Statistical mechanical prediction of ligand perturbation to RNA secondary structure and application to riboswitches
暂无分享,去创建一个
[1] Tao Pan,et al. Folding of noncoding RNAs during transcription facilitated by pausing-induced nonnative structures , 2007, Proceedings of the National Academy of Sciences.
[2] Shantenu Jha,et al. The Impact of a Ligand Binding on Strand Migration in the SAM-I Riboswitch , 2013, PLoS Comput. Biol..
[3] Shi-jie Chen,et al. Predicting Cotranscriptional Folding Kinetics For Riboswitch. , 2018, The journal of physical chemistry. B.
[4] Fareed Aboul-Ela,et al. Basis for ligand discrimination between ON and OFF state riboswitch conformations: the case of the SAM-I riboswitch. , 2012, RNA.
[5] R. Breaker,et al. Riboswitches that sense S-adenosylhomocysteine and activate genes involved in coenzyme recycling. , 2008, Molecular cell.
[6] Ivo L Hofacker,et al. Energy-directed RNA structure prediction. , 2014, Methods in molecular biology.
[7] D. Turner,et al. A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation , 2006, Nucleic acids research.
[8] A. Laederach,et al. Transcending the prediction paradigm: novel applications of SHAPE to RNA function and evolution , 2016, Wiley interdisciplinary reviews. RNA.
[9] Siqi Tian,et al. RNA structure through multidimensional chemical mapping , 2016, bioRxiv.
[10] C. Yanofsky,et al. Regulation by transcription attenuation in bacteria: how RNA provides instructions for transcription termination/antitermination decisions. , 2002, BioEssays : news and reviews in molecular, cellular and developmental biology.
[11] Christoph Flamm,et al. In silico design of ligand triggered RNA switches , 2018, bioRxiv.
[12] Katarzyna J Purzycka,et al. RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme. , 2017, RNA.
[13] T. Henkin,et al. Riboswitch RNAs: Regulation of gene expression by direct monitoring of a physiological signal , 2010, RNA biology.
[14] J. Onuchic,et al. Magnesium controls aptamer-expression platform switching in the SAM-I riboswitch , 2019, Nucleic acids research.
[15] Ali Nahvi,et al. An mRNA structure that controls gene expression by binding S-adenosylmethionine , 2003, Nature Structural Biology.
[16] T. Henkin,et al. Crystal structures of the SAM-III/SMK riboswitch reveal the SAM-dependent translation inhibition mechanism , 2008, Nature Structural &Molecular Biology.
[17] Peter Daldrop,et al. RNA Tertiary Interactions in a Riboswitch Stabilize the Structure of a Kink Turn , 2011, Structure.
[18] Feng Ding,et al. RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction. , 2012, RNA.
[19] Jonathan Perreault,et al. Transcriptional pausing at the translation start site operates as a critical checkpoint for riboswitch regulation , 2017, Nature Communications.
[20] D. Crothers,et al. The kinetics of ligand binding by an adenine-sensing riboswitch. , 2005, Biochemistry.
[21] J. Steitz,et al. The Noncoding RNA Revolution—Trashing Old Rules to Forge New Ones , 2014, Cell.
[22] S. Strobel,et al. Gene regulation by a glycine riboswitch singlet uses a finely tuned energetic landscape for helical switching , 2018, RNA.
[23] Daniel Herschlag,et al. The roles of structural dynamics in the cellular functions of RNAs , 2019, Nature Reviews Molecular Cell Biology.
[24] G. Nienhaus,et al. Single-molecule FRET reveals the energy landscape of the full-length SAM-I riboswitch. , 2017, Nature chemical biology.
[25] Wei Huang,et al. Linking aptamer‐ligand binding and expression platform folding in riboswitches: prospects for mechanistic modeling and design , 2015, Wiley interdisciplinary reviews. RNA.
[26] D. Nesbitt,et al. Single-Molecule FRET Kinetics of the Mn2+ Riboswitch: Evidence for Allosteric Mg2+ Control of "Induced-Fit" vs "Conformational Selection" Folding Pathways. , 2019, The journal of physical chemistry. B.
[27] Ronny Lorenz,et al. The Vienna RNA Websuite , 2008, Nucleic Acids Res..
[28] G. Nienhaus,et al. The multi-state energy landscape of the SAM-I riboswitch: A single-molecule Förster resonance energy transfer spectroscopy study. , 2018, The Journal of chemical physics.
[29] M. Woodside,et al. Transition path times for nucleic Acid folding determined from energy-landscape analysis of single-molecule trajectories. , 2012, Physical review letters.
[30] R. Breaker,et al. Regulation of bacterial gene expression by riboswitches. , 2005, Annual review of microbiology.
[31] Vitaly Epshtein,et al. The riboswitch-mediated control of sulfur metabolism in bacteria , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[32] Tina M. Henkin,et al. Natural Variability in S-Adenosylmethionine (SAM)-Dependent Riboswitches: S-Box Elements in Bacillus subtilis Exhibit Differential Sensitivity to SAM In Vivo and In Vitro , 2007, Journal of bacteriology.
[33] R. Breaker,et al. The structural and functional diversity of metabolite-binding riboswitches. , 2009, Annual review of biochemistry.
[34] T. Henkin,et al. S-adenosylmethionine directly inhibits binding of 30S ribosomal subunits to the SMK box translational riboswitch RNA , 2007, Proceedings of the National Academy of Sciences.
[35] C. Brooks,et al. Ligand Modulates Cross-Coupling between Riboswitch Folding and Transcriptional Pausing , 2018, bioRxiv.
[36] Michael T. Wolfinger,et al. NMR Structural Profiling of Transcriptional Intermediates Reveals Riboswitch Regulation by Metastable RNA Conformations. , 2017, Journal of the American Chemical Society.
[37] Karissa Y. Sanbonmatsu,et al. The expression platform and the aptamer: cooperativity between Mg2+ and ligand in the SAM-I riboswitch , 2012, Nucleic acids research.
[38] David H Mathews,et al. Prediction of RNA secondary structure by free energy minimization. , 2006, Current opinion in structural biology.
[39] D. Thirumalai,et al. Relative stability of helices determines the folding landscape of adenine riboswitch aptamers. , 2008, Journal of the American Chemical Society.
[40] J. Changeux,et al. ON THE NATURE OF ALLOSTERIC TRANSITIONS: A PLAUSIBLE MODEL. , 1965, Journal of molecular biology.
[41] D. Turner,et al. Predicting oligonucleotide affinity to nucleic acid targets. , 1999, RNA.
[42] Michael F. Sloma,et al. Exact calculation of loop formation probability identifies folding motifs in RNA secondary structures , 2016, RNA.
[43] Robert Giegerich,et al. Lost in folding space? Comparing four variants of the thermodynamic model for RNA secondary structure prediction , 2011, BMC Bioinformatics.
[44] Peter F. Stadler,et al. ViennaRNA Package 2.0 , 2011, Algorithms for Molecular Biology.
[45] D. Lafontaine,et al. Folding of the SAM aptamer is determined by the formation of a K-turn-dependent pseudoknot. , 2008, Biochemistry.
[46] Tamar Schlick,et al. Dynamic Energy Landscapes of Riboswitches Help Interpret Conformational Rearrangements and Function , 2012, PLoS Comput. Biol..
[47] R. Parker,et al. A multicolor riboswitch-based platform for imaging of RNA in live mammalian cells , 2018, Nature Chemical Biology.
[48] J. Onuchic,et al. Cooperation between Magnesium and Metabolite Controls Collapse of the SAM-I Riboswitch. , 2017, Biophysical journal.
[49] D. Turner,et al. 2 – Thermodynamics of RNA Secondary Structure Formation , 2001 .
[50] T. Henkin,et al. The S box regulon: a new global transcription termination control system for methionine and cysteine biosynthesis genes in Gram‐positive bacteria , 1998, Molecular microbiology.
[51] D. Lafontaine,et al. Molecular insights into the ligand-controlled organization of the SAM-I riboswitch. , 2011, Nature chemical biology.
[52] P. Stadler,et al. The effect of RNA secondary structures on RNA-ligand binding and the modifier RNA mechanism: a quantitative model. , 2005, Gene.
[53] R. M. Harris,et al. Physical chemistry for the life sciences , 1980, Nature.
[54] T. Pan,et al. Transcriptional pausing coordinates folding of the aptamer domain and the expression platform of a riboswitch , 2012, Proceedings of the National Academy of Sciences.
[55] É. Massé,et al. Comparative Study between Transcriptionally- and Translationally-Acting Adenine Riboswitches Reveals Key Differences in Riboswitch Regulatory Mechanisms , 2011, PLoS genetics.
[56] Harald Schwalbe,et al. Three-state mechanism couples ligand and temperature sensing in riboswitches , 2013, Nature.
[57] A. Serganov,et al. A Decade of Riboswitches , 2013, Cell.
[58] D. Lafontaine,et al. Ligand recognition and helical stacking formation are intimately linked in the SAM-I riboswitch regulatory mechanism , 2017, RNA.
[59] Jan Gorodkin,et al. RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods , 2014, Methods in Molecular Biology.
[60] D. Crothers,et al. The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch. , 2005, Molecular cell.
[61] D Thirumalai,et al. Gene regulation by riboswitches with and without negative feedback loop. , 2012, Biophysical journal.
[62] Walter N. Moss,et al. Folding and finding RNA secondary structure. , 2010, Cold Spring Harbor perspectives in biology.
[63] E. Nudler,et al. The riboswitch control of bacterial metabolism. , 2004, Trends in biochemical sciences.
[64] Yanli Wang,et al. Co-Transcriptional Folding and Regulation Mechanisms of Riboswitches , 2017, Molecules.
[65] T. Henkin,et al. The SMK box is a new SAM-binding RNA for translational regulation of SAM synthetase , 2006, Nature Structural &Molecular Biology.
[66] Tina M Henkin,et al. Variable sequences outside the SAM-binding core critically influence the conformational dynamics of the SAM-III/SMK box riboswitch. , 2011, Journal of molecular biology.
[67] R. Montange,et al. Structure of the S-adenosylmethionine riboswitch regulatory mRNA element , 2006, Nature.
[68] S. Jha,et al. Conformational heterogeneity of the SAM-I riboswitch transcriptional ON state: a chaperone-like role for S-adenosyl methionine. , 2012, Journal of molecular biology.
[69] H. Schwalbe,et al. Ligand-modulated folding of the full-length adenine riboswitch probed by NMR and single-molecule FRET spectroscopy , 2017, Nucleic acids research.
[70] Alexander Schug,et al. Nonlocal helix formation is key to understanding S-adenosylmethionine-1 riboswitch function. , 2009, Biophysical journal.