An integrated perspective on RNA aptamer ligand-recognition models: clearing muddy waters

Fluorescence-Based Strategies to Investigate the Structure and Dynamics of Aptamer-Ligand Complexes

(2016) Cibran Perez-Gonzalez et al.   Frontiers in Chemistry

Mg2+ Shifts Ligand-Mediated Folding of a Riboswitch from Induced-Fit to Conformational Selection

(2015) Krishna C. Suddala et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

RNA-mediated epigenetic regulation of gene expression

(2015) Daniel Holoch et al.   NATURE REVIEWS GENETICS

Linking aptamer-ligand binding and expression platform folding in riboswitches: prospects for mechanistic modeling and design

(2015) Fareed Aboul-ela et al.   Wiley Interdisciplinary Reviews-RNA

Fluorescence tools to investigate riboswitch structural dynamics

(2014) Patrick St-Pierre et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Single-molecule studies of riboswitch folding

(2014) Andrew Savinov et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Distinguishing induced fit from conformational selection

(2014) Stefano Gianni et al.   BIOPHYSICAL CHEMISTRY

Single-Molecule Conformational Dynamics of a Biologically Functional Hydroxocobalamin Riboswitch

(2014) Erik D. Holmstrom et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The rise of regulatory RNA

(2014) Kevin V. Morris et al.   NATURE REVIEWS GENETICS

Conformational Selection Is a Dominant Mechanism of Ligand Binding

(2013) Austin D. Vogt et al.   BIOCHEMISTRY

Kinetics and Energetics of Biomolecular Folding and Binding

(2013) Christopher A. Pierse et al.   BIOPHYSICAL JOURNAL

Kinetics of Ligand-Receptor Interaction Reveals an Induced-Fit Mode of Binding in a Cyclic Nucleotide-Activated Protein

(2013) Sebastian Peuker et al.   BIOPHYSICAL JOURNAL

Ligand Concentration Regulates the Pathways of Coupled Protein Folding and Binding

(2013) Kyle G. Daniels et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Single-molecule chemical denaturation of riboswitches

(2013) Paul A. Dalgarno et al.   NUCLEIC ACIDS RESEARCH

Folding and ligand recognition of the TPP riboswitch aptamer at single-molecule resolution

(2013) Andrea Haller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-Molecule Studies of the Lysine Riboswitch Reveal Effector-Dependent Conformational Dynamics of the Aptamer Domain

(2012) Larry R. Fiegland et al.   BIOCHEMISTRY

Conformational Selection or Induced Fit? A Critical Appraisal of the Kinetic Mechanism

(2012) Austin D. Vogt et al.   BIOCHEMISTRY

Folding of the SAM-I riboswitch

(2012) Sébastien H Eschbach et al.   RNA Biology

The Dynamic Nature of RNA as Key to Understanding Riboswitch Mechanisms

(2011) Andrea Haller et al.   ACCOUNTS OF CHEMICAL RESEARCH

Induced Fit or Conformational Selection? The Role of the Semi-closed State in the Maltose Binding Protein

(2011) Denis Bucher et al.   BIOCHEMISTRY

Free-Energy Landscapes of Protein Domain Movements upon Ligand Binding

(2011) Hiroko X. Kondo et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Molecular insights into the ligand-controlled organization of the SAM-I riboswitch

(2011) Benoit Heppell et al.   Nature Chemical Biology

Conformational capture of the SAM-II riboswitch

(2011) Andrea Haller et al.   Nature Chemical Biology

Influence of ground-state structure and Mg 2+ binding on folding kinetics of the guanine-sensing riboswitch aptamer domain

(2011) Janina Buck et al.   NUCLEIC ACIDS RESEARCH

Single-molecule force spectroscopy of the add adenine riboswitch relates folding to regulatory mechanism

(2011) Krishna Neupane et al.   NUCLEIC ACIDS RESEARCH

Widespread Genetic Switches and Toxicity Resistance Proteins for Fluoride

(2011) J. L. Baker et al.   SCIENCE

Archaeal CRISPR-based immune systems: exchangeable functional modules

(2011) Roger A. Garrett et al.   TRENDS IN MICROBIOLOGY

A Role for Both Conformational Selection and Induced Fit in Ligand Binding by the LAO Protein

(2011) Daniel-Adriano Silva et al.   PLoS Computational Biology

Comparative Study between Transcriptionally- and Translationally-Acting Adenine Riboswitches Reveals Key Differences in Riboswitch Regulatory Mechanisms

(2011) Jean-François Lemay et al.   PLoS Genetics

From Induced Fit to Conformational Selection: A Continuum of Binding Mechanism Controlled by the Timescale of Conformational Transitions

(2010) Huan-Xiang Zhou   BIOPHYSICAL JOURNAL

Enzyme dynamics point to stepwise conformational selection in catalysis

(2010) Buyong Ma et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Real-time multidimensional NMR follows RNA folding with second resolution

(2010) M.-K. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Topology Links RNA Secondary Structure with Global Conformation, Dynamics, and Adaptation

(2010) M. H. Bailor et al.   SCIENCE

Induced fit, conformational selection and independent dynamic segments: an extended view of binding events

(2010) Peter Csermely et al.   TRENDS IN BIOCHEMICAL SCIENCES

Reconciling binding mechanisms of intrinsically disordered proteins

(2009) L. Michel Espinoza-Fonseca   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Binding Kinetics of Glucose and Allosteric Activators to Human Glucokinase Reveal Multiple Conformational States

(2009) Mathias Antoine et al.   BIOCHEMISTRY

The Cluster of Hydrophobic Residues Controls the Entrance to the Active Site of Choline Oxidase

(2009) Yao Xin et al.   BIOCHEMISTRY

Amino acid recognition and gene regulation by riboswitches

(2009) Alexander Serganov et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

The Dynamic Landscapes of RNA Architecture

(2009) José Almeida Cruz et al.   CELL

Origins and Mechanisms of miRNAs and siRNAs

(2009) Richard W. Carthew et al.   CELL

Substrate Induced Population Shifts and Stochastic Gating in the PBCV-1 mRNA Capping Enzyme

(2009) Robert V. Swift et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The role of dynamic conformational ensembles in biomolecular recognition

(2009) David D Boehr et al.   Nature Chemical Biology

Constructing RNA dynamical ensembles by combining MD and motionally decoupled NMR RDCs: new insights into RNA dynamics and adaptive ligand recognition

(2009) Aaron T. Frank et al.   NUCLEIC ACIDS RESEARCH

Conformational selection or induced fit: A flux description of reaction mechanism

(2009) G. G. Hammes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conformational selection and induced fit mechanism underlie specificity in noncovalent interactions with ubiquitin

(2009) T. Wlodarski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conformational sampling, catalysis, and evolution of the bacterial phosphotriesterase

(2009) C. J. Jackson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ligand binding to proteins: The binding landscape model

(2009) David W. Miller et al.   PROTEIN SCIENCE

Riboswitches: Ancient and Promising Genetic Regulators

(2008) Simon Blouin et al.   CHEMBIOCHEM

Crystal Structure of the Lysine Riboswitch Regulatory mRNA Element

(2008) Andrew D. Garst et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Thrombin

(2008) Enrico Di Cera   MOLECULAR ASPECTS OF MEDICINE

Structural insights into amino acid binding and gene control by a lysine riboswitch

(2008) Alexander Serganov et al.   NATURE

Enzymes with lid-gated active sites must operate by an induced fit mechanism instead of conformational selection

(2008) S. M. Sullivan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Theory, analysis, and interpretation of single-molecule force spectroscopy experiments

(2008) O. K. Dudko et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamic energy landscape view of coupled binding and protein conformational change: Induced-fit versus population-shift mechanisms

(2008) K.-i. Okazaki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Selected-fit versus induced-fit protein binding: Kinetic differences and mutational analysis

(2008) Thomas R. Weikl et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Mechanism of induced folding: Both folding before binding and binding before folding can be realized in staphylococcal nuclease mutants

(2008) Masayoshi Onitsuka et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Direct Observation of Hierarchical Folding in Single Riboswitch Aptamers

(2008) W. J. Greenleaf et al.   SCIENCE