Published in Proc Natl Acad Sci U S A on April 11, 2011
Folding and assembly of the large molecular machine Hsp90 studied in single-molecule experiments. Proc Natl Acad Sci U S A (2016) 0.83
The unexpected role of polyubiquitin chains in the formation of fibrillar aggregates. Nat Commun (2015) 0.78
Structural Determinants of Misfolding in Multidomain Proteins. PLoS Comput Biol (2016) 0.75
Structure of ubiquitin refined at 1.8 A resolution. J Mol Biol (1987) 9.19
Contact order, transition state placement and the refolding rates of single domain proteins. J Mol Biol (1998) 8.51
Theory of protein folding. Curr Opin Struct Biol (2004) 7.64
Force-clamp spectroscopy monitors the folding trajectory of a single protein. Science (2004) 6.82
3D domain swapping: a mechanism for oligomer assembly. Protein Sci (1995) 4.96
The mechanical stability of ubiquitin is linkage dependent. Nat Struct Biol (2003) 4.66
The protein folding problem. Annu Rev Biophys (2008) 4.43
Protein folding studied by single-molecule FRET. Curr Opin Struct Biol (2008) 4.33
Domain swapping: entangling alliances between proteins. Proc Natl Acad Sci U S A (1994) 4.20
Intrinsic rates and activation free energies from single-molecule pulling experiments. Phys Rev Lett (2006) 4.04
The unfolding kinetics of ubiquitin captured with single-molecule force-clamp techniques. Proc Natl Acad Sci U S A (2004) 3.18
Kinetics and thermodynamics of folding in model proteins. Proc Natl Acad Sci U S A (1993) 3.08
The human ubiquitin multigene family: some genes contain multiple directly repeated ubiquitin coding sequences. EMBO J (1985) 3.06
Evidence for a three-state model of protein folding from kinetic analysis of ubiquitin variants with altered core residues. Nat Struct Biol (1996) 2.71
Protein folding thermodynamics and dynamics: where physics, chemistry, and biology meet. Chem Rev (2006) 2.48
RNA and protein folding: common themes and variations. Biochemistry (2005) 2.47
Single-molecule studies of protein folding. Annu Rev Biochem (2008) 2.22
How native-state topology affects the folding of dihydrofolate reductase and interleukin-1beta. Proc Natl Acad Sci U S A (2000) 2.11
Native topology determines force-induced unfolding pathways in globular proteins. Proc Natl Acad Sci U S A (2000) 2.09
Kinetics and thermodynamics of folding of a de novo designed four-helix bundle protein. J Mol Biol (1996) 1.95
The unfolding story of three-dimensional domain swapping. Structure (2003) 1.89
Deposition diseases and 3D domain swapping. Structure (2006) 1.88
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
Force-clamp spectroscopy of single-protein monomers reveals the individual unfolding and folding pathways of I27 and ubiquitin. Biophys J (2007) 1.63
Pathways and kinetic barriers in mechanical unfolding and refolding of RNA and proteins. Structure (2006) 1.58
Theoretical perspectives on protein folding. Annu Rev Biophys (2010) 1.53
Pulling direction as a reaction coordinate for the mechanical unfolding of single molecules. J Phys Chem B (2008) 1.46
Stretching single-domain proteins: phase diagram and kinetics of force-induced unfolding. Proc Natl Acad Sci U S A (1999) 1.41
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
Multiple stepwise refolding of immunoglobulin domain I27 upon force quench depends on initial conditions. Proc Natl Acad Sci U S A (2005) 1.32
Molecular dynamics simulations of hydrophobic collapse of ubiquitin. Protein Sci (1998) 1.25
Signatures of hydrophobic collapse in extended proteins captured with force spectroscopy. Proc Natl Acad Sci U S A (2007) 1.24
Reversible mechanical unfolding of single ubiquitin molecules. Biophys J (2004) 1.14
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 reveal a native-like intermediate during low-temperature refolding of ubiquitin. J Mol Biol (2004) 1.07
Refolding dynamics of stretched biopolymers upon force quench. Proc Natl Acad Sci U S A (2009) 1.04
Dissecting the mechanical unfolding of ubiquitin. Proc Natl Acad Sci U S A (2005) 1.02
The folding pathway of ubiquitin from all-atom molecular dynamics simulations. Biophys Chem (2004) 0.99
Fluctuations of primary ubiquitin folding intermediates in a force clamp. J Struct Biol (2006) 0.98
Refolding upon force quench and pathways of mechanical and thermal unfolding of ubiquitin. Biophys J (2006) 0.93
Comment on "Force-clamp spectroscopy monitors the folding trajectory of a single protein". Science (2004) 0.92
Multiple folding mechanisms of protein ubiquitin. Proteins (2005) 0.85
Probing protein-protein interactions by dynamic force correlation spectroscopy. Phys Rev Lett (2005) 0.84
New force replica exchange method and protein folding pathways probed by force-clamp technique. J Chem Phys (2008) 0.83
Molecular anatomy of a trafficking organelle. Cell (2006) 11.47
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
Structure and mechanism of the reversible photoswitch of a fluorescent protein. Proc Natl Acad Sci U S A (2005) 2.21
Probing the chemistry of thioredoxin catalysis with force. Nature (2007) 2.17
Mechanoenzymatics of titin kinase. Proc Natl Acad Sci U S A (2008) 2.17
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
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
Development of novel statistical potentials for protein fold recognition. Curr Opin Struct Biol (2004) 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
Size, shape, and flexibility of RNA structures. J Chem Phys (2006) 1.31
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
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
Mechanical network in titin immunoglobulin from force distribution analysis. PLoS Comput Biol (2009) 1.25
Relative stability of helices determines the folding landscape of adenine riboswitch aptamers. J Am Chem Soc (2008) 1.24
Signatures of hydrophobic collapse in extended proteins captured with force spectroscopy. Proc Natl Acad Sci U S A (2007) 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
Mechanical response of silk crystalline units from force-distribution analysis. Biophys J (2009) 1.21
Dynamic allostery in the methionine repressor revealed by force distribution analysis. PLoS Comput Biol (2009) 1.21
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
A novel calcium-binding site of von Willebrand factor A2 domain regulates its cleavage by ADAMTS13. Blood (2011) 1.06
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