NMR paper Simultaneous NMR characterisation of multiple minima in the free energy landscape of an RNA UUCG tetraloop.

		BioNMR > Educational resources > Journal club
[NMR paper] Simultaneous NMR characterisation of multiple minima in the free energy landscape of an RNA UUCG tetraloop.

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

01-12-2017, 03:48 AM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,714

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

Simultaneous NMR characterisation of multiple minima in the free energy landscape of an RNA UUCG tetraloop.

Related Articles Simultaneous NMR characterisation of multiple minima in the free energy landscape of an RNA UUCG tetraloop.

Phys Chem Chem Phys. 2017 Jan 09;:

Authors: Borkar AN, Vallurupalli P, Camilloni C, Kay LE, Vendruscolo M

Abstract
RNA molecules in solution tend to undergo structural fluctuations of relatively large amplitude and to populate a range of different conformations some of which with low populations. It is still very challenging, however, to characterise the structures of these low populated states and to understand their functional roles. In the present study, we address this problem by using NMR residual dipolar couplings (RDCs) as structural restraints in replica-averaged metadynamics (RAM) simulations. By applying this approach to a 14-mer RNA hairpin containing the prototypical UUCG tetraloop motif, we show that it is possible to construct the free energy landscape of this RNA molecule. This free energy landscapes reveals the surprisingly rich dynamics of the UUCG tetraloop and identifies the multiple substates that exist in equilibrium owing to thermal fluctuations. The approach that we present is general and can be applied to the study of the free energy landscapes of other RNA or RNA-protein systems.

PMID: 28067358 [PubMed - as supplied by publisher]

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Simultaneous Chirality Sensing of Multiple Amines by 19F NMR Simultaneous Chirality Sensing of Multiple Amines by 19F NMR Yanchuan Zhao and Timothy M. Swager http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/jacs.5b00556/20150227/images/medium/ja-2015-00556n_0007.gif Journal of the American Chemical Society DOI: 10.1021/jacs.5b00556 http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA http://www.bionmr.com//feeds.feedburner.com/~r/acs/jacsat/~4/EZ7QKbt4vFY	nmrlearner	Journal club	0	02-27-2015 11:25 PM
[NMR paper] Probing the Free Energy Landscape of the Fast-Folding gpW Protein by Relaxation Dispersion NMR. Probing the Free Energy Landscape of the Fast-Folding gpW Protein by Relaxation Dispersion NMR. Related Articles Probing the Free Energy Landscape of the Fast-Folding gpW Protein by Relaxation Dispersion NMR. J Am Chem Soc. 2014 May 8; Authors: Sanchez-Medina C, Sekhar A, Vallurupalli P, Cerminara M, Muñoz V, Kay LE Abstract The topographic features of the free energy landscapes that govern the thermodynamics and kinetics of conformational transitions in proteins, which in turn are integral for function, are not well understood....	nmrlearner	Journal club	0	05-09-2014 07:01 PM
Probing the Free Energy Landscape of the Fast-Folding gpW Protein by Relaxation Dispersion NMR Probing the Free Energy Landscape of the Fast-Folding gpW Protein by Relaxation Dispersion NMR Celia Sanchez-Medina, Ashok Sekhar, Pramodh Vallurupalli, Michele Cerminara, Victor Mun?oz and Lewis E. Kay http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja502705y/aop/images/medium/ja-2014-02705y_0007.gif Journal of the American Chemical Society DOI: 10.1021/ja502705y http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/jacsat/~4/uht26log5zQ	nmrlearner	Journal club	0	05-08-2014 05:38 PM
NMR Studies of the free Energy Landscape of Intrinsically Disordered Proteins in their free and Bound Forms NMR Studies of the free Energy Landscape of Intrinsically Disordered Proteins in their free and Bound Forms Publication date: 28 January 2014 Source:Biophysical Journal, Volume 106, Issue 2, Supplement 1</br> Author(s): Martin Blackledge</br> </br></br> </br></br> More...	nmrlearner	Journal club	0	01-29-2014 12:50 AM
Characterization of Free Energy Landscapes of Proteins using NMR Spectroscopy Characterization of Free Energy Landscapes of Proteins using NMR Spectroscopy 29 January 2013 Publication year: 2013 Source:Biophysical Journal, Volume 104, Issue 2, Supplement 1</br> </br> </br> </br></br>	nmrlearner	Journal club	0	02-03-2013 10:13 AM
[NMR paper] Extending the family of UNCG-like tetraloop motifs: NMR structure of a CACG tetraloop Extending the family of UNCG-like tetraloop motifs: NMR structure of a CACG tetraloop from coxsackievirus B3. Related Articles Extending the family of UNCG-like tetraloop motifs: NMR structure of a CACG tetraloop from coxsackievirus B3. Biochemistry. 2003 Apr 22;42(15):4373-83 Authors: Du Z, Yu J, Andino R, James TL Stable RNA tetraloop motifs are found frequently in biologically active RNAs. These motifs carry out a wide variety of functions in RNA folding, in RNA-RNA and RNA-protein interactions. A great deal of knowledge about the...	nmrlearner	Journal club	0	11-24-2010 09:01 PM
[NMR paper] The pressure-temperature free energy-landscape of staphylococcal nuclease monitored b The pressure-temperature free energy-landscape of staphylococcal nuclease monitored by (1)H NMR. Related Articles The pressure-temperature free energy-landscape of staphylococcal nuclease monitored by (1)H NMR. J Mol Biol. 2000 Apr 28;298(2):293-302 Authors: Lassalle MW, Yamada H, Akasaka K The thermodynamic stability of staphylococcal nuclease was studied against the variation of both temperature and pressure by utilizing (1)H NMR spectroscopy at 750 MHz in 20 mM Mes buffer containing 99.9 % (2)H(2)O, pH 5.3. Equilibrium fractions of folded...	nmrlearner	Journal club	0	11-18-2010 09:15 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