Related ArticlesCu(II)-Based Paramagnetic Probe to Study RNA-Protein Interactions by NMR.
Inorg Chem. 2017 Mar 22;
Authors: Seebald LM, DeMott CM, Ranganathan S, Asare Okai PN, Glazunova A, Chen A, Shekhtman A, Royzen M
Abstract
Paramagnetic NMR techniques allow for studying three-dimensional structures of RNA-protein complexes. In particular, paramagnetic relaxation enhancement (PRE) data can provide valuable information about long-range distances between different structural components. For PRE NMR experiments, oligonucleotides are typically spin-labeled using nitroxide reagents. The current work describes an alternative approach involving a Cu(II) cyclen-based probe that can be covalently attached to an RNA strand in the vicinity of the protein's binding site using "click" chemistry. The approach has been applied to study binding of HIV-1 nucleocapsid protein 7 (NCp7) to a model RNA pentanucleotide, 5'-ACGCU-3'. Coordination of the paramagnetic metal to glutamic acid residue of NCp7 reduced flexibility of the probe, thus simplifying interpretation of the PRE data. NMR experiments showed attenuation of signal intensities from protein residues localized in proximity to the paramagnetic probe as the result of RNA-protein interactions. The extent of the attenuation was related to the probe's proximity allowing us to construct the protein's contact surface map.
PMID: 28328212 [PubMed - as supplied by publisher]
[NMR paper] Cobalt-based paramagnetic probe to study RNA-protein interactions by NMR.
Cobalt-based paramagnetic probe to study RNA-protein interactions by NMR.
Related Articles Cobalt-based paramagnetic probe to study RNA-protein interactions by NMR.
J Inorg Biochem. 2017 Feb 24;170:202-208
Authors: Seebald LM, DeMott CM, Ranganathan S, Asare-Okai PN, Glazunova A, Chen A, Shekhtman A, Royzen M
Abstract
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Cobalt-based paramagnetic probe to study RNA-protein interactions by NMR
Cobalt-based paramagnetic probe to study RNA-protein interactions by NMR
Publication date: Available online 24 February 2017
Source:Journal of Inorganic Biochemistry</br>
Author(s): Leah M. Seebald, Christopher M. DeMott, Srivathsan Ranganathan, Papa Nii Asare Okai, Anastasia Glazunova, Alan Chen, Alexander Shekhtman, Maksim Royzen</br>
Paramagnetic resonance enhancement (PRE) is an NMR technique that allows studying three-dimensional structures of RNA-protein complexes in solution. RNA strands are typically spin labeled using nitroxide reagents,...
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02-25-2017 06:21 AM
[NMR paper] Structure-based drug design: NMR-based approach for ligand-protein interactions.
Structure-based drug design: NMR-based approach for ligand-protein interactions.
Related Articles Structure-based drug design: NMR-based approach for ligand-protein interactions.
Drug Discov Today Technol. 2006;3(3):241-5
Authors: Zhang X, Tang H, Ye C, Liu M
Abstract
The realization of the powerfulness in analyzing ligand-protein interactions at the atomic resolution has made NMR techniques increasingly attractive in drug discovery and development. With some significant new method developments during the past few years,...
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07-06-2014 08:28 PM
[NMR paper] (19) F NMR Spectroscopy as a Probe of Cytoplasmic Viscosity and Weak Protein Interactions in Living Cells.
(19) F NMR Spectroscopy as a Probe of Cytoplasmic Viscosity and Weak Protein Interactions in Living Cells.
(19) F NMR Spectroscopy as a Probe of Cytoplasmic Viscosity and Weak Protein Interactions in Living Cells.
Chemistry. 2013 Aug 6;
Authors: Ye Y, Liu X, Zhang Z, Wu Q, Jiang B, Jiang L, Zhang X, Liu M, Pielak GJ, Li C
Abstract
Protein mobility in living cells is vital for cell function. Both cytosolic viscosity and weak protein-protein interactions affect mobility, but examining viscosity and weak interaction effects is challenging....
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08-08-2013 03:46 PM
An NMR strategy for fragment-based ligand screening utilizing a paramagnetic lanthanide probe.
An NMR strategy for fragment-based ligand screening utilizing a paramagnetic lanthanide probe.
An NMR strategy for fragment-based ligand screening utilizing a paramagnetic lanthanide probe.
J Biomol NMR. 2011 Sep 17;
Authors: Saio T, Ogura K, Shimizu K, Yokochi M, Burke TR, Inagaki F
Abstract
A nuclear magnetic resonance-based ligand screening strategy utilizing a paramagnetic lanthanide probe is presented. By fixing a paramagnetic lanthanide ion to a target protein, a pseudo-contact shift (PCS) and a paramagnetic relaxation...
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09-20-2011 03:10 PM
An NMR strategy for fragment-based ligand screening utilizing a paramagnetic lanthanide probe
An NMR strategy for fragment-based ligand screening utilizing a paramagnetic lanthanide probe
Abstract A nuclear magnetic resonance-based ligand screening strategy utilizing a paramagnetic lanthanide probe is presented. By fixing a paramagnetic lanthanide ion to a target protein, a pseudo-contact shift (PCS) and a paramagnetic relaxation enhancement (PRE) can be observed for both the target protein and its bound ligand. Based on PRE and PCS information, the bound ligand is then screened from the compound library and the structure of the ligandâ??protein complex is determined. PRE is an...
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09-20-2011 05:02 AM
[NMR paper] Oxygen as a paramagnetic probe of membrane protein structure by cysteine mutagenesis
Oxygen as a paramagnetic probe of membrane protein structure by cysteine mutagenesis and (19)F NMR spectroscopy.
Related Articles Oxygen as a paramagnetic probe of membrane protein structure by cysteine mutagenesis and (19)F NMR spectroscopy.
J Am Chem Soc. 2002 Feb 27;124(8):1778-81
Authors: Luchette PA, Prosser RS, Sanders CR
Oxygen solubility increases toward the hydrophobic interior of membranes. Using NMR, this O(2) solubility gradient gives rise to an exquisite range of position-dependent paramagnetic effects at partial pressures of 100...
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[NMR paper] Probing the surface of a sweet protein: NMR study of MNEI with a paramagnetic probe.
Probing the surface of a sweet protein: NMR study of MNEI with a paramagnetic probe.
Related Articles Probing the surface of a sweet protein: NMR study of MNEI with a paramagnetic probe.
Protein Sci. 2001 Aug;10(8):1498-507
Authors: Niccolai N, Spadaccini R, Scarselli M, Bernini A, Crescenzi O, Spiga O, Ciutti A, Di Maro D, Bracci L, Dalvit C, Temussi PA
The design of safe sweeteners is very important for people who are affected by diabetes, hyperlipemia, and caries and other diseases that are linked to the consumption of sugars. Sweet...
Cu(II)-Based Paramagnetic Probe to Study RNA-Protein Interactions by NMR.
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