2H NMR Spin Relaxation for studying RNA dynamics

		BioNMR > Educational resources > Journal club
2H NMR Spin Relaxation for studying RNA dynamics

Webservers

NMR processing:

MDD

NMR assignment:

Backbone:

Side-chains:

NOEs:

Structure from NMR restraints:

Ab initio:

Fragment-based:

Rosetta-NMR (Robetta)

Template-based:

GeNMR

I-TASSER

Refinement:

Amber

Structure from chemical shifts:

Fragment-based:

Homology-based:

Torsion angles from chemical shifts:

Preditor

TALOS

Promega- Proline

Secondary structure from chemical shifts:

CSI (via RCI server)

TALOS

MICS caps, β-turns

d2D

PECAN

Flexibility from chemical shifts:

RCI

Interactions from chemical shifts:

HADDOCK

Chemical shifts re-referencing:

NMR model quality:

NOEs, other restraints:

Chemical shifts:

RDCs:

Pseudocontact shifts:

Protein geomtery:

SAVES2 or SAVES4

Quality Control Check

NMR spectrum prediction:

FANDAS

MestReS

V-NMR

Flexibility from structure:

Backbone S2

Methyl S2

B-factor

Molecular dynamics:

Gromacs

Amber

Antechamber

Chemical shifts prediction:

From structure:

Shiftx2

Sparta+

Camshift

CH3shift- Methyl

ArShift- Aromatic

ShiftS

Proshift

PPM

CheShift-2- Cα

From sequence:

Shifty

Camcoil

Poulsen_rc_CS

Disordered proteins:

MAXOCC

Format conversion & validation:

CCPN

From NMR-STAR 3.1

Validate NMR-STAR 3.1

NMR sample preparation:

Protein disorder:

DisMeta

Protein solubility:

Isotope labeling:

Solid-state NMR:

View First Unread

Thread Tools

Search this Thread

Rate Thread

Display Modes

05-19-2005, 08:44 AM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,174

Points: 193,617, Level: 100

Level up: 0%, 0 Points needed

Activity: 50.7%

Last Achievements

Award-Showcase

NMR Credits: 0

NMR Points: 193,617

Downloads: 0

Uploads: 0

A Suite of 2H NMR Spin Relaxation Experiments for the Measurement of RNA Dynamics
Pramodh Vallurupalli and Lewis E. Kay, J. Am. Chem. Soc.; 2005; 127 (18) pp 6893 - 6901

ABSTRACT:

A suite of (2)H-based spin relaxation NMR experiments is presented for the measurement of molecular dynamics in a site-specific manner in uniformly (13)C, randomly fractionally deuterated ( approximately 50%) RNA molecules. The experiments quantify (2)H R(1) and R(2) relaxation rates that can subsequently be analyzed to obtain information about dynamics on a pico- to nanosecond time scale. Sensitivity permitting, the consistency of the data can be evaluated by measuring all five rates that are accessible for a spin 1 particle and establishing that the rates obey relations that are predicted from theory. The utility of the methodology is demonstrated with studies of the dynamics of a 14-mer RNA containing the UUCG tetraloop at temperatures of 25 and 5 degrees C. The high quality of the data, even at 5 degrees C, suggests that the experiments will be of use for the study of RNA molecules that are as large as 30 nucleotides.

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Water proton spin saturation affects measured protein backboneN spin relaxation rates Water proton spin saturation affects measured protein backboneN spin relaxation rates Publication year: 2011 Source: Journal of Magnetic Resonance, Available online 1 October 2011</br> KangChen, NicoTjandra</br> Protein backboneN NMR spin relaxation rates are useful in characterizing the protein dynamics and structures. To observe the protein nuclear-spin resonances a pulse sequence has to include a water suppression scheme. There are two commonly employed methods, saturating or dephasing the water spins with pulse field gradients and keeping them unperturbed with flip-back pulses....	nmrlearner	Journal club	0	10-02-2011 08:25 AM
Active site dynamics in NADH oxidase from Thermus thermophilus studied by NMR spin relaxation Active site dynamics in NADH oxidase from Thermus thermophilus studied by NMR spin relaxation Abstract We have characterized the backbone dynamics of NADH oxidase from Thermus thermophilus (NOX) using a recently-developed suite of NMR experiments designed to isolate exchange broadening, together with 15N R 1, R 1Ï? , and {1H}-15N steady-state NOE relaxation measurements performed at 11.7 and 18.8 T. NOX is a 54 kDa homodimeric enzyme that belongs to a family of structurally homologous flavin reductases and nitroreductases with many potential biotechnology applications. Prior studies...	nmrlearner	Journal club	0	09-30-2011 08:01 PM
[NMR tweet] http://www.pulist.net/spin-dynamics-basics-of-nuclear-magnetic-resonance.html #quarks #and #nucleons #nuclear Spin Dynamics: Basics of N http://www.pulist.net/spin-dynamics-basics-of-nuclear-magnetic-resonance.html #quarks #and #nucleons #nuclear Spin Dynamics: Basics of N Published by pubooks (Joel Michal) on 2011-03-31T07:54:11Z Source: Twitter	nmrlearner	Twitter NMR	0	03-31-2011 08:09 AM
Structure, Dynamics, and Kinetics of Weak Protein-Protein Complexes from NMR Spin Relaxation Measurements of Titrated Solutions. Structure, Dynamics, and Kinetics of Weak Protein-Protein Complexes from NMR Spin Relaxation Measurements of Titrated Solutions. Structure, Dynamics, and Kinetics of Weak Protein-Protein Complexes from NMR Spin Relaxation Measurements of Titrated Solutions. Angew Chem Int Ed Engl. 2011 Mar 18; Authors: Salmon L, Ortega Roldan JL, Lescop E, Licinio A, van Nuland N, Jensen MR, Blackledge M	nmrlearner	Journal club	0	03-23-2011 05:41 PM
A Practical Guide to Protein Dynamics From 15N Spin Relaxation in Solution A Practical Guide to Protein Dynamics From 15N Spin Relaxation in Solution Publication year: 2011 Source: Progress in Nuclear Magnetic Resonance Spectroscopy, In Press, Accepted Manuscript, Available online 7 January 2011</br> S. Bastien, Morin</br> More...	nmrlearner	Journal club	0	01-08-2011 12:25 PM
[NMR tweet] Nuclear Spin Relaxation in Liquids: Nuclear Spin Relaxation in LiquidsNuclear magnetic resonance (NMR) is wide... http://bit.ly/hDdW99 Nuclear Spin Relaxation in Liquids: Nuclear Spin Relaxation in LiquidsNuclear magnetic resonance (NMR) is wide... http://bit.ly/hDdW99 Published by booksvariety (BooksVariety.com) on 2010-12-04T23:02:54Z Source: Twitter	nmrlearner	Twitter NMR	0	12-04-2010 11:36 PM
[NMR paper] Side chain dynamics in unfolded protein states: an NMR based 2H spin relaxation study Side chain dynamics in unfolded protein states: an NMR based 2H spin relaxation study of delta131delta. Related Articles Side chain dynamics in unfolded protein states: an NMR based 2H spin relaxation study of delta131delta. J Am Chem Soc. 2003 Feb 19;125(7):1748-58 Authors: Choy WY, Shortle D, Kay LE NMR relaxation data on disordered proteins can provide insight into both structural and dynamic properties of these molecules. Because of chemical shift degeneracy in correlation spectra, detailed site-specific analyses of side chain dynamics...	nmrlearner	Journal club	0	11-24-2010 09:01 PM
[NMR paper] 19F-NMR spin-spin relaxation (T2) method for characterizing volatile anesthetic bindi 19F-NMR spin-spin relaxation (T2) method for characterizing volatile anesthetic binding to proteins. Analysis of isoflurane binding to serum albumin. Related Articles 19F-NMR spin-spin relaxation (T2) method for characterizing volatile anesthetic binding to proteins. Analysis of isoflurane binding to serum albumin. Biochemistry. 1992 Aug 11;31(31):7069-76 Authors: Dubois BW, Evers AS This paper characterizes the low-affinity ligand binding interactions of a fluorinated volatile anesthetic, isoflurane (CHF2OCHClCF3), with bovine serum albumin...	nmrlearner	Journal club	0	08-21-2010 11:45 PM

« Previous Thread | Next Thread »

Posting Rules
You may not post new threads You may not post replies You may not post attachments You may not edit your posts BB code is On Smilies are On [IMG] code is On HTML code is On Trackbacks are Off Pingbacks are Off Refbacks are Off