Interaction cutoff effect on ruggedness of protein-protein energy landscape

The concept of the energy landscape is important for better understanding of protein–protein interactions and for designing adequate docking procedures. The intermolecular landscape has a rugged terrain that impedes search procedures. Its inherent ruggedness is related to the conformational characteristics of the molecules and to the form of the potential function—more rugged for short‐range potentials and less rugged for “soft,” typically long‐range potentials. Our study determined that the landscape ruggedness is further substantially exacerbated by truncation of the potentials. This additional ruggedness appears below certain critical interaction ranges that depend on the form of the potential. The theoretical model describing the cutoff effect on the landscape ruggedness is confirmed by the energy calculation on a dataset of protein–protein complexes. The negative effect of the potentials cutoff is well known. However, revealing its physical basis in terms of the energy landscape is important for better understanding of intermolecular interactions. Proteins 2008. © 2007 Wiley‐Liss, Inc.