Treating Conformational Flexibility in Protein-Protein Docking

Modelling how proteins bind to one another is a challenging task, in part due to the conformational changes that can occur upon complex formation. We here describe the various types of motion that occur upon protein binding and discuss their treatment in computational protein-protein docking methods to predict the structure of the bound complex. Considered are five different categories of structural change, that cover timescales from picoseconds to milliseconds and amplitudes extending to tens of angstroms. First small-scale motion, which includes bond stretching, bond angle bending and dihedral rotation is addressed. This is followed by larger motions of the protein main-chain, the loops and entire protein domains. Finally, we consider the class of intrinsically disordered proteins including protein segments that refold upon binding. For each category, the capabilities and limitations of current docking procedures are discussed by means of an illustrative example.