Analysis of a preQ1-I riboswitch in effector-free and bound states reveals a metabolite-programmed nucleobase-stacking spine that controls gene regulation

Schroeder, Griffin M.; Dutta, Debapratim; Cavender, Chapin E.; Jenkins, Jermaine L.; Pritchett, Elizabeth M.; Baker, Cameron D.; Ashton, John M.; Mathews, David H.; Wedekind, Joseph E.

doi:10.1093/nar/gkaa546

Title: Analysis of a preQ1-I riboswitch in effector-free and bound states reveals a metabolite-programmed nucleobase-stacking spine that controls gene regulation

Journal Article · Mon Jun 29 00:00:00 EDT 2020 · Nucleic Acids Research

DOI:https://doi.org/10.1093/nar/gkaa546· OSTI ID:1635308

^[1]; Dutta, Debapratim ^[1];

^[1];

^[1]; Pritchett, Elizabeth M. ^[2]; Baker, Cameron D. ^[2]; Ashton, John M. ^[2];

^[1];

^[1]

Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA, Center for RNA Biology, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA
Genomics Research Center, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA

Riboswitches are structured RNA motifs that recognize metabolites to alter the conformations of downstream sequences, leading to gene regulation. To investigate this molecular framework, we determined crystal structures of a preQ₁-I riboswitch in effector-free and bound states at 2.00 Å and 2.65 Å-resolution. Both pseudoknots exhibited the elusive L2 loop, which displayed distinct conformations. Conversely, the Shine-Dalgarno sequence (SDS) in the S2 helix of each structure remained unbroken. The expectation that the effector-free state should expose the SDS prompted us to conduct solution experiments to delineate environmental changes to specific nucleobases in response to preQ₁. We then used nudged elastic band computational methods to derive conformational-change pathways linking the crystallographically-determined effector-free and bound-state structures. Pathways featured: (i) unstacking and unpairing of L2 and S2 nucleobases without preQ₁—exposing the SDS for translation and (ii) stacking and pairing L2 and S2 nucleobases with preQ₁—sequestering the SDS. Our results reveal how preQ₁ binding reorganizes L2 into a nucleobase-stacking spine that sequesters the SDS, linking effector recognition to biological function. The generality of stacking spines as conduits for effector-dependent, interdomain communication is discussed in light of their existence in adenine riboswitches, as well as the turnip yellow mosaic virus ribosome sensor.

View Journal Article

Cite

Export

Save

Research Organization:: SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States). Stanford Synchrotron Radiation Lightsource (SSRL); University of Rochester, NY (United States). School of Medicine and Dentistry

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES); USDOE Office of Science (SC), Biological and Environmental Research (BER); National Institutes of Health (NIH)

Grant/Contract Number:: AC02-76SF00515; P41 GM103393; GM132185; GM063162; T32 AI049815; T32 GM118283

OSTI ID:: 1635308

Alternate ID(s):: OSTI ID: 1903962

Journal Information:: Nucleic Acids Research, Journal Name: Nucleic Acids Research Vol. 48 Journal Issue: 14; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United Kingdom

Language:: English

References (90)

RNA SHAPE analysis in living cells Spitale, Robert C.; Crisalli, Pete; Flynn, Ryan A. Nature Chemical Biology, Vol. 9, Issue 1 https://doi.org/10.1038/nchembio.1131	journal	November 2012
Structural insights into amino acid binding and gene control by a lysine riboswitch Serganov, Alexander; Huang, Lili; Patel, Dinshaw J. Nature, Vol. 455, Issue 7217 https://doi.org/10.1038/nature07326	journal	September 2008
Linking Crystallographic Model and Data Quality Karplus, P. A.; Diederichs, K. Science, Vol. 336, Issue 6084 https://doi.org/10.1126/science.1218231	journal	May 2012
Mg ²⁺ ions: do they bind to nucleobase nitrogens? Leonarski, Filip; D'Ascenzo, Luigi; Auffinger, Pascal Nucleic Acids Research, Vol. 45, Issue 2 https://doi.org/10.1093/nar/gkw1175	journal	December 2016
Overview of the CCP 4 suite and current developments Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D. Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S0907444910045749	journal	March 2011
A solution for the best rotation to relate two sets of vectors Kabsch, W. Acta Crystallographica Section A, Vol. 32, Issue 5 https://doi.org/10.1107/S0567739476001873	journal	September 1976
A partial nudged elastic band implementation for use with large or explicitly solvated systems Bergonzo, Christina; Campbell, Arthur J.; Walker, Ross C. International Journal of Quantum Chemistry, Vol. 109, Issue 15 https://doi.org/10.1002/qua.22405	journal	December 2009
Long-Range Interactions in Riboswitch Control of Gene Expression Jones, Christopher P.; Ferré-D'Amaré, Adrian R. Annual Review of Biophysics, Vol. 46, Issue 1 https://doi.org/10.1146/annurev-biophys-070816-034042	journal	May 2017
Lightweight object oriented structure analysis: Tools for building tools to analyze molecular dynamics simulations Romo, Tod D.; Leioatts, Nicholas; Grossfield, Alan Journal of Computational Chemistry, Vol. 35, Issue 32 https://doi.org/10.1002/jcc.23753	journal	October 2014
Structural Insights into Riboswitch Control of the Biosynthesis of Queuosine, a Modified Nucleotide Found in the Anticodon of tRNA Kang, Mijeong; Peterson, Robert; Feigon, Juli Molecular Cell, Vol. 33, Issue 6 https://doi.org/10.1016/j.molcel.2009.02.019	journal	March 2009
Cryo-EM structure of a 40 kDa SAM-IV riboswitch RNA at 3.7 Å resolution Zhang, Kaiming; Li, Shanshan; Kappel, Kalli Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-13494-7	journal	December 2019
Single transcriptional and translational preQ1 riboswitches adopt similar pre-folded ensembles that follow distinct folding pathways into the same ligand-bound structure Suddala, Krishna C.; Rinaldi, Arlie J.; Feng, Jun Nucleic Acids Research, Vol. 41, Issue 22 https://doi.org/10.1093/nar/gkt798	journal	September 2013
Structure and function of pseudoknots involved in gene expression control: Structure and function of pseudoknots Peselis, Alla; Serganov, Alexander Wiley Interdisciplinary Reviews: RNA, Vol. 5, Issue 6 https://doi.org/10.1002/wrna.1247	journal	July 2014
Ribosome-induced RNA conformational changes in a viral 3′-UTR sense and regulate translation levels Hartwick, Erik W.; Costantino, David A.; MacFadden, Andrea Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-07542-x	journal	November 2018
Riboswitches: Structures and Mechanisms Garst, A. D.; Edwards, A. L.; Batey, R. T. Cold Spring Harbor Perspectives in Biology, Vol. 3, Issue 6 https://doi.org/10.1101/cshperspect.a003533	journal	October 2010
Structure–Activity Relationship of Flavin Analogues That Target the Flavin Mononucleotide Riboswitch Vicens, Quentin; Mondragón, Estefanía; Reyes, Francis E. ACS Chemical Biology, Vol. 13, Issue 10 https://doi.org/10.1021/acschembio.8b00533	journal	August 2018
Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes Ryckaert, Jean-Paul; Ciccotti, Giovanni; Berendsen, Herman J. C. Journal of Computational Physics, Vol. 23, Issue 3 https://doi.org/10.1016/0021-9991(77)90098-5	journal	March 1977
Nudged Elastic Band Calculation of Minimal Energy Paths for the Conformational Change of a GG Non-canonical Pair Mathews, David H.; Case, David A. Journal of Molecular Biology, Vol. 357, Issue 5 https://doi.org/10.1016/j.jmb.2006.01.054	journal	April 2006
Structural analysis of a class III preQ ₁ riboswitch reveals an aptamer distant from a ribosome-binding site regulated by fast dynamics Liberman, Joseph A.; Suddala, Krishna C.; Aytenfisu, Asaminew Proceedings of the National Academy of Sciences, Vol. 112, Issue 27 https://doi.org/10.1073/pnas.1503955112	journal	June 2015
Metalloriboswitches: RNA-based inorganic ion sensors that regulate genes Wedekind, Joseph E.; Dutta, Debapratim; Belashov, Ivan A. Journal of Biological Chemistry, Vol. 292, Issue 23 https://doi.org/10.1074/jbc.R117.787713	journal	April 2017
Quantum and thermal effects in $H_{2}$ dissociative adsorption: Evaluation of free energy barriers in multidimensional quantum systems Mills, Greg; Jónsson, Hannes Physical Review Letters, Vol. 72, Issue 7 https://doi.org/10.1103/PhysRevLett.72.1124	journal	February 1994
Structural and Dynamic Basis for Low-Affinity, High-Selectivity Binding of L-Glutamine by the Glutamine Riboswitch Ren, Aiming; Xue, Yi; Peselis, Alla Cell Reports, Vol. 13, Issue 9 https://doi.org/10.1016/j.celrep.2015.10.062	journal	December 2015
The Structural and Functional Diversity of Metabolite-Binding Riboswitches Roth, Adam; Breaker, Ronald R. Annual Review of Biochemistry, Vol. 78, Issue 1 https://doi.org/10.1146/annurev.biochem.78.070507.135656	journal	June 2009
Comparative Study between Transcriptionally- and Translationally-Acting Adenine Riboswitches Reveals Key Differences in Riboswitch Regulatory Mechanisms Lemay, Jean-François; Desnoyers, Guillaume; Blouin, Simon PLoS Genetics, Vol. 7, Issue 1 https://doi.org/10.1371/journal.pgen.1001278	journal	January 2011
Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald Salomon-Ferrer, Romelia; Götz, Andreas W.; Poole, Duncan Journal of Chemical Theory and Computation, Vol. 9, Issue 9 https://doi.org/10.1021/ct400314y	journal	August 2013
Modeling and automation of sequencing-based characterization of RNA structure Aviran, S.; Trapnell, C.; Lucks, J. B. Proceedings of the National Academy of Sciences, Vol. 108, Issue 27 https://doi.org/10.1073/pnas.1106541108	journal	June 2011
Riboswitch diversity and distribution McCown, Phillip J.; Corbino, Keith A.; Stav, Shira RNA, Vol. 23, Issue 7 https://doi.org/10.1261/rna.061234.117	journal	April 2017
Structural Insights into Ligand Recognition by a Sensing Domain of the Cooperative Glycine Riboswitch Huang, Lili; Serganov, Alexander; Patel, Dinshaw J. Molecular Cell, Vol. 40, Issue 5 https://doi.org/10.1016/j.molcel.2010.11.026	journal	December 2010
Crystallographic Analysis of Small Ribozymes and Riboswitches Lippa, Geoffrey M.; Liberman, Joseph A.; Jenkins, Jermaine L. Methods in Molecular Biology https://doi.org/10.1007/978-1-61779-545-9_11	book	January 2012
How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? Wang, Junmei; Cieplak, Piotr; Kollman, Peter A. Journal of Computational Chemistry, Vol. 21, Issue 12 https://doi.org/10.1002/1096-987X(200009)21:12<1049::AID-JCC3>3.0.CO;2-F	journal	January 2000
Cocrystal structure of a class I preQ1 riboswitch reveals a pseudoknot recognizing an essential hypermodified nucleobase Klein, Daniel J.; Edwards, Thomas E.; Ferré-D'Amaré, Adrian R. Nature Structural & Molecular Biology, Vol. 16, Issue 3 https://doi.org/10.1038/nsmb.1563	journal	February 2009
DMS footprinting of structured RNAs and RNA–protein complexes Tijerina, Pilar; Mohr, Sabine; Russell, Rick Nature Protocols, Vol. 2, Issue 10 https://doi.org/10.1038/nprot.2007.380	journal	October 2007
Molecular mechanism for preQ ₁ -II riboswitch function revealed by molecular dynamics Aytenfisu, Asaminew H.; Liberman, Joseph A.; Wedekind, Joseph E. RNA, Vol. 21, Issue 11 https://doi.org/10.1261/rna.051367.115	journal	September 2015
Structure of HIV TAR in complex with a Lab-Evolved RRM provides insight into duplex RNA recognition and synthesis of a constrained peptide that impairs transcription Belashov, Ivan A.; Crawford, David W.; Cavender, Chapin E. Nucleic Acids Research, Vol. 46, Issue 13 https://doi.org/10.1093/nar/gky529	journal	June 2018
Strong Correlation between SHAPE Chemistry and the Generalized NMR Order Parameter ( S ² ) in RNA Gherghe, Costin M.; Shajani, Zahra; Wilkinson, Kevin A. Journal of the American Chemical Society, Vol. 130, Issue 37 https://doi.org/10.1021/ja804541s	journal	September 2008
Folding of a transcriptionally acting PreQ1 riboswitch Rieder, U.; Kreutz, C.; Micura, R. Proceedings of the National Academy of Sciences, Vol. 107, Issue 24 https://doi.org/10.1073/pnas.0914925107	journal	June 2010
The tRNA-like structure of Turnip yellow mosaic virus RNA is a 3′-translational enhancer Matsuda, Daiki; Dreher, Theo W. Virology, Vol. 321, Issue 1 https://doi.org/10.1016/j.virol.2003.10.023	journal	March 2004
Crystal Structure of the Lysine Riboswitch Regulatory mRNA Element Garst, Andrew D.; Héroux, Annie; Rambo, Robert P. Journal of Biological Chemistry, Vol. 283, Issue 33 https://doi.org/10.1074/jbc.C800120200	journal	July 2008
Global indicators of X-ray data quality Weiss, Manfred S. Journal of Applied Crystallography, Vol. 34, Issue 2 https://doi.org/10.1107/S0021889800018227	journal	April 2001
Amino acid recognition and gene regulation by riboswitches Serganov, Alexander; Patel, Dinshaw J. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Vol. 1789, Issue 9-10 https://doi.org/10.1016/j.bbagrm.2009.07.002	journal	September 2009
SLTCAP: A Simple Method for Calculating the Number of Ions Needed for MD Simulation Schmit, Jeremy D.; Kariyawasam, Nilusha L.; Needham, Vince Journal of Chemical Theory and Computation, Vol. 14, Issue 4 https://doi.org/10.1021/acs.jctc.7b01254	journal	March 2018
The Structure of the Guanidine-II Riboswitch Huang, Lin; Wang, Jia; Lilley, David M. J. Cell Chemical Biology, Vol. 24, Issue 6 https://doi.org/10.1016/j.chembiol.2017.05.014	journal	June 2017
Coupling Green Fluorescent Protein Expression with Chemical Modification to Probe Functionally Relevant Riboswitch Conformations in Live Bacteria Dutta, Debapratim; Belashov, Ivan A.; Wedekind, Joseph E. Biochemistry, Vol. 57, Issue 31 https://doi.org/10.1021/acs.biochem.8b00316	journal	April 2018
Protein unties the pseudoknot: S1-mediated unfolding of RNA higher order structure Lund, Paul E.; Chatterjee, Surajit; Daher, May Nucleic Acids Research, Vol. 48, Issue 4 https://doi.org/10.1093/nar/gkz1166	journal	December 2019
Structure of the Eukaryotic Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand Thore, S. Science, Vol. 312, Issue 5777 https://doi.org/10.1126/science.1128451	journal	May 2006
Deciphering Deazapurine Biosynthesis: Pathway for Pyrrolopyrimidine Nucleosides Toyocamycin and Sangivamycin McCarty, Reid M.; Bandarian, Vahe Chemistry & Biology, Vol. 15, Issue 8 https://doi.org/10.1016/j.chembiol.2008.07.012	journal	August 2008
Structural basis for recognition of S-adenosylhomocysteine by riboswitches Edwards, A. L.; Reyes, F. E.; Heroux, A. RNA, Vol. 16, Issue 11 https://doi.org/10.1261/rna.2341610	journal	September 2010
Nudged elastic band method for finding minimum energy paths of transitions JÓNsson, Hannes; Mills, Greg; Jacobsen, Karsten W. Proceedings of the International School of Physics, Classical and Quantum Dynamics in Condensed Phase Simulations https://doi.org/10.1142/9789812839664_0016	conference	November 2011
The Structural Basis for Recognition of the PreQ ₀ Metabolite by an Unusually Small Riboswitch Aptamer Domain Spitale, Robert C.; Torelli, Andrew T.; Krucinska, Jolanta Journal of Biological Chemistry, Vol. 284, Issue 17 https://doi.org/10.1074/jbc.C900024200	journal	March 2009
Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems Darden, Tom; York, Darrin; Pedersen, Lee The Journal of Chemical Physics, Vol. 98, Issue 12 https://doi.org/10.1063/1.464397	journal	June 1993
Ultraviolet Shadowing of RNA Can Cause Significant Chemical Damage in Seconds Kladwang, Wipapat; Hum, Justine; Das, Rhiju Scientific Reports, Vol. 2, Issue 1 https://doi.org/10.1038/srep00517	journal	July 2012
MolProbity : all-atom structure validation for macromolecular crystallography Chen, Vincent B.; Arendall, W. Bryan; Headd, Jeffrey J. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1 https://doi.org/10.1107/S0907444909042073	journal	December 2009
Checking your imagination: applications of the free R value Kleywegt, Gerard J.; Brünger, Axel T. Structure, Vol. 4, Issue 8 https://doi.org/10.1016/S0969-2126(96)00097-4	journal	August 1996
Features and development of Coot Emsley, P.; Lohkamp, B.; Scott, W. G. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/S0907444910007493	journal	March 2010
Free State Conformational Sampling of the SAM-I Riboswitch Aptamer Domain Stoddard, Colby D.; Montange, Rebecca K.; Hennelly, Scott P. Structure, Vol. 18, Issue 7 https://doi.org/10.1016/j.str.2010.04.006	journal	July 2010
Geometric nomenclature and classification of RNA base pairs Leontis, Neocles B.; Westhof, Eric RNA, Vol. 7, Issue 4 https://doi.org/10.1017/S1355838201002515	journal	April 2001
Ligand-induced changes in 2-aminopurine fluorescence as a probe for small molecule binding to HIV-1 TAR RNA Bradrick, T. D. RNA, Vol. 10, Issue 9 https://doi.org/10.1261/rna.7620304	journal	September 2004
Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of α/γ Conformers Pérez, Alberto; Marchán, Iván; Svozil, Daniel Biophysical Journal, Vol. 92, Issue 11 https://doi.org/10.1529/biophysj.106.097782	journal	June 2007
Principles for targeting RNA with drug-like small molecules Warner, Katherine Deigan; Hajdin, Christine E.; Weeks, Kevin M. Nature Reviews Drug Discovery, Vol. 17, Issue 8 https://doi.org/10.1038/nrd.2018.93	journal	July 2018
Structures of riboswitch RNA reaction states by mix-and-inject XFEL serial crystallography Stagno, J. R.; Liu, Y.; Bhandari, Y. R. Nature, Vol. 541, Issue 7636 https://doi.org/10.1038/nature20599	journal	November 2016
2-aminopurine as a fluorescent probe of DNA conformation and the DNA–enzyme interface Jones, Anita C.; Neely, Robert K. Quarterly Reviews of Biophysics, Vol. 48, Issue 2 https://doi.org/10.1017/S0033583514000158	journal	April 2015
PHENIX: a comprehensive Python-based system for macromolecular structure solution Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221 https://doi.org/10.1107/S0907444909052925	journal	January 2010
Characterizing RNA structures in vitro and in vivo with selective 2′-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq) Watters, Kyle E.; Yu, Angela M.; Strobel, Eric J. Methods, Vol. 103 https://doi.org/10.1016/j.ymeth.2016.04.002	journal	July 2016
Conformational Rearrangements of Individual Nucleotides during RNA-Ligand Binding Are Rate-Differentiated Frener, Marina; Micura, Ronald Journal of the American Chemical Society, Vol. 138, Issue 11 https://doi.org/10.1021/jacs.5b11876	journal	March 2016
Crystal Structures of the Thi-Box Riboswitch Bound to Thiamine Pyrophosphate Analogs Reveal Adaptive RNA-Small Molecule Recognition Edwards, Thomas E.; Ferré-D'Amaré, Adrian R. Structure, Vol. 14, Issue 9 https://doi.org/10.1016/j.str.2006.07.008	journal	September 2006
Structural Basis of Thiamine Pyrophosphate Analogues Binding to the Eukaryotic Riboswitch Thore, Stéphane; Frick, Christian; Ban, Nenad Journal of the American Chemical Society, Vol. 130, Issue 26 https://doi.org/10.1021/ja801708e	journal	July 2008
Synthetic ligands for PreQ1 riboswitches provide structural and mechanistic insights into targeting RNA tertiary structure Connelly, Colleen M.; Numata, Tomoyuki; Boer, Robert E. Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-09493-3	journal	April 2019
The interpretation of protein structures: Estimation of static accessibility Lee, B.; Richards, F. M. Journal of Molecular Biology, Vol. 55, Issue 3 https://doi.org/10.1016/0022-2836(71)90324-X	journal	February 1971
Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles Zgarbová, Marie; Otyepka, Michal; Šponer, Jiří Journal of Chemical Theory and Computation, Vol. 7, Issue 9 https://doi.org/10.1021/ct200162x	journal	August 2011
The purine riboswitch as a model system for exploring RNA biology and chemistry Porter, Ely B.; Marcano-Velázquez, Joan G.; Batey, Robert T. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Vol. 1839, Issue 10 https://doi.org/10.1016/j.bbagrm.2014.02.014	journal	October 2014
The Shine-Dalgarno sequence of riboswitch-regulated single mRNAs shows ligand-dependent accessibility bursts Rinaldi, Arlie J.; Lund, Paul E.; Blanco, Mario R. Nature Communications, Vol. 7, Issue 1 https://doi.org/10.1038/ncomms9976	journal	January 2016
Comparison of a PreQ ₁ Riboswitch Aptamer in Metabolite-bound and Free States with Implications for Gene Regulation Jenkins, Jermaine L.; Krucinska, Jolanta; McCarty, Reid M. Journal of Biological Chemistry, Vol. 286, Issue 28 https://doi.org/10.1074/jbc.M111.230375	journal	May 2011
A Decade of Riboswitches Serganov, Alexander; Nudler, Evgeny Cell, Vol. 152, Issue 1-2 https://doi.org/10.1016/j.cell.2012.12.024	journal	January 2013
Building Water Models: A Different Approach Izadi, Saeed; Anandakrishnan, Ramu; Onufriev, Alexey V. The Journal of Physical Chemistry Letters, Vol. 5, Issue 21 https://doi.org/10.1021/jz501780a	journal	October 2014
ykkC riboswitches employ an add-on helix to adjust specificity for polyanionic ligands Peselis, Alla; Serganov, Alexander Nature Chemical Biology, Vol. 14, Issue 9 https://doi.org/10.1038/s41589-018-0114-4	journal	August 2018
Molecular sensing by the aptamer domain of the FMN riboswitch: a general model for ligand binding by conformational selection Vicens, Quentin; Mondragón, Estefanía; Batey, Robert T. Nucleic Acids Research, Vol. 39, Issue 19 https://doi.org/10.1093/nar/gkr565	journal	July 2011
Riboswitch structure in the ligand-free state: Riboswitch structure in the ligand-free state Liberman, Joseph A.; Wedekind, Joseph E. Wiley Interdisciplinary Reviews: RNA, Vol. 3, Issue 3 https://doi.org/10.1002/wrna.114	journal	September 2011
Selective small-molecule inhibition of an RNA structural element Howe, John A.; Wang, Hao; Fischmann, Thierry O. Nature, Vol. 526, Issue 7575 https://doi.org/10.1038/nature15542	journal	September 2015
Solution Structure of a Luteoviral P1–P2 Frameshifting mRNA Pseudoknot Nixon, Paul L.; Rangan, Anupama; Kim, Y. -G Journal of Molecular Biology, Vol. 322, Issue 3 https://doi.org/10.1016/S0022-2836(02)00779-9	journal	September 2002
Nucleobase mutants of a bacterial preQ ₁ -II riboswitch that uncouple metabolite sensing from gene regulation Dutta, Debapratim; Wedekind, Joseph E. Journal of Biological Chemistry, Vol. 295, Issue 9 https://doi.org/10.1074/jbc.RA119.010755	journal	October 2019
Force Field for Mg ²⁺ , Mn ²⁺ , Zn ²⁺ , and Cd ²⁺ Ions That Have Balanced Interactions with Nucleic Acids Panteva, Maria T.; Giambaşu, George M.; York, Darrin M. The Journal of Physical Chemistry B, Vol. 119, Issue 50 https://doi.org/10.1021/acs.jpcb.5b10423	journal	December 2015
Molecular Mechanism of preQ ₁ Riboswitch Action: A Molecular Dynamics Study Banáš, Pavel; Sklenovský, Petr; Wedekind, Joseph E. The Journal of Physical Chemistry B, Vol. 116, Issue 42 https://doi.org/10.1021/jp309230v	journal	October 2012
Improving biosensor analysis Myszka, David G. Journal of Molecular Recognition, Vol. 12, Issue 5 https://doi.org/10.1002/(SICI)1099-1352(199909/10)12:5<279::AID-JMR473>3.0.CO;2-3	journal	September 1999
Structure of the Guanidine III Riboswitch Huang, Lin; Wang, Jia; Wilson, Timothy J. Cell Chemical Biology, Vol. 24, Issue 11 https://doi.org/10.1016/j.chembiol.2017.08.021	journal	November 2017
RNA SHAPE Chemistry Reveals Nonhierarchical Interactions Dominate Equilibrium Structural Transitions in tRNA ^Asp Transcripts Wilkinson, Kevin A.; Merino, Edward J.; Weeks, Kevin M. Journal of the American Chemical Society, Vol. 127, Issue 13 https://doi.org/10.1021/ja0436749	journal	April 2005
Selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution Wilkinson, Kevin A.; Merino, Edward J.; Weeks, Kevin M. Nature Protocols, Vol. 1, Issue 3 https://doi.org/10.1038/nprot.2006.249	journal	August 2006
Systematic Parameterization of Monovalent Ions Employing the Nonbonded Model Li, Pengfei; Song, Lin Frank; Merz, Kenneth M. Journal of Chemical Theory and Computation, Vol. 11, Issue 4 https://doi.org/10.1021/ct500918t	journal	March 2015
Coenzyme recognition and gene regulation by a flavin mononucleotide riboswitch Serganov, Alexander; Huang, Lili; Patel, Dinshaw J. Nature, Vol. 458, Issue 7235 https://doi.org/10.1038/nature07642	journal	January 2009
Base ionization and ligand binding: how small ribozymes and riboswitches gain a foothold in a protein world Liberman, Joseph A.; Wedekind, Joseph E. Current Opinion in Structural Biology, Vol. 21, Issue 3 https://doi.org/10.1016/j.sbi.2011.03.016	journal	June 2011
The Mechanisms of RNA SHAPE Chemistry McGinnis, Jennifer L.; Dunkle, Jack A.; Cate, Jamie H. D. Journal of the American Chemical Society, Vol. 134, Issue 15 https://doi.org/10.1021/ja2104075	journal	April 2012

Similar Records

A small RNA that cooperatively senses two stacked metabolites in one pocket for gene control

Journal Article · Tue Jan 11 00:00:00 EST 2022 · Nature Communications · OSTI ID:1635308

Schroeder, Griffin M.; Cavender, Chapin E.; Blau, Maya E.; +3 more

Structural analysis of a class III preQ₁ riboswitch reveals an aptamer distant from a ribosome-binding site regulated by fast dynamics

Journal Article · Tue Jun 23 00:00:00 EDT 2015 · Proceedings of the National Academy of Sciences of the United States of America · OSTI ID:1635308

Liberman, Joseph A.; Suddala, Krishna C.; Aytenfisu, Asaminew; +7 more

Structural Investigation of the GlmS Ribozyme Bound to Its Catalytic Cofactor

Journal Article · Mon Jan 01 00:00:00 EST 2007 · Chemistry & Biology · OSTI ID:1635308

Cochrane, J; Lipchock, S; Strobel, S

Related Subjects

59 BASIC BIOLOGICAL SCIENCES

Title: Analysis of a preQ1-I riboswitch in effector-free and bound states reveals a metabolite-programmed nucleobase-stacking spine that controls gene regulation

Citation Formats

References (90)

Similar Records

Related Subjects