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.
Keywords: Backbone motion, Conformational change, Domain motion, Flexible docking, Intrinsically disordered protein,
Loop motion, Protein binding, Protein complex, Protein conformation, Protein dynamics, Protein flexibility, Protein motion,
Protein-protein docking, Protein-protein interaction, Structural change
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