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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.

SUBMITTER: Ryabov Y

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

REPOSITORIES: biostudies-literature

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

Ryabov Yaroslav Y Clore G Marius GM Schwieters Charles D CD

Journal of the American Chemical Society 20100501 17

(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 tenso ...[more]

PMID: 20392103

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Project description:Protein backbone (15)N spin relaxation rates measured by solution NMR provide useful dynamic information with a site-specific resolution. The conventional method is to record a series of 2D (1)H-(15)N HSQC spectra with varied relaxation delays, and derive relaxation rate from the following curve fitting on the resonance intensities. Proteins with poorly resolved spectra often require several 3D HNCO spectra to be collected on a (15)N/(13)C double labeled protein sample. In order to reduce the relaxation dimension Carr et al. (P.A. Carr, D.A. Fearing, A.G. Palmer, 3D accordion spectroscopy for measuring N-15 and (CO)-Carbon-13 relaxation rates in poorly resolved NMR spectra, J. Magn. Reson. 132 (1998) 25-33) employed an Accordion type HNCO pulse sequence to obtain (15)N or (13)C T(1) relaxation rates by numerical fitting of the relaxation interfered free induction decay (FID) data. To avoid intensive analysis of the time domain data, we propose a modified protocol to measure (15)N T(1) and T(2) relaxation rates from easily obtained line-widths in an Accordion HNCO spectrum. Both T(1) and T(2) relaxation could be simultaneously convoluted into the constant-time evolution periods of (13)C' and (15)N, respectively. The relaxation delay was allowed to reach at least 3 x T(1) or 3 x T(2) so that the signal was substantially decayed by the end of the FID, and the resulting peak full-width at half height (FWHH) could be directly used to calculate relaxation rate. When applied to the 76-residue Ubiquitin and the 226-residue glutamine-binding protein (GlnBP), this method yielded T(1) and T(2) values deviating on average by 4-6% and 5-7%, respectively, from the measurements based on the conventional 2D method. In comparison, the conventional methods possessed intrinsic error ranges of 2-4% for T(1) and 3-6% for T(2). In addition to comparable accuracy, the fully-relaxed Accordion HNCO method presented here allowed measurements of relaxation rates for resonances unresolved in 2D spectra, thus providing a more complete dynamic picture of the protein.

Dataset Information

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

Publications

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

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