Comparison of Solution and Crystal Structures of PreQ 1 Riboswitch Reveals Calcium-Induced Changes in Conformation and Dynamics

Zhang, Qi; Kang, Mijeong; Peterson, Robert D.; Feigon, Juli

doi:10.1021/ja111769g

Title: Comparison of Solution and Crystal Structures of PreQ ₁ Riboswitch Reveals Calcium-Induced Changes in Conformation and Dynamics

Journal Article · Wed Mar 16 00:00:00 EDT 2011 · Journal of the American Chemical Society

DOI:https://doi.org/10.1021/ja111769g· OSTI ID:1123352

Zhang, Qi ^[1]; Kang, Mijeong ^[1]; Peterson, Robert D. ^[1]; Feigon, Juli ^[1]

Department of Chemistry and Biochemistry and ‡UCLA−DOE Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095-1569, United States

View Journal Article

Cite

Export

Save

Sponsoring Organization:: USDOE

OSTI ID:: 1123352

Journal Information:: Journal of the American Chemical Society, Journal Name: Journal of the American Chemical Society Vol. 133 Journal Issue: 14; ISSN 0002-7863

Publisher:: American Chemical SocietyCopyright Statement

Country of Publication:: United States

Language:: English

Citation Metrics:

Cited by: 49 works

Citation information provided by
Web of Science

References (27)

NMR structures of biomolecules using field oriented media and residual dipolar couplings Prestegard, J. H.; Al-Hashimi, H. M.; Tolman, J. R. Quarterly Reviews of Biophysics, Vol. 33, Issue 4 https://doi.org/10.1017/S0033583500003656	journal	November 2000
Roles of Mg ²⁺ in TPP-dependent riboswitch Yamauchi, Takahiro; Miyoshi, Daisuke; Kubodera, Takafumi FEBS Letters, Vol. 579, Issue 12 https://doi.org/10.1016/j.febslet.2005.03.074	journal	April 2005
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
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
Ribozymes and Riboswitches: Modulation of RNA Function by Small Molecules Zhang, Jinwei; Lau, Matthew W.; Ferré-D’Amaré, Adrian R. Biochemistry, Vol. 49, Issue 43 https://doi.org/10.1021/bi1012645	journal	November 2010
The Ligand-Free State of the TPP Riboswitch: A Partially Folded RNA Structure Ali, Mona; Lipfert, Jan; Seifert, Soenke Journal of Molecular Biology, Vol. 396, Issue 1 https://doi.org/10.1016/j.jmb.2009.11.030	journal	February 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
Idiosyncratically tuned switching behavior of riboswitch aptamer domains revealed by comparative small-angle X-ray scattering analysis Baird, N. J.; Ferre-D'Amare, A. R. RNA, Vol. 16, Issue 3 https://doi.org/10.1261/rna.1852310	journal	January 2010
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
Time-resolved NMR methods resolving ligand-induced RNA folding at atomic resolution Buck, J.; Furtig, B.; Noeske, J. Proceedings of the National Academy of Sciences, Vol. 104, Issue 40 https://doi.org/10.1073/pnas.0703182104	journal	September 2007
Calcium signalling in bacteria: Calcium in bacteria Dominguez, Delfina C. Molecular Microbiology, Vol. 54, Issue 2 https://doi.org/10.1111/j.1365-2958.2004.04276.x	journal	August 2004
Riboswitches: Emerging Themes in RNA Structure and Function Montange, Rebecca K.; Batey, Robert T. Annual Review of Biophysics, Vol. 37, Issue 1 https://doi.org/10.1146/annurev.biophys.37.032807.130000	journal	June 2008
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
A riboswitch selective for the queuosine precursor preQ1 contains an unusually small aptamer domain Roth, Adam; Winkler, Wade C.; Regulski, Elizabeth E. Nature Structural & Molecular Biology, Vol. 14, Issue 4 https://doi.org/10.1038/nsmb1224	journal	March 2007
Direct Measurement of Distances and Angles in Biomolecules by NMR in a Dilute Liquid Crystalline Medium Tjandra, N. Science, Vol. 278, Issue 5340 https://doi.org/10.1126/science.278.5340.1111	journal	November 1997
Measurement of Proton, Nitrogen, and Carbonyl Chemical Shielding Anisotropies in a Protein Dissolved in a Dilute Liquid Crystalline Phase Cornilescu, Gabriel; Bax, Ad Journal of the American Chemical Society, Vol. 122, Issue 41 https://doi.org/10.1021/ja0016194	journal	October 2000
Characterizing Complex Dynamics in the Transactivation Response Element Apical Loop and Motional Correlations with the Bulge by NMR, Molecular Dynamics, and Mutagenesis Dethoff, Elizabeth A.; Hansen, Alexandar L.; Musselman, Catherine Biophysical Journal, Vol. 95, Issue 8 https://doi.org/10.1529/biophysj.108.140285	journal	October 2008
Characterizing the relative orientation and dynamics of RNA A-form helices using NMR residual dipolar couplings Bailor, Maximillian H.; Musselman, Catherine; Hansen, Alexandar L. Nature Protocols, Vol. 2, Issue 6 https://doi.org/10.1038/nprot.2007.221	journal	June 2007
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
RNA Folding: Thermodynamic and Molecular Descriptions of the Roles of Ions Draper, David E. Biophysical Journal, Vol. 95, Issue 12 https://doi.org/10.1529/biophysj.108.131813	journal	December 2008
Highly Modular Structure and Ligand Binding by Conformational Capture in a Minimalistic Riboswitch Duchardt-Ferner, Elke; Weigand, Julia E.; Ohlenschläger, Oliver Angewandte Chemie International Edition, Vol. 49, Issue 35 https://doi.org/10.1002/anie.201001339	journal	July 2010
Extending the Range of Microsecond-to-Millisecond Chemical Exchange Detected in Labeled and Unlabeled Nucleic Acids by Selective Carbon R _1ρ NMR Spectroscopy Hansen, Alexandar L.; Nikolova, Evgenia N.; Casiano-Negroni, Anette Journal of the American Chemical Society, Vol. 131, Issue 11 https://doi.org/10.1021/ja8091399	journal	February 2009
Dynamics of Large Elongated RNA by NMR Carbon Relaxation Hansen, Alexandar L.; Al-Hashimi, Hashim M. Journal of the American Chemical Society, Vol. 129, Issue 51 https://doi.org/10.1021/ja0757982	journal	December 2007
Direct Observation of Hierarchical Folding in Single Riboswitch Aptamers Greenleaf, W. J.; Frieda, K. L.; Foster, D. A. N. Science, Vol. 319, Issue 5863 https://doi.org/10.1126/science.1151298	journal	January 2008
Confirmation of a second natural preQ1 aptamer class in Streptococcaceae bacteria Meyer, M. M.; Roth, A.; Chervin, S. M. RNA, Vol. 14, Issue 4 https://doi.org/10.1261/rna.937308	journal	February 2008
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
Real-time multidimensional NMR follows RNA folding with second resolution Lee, M. -K.; Gal, M.; Frydman, L. Proceedings of the National Academy of Sciences, Vol. 107, Issue 20 https://doi.org/10.1073/pnas.1001195107	journal	May 2010

Similar Records

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:1123352

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

Ligand Binding Induces Conformational Changes in Human Cellular Retinol-binding Protein 1 (CRBP1) Revealed by Atomic Resolution Crystal Structures

Journal Article · Sun Feb 21 00:00:00 EST 2016 · Journal of Biological Chemistry · OSTI ID:1123352

Silvaroli, Josie A.; Arne, Jason M.; Chelstowska, Sylwia; +3 more

CRYSTAL STRUCTURE OF UNLIGATED GUANYLATE KINASE FROM YEAST REVEALS GMP-INDUCED CONFORMATIONAL CHANGES

Journal Article · Mon Jan 01 00:00:00 EST 2001 · Journal of Molecular Biology · OSTI ID:1123352

BLASZCZYK, J; LI, Y; YAN, H; +1 more

Title: Comparison of Solution and Crystal Structures of PreQ 1 Riboswitch Reveals Calcium-Induced Changes in Conformation and Dynamics

Citation Formats

References (27)

Similar Records

Related Subjects

Title: Comparison of Solution and Crystal Structures of PreQ ₁ Riboswitch Reveals Calcium-Induced Changes in Conformation and Dynamics