NMR paper Ultraslow Domain Motions in HIV-1 TAR RNA Revealed by Solid-State Deuterium NMR.

		BioNMR > Educational resources > Journal club
[NMR paper] Ultraslow Domain Motions in HIV-1 TAR RNA Revealed by Solid-State Deuterium NMR.

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:

Thread Tools

Search this Thread

Rate Thread

Display Modes

12-09-2016, 06:09 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,732

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

Ultraslow Domain Motions in HIV-1 TAR RNA Revealed by Solid-State Deuterium NMR.

Ultraslow Domain Motions in HIV-1 TAR RNA Revealed by Solid-State Deuterium NMR.

Ultraslow Domain Motions in HIV-1 TAR RNA Revealed by Solid-State Deuterium NMR.

J Phys Chem B. 2016 Dec 08;

Authors: Huang W, Emani PS, Varani G, Drobny GP

Abstract
Intrinsic motions may allow HIV-1 TAR RNA to change its conformation to form a functional complex with the Tat protein, which is essential for viral replication. Understanding the dynamic properties of TAR necessitates determining motion on the intermediate ns-?s time scale. To this end, we performed solid-state deuterium NMR line shape and T1Z relaxation time experiments to measure intermediate motions for two uridine residues, U40 and U42, within the lower helix of TAR. We infer global motions at rates of ~10(5) s(-1) in the lower helix, which are much slower than those of the upper helix (~10(6) s(-1)), indicating the two helical domains reorient independently of one another in the solid-state sample. These results contribute to the aim of fully describing the properties of functional motions in TAR RNA.

PMID: 27930881 [PubMed - as supplied by publisher]

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Site-SpecificInternal Motions in GB1 Protein MicrocrystalsRevealed by 3D 2H–13C–13C Solid-State NMR Spectroscopy Site-SpecificInternal Motions in GB1 Protein MicrocrystalsRevealed by 3D 2H–13C–13C Solid-State NMR Spectroscopy Xiangyan Shi and Chad M. Rienstra http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/jacs.5b12974/20160318-01/images/medium/ja-2015-129748_0009.gif Journal of the American Chemical Society DOI: 10.1021/jacs.5b12974 http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/jacsat/~4/hmGFpLGOae8	nmrlearner	Journal club	0	03-19-2016 06:39 AM
Site-Specific Protein Internal Motions Revealed by 2H Solid-State NMR Spectroscopy Site-Specific Protein Internal Motions Revealed by 2H Solid-State NMR Spectroscopy Publication date: 16 February 2016 Source:Biophysical Journal, Volume 110, Issue 3, Supplement 1</br> Author(s): Xiangyan Shi, Deborah A. Berthold, Chad M. Rienstra</br> </br></br> </br></br> More...	nmrlearner	Journal club	0	02-17-2016 07:50 PM
[NMR paper] Site-Specific Internal Motions in GB1 Protein Microcrystals Revealed by 3D (2)H-(13)C-(13)C Solid-State NMR Spectroscopy. Site-Specific Internal Motions in GB1 Protein Microcrystals Revealed by 3D (2)H-(13)C-(13)C Solid-State NMR Spectroscopy. Related Articles Site-Specific Internal Motions in GB1 Protein Microcrystals Revealed by 3D (2)H-(13)C-(13)C Solid-State NMR Spectroscopy. J Am Chem Soc. 2016 Feb 5; Authors: Shi X, Rienstra CM Abstract (2)H quadrupolar line shapes deliver rich information about protein dynamics. A newly designed 3D (2)H-(13)C-(13)Csolid-state NMR magic angle spinning (MAS) experiment is presented and demonstrated on the...	nmrlearner	Journal club	0	02-06-2016 03:10 PM
[NMR paper] Investigation of rhodopsin dynamics in its signaling state by solid-state deuterium NMR spectroscopy. Investigation of rhodopsin dynamics in its signaling state by solid-state deuterium NMR spectroscopy. Investigation of rhodopsin dynamics in its signaling state by solid-state deuterium NMR spectroscopy. Methods Mol Biol. 2015;1271:133-58 Authors: Struts AV, Chawla U, Perera SM, Brown MF Abstract Site-directed deuterium NMR spectroscopy is a valuable tool to study the structural dynamics of biomolecules in cases where solution NMR is inapplicable. Solid-state (2)H NMR spectral studies of aligned membrane samples of rhodopsin...	nmrlearner	Journal club	0	02-24-2015 02:48 PM
[NMR paper] Insights into Domain-Domain Motions in Proteins and RNA from Solution NMR. Insights into Domain-Domain Motions in Proteins and RNA from Solution NMR. Related Articles Insights into Domain-Domain Motions in Proteins and RNA from Solution NMR. Acc Chem Res. 2014 Aug 22; Authors: Ravera E, Salmon L, Fragai M, Parigi G, Al-Hashimi H, Luchinat C Abstract Conspectus Many multidomain proteins and ribonucleic acids consist of domains that autonomously fold and that are linked together by flexible junctions. This architectural design allows domains to sample a wide range of positions with respect to one another,...	nmrlearner	Journal club	0	08-26-2014 01:25 PM
[NMR paper] Nanosecond timescale motions in proteins revealed by high-resolution NMR relaxometry. Nanosecond timescale motions in proteins revealed by high-resolution NMR relaxometry. Related Articles Nanosecond timescale motions in proteins revealed by high-resolution NMR relaxometry. J Am Chem Soc. 2013 Nov 14; Authors: Charlier CD, Khan SN, Marquardsen T, Pelupessy P, Reiss V, Sakellariou D, Bodenhausen G, Engelke F, Ferrage F Abstract Understanding the molecular determinants underlying protein function requires the characterization of both structure and dynamics at atomic resolution. Nuclear relaxation rates allow a precise...	nmrlearner	Journal club	0	11-16-2013 03:14 PM
Quantification of protein backbone hydrogen-deuterium exchange rates by solid state N Quantification of protein backbone hydrogen-deuterium exchange rates by solid state NMR spectroscopy Abstract We present the quantification of backbone amide hydrogen-deuterium exchange rates (HDX) for immobilized proteins. The experiments make use of the deuterium isotope effect on the amide nitrogen chemical shift, as well as on proton dilution by deuteration. We find that backbone amides in the microcrystalline Î±-spectrin SH3 domain exchange rather slowly with the solvent (with exchange rates negligible within the individual 15Nâ??T 1 timescales). We observed chemical exchange for 6...	nmrlearner	Journal club	0	10-27-2010 08:51 AM
Quantification of protein backbone hydrogen-deuterium exchange rates by solid state N Quantification of protein backbone hydrogen-deuterium exchange rates by solid state NMR spectroscopy. Related Articles Quantification of protein backbone hydrogen-deuterium exchange rates by solid state NMR spectroscopy. J Biomol NMR. 2010 Oct 20; Authors: Del Amo JM, Fink U, Reif B We present the quantification of backbone amide hydrogen-deuterium exchange rates (HDX) for immobilized proteins. The experiments make use of the deuterium isotope effect on the amide nitrogen chemical shift, as well as on proton dilution by deuteration. We find that...	nmrlearner	Journal club	0	10-22-2010 06:02 AM

« 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