Journal of the American Chemical Society, Vol.132, No.17, 5987-5987, 2010
Direct Use of N-15 Relaxation Rates as Experimental Restraints on Molecular Shape and Orientation for Docking of Protein-Protein Complexes
N-15 relaxation rates contain information on overall molecular shape and size, as well as residue specific orientations of N-H bond vectors relative to the axes of the diffusion tensor. Here we describe a pseudopotential E-relax that permits direct use of N-15 relaxation rates, in the form of R-2/R-1 ratios, as experimental restraints in structure calculations without requiring prior information to be extracted from a known molecular structure. The elements of the rotational diffusion tensor are calculated from the atomic coordinates at each step of the structure calculation and then used together with the N-H bond vector orientations to compute the N-15 R-2/R-1 ratios. We show that the E-relax term can be reliably used for protein-protein docking of complexes and illustrate its applicability to the 40 kDa complex of the N-terminal domain of enzyme I and the histidine phosphocarrier protein HPr and to the symmetric HIV-1 protease dimer.