NMR Research Today is a free monthly online journal that collates and summarizes the latest research about NMR, including details on nuclear magnetic resonance, structural determination, techniques.

Backbone amide dynamics studies of Apo-L75F-TrpR, a temperature-sensitive mutant of the tryptophan repressor protein (TrpR): comparison with the (15)N NMR relaxation profiles of wild-type and A77V mutant Apo-TrpR repressors.

Goel A, Tripet BP, Tyler RC, Nebert LD, Copié V

Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, USA.

Backbone amide dynamics studies were conducted on a temperature-sensitive mutant (L75F-TrpR) of the tryptophan repressor protein (TrpR) of Escherichia coli in its apo (i.e., no l-tryptophan corepressor-bound) form. The (15)N NMR relaxation profiles of apo-L75F-TrpR were analyzed and compared to those of wild-type (WT) and super-repressor mutant (A77V) TrpR proteins, also in their apo forms. The (15)N NMR relaxation data ((15)N-T(1), (15)N-T(2), and heteronuclear (15)N-{(1)H}-nOe) recorded on all three aporepressors at a magnetic field strength of 600 MHz ((1)H Larmor frequency) were analyzed to extract dynamics parameters, including diffusion tensor ratios (D(∥)/D(⊥)), correlation times (τ(m)) for overall reorientations of the proteins in solution, reduced spectral density terms [J(eff)(0), J(0.87ω(H)), J(ω(N))], and generalized order parameters (S(2)), which report on protein internal motions on the picosecond to nanosecond and slower microsecond to millisecond chemical exchange time scales. Our results indicate that all three aporepressors exhibit comparable D(∥)/D(⊥) ratios and characteristic time constants, τ(m), for overall global reorientation, indicating that in solution, all three apoproteins display very similar overall shape, structure, and rotational diffusion properties. Comparison of (15)N NMR relaxation data, reduced spectral density profiles, and generalized S(2) order parameters indicated that these parameters are quite uniform for backbone amides positioned within the four (A-C and F) core α-helices of all three aporepressors. In contrast, small but noticeable differences in internal dynamics were observed for backbone amides located within the helix D-turn-helix E DNA-binding domain of the apo-TrpR proteins. The significance of these dynamics differences in terms of the biophysical characteristics and ligand binding properties of the three apo-TrpR proteins is discussed.

Published 14 September 2010 in Biochemistry, 49(37): 8006-19.
Full-text of this article is available online (may require subscription).

Articles on NMR published 14 September 2010:

NMR studies of translocation of the Zif268 protein between its target DNA Sites.   Biochemistry, 49(37): 7998-8005.

Zif268 is a zinc-finger protein containing three Cys(2)-His(2)-type zinc-finger domains that bind the target DNA sequence GCGTGGGCG in a cooperative manner. In this work, we characterized translocation of the Zif268 protein between its target DNA sites using NMR spectroscopy. The residual dipolar coupling data and NMR chemical shift data suggested that the structure of the sequence-specific complex between Zif268 and its target DNA in solution is the same as the crystal structure. Using ... [Abstract] [Full-text]

Articles on NMR published 1 September 2009:

Enzymology with a spin-labeled phospholipase C: soluble substrate binding by 31P NMR from 0.005 to 11.7 T.   Biochemistry, 48(35): 8282-4.

31P NMR relaxation studies from 0.005 to 11.7 T are used to monitor water-soluble inositol 1,2-(cyclic) phosphate (cIP) binding to phosphatidylinositol-specific phospholipase C spin-labeled at H82C, a position near the active site of the enzyme, and to determine how activating phosphatidylcholine (PC) molecules affect this interaction. We show that, in the absence of an interface, cIP binding to the protein is not rate-limiting, and that lower activation by PC vesicles as opposed to micelles is ... [Abstract] [Full-text]

Articles on NMR published 17 August 2009:

A nonlinear BOLD model accounting for refractory effect by applying the longitudinal relaxation in NMR to the linear BOLD model.   Magn Reson Imaging, 27(7): 907-12.

A mathematical model to regress the nonlinear blood oxygen level-dependent (BOLD) fMRI signal has been developed by incorporating the refractory effect into the linear BOLD model of the biphasic gamma variate function. The refractory effect was modeled as a relaxation of two separate BOLD capacities corresponding to the biphasic components of the BOLD signal in analogy with longitudinal relaxation of magnetization in NMR. When tested with the published fMRI data of finger tapping, the nonlinear ... [Abstract] [Full-text]

Articles on NMR published 15 June 2009:

1H NMR titration and quantum calculation for the inclusion complexes of cis-cyclooctene, cis, cis-1, 3-cyclooctadiene and cis, cis-1, 5-cyclooctadiene with beta-cyclodextrin.   Spectrochim Acta A Mol Biomol Spectrosc, 73(4): 713-8.

The inclusion behavior of cis-cyclooctene, cis, cis-1, 3-cyclooctadiene and cis, cis-1, 5-cyclooctadiene with beta-cyclodextrin (beta-CD) was studied by using (1)H NMR method in D(2)O/CD(3)OD solution and PM3 quantum-chemical simulation in vacuum. The experimental results indicate that each guest molecule penetrates deeply into beta-CD cavity and forms equimolecular inclusion complex with the host. The association constants of the complexes were determined by non-linear least-square method on ... [Abstract] [Full-text]

Articles on NMR published 27 March 2009:

Reversible interactions with para-hydrogen enhance NMR sensitivity by polarization transfer.   Science, 323(5922): 1708-11.

The sensitivity of both nuclear magnetic resonance spectroscopy and magnetic resonance imaging is very low because the detected signal strength depends on the small population difference between spin states even in high magnetic fields. Hyperpolarization methods can be used to increase this difference and thereby enhance signal strength. This has been achieved previously by incorporating the molecular spin singlet para-hydrogen into hydrogenation reaction products. We show here that a metal ... [Abstract] [Full-text]

Articles on NMR published 27 February 2009:

Metabolic and hemodynamic events after changes in neuronal activity: current hypotheses, theoretical predictions and in vivo NMR experimental findings.   J Cereb Blood Flow Metab, 29(3): 441-63.

Unraveling the energy metabolism and the hemodynamic outcomes of excitatory and inhibitory neuronal activity is critical not only for our basic understanding of overall brain function, but also for the understanding of many brain disorders. Methodologies of magnetic resonance spectroscopy (MRS) and magnetic resonance imaging (MRI) are powerful tools for the noninvasive investigation of brain metabolism and physiology. However, the temporal and spatial resolution of in vivo MRS and MRI is not ... [Abstract] [Full-text]

Articles on NMR published 8 January 2009:

Water and salt distribution in Atlantic salmon (Salmo salar) studied by low-field 1H NMR, 1H and 23Na MRI and light microscopy: effects of raw material quality and brine salting.   J Agric Food Chem, 57(1): 46-54.

The effect of different Atlantic salmon raw materials (prerigor, postrigor and frozen/thawed) on water mobility and salt uptake after brine salting was investigated by using LF 1H NMR T2 relaxation,1H and 23Na MRI and light microscopy. Distributed exponential analysis of the T2 relaxation data revealed two main water pools in all raw materials, T21 and T22, with relaxation times in the range of 20-100 ms and 100-300 ms, respectively. Raw material differences were reflected in the T2 relaxation ... [Abstract] [Full-text]

Articles on NMR published 21 November 2008:

Dynamic NMR effects in breast cancer dynamic-contrast-enhanced MRI.   Proc Natl Acad Sci U S A, 105(46): 17937-42.

The passage of a vascular-injected paramagnetic contrast reagent (CR) bolus through a region-of-interest affects tissue (1)H(2)O relaxation and thus MR image intensity. For longitudinal relaxation [R(1) identical with (T(1))(-1)], the CR must have transient molecular interactions with water. Because the CR and water molecules are never uniformly distributed in the histological-scale tissue compartments, the kinetics of equilibrium water compartmental interchange are competitive. In particular, ... [Abstract] [Full-text]

© 2005-2011 NMR Research Today. All Rights Reserved.