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[NMR paper] Investigation of Intrinsically Disordered Proteins through Exchange with Hyperpolarized Water
Dec 05, 2016 - 1:06 PM - by nmrlearner
nmrlearner's Avatar Investigation of Intrinsically Disordered Proteins through Exchange with Hyperpolarized Water


Hyperpolarized water can selectively enhance NMR signals of rapidly exchanging protons in osteopontin (OPN), a metastasis-associated intrinsically disordered protein (IDP), at near-physiological pH and temperature. The transfer of magnetization from hyperpolarized water is limited to solvent-exposed residues and therefore selectively enhances signals in 1H-15N correlation spectra. Binding to the polysaccharide heparin was found to induce the unfolding of preformed structural elements in OPN.A fair exchange: The study of intrinsically disordered proteins under physiological conditions is often impeded by weak and overlapping NMR signals. This bottle-neck can be overcome by means of dissolution dynamic nuclear polarization (D-DNP). Selective proton exchange between hyperpolarized water with solvent-exposed amino acids in osteopontin, a metastasis-associated protein, casts light on the binding of this IDP to heparin.

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0 Replies | 7 Views
[Stan NMR blog] Is NMR Stuck?
Dec 04, 2016 - 2:24 AM - by nmrlearner
nmrlearner's Avatar Is NMR Stuck?

A frank Talk about the current state of NMR (not MRI).

Source: Stan blog library
0 Replies | 8 Views
[Stan NMR blog] Update of the popular Mathematical Constants page
Dec 04, 2016 - 2:24 AM - by nmrlearner
nmrlearner's Avatar Update of the popular Mathematical Constants page

All Links and References checked and updated. Also in PDF version.

Source: Stan blog library
0 Replies | 8 Views
[NMR paper] Spin Saturation Transfer Difference NMR (SSTD NMR): A New Tool to Obtain Kinetic Parameters of Chemical Exchange Processes.
Dec 04, 2016 - 2:24 AM - by nmrlearner
nmrlearner's Avatar Spin Saturation Transfer Difference NMR (SSTD NMR): A New Tool to Obtain Kinetic Parameters of Chemical Exchange Processes.

Spin Saturation Transfer Difference NMR (SSTD NMR): A New Tool to Obtain Kinetic Parameters of Chemical Exchange Processes.

J Vis Exp. 2016 Nov 12;(117):

Authors: Quirós MT, Macdonald C, Angulo J, Muñoz MP

Abstract
This detailed protocol describes the new Spin Saturation Transfer Difference Nuclear Magnetic Resonance protocol (SSTD NMR), recently developed in our group to study processes of mutual-site chemical exchange that are difficult to analyze by traditional methods. As the name suggests, this method combines the Spin Saturation Transfer method used for small molecules, with the Saturation Transfer Difference (STD) NMR method employed for the study of protein-ligand interactions, by measuring transient spin saturation transfer along increasing saturation times (build-up curves) in small organic and organometallic molecules undergoing chemical exchange. Advantages of this method over existing ones are: there is no need to reach coalescence of the exchanging signals; the method can be applied as long as one signal of the exchanging sites is isolated; there is no need to measure T1 or reach steady state saturation; rate constant values are measured directly, and T1 values are obtained in the same experiment, using only one set of experiments. To test the method, we have studied the dynamics of the hindered rotation of N,N-dimethylamides, for which much data is available for comparison. The thermodynamic parameters obtained using SSTD are very similar to the reported ones (spin-saturation transfer techniques and... [Read More]
0 Replies | 15 Views
[NMR paper] Orthogonal spin labeling using click chemistry for in vitro and in vivo applications
Dec 03, 2016 - 2:09 PM - by nmrlearner
nmrlearner's Avatar Orthogonal spin labeling using click chemistry for in vitro and in vivo applications

Publication date: Available online 2 December 2016
Source:Journal of Magnetic Resonance

Author(s): Svetlana Kucher, Sergei Korneev, Swati Tyagi, Ronja Apfelbaum, Dina Grohmann, Edward A. Lemke, Johann P. Klare, Heinz-Jürgen Steinhoff, Daniel Klose

Site-directed spin labeling for EPR- and NMR spectroscopy has mainly been achieved exploiting the specific reactivity of cysteines. For proteins with native cysteines or for in vivo applications, an alternative coupling strategy is required. In these cases click chemistry offers major benefits by providing a fast and highly selective, biocompatible reaction between azide and alkyne groups. Here, we establish click chemistry as a tool to target unnatural amino acids in vitro and in vivo using azide- and alkyne-functionalized spin labels. The approach is compatible with a variety of labels including reduction-sensitive nitroxides. Comparing spin labeling efficiencies from the copper-free with the strongly reducing copper(I)-catalyzed azide-alkyne click reaction, we find that the faster kinetics for the catalyzed reaction outrun reduction of the labile nitroxide spin labels and allow quantitative labeling yields within short reaction times. Inter-spin distance measurements demonstrate that the novel side chain is suitable for paramagnetic NMR- or EPR-based conformational studies of macromolecular complexes.
... [Read More]
0 Replies | 10 Views
Seven UCD faculty members elected as AAAS fellows - Davis Enterprise
Dec 02, 2016 - 7:56 PM - by nmrlearner
nmrlearner's Avatar

Seven UCD faculty members elected as AAAS fellows
Davis Enterprise
Ames combines powerful nuclear magnetic resonance techniques with biophysical approaches to make discoveries about the shape and structure of this important family of proteins. Ames' laboratory's long-term goal is to understand how calcium sensor ...

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Seven UCD faculty members elected as AAAS fellows - Davis Enterprise
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0 Replies | 13 Views
[NMR paper] Effect of Glu12-His89 Interaction on Dynamic Structures in HIV-1 p17 Matrix Protein Elucidated by NMR.
Dec 02, 2016 - 7:56 PM - by nmrlearner
nmrlearner's Avatar Effect of Glu12-His89 Interaction on Dynamic Structures in HIV-1 p17 Matrix Protein Elucidated by NMR.

Related Articles Effect of Glu12-His89 Interaction on Dynamic Structures in HIV-1 p17 Matrix Protein Elucidated by NMR.

PLoS One. 2016;11(12):e0167176

Authors: Konagaya Y, Miyakawa R, Sato M, Matsugami A, Watanabe S, Hayashi F, Kigawa T, Nishimura C

Abstract
To test the existence of the salt bridge and stability of the HIV-1 p17 matrix protein, an E12A (mutated at helix 1) was established to abolish possible electrostatic interactions. The chemical shift perturbation from the comparison between wild type and E12A suggested the existence of an electrostatic interaction in wild type between E12 and H89 (located in helix 4). Unexpectedly, the studies using urea denaturation indicated that the E12A substitution slightly stabilized the protein. The dynamic structure of E12A was examined under physiological conditions by both amide proton exchange and relaxation studies. The quick exchange method of amide protons revealed that the residues with faster exchange were located at the mutated region, around A12, compared to those of the wild-type protein. In addition, some residues at the region of helix 4, including H89, exhibited faster exchange in the mutant. In contrast, the average values of the kinetic rate constants for amide proton exchange for residues located in all loop regions were slightly lower in E12A than in wild type. Furthermore, the analyses of the order... [Read More]
0 Replies | 18 Views
Nuclear spin-lattice relaxation in nitroxide spin-label EPR
Dec 02, 2016 - 7:56 PM - by nmrlearner
nmrlearner's Avatar From The DNP-NMR Blog:

Nuclear spin-lattice relaxation in nitroxide spin-label EPR

p.p1 {margin: 0.0px 0.0px 0.0px 36.0px; text-indent: -36.0px; font: 12.0px Helvetica}
Marsh, D., Nuclear spin-lattice relaxation in nitroxide spin-label EPR. J Magn Reson, 2016. 272: p. 166-171.


https://www.ncbi.nlm.nih.gov/pubmed/27712989


Nuclear relaxation is a sensitive monitor of rotational dynamics in spin-label EPR. It also contributes competing saturation transfer pathways in T1-exchange spectroscopy, and the determination of paramagnetic relaxation enhancement in site-directed spin labelling. A survey shows that the definition of nitrogen nuclear relaxation rate Wn commonly used in the CW-EPR literature for 14N-nitroxyl spin labels is inconsistent with that currently adopted in time-resolved EPR measurements of saturation recovery. Redefinition of the normalised 14N spin-lattice relaxation rate, b=Wn/(2We), preserves the expressions used for CW-EPR, whilst rendering them consistent with expressions for saturation recovery rates in pulsed EPR. Furthermore, values routinely quoted for nuclear relaxation times that are deduced from EPR spectral diffusion rates in 14N-nitroxyl spin labels do not accord with conventional analysis of spin-lattice relaxation in this three-level system. Expressions for CW-saturation EPR with the revised definitions are summarised. Data on nitrogen nuclear spin-lattice relaxation times are compiled according to the three-level scheme for 14N-relaxation: T1n=1/Wn. Results are compared and contrasted with those for the two-level 15N-nitroxide system.
... [Read More]
0 Replies | 14 Views
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