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Subsite Ligand Recognition and Cooperativity in the TPP Riboswitch: Implications for Fragment-Linkin

Journal Article · · ACS Chem. Biol.
Research Organization:
Advanced Photon Source (APS), Argonne National Laboratory (ANL), Argonne, IL (US)
Sponsoring Organization:
DOE - Office Of Science; NIH
OSTI ID:
1847154
Journal Information:
ACS Chem. Biol., Journal Name: ACS Chem. Biol. Journal Issue: (2) Vol. 17
Country of Publication:
United States
Language:
ENGLISH

References (53)

Cooperativity in macromolecular assembly journal July 2008
Cooperative and anticooperative binding to a ribozyme. journal September 1993
Validating Fragment-Based Drug Discovery for Biological RNAs: Lead Fragments Bind and Remodel the TPP Riboswitch Specifically journal May 2014
What is Cooperativity? journal September 2009
Stromelysin Inhibitors Designed from Weakly Bound Fragments:  Effects of Linking and Cooperativity journal June 1997
Molecular sensing by the aptamer domain of the FMN riboswitch: a general model for ligand binding by conformational selection journal July 2011
RNA base-pairing complexity in living cells visualized by correlated chemical probing journal November 2019
Thermodynamic analysis of ligand binding and ligand binding-induced tertiary structure formation by the thiamine pyrophosphate riboswitch journal November 2009
XDS journal January 2010
Principles for targeting RNA with drug-like small molecules journal July 2018
Cooperativity, allostery and synergism in ligand binding to riboswitches journal October 2015
Fragment based search for small molecule inhibitors of HIV-1 Tat-TAR journal December 2014
Discovery of Key Physicochemical, Structural, and Spatial Properties of RNA-Targeted Bioactive Ligands journal September 2017
Discovery of Potent Nonpeptide Inhibitors of Stromelysin Using SAR by NMR journal June 1997
Small molecules targeting viral RNA: Small molecules targeting viral RNA journal June 2016
On the attribution and additivity of binding energies journal July 1981
Identification of Biologically Active, HIV TAR RNA-Binding Small Molecules Using Small Molecule Microarrays journal May 2014
Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix journal October 2019
Fragment screening against the thiamine pyrophosphate riboswitchthiM journal January 2011
Discovering High-Affinity Ligands for Proteins: SAR by NMR journal November 1996
Synthesis of Stable Analogues of Thiamine Di- and Triphosphate as Tools for Probing a New Phosphorylation Pathway journal October 2002
Structure and ligand binding of the SAM-V riboswitch journal June 2018
RNA as a small molecule druggable target journal December 2017
Inference of Macromolecular Assemblies from Crystalline State journal September 2007
A Fragment-Based Approach to Identifying Ligands for Riboswitches journal February 2010
Design of small molecules targeting RNA structure from sequence journal January 2020
Selective Monodeprotection of Phosphate, Phosphite, Phosphonate, and Phosphoramide Benzyl Esters journal May 1995
Ligand efficiency as a guide in fragment hit selection and optimization journal October 2010
Accurate detection of chemical modifications in RNA by mutational profiling (MaP) with ShapeMapper 2 journal November 2017
Coenzyme recognition and gene regulation by a flavin mononucleotide riboswitch journal January 2009
Probing the Tetrahymena Group I Ribozyme Reaction in Both Directions journal August 2002
Ligand-induced folding of the thiM TPP riboswitch investigated by a structure-based fluorescence spectroscopic approach journal August 2007
RNA Structure Analysis at Single Nucleotide Resolution by Selective 2‘-Hydroxyl Acylation and Primer Extension (SHAPE) journal March 2005
Fingerprinting Noncanonical and Tertiary RNA Structures by Differential SHAPE Reactivity journal August 2012
Structural basis of ligand binding by a c-di-GMP riboswitch journal November 2009
Riboswitch diversity and distribution journal April 2017
The ways and means of fragment-based drug design journal November 2016
Monofluoro- and difluoro-methylenebisphosphonic acids: isopolar analogues of pyrophosphoric acid journal January 1981
Compound Design by Fragment-Linking journal April 2011
HOLLOW: Generating Accurate Representations of Channel and Interior Surfaces in Molecular Structures journal January 2008
Fragment-based design of small RNA binders: Promising developments and contribution of NMR journal July 2012
Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch journal May 2006
A general fragment-based approach to identify and optimize bioactive ligands targeting RNA journal December 2020
Probing riboswitch–ligand interactions using thiamine pyrophosphate analogues journal January 2012
Guidelines for SHAPE Reagent Choice and Detection Strategy for RNA Structure Probing Studies journal May 2019
Selective 2′-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) for direct, versatile and accurate RNA structure analysis journal October 2015
Exploring the Druggability of Conserved RNA Regulatory Elements in the SARS‐CoV‐2 Genome journal August 2021
Crystal Structures of the Thi-Box Riboswitch Bound to Thiamine Pyrophosphate Analogs Reveal Adaptive RNA-Small Molecule Recognition journal September 2006
Complex Ligand-Induced Conformational Changes in tRNA Asp Revealed by Single-Nucleotide Resolution SHAPE Chemistry journal March 2008
Parallel Discovery Strategies Provide a Basis for Riboswitch Ligand Design journal October 2020
Targeting Influenza A Virus RNA Promoter journal March 2015
Single-molecule correlated chemical probing of RNA journal September 2014
Discovery of Selective Ligands for Telomeric RNA G-quadruplexes (TERRA) through 19 F-NMR Based Fragment Screening journal May 2014