title: 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 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.
authors.affiliation: Division of Computational Bioscience, Building 12A, Center for Information Technology, National Institutes of Health, Bethesda, Maryland 20892-5624, USA.
authors.forename: Yaroslav
authors.initials: Y
authors.lastname: Ryabov
authors.forename: G Marius
authors.initials: GM
authors.lastname: Clore
authors.forename: Charles D
authors.initials: CD
authors.lastname: Schwieters
mesh_terms: D009587:Nitrogen Isotopes / Q000737:chemistry*; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*
chemical_list: D009587:Nitrogen Isotopes; D011506:Proteins
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