Related ArticlesSimultaneous 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]
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, Muņoz 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
[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...