  Conformational changes upon protein-protein association are the key element
of the binding mechanism. The study presents a systematic large-scale analysis
of such conformational changes in the side chains. The results indicate that
short and long side chains have different propensities for the conformational
changes. Long side chains with three or more dihedral angles are often subject
to large conformational transition. Shorter residues with one or two dihedral
angles typically undergo local conformational changes not leading to a
conformational transition. The relationship between the local readjustments and
the equilibrium fluctuations of a side chain around its unbound conformation is
suggested. Most of the side chains undergo larger changes in the dihedral angle
most distant from the backbone. The amino acids with symmetric aromatic (Phe
and Tyr) and charged (Asp and Glu) groups show the opposite trend where the
near-backbone dihedral angles change the most. The frequencies of the
core-to-surface interface transitions of six nonpolar residues and Tyr exceed
the frequencies of the opposite, surface-to-core transitions. The binding
increases both polar and nonpolar interface areas. However, the increase of the
nonpolar area is larger for all considered classes of protein complexes. The
results suggest that the protein association perturbs the unbound interfaces to
increase the hydrophobic forces. The results facilitate better understanding of
the conformational changes in proteins and suggest directions for efficient
conformational sampling in docking protocols.
