Paramagnetic relaxation enhancement (PRE) is a versatile tool for NMR spectroscopic structural and kinetic studies in biological macromolecules. Here, we compare the quality of PRE data derived from two spin labels with markedly different dynamic properties for large RNAs using the I-A riboswitch aptamer domain (78 nt) from Mesoplamsa florum as model system. We designed two I-A aptamer constructs that were spin-labeled by noncovalent hybridization of short spin-labeled oligomer fragments. As an example of a flexible spin label, UreidoU-TEMPO was incorporated into the 3â?² terminal end of helix P1 while, the recently developed rigid spin-label Ã?m was incorporated in the 5â?² terminal end of helix P1. We determined PRE rates obtained from aromatic 13C bound proton intensities and compared these rates to PREs derived from imino proton intensities in this sizeable RNA (~78 nt). PRE restraints derived from both imino and aromatic protons yielded similar data quality, and hence can both be reliably used for PRE determination. For NMR, the data quality derived from the rigid spin label Ã?m is slightly better than the data quality for the flexible UreidoTEMPO as judged by comparison of the structural agreement with the I-A aptamer crystal structure (3SKI).
[NMR paper] A Triarylmethyl Spin Label for Long-Range Distance Measurement at Physiological Temperatures Using T1 Relaxation Enhancement
A Triarylmethyl Spin Label for Long-Range Distance Measurement at Physiological Temperatures Using T1 Relaxation Enhancement
Publication date: Available online 10 May 2016
Source:Journal of Magnetic Resonance</br>
Author(s): Zhongyu Yang, Michael D. Bridges, Carlos J. López, Olga Yu. Rogozhnikova, Dmitry V. Trukhin, Evan K. Brooks, Victor Tormyshev, Howard J. Halpern, Wayne L. Hubbell</br>
Site-directed spin labeling (SDSL) in combination with Electron Paramagnetic Resonance (EPR) spectroscopy has become an important tool for measuring distances in...
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05-11-2016 08:04 PM
The Spatial Effect of Protein Deuteration on Nitroxide Spin-label Relaxation: Implications for EPR Distance Measurement
The Spatial Effect of Protein Deuteration on Nitroxide Spin-label Relaxation: Implications for EPR Distance Measurement
Publication date: Available online 28 September 2014
Source:Journal of Magnetic Resonance</br>
Author(s): Hassane. El Mkami , Richard Ward , Andrew Bowman , Tom Owen-Hughes , David G. Norman</br>
Pulsed electron-electron double resonance (PELDOR) coupled with site-directed spin labeling is a powerful technique for the elucidation of protein or nucleic acid, macromolecular structure and interactions. The intrinsic high sensitivity of electron...
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09-28-2014 08:03 PM
VITAL NMR: using chemical shift derived secondary structure information for a limited set of amino acids to assess homology model accuracy
VITAL NMR: using chemical shift derived secondary structure information for a limited set of amino acids to assess homology model accuracy
Abstract Homology modeling is a powerful tool for predicting protein structures, whose success depends on obtaining a reasonable alignment between a given structural template and the protein sequence being analyzed. In order to leverage greater predictive power for proteins with few structural templates, we have developed a method to rank homology models based upon their compliance to secondary structure derived from experimental solid-state NMR...
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12-22-2011 06:50 AM
Impact of (15)N R(2)/R(1) Relaxation Restraints on Molecular Size, Shape, and Bond Vector Orientation for NMR Protein Structure Determination with Sparse Distance Restraints.
Impact of (15)N R(2)/R(1) Relaxation Restraints on Molecular Size, Shape, and Bond Vector Orientation for NMR Protein Structure Determination with Sparse Distance Restraints.
Impact of (15)N R(2)/R(1) Relaxation Restraints on Molecular Size, Shape, and Bond Vector Orientation for NMR Protein Structure Determination with Sparse Distance Restraints.
J Am Chem Soc. 2011 Apr 4;
Authors: Ryabov Y, Schwieters CD, Clore GM
(15)N R(2)/R(1) relaxation data contain information on molecular shape and size as well as on bond vector orientations relative to...
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Impact of 15N R2/R1 Relaxation Restraints on Molecular Size, Shape, and Bond Vector Orientation for NMR Protein Structure Determination with Sparse Distance Restraints
Impact of 15N R2/R1 Relaxation Restraints on Molecular Size, Shape, and Bond Vector Orientation for NMR Protein Structure Determination with Sparse Distance Restraints
Yaroslav Ryabov, Charles D. Schwieters and G. Marius Clore
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja201020c/aop/images/medium/ja-2011-01020c_0002.gif
Journal of the American Chemical Society
DOI: 10.1021/ja201020c
http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA
http://feeds.feedburner.com/~r/acs/jacsat/~4/3J1IyCLkQMQ
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04-05-2011 10:37 AM
[NMR paper] Increased rigidity of eglin c at acidic pH: evidence from NMR spin relaxation and MD
Increased rigidity of eglin c at acidic pH: evidence from NMR spin relaxation and MD simulations.
Related Articles Increased rigidity of eglin c at acidic pH: evidence from NMR spin relaxation and MD simulations.
Biochemistry. 2003 Dec 2;42(47):13856-68
Authors: Hu H, Clarkson MW, Hermans J, Lee AL
To gain physical insights into how proteins respond to changes in pH, the picosecond to nanosecond time scale dynamics of the small serine protease inhibitor eglin c have been studied by NMR spin relaxation experiments and MD simulations under two...
Impact of spin label rigidity on extent and accuracy of distance information from PRE data
Linear Mode
