Protein-Protein interactions:

Using explicit water molecular dynamics simulations and free energy estimates we try to understand the mechanisms of protein recognition. Our efforts have recently unveiled a new view on this subject, emphasizing the role of desolvation as a dominant force in recognition. We have also found that nanoscale receptor-ligand interactions stemming from electrostatic and solvation effects tunes the association time scales over a range spanning as much as 5 orders of magnitude in complexes where long electrostatics provide the specificty for recognition. Desolvation mediated complexes only span 3 order magnitude. Simulations have explicitly revealed that recognition arises from an optimized molecular key already encoded in the protein's primary structure. Similarly, well defined non-covalent, and non-specific, bonds are responsible for locking the encounter complex in place.

See Anchor residues in protein-protein interactions, PNAS 2004
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