2H NMR Spin Relaxation for studying RNA dynamics

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2H NMR Spin Relaxation for studying RNA dynamics

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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:

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05-19-2005, 08:44 AM

nmrlearner

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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.

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