Large-scale characteristics of the energy landscape in protein-protein interactions

Characterization of intermolecular energy landscapes in protein-protein interactions is important for understanding the mechanisms of these interactions as well as for designing better protein docking methods. A simplified representation of the landscape was used for a systematic study of its large-scale characteristics in a large nonredundant dataset of protein complexes. The focus of the study is on the basic features of the low-resolution energy basins and their distribution on the landscape. The results clearly show that, in general, the number of such basins is small, these basins are well formed, correlated with actual binding modes, and the pattern of basins distribution depends on the type of the complex. For docking studies, the results suggest that adequate starting points for the structural refinement are detectable by low-resolution procedures and the number of such starting points is relatively small.