Using the experimentally determined components of the overall rotational diffusion tensor to restrain molecular shape and size in NMR structure determination of globular proteins and protein-protein complexes.
This paper describes an approach for making use of the components of the experimentally determined rotational diffusion tensor derived from NMR relaxation measurements in macromolecular structure determination. The parameters of the rotational diffusion tensor describe the shape and size of the macromolecule or macromolecular complex, and are therefore complementary to traditional NMR restraints. The structural information contained in the rotational diffusion tensor is not dissimilar to that present in the small-angle region of solution X-ray scattering profiles. We demonstrate the utility of rotational diffusion tensor restraints for protein structure refinement using the N-terminal domain of enzyme I (EIN) as an example and validate the results by solution small-angle X-ray scattering. We also show how rotational diffusion tensor restraints can be used for docking complexes using the dimeric HIV-1 protease and the EIN-HPr complexes as examples. In the former case, the rotational diffusion tensor restraints are sufficient in their own right to determine the position of one subunit relative to another. In the latter case, rotational diffusion tensor restraints complemented by highly ambiguous distance restraints derived from chemical shift perturbation mapping and a hydrophobic contact potential are sufficient to correctly dock EIN to HPr. In each case, the cluster containing the lowest-energy structure corresponds to the correct solution.
Ryabov
Yaroslav
Y
Division of Computational Bioscience, Building 12A, Center for Information Technology, National Institutes of Health, Bethesda, Maryland 20892-5624, USA.
Suh
Jeong-Yong
JY
Grishaev
Alexander
A
Clore
G Marius
GM
Schwieters
Charles D
CD
D001426:Bacterial Proteins / Q000737:chemistry*; D003198:Computer Simulation; D004058:Diffusion; D019281:Dimerization; D016333:HIV Protease / Q000737:chemistry; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D017434:Protein Structure, Tertiary
D001426:Bacterial Proteins; D016333:HIV Protease; C514803:p16 protease, Human immunodeficiency virus 1