computational and experimental approaches. These studies are essential to (i) understand the molecular basis of normal immune function associated with IgSFs; (ii) define the mechanisms underlying IgSF-associated dysfunction and disease, and (iii) define strategies to re-engineer IgSF receptor:ligand interactions for the realization of surgically defined mutants with altered affinities and selectivities, which can act as biologic drugs
Modeling protein structures, designing novel folds
We are developing a computational approach to model proteins for which a limited number of experimental restraints are available. We utilize our recently developed fragment library of supersecondary structure elements (Smotifs) that was shown to have saturated almost 10 years ago. We hypothesize that all protein folds should be possible to build from this library. We are developing algorithms that take advantage of NMR chemical shift information to identify a subset of Smotifs that form a protein and setting up optimization approaches that will rapidly assemble overlapping Smotifs into compact folds.
Evolution of robustness in gene networks (Protein-DNA interactions, structure based prediction of DNA binding motifs.)
Previous research has shown gene regulatory networks are robust to perturbations at the level of the connections between transcription factors. We investigate the mechanisms underlying the evolution of robustness in gene networks using a modeling approach, which considers three levels: binding of individual transcription factors to DNA, dynamics of gene expression levels, and fitness effects at the population level.