Free state conformational sampling of the SAM-I riboswitch aptamer domain.

Structure
Colby D StoddardRobert T Batey

Abstract

Riboswitches are highly structured elements residing in the 5' untranslated region of messenger RNAs that specifically bind cellular metabolites to alter gene expression. While there are many structures of ligand-bound riboswitches that reveal details of bimolecular recognition, their unliganded structures remain poorly characterized. Characterizing the molecular details of the unliganded state is crucial for understanding the riboswitch's mechanism of action because it is this state that actively interrogates the cellular environment and helps direct the regulatory outcome. To develop a detailed description of the ligand-free form of an S-adenosylmethionine binding riboswitch at the local and global levels, we have employed a series of biochemical, biophysical, and computational methods. Our data reveal that the ligand binding domain adopts an ensemble of states that minimizes the energy barrier between the free and bound states to establish an efficient decision making branchpoint in the regulatory process.

References

Oct 3, 1998·Acta Crystallographica. Section D, Biological Crystallography·A T BrüngerG L Warren
Apr 20, 1999·Methods : a Companion to Methods in Enzymology·S P Ryder, S A Strobel
Jun 11, 1999·Current Opinion in Structural Biology·S A Strobel
Oct 26, 1999·Acta Crystallographica. Section D, Biological Crystallography·J W Pflugrath
Jan 10, 2003·Nucleic Acids Research·Sam Griffiths-JonesSean R Eddy
Apr 19, 2003·Proceedings of the National Academy of Sciences of the United States of America·Vitaly EpshteinEvgeny Nudler
Aug 12, 2003·Nature Structural Biology·Wade C WinklerRonald R Breaker
Nov 5, 2003·Genes & Development·Narasimhan SudarsanRonald R Breaker
Mar 24, 2005·Journal of the American Chemical Society·Edward J MerinoKevin M Weeks
Apr 6, 2005·Molecular Cell·J Kenneth WickiserDonald M Crothers
May 3, 2006·Journal of Molecular Biology·Sunny D GilbertRobert T Batey
Jul 1, 2006·Nature·Rebecca K Montange, Robert T Batey
Aug 15, 2006·Biochimie·K Y Sanbonmatsu
Jan 24, 2007·ACS Chemical Biology·Colby D Stoddard, Robert T Batey
Feb 8, 2007·Annual Review of Biophysics and Biomolecular Structure·Jan Lipfert, Sebastian Doniach
Apr 7, 2007·Journal of the American Chemical Society·Pau BernadóDmitri I Svergun
Nov 14, 2007·Genome Biology·Jeffrey E Barrick, Ronald R Breaker
Dec 25, 2007·Journal of the American Chemical Society·Angel E Garcia, Dietmar Paschek
Jan 22, 2008·Biochemistry·Benoit Heppell, Daniel A Lafontaine
Feb 19, 2008·Biophysical Journal·Simone Fulle, Holger Gohlke
Feb 20, 2008·PLoS Computational Biology·Douglas L Theobald, Deborah S Wuttke
Apr 11, 2008·Biochemistry·Lukasz PopendaZofia Gdaniec
Jun 25, 2008·Annual Review of Biophysics·Rebecca K Montange, Robert T Batey
Jul 3, 2008·The Journal of Biological Chemistry·Andrew D GarstRobert T Batey
Jan 17, 2009·Journal of Molecular Biology·Andrea C Vaiana, Kevin Y Sanbonmatsu
Mar 21, 2009·Annual Review of Biochemistry·Adam Roth, Ronald R Breaker
Jul 15, 2009·Biochimica Et Biophysica Acta·Andrew D Garst, Robert T Batey
Aug 4, 2009·Trends in Biochemical Sciences·James B MunroScott C Blanchard
Oct 21, 2009·Nature Chemical Biology·David D BoehrPeter E Wright
Dec 17, 2009·Journal of Molecular Biology·Rebecca K MontangeRobert T Batey

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Citations

Dec 25, 2013·Annual Review of Physical Chemistry·Loïc SalmonHashim M Al-Hashimi
May 15, 2012·Annual Review of Biophysics·Alexander Serganov, Dinshaw J Patel
Mar 13, 2014·Annual Review of Biochemistry·Anthony M MustoeHashim M Al-Hashimi
May 14, 2014·Nature Reviews. Genetics·Stefanie A MortimerJennifer A Doudna
Mar 19, 2013·Annual Review of Biophysics·Robert P Rambo, John A Tainer
Apr 23, 2014·Proceedings of the National Academy of Sciences of the United States of America·Jeremiah J TrauschRobert T Batey
Aug 12, 2014·The Journal of Chemical Physics·Yuhong Zhu, Shi-Jie Chen
Aug 10, 2013·Methods : a Companion to Methods in Enzymology·Irina V NovikovaKarissa Y Sanbonmatsu
May 3, 2011·RNA·Alexei V KazantsevNorman R Pace
May 18, 2011·Nucleic Acids Research·Anna WackerHarald Schwalbe
May 28, 2011·Accounts of Chemical Research·Katherine E Deigan, Adrian R Ferré-D'Amaré
Jun 17, 2011·The Journal of Biological Chemistry·Renaud TremblayDaniel A Lafontaine
Aug 30, 2011·The Journal of Physical Chemistry. a·Prashant S EmaniGary P Drobny
Feb 24, 2012·PLoS Computational Biology·Giulio QuartaTamar Schlick
May 29, 2012·European Biophysics Journal : EBJ·Michal Hammel
May 25, 2013·PLoS Computational Biology·Wei HuangFareed Aboul-ela
Dec 7, 2013·International Journal of Molecular Sciences·Irina V NovikovaKarissa Y Sanbonmatsu
Aug 2, 2012·Quarterly Reviews of Biophysics·Robert T Batey
Dec 20, 2015·Biophysical Journal·Julie L Sutton, Lois Pollack
Sep 8, 2015·Journal of Molecular Biology·Christopher WostenbergRobert T Batey
Mar 8, 2013·Journal of Molecular Biology·Irina V NovikovaKarissa Y Sanbonmatsu
May 15, 2012·Current Opinion in Structural Biology·Alexander Serganov, Dinshaw J Patel
Aug 13, 2011·Journal of Molecular Graphics & Modelling·Paula M PetroneAndrea K Pomerantz
Apr 19, 2011·Current Opinion in Structural Biology·Maximillian H BailorHashim M Al-Hashimi
Nov 6, 2015·Biochimica Et Biophysica Acta·Karissa Sanbonmatsu
Mar 3, 2015·Current Opinion in Structural Biology·Boris FürtigHarald Schwalbe
May 28, 2014·Biochimica Et Biophysica Acta·Ian R PriceAilong Ke
Jun 24, 2014·Biochimica Et Biophysica Acta·Karissa Y Sanbonmatsu
Mar 4, 2014·Biochimica Et Biophysica Acta·Alla Peselis, Alexander Serganov
Oct 1, 2011·Wiley Interdisciplinary Reviews. RNA·Joseph A Liberman, Joseph E Wedekind
Oct 1, 2011·Wiley Interdisciplinary Reviews. RNA·Robert T Batey
Aug 19, 2014·Wiley Interdisciplinary Reviews. RNA·Robert C SpitaleHoward Y Chang
Apr 8, 2014·Biophysical Journal·Ryan L HayesJosé N Onuchic
Mar 15, 2013·Journal of Molecular Biology·Colby D StoddardRobert T Batey
Nov 16, 2010·Journal of Molecular Biology·Ross C WilsonMark P Foster
Aug 4, 2015·The Journal of Chemical Physics·Sha GongWenbing Zhang

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