Protein-protein recognition is key to many biological processes, including immune response and signal transduction. Understanding the molecular interactions responsible for specificity is a real challenge. As an example, we take a close look at the interaction between the peptide-MHC and T Cell receptor proteins. Using molecular dynamics, we dissect hydrogen bonding patterns and energetic contributions of single side chains and of the solvent at the interface. Next, a computational method inspired by double mutants studies is introduced, in order to understand the cooperativity of side chain interactions in protein-protein recognition.
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