Direct use of 15N relaxation rates as experimental restraints on molecular shape and orientation for docking of protein-protein complexes.

ABSTRACT: (15)N 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 (15)N 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 (15)N 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 a

SUBMITTER: Ryabov Y 

PROVIDER: S-EPMC2872242 | biostudies-literature | 2010 May

REPOSITORIES: biostudies-literature