Published in J Am Chem Soc on October 22, 2013
Common themes and differences in SAM recognition among SAM riboswitches. Biochim Biophys Acta (2014) 0.82
Understanding the kinetic mechanism of RNA single base pair formation. Proc Natl Acad Sci U S A (2015) 0.79
Generalized Manning Condensation Model Captures the RNA Ion Atmosphere. Phys Rev Lett (2015) 0.78
SOP-GPU: influence of solvent-induced hydrodynamic interactions on dynamic structural transitions in protein assemblies. J Comput Chem (2016) 0.75
Regulation of bacterial gene expression by riboswitches. Annu Rev Microbiol (2005) 5.66
Cooperation between translating ribosomes and RNA polymerase in transcription elongation. Science (2010) 3.87
Control of alternative RNA splicing and gene expression by eukaryotic riboswitches. Nature (2007) 3.87
An mRNA structure that controls gene expression by binding S-adenosylmethionine. Nat Struct Biol (2003) 3.75
Riboswitches: emerging themes in RNA structure and function. Annu Rev Biophys (2008) 3.75
The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch. Mol Cell (2005) 3.62
A decade of riboswitches. Cell (2013) 3.26
Direct observation of hierarchical folding in single riboswitch aptamers. Science (2008) 3.22
Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes. Genome Biol (2010) 3.19
Protein folding kinetics: timescales, pathways and energy landscapes in terms of sequence-dependent properties. Fold Des (1997) 3.14
Structure of the SAM-II riboswitch bound to S-adenosylmethionine. Nat Struct Mol Biol (2008) 3.13
Evidence for a second class of S-adenosylmethionine riboswitches and other regulatory RNA motifs in alpha-proteobacteria. Genome Biol (2005) 2.32
The S(MK) box is a new SAM-binding RNA for translational regulation of SAM synthetase. Nat Struct Mol Biol (2006) 2.08
Dynamics of allosteric transitions in GroEL. Proc Natl Acad Sci U S A (2006) 1.88
Probing the mechanical folding kinetics of TAR RNA by hopping, force-jump, and force-ramp methods. Biophys J (2005) 1.86
Full distance-resolved folding energy landscape of one single protein molecule. Proc Natl Acad Sci U S A (2010) 1.85
Revealing the bifurcation in the unfolding pathways of GFP by using single-molecule experiments and simulations. Proc Natl Acad Sci U S A (2007) 1.74
Complex riboswitches. Science (2008) 1.70
Force unfolding kinetics of RNA using optical tweezers. I. Effects of experimental variables on measured results. Biophys J (2007) 1.61
Pathways and kinetic barriers in mechanical unfolding and refolding of RNA and proteins. Structure (2006) 1.58
Crystal structures of the SAM-III/S(MK) riboswitch reveal the SAM-dependent translation inhibition mechanism. Nat Struct Mol Biol (2008) 1.54
Nonlocal helix formation is key to understanding S-adenosylmethionine-1 riboswitch function. Biophys J (2009) 1.51
Design principles for riboswitch function. PLoS Comput Biol (2009) 1.44
The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches. RNA (2008) 1.39
Riboswitches that sense S-adenosylhomocysteine and activate genes involved in coenzyme recycling. Mol Cell (2008) 1.38
Direct observation of an ensemble of stable collapsed states in the mechanical folding of ubiquitin. Proc Natl Acad Sci U S A (2009) 1.35
Force-dependent hopping rates of RNA hairpins can be estimated from accurate measurement of the folding landscapes. Proc Natl Acad Sci U S A (2008) 1.33
A variant riboswitch aptamer class for S-adenosylmethionine common in marine bacteria. RNA (2009) 1.32
Mechanical unfolding of RNA: from hairpins to structures with internal multiloops. Biophys J (2006) 1.27
Relative stability of helices determines the folding landscape of adenine riboswitch aptamers. J Am Chem Soc (2008) 1.24
Single-molecule studies of RNA polymerase: one singular sensation, every little step it takes. Mol Cell (2011) 1.21
Single-molecule force spectroscopy of the add adenine riboswitch relates folding to regulatory mechanism. Nucleic Acids Res (2011) 1.17
Force unfolding kinetics of RNA using optical tweezers. II. Modeling experiments. Biophys J (2007) 1.16
Direct observation of cotranscriptional folding in an adenine riboswitch. Science (2012) 1.13
From mechanical folding trajectories to intrinsic energy landscapes of biopolymers. Proc Natl Acad Sci U S A (2013) 1.10
Folding energy landscape of the thiamine pyrophosphate riboswitch aptamer. Proc Natl Acad Sci U S A (2012) 1.07
Cooperative and directional folding of the preQ1 riboswitch aptamer domain. J Am Chem Soc (2011) 1.05
Role of the adenine ligand on the stabilization of the secondary and tertiary interactions in the adenine riboswitch. J Mol Biol (2009) 1.01
Dynamic energy landscapes of riboswitches help interpret conformational rearrangements and function. PLoS Comput Biol (2012) 0.92
Variable sequences outside the SAM-binding core critically influence the conformational dynamics of the SAM-III/SMK box riboswitch. J Mol Biol (2011) 0.92
Single-molecule studies of the lysine riboswitch reveal effector-dependent conformational dynamics of the aptamer domain. Biochemistry (2012) 0.91
Chain length determines the folding rates of RNA. Biophys J (2012) 0.91
Loop-loop interaction in an adenine-sensing riboswitch: a molecular dynamics study. RNA (2013) 0.91
The SAM-responsive S(MK) box is a reversible riboswitch. Mol Microbiol (2010) 0.90
Probing protein-protein interactions by dynamic force correlation spectroscopy. Phys Rev Lett (2005) 0.84
RNA under tension: Folding Landscapes, Kinetic partitioning Mechanism, and Molecular Tensegrity. J Phys Chem Lett (2012) 0.80
Gene regulation by riboswitches with and without negative feedback loop. Biophys J (2012) 0.77
Navigating the folding routes. Science (1995) 7.34
Metastability of the folded states of globular proteins. Proc Natl Acad Sci U S A (1990) 3.79
Molecular crowding enhances native state stability and refolding rates of globular proteins. Proc Natl Acad Sci U S A (2005) 3.29
Dissecting the assembly of Abeta16-22 amyloid peptides into antiparallel beta sheets. Structure (2003) 3.18
Protein folding kinetics: timescales, pathways and energy landscapes in terms of sequence-dependent properties. Fold Des (1997) 3.14
Kinetics and thermodynamics of folding in model proteins. Proc Natl Acad Sci U S A (1993) 3.08
The nature of folded states of globular proteins. Biopolymers (1992) 2.91
Mechanisms and kinetics of beta-hairpin formation. Proc Natl Acad Sci U S A (2000) 2.66
Pair potentials for protein folding: choice of reference states and sensitivity of predicted native states to variations in the interaction schemes. Protein Sci (1999) 2.41
Folding of RNA involves parallel pathways. J Mol Biol (1997) 2.22
Native topology determines force-induced unfolding pathways in globular proteins. Proc Natl Acad Sci U S A (2000) 2.09
Urea denaturation by stronger dispersion interactions with proteins than water implies a 2-stage unfolding. Proc Natl Acad Sci U S A (2008) 2.03
Monomer adds to preformed structured oligomers of Abeta-peptides by a two-stage dock-lock mechanism. Proc Natl Acad Sci U S A (2006) 2.01
Simulations of beta-hairpin folding confined to spherical pores using distributed computing. Proc Natl Acad Sci U S A (2002) 1.99
Kinetics and thermodynamics of folding of a de novo designed four-helix bundle protein. J Mol Biol (1996) 1.95
Interactions between hydrophobic and ionic solutes in aqueous guanidinium chloride and urea solutions: lessons for protein denaturation mechanism. J Am Chem Soc (2007) 1.90
Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations. Proc Natl Acad Sci U S A (2006) 1.90
Dynamics of allosteric transitions in GroEL. Proc Natl Acad Sci U S A (2006) 1.88
Exploring the kinetic requirements for enhancement of protein folding rates in the GroEL cavity. J Mol Biol (1999) 1.85
Chaperonin-facilitated protein folding: optimization of rate and yield by an iterative annealing mechanism. Proc Natl Acad Sci U S A (1996) 1.79
Role of counterion condensation in folding of the Tetrahymena ribozyme. I. Equilibrium stabilization by cations. J Mol Biol (2001) 1.78
Exploring protein aggregation and self-propagation using lattice models: phase diagram and kinetics. Protein Sci (2002) 1.77
Can energy landscape roughness of proteins and RNA be measured by using mechanical unfolding experiments? Proc Natl Acad Sci U S A (2003) 1.76
Revealing the bifurcation in the unfolding pathways of GFP by using single-molecule experiments and simulations. Proc Natl Acad Sci U S A (2007) 1.74
Theoretical predictions of folding pathways by using the proximity rule, with applications to bovine pancreatic trypsin inhibitor. Proc Natl Acad Sci U S A (1995) 1.73
Dynamics of Asp23-Lys28 salt-bridge formation in Abeta10-35 monomers. J Am Chem Soc (2006) 1.63
Multiple protein folding nuclei and the transition state ensemble in two-state proteins. Proteins (2001) 1.61
Role of counterion condensation in folding of the Tetrahymena ribozyme. II. Counterion-dependence of folding kinetics. J Mol Biol (2001) 1.61
Network of dynamically important residues in the open/closed transition in polymerases is strongly conserved. Structure (2005) 1.60
Dynamics of unbinding of cell adhesion molecules: transition from catch to slip bonds. Proc Natl Acad Sci U S A (2005) 1.59
Pathways and kinetic barriers in mechanical unfolding and refolding of RNA and proteins. Structure (2006) 1.58
Mechanical unfolding of RNA hairpins. Proc Natl Acad Sci U S A (2005) 1.57
Charge density of divalent metal cations determines RNA stability. J Am Chem Soc (2007) 1.56
Effects of denaturants and osmolytes on proteins are accurately predicted by the molecular transfer model. Proc Natl Acad Sci U S A (2008) 1.52
Lattice models for proteins reveal multiple folding nuclei for nucleation-collapse mechanism. J Mol Biol (1998) 1.50
Molecular dynamics simulations of end-to-end contact formation in hydrocarbon chains in water and aqueous urea solution. J Am Chem Soc (2003) 1.44
Toward a molecular theory of early and late events in monomer to amyloid fibril formation. Annu Rev Phys Chem (2011) 1.43
Forced-unfolding and force-quench refolding of RNA hairpins. Biophys J (2006) 1.42
Collapse transition in proteins. Phys Chem Chem Phys (2008) 1.41
Stretching single-domain proteins: phase diagram and kinetics of force-induced unfolding. Proc Natl Acad Sci U S A (1999) 1.41
Magnesium-dependent folding of self-splicing RNA: exploring the link between cooperativity, thermodynamics, and kinetics. Proc Natl Acad Sci U S A (1999) 1.38
Rigor to post-rigor transition in myosin V: link between the dynamics and the supporting architecture. Structure (2010) 1.37
Ribosome exit tunnel can entropically stabilize alpha-helices. Proc Natl Acad Sci U S A (2005) 1.36
RNA tertiary interactions mediate native collapse of a bacterial group I ribozyme. J Mol Biol (2005) 1.36
Determination of network of residues that regulate allostery in protein families using sequence analysis. Protein Sci (2006) 1.35
Cooperativity in protein folding: from lattice models with sidechains to real proteins. Fold Des (1998) 1.34
Aqueous urea solution destabilizes Abeta(16-22) oligomers. Proc Natl Acad Sci U S A (2004) 1.34
Development of novel statistical potentials for protein fold recognition. Curr Opin Struct Biol (2004) 1.33
Force-dependent hopping rates of RNA hairpins can be estimated from accurate measurement of the folding landscapes. Proc Natl Acad Sci U S A (2008) 1.33
Capturing the essence of folding and functions of biomolecules using coarse-grained models. Nat Commun (2011) 1.32
Multiple stepwise refolding of immunoglobulin domain I27 upon force quench depends on initial conditions. Proc Natl Acad Sci U S A (2005) 1.32
Exploring the energy landscape in proteins. Proc Natl Acad Sci U S A (1993) 1.32
Allosteric transitions in the chaperonin GroEL are captured by a dominant normal mode that is most robust to sequence variations. Biophys J (2007) 1.31
Size, shape, and flexibility of RNA structures. J Chem Phys (2006) 1.31
Probing the instabilities in the dynamics of helical fragments from mouse PrPC. Proc Natl Acad Sci U S A (2004) 1.31
Mechanical unfolding of RNA: from hairpins to structures with internal multiloops. Biophys J (2006) 1.27
Compaction of a bacterial group I ribozyme coincides with the assembly of core helices. Biochemistry (2004) 1.26
Relative stability of helices determines the folding landscape of adenine riboswitch aptamers. J Am Chem Soc (2008) 1.24
Persistence length changes dramatically as RNA folds. Phys Rev Lett (2005) 1.23
Folding of the Tetrahymena ribozyme by polyamines: importance of counterion valence and size. J Mol Biol (2004) 1.23
Allosteric communication in dihydrofolate reductase: signaling network and pathways for closed to occluded transition and back. J Mol Biol (2007) 1.22
Extracting stacking interaction parameters for RNA from the data set of native structures. J Mol Biol (2005) 1.22
Nanopore-protein interactions dramatically alter stability and yield of the native state in restricted spaces. J Mol Biol (2006) 1.22
Metal ion dependence of cooperative collapse transitions in RNA. J Mol Biol (2009) 1.20
Effects of crowding and confinement on the structures of the transition state ensemble in proteins. J Phys Chem B (2007) 1.20
Symmetric connectivity of secondary structure elements enhances the diversity of folding pathways. J Mol Biol (2005) 1.19
Charge states rather than propensity for beta-structure determine enhanced fibrillogenesis in wild-type Alzheimer's beta-amyloid peptide compared to E22Q Dutch mutant. Protein Sci (2002) 1.19
Factors governing the foldability of proteins. Proteins (1996) 1.18
Kinetics of peptide folding: computer simulations of SYPFDV and peptide variants in water. J Mol Biol (1997) 1.18
Assembly mechanisms of RNA pseudoknots are determined by the stabilities of constituent secondary structures. Proc Natl Acad Sci U S A (2009) 1.16
Stiffness of the distal loop restricts the structural heterogeneity of the transition state ensemble in SH3 domains. J Mol Biol (2002) 1.16
Dynamics of locking of peptides onto growing amyloid fibrils. Proc Natl Acad Sci U S A (2009) 1.15
Virtual atom representation of hydrogen bonds in minimal off-lattice models of alpha helices: effect on stability, cooperativity and kinetics. Fold Des (1998) 1.14
Multiple probes are required to explore and control the rugged energy landscape of RNA hairpins. J Am Chem Soc (2008) 1.13
Probing the initial stage of aggregation of the Abeta(10-35)-protein: assessing the propensity for peptide dimerization. J Mol Biol (2004) 1.12
Dynamic transition in tRNA is solvent induced. J Am Chem Soc (2006) 1.11
From mechanical folding trajectories to intrinsic energy landscapes of biopolymers. Proc Natl Acad Sci U S A (2013) 1.10
Kinetics of loop formation in polymer chains. J Phys Chem B (2008) 1.10
Annealing function of GroEL: structural and bioinformatic analysis. Biophys Chem (2003) 1.10
Compression and stretching of a self-avoiding chain in cylindrical nanopores. Phys Rev Lett (2008) 1.09
Entropic stabilization of proteins by TMAO. J Phys Chem B (2011) 1.09
Probing the mechanisms of fibril formation using lattice models. J Chem Phys (2008) 1.08
Kinetics of interior loop formation in semiflexible chains. J Chem Phys (2006) 1.08
Influence of preformed Asp23-Lys28 salt bridge on the conformational fluctuations of monomers and dimers of Abeta peptides with implications for rates of fibril formation. J Phys Chem B (2009) 1.08
Counterion charge density determines the position and plasticity of RNA folding transition states. J Mol Biol (2006) 1.07
Minimal models for proteins and RNA from folding to function. Prog Mol Biol Transl Sci (2008) 1.05
Refolding dynamics of stretched biopolymers upon force quench. Proc Natl Acad Sci U S A (2009) 1.04
Interactions between amino acid side chains in cylindrical hydrophobic nanopores with applications to peptide stability. Proc Natl Acad Sci U S A (2008) 1.04
Transmembrane structures of amyloid precursor protein dimer predicted by replica-exchange molecular dynamics simulations. J Am Chem Soc (2009) 1.04
Modeling the role of disulfide bonds in protein folding: entropic barriers and pathways. Proteins (1995) 1.04
Factors governing fibrillogenesis of polypeptide chains revealed by lattice models. Phys Rev Lett (2010) 1.03
Allostery wiring diagrams in the transitions that drive the GroEL reaction cycle. J Mol Biol (2008) 1.03
Effect of finite size on cooperativity and rates of protein folding. J Phys Chem A (2006) 1.03
Effects of trimethylamine N-oxide (TMAO) and crowding agents on the stability of RNA hairpins. J Am Chem Soc (2008) 1.03
Factors governing helix formation in peptides confined to carbon nanotubes. Nano Lett (2008) 1.03
How accurate are polymer models in the analysis of Förster resonance energy transfer experiments on proteins? J Chem Phys (2009) 1.02
Residues in substrate proteins that interact with GroEL in the capture process are buried in the native state. Proc Natl Acad Sci U S A (2006) 1.02
Compaction and tensile forces determine the accuracy of folding landscape parameters from single molecule pulling experiments. Phys Rev Lett (2011) 1.01
Structures and free-energy landscapes of the wild type and mutants of the Abeta(21-30) peptide are determined by an interplay between intrapeptide electrostatic and hydrophobic interactions. J Mol Biol (2008) 1.01
Molecular origin of constant m-values, denatured state collapse, and residue-dependent transition midpoints in globular proteins. Biochemistry (2009) 1.00