Revealing the bifurcation in the unfolding pathways of GFP by using single-molecule experiments and simulations.

PubWeight™: 1.74‹?› | Rank: Top 3%

🔗 View Article (PMC 2154420)

Published in Proc Natl Acad Sci U S A on December 13, 2007

Authors

Moritz Mickler1, Ruxandra I Dima, Hendrik Dietz, Changbong Hyeon, D Thirumalai, Matthias Rief

Author Affiliations

1: Physik Department E22, Technische Universität München, James-Franck-Strasse, D-85748 Garching, Germany.

Articles citing this

ClpX(P) generates mechanical force to unfold and translocate its protein substrates. Cell (2011) 2.31

Mechanism of fibrin(ogen) forced unfolding. Structure (2011) 1.72

An expanding arsenal of experimental methods yields an explosion of insights into protein folding mechanisms. Nat Struct Mol Biol (2009) 1.43

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

Dependence of protein folding stability and dynamics on the density and composition of macromolecular crowders. Biophys J (2010) 1.16

The dual-basin landscape in GFP folding. Proc Natl Acad Sci U S A (2008) 1.16

From mechanical folding trajectories to intrinsic energy landscapes of biopolymers. Proc Natl Acad Sci U S A (2013) 1.10

Direct single-molecule observation of a protein living in two opposed native structures. Proc Natl Acad Sci U S A (2009) 1.07

Tightening the knot in phytochrome by single-molecule atomic force microscopy. Biophys J (2009) 1.06

Nanomechanics of HaloTag tethers. J Am Chem Soc (2013) 1.03

Hidden complexity in the isomerization dynamics of Holliday junctions. Nat Chem (2012) 0.99

Crowding effects on the mechanical stability and unfolding pathways of ubiquitin. J Phys Chem B (2009) 0.97

Promoter melting triggered by bacterial RNA polymerase occurs in three steps. Proc Natl Acad Sci U S A (2010) 0.97

Force-dependent switch in protein unfolding pathways and transition-state movements. Proc Natl Acad Sci U S A (2016) 0.93

Structural transitions and energy landscape for Cowpea Chlorotic Mottle Virus capsid mechanics from nanomanipulation in vitro and in silico. Biophys J (2013) 0.93

Denaturant-dependent folding of GFP. Proc Natl Acad Sci U S A (2012) 0.92

Probing the origin of tubulin rigidity with molecular simulations. Proc Natl Acad Sci U S A (2008) 0.92

Multicolor single-molecule FRET to explore protein folding and binding. Mol Biosyst (2010) 0.90

Propensity to form amyloid fibrils is encoded as excitations in the free energy landscape of monomeric proteins. J Mol Biol (2014) 0.90

Beta-barrel scaffold of fluorescent proteins: folding, stability and role in chromophore formation. Int Rev Cell Mol Biol (2013) 0.89

Hysteresis as a Marker for Complex, Overlapping Landscapes in Proteins. J Phys Chem Lett (2012) 0.88

Order statistics theory of unfolding of multimeric proteins. Biophys J (2010) 0.88

Full reconstruction of a vectorial protein folding pathway by atomic force microscopy and molecular dynamics simulations. J Biol Chem (2010) 0.86

Mechanically untying a protein slipknot: multiple pathways revealed by force spectroscopy and steered molecular dynamics simulations. J Am Chem Soc (2012) 0.86

The origin of nonmonotonic complex behavior and the effects of nonnative interactions on the diffusive properties of protein folding. Biophys J (2010) 0.85

Low folding cooperativity of HP35 revealed by single-molecule force spectroscopy and molecular dynamics simulation. Biophys J (2012) 0.84

Mutation of conserved histidines alters tertiary structure and nanomechanics of consensus ankyrin repeats. J Biol Chem (2012) 0.83

Unfolding and translocation pathway of substrate protein controlled by structure in repetitive allosteric cycles of the ClpY ATPase. Proc Natl Acad Sci U S A (2011) 0.82

Structure-Based Prediction of Protein-Folding Transition Paths. Biophys J (2016) 0.82

Folding study of Venus reveals a strong ion dependence of its yellow fluorescence under mildly acidic conditions. J Biol Chem (2009) 0.82

Mechanisms of cellular proteostasis: insights from single-molecule approaches. Annu Rev Biophys (2014) 0.81

Tracking unfolding and refolding reactions of single proteins using atomic force microscopy methods. Methods (2013) 0.80

Kinetics of allosteric transitions in S-adenosylmethionine riboswitch are accurately predicted from the folding landscape. J Am Chem Soc (2013) 0.80

Structural Consequences of Chromophore Formation and Exploration of Conserved Lid Residues amongst Naturally Occurring Fluorescent Proteins. Chem Phys (2014) 0.79

Single-molecule experiments reveal the flexibility of a Per-ARNT-Sim domain and the kinetic partitioning in the unfolding pathway under force. Biophys J (2012) 0.79

Minimum energy compact structures in force-quench polyubiquitin folding are domain swapped. Proc Natl Acad Sci U S A (2011) 0.79

Helices 2 and 3 are the initiation sites in the PrP(C) → PrP(SC) transition. Biochemistry (2012) 0.78

Contact Statistics Highlight Distinct Organizing Principles of Proteins and RNA. Biophys J (2016) 0.78

Mechanical anisotropy of ankyrin repeats. Biophys J (2012) 0.78

Coarse-Grained Simulations of Topology-Dependent Mechanisms of Protein Unfolding and Translocation Mediated by ClpY ATPase Nanomachines. PLoS Comput Biol (2016) 0.78

Nucleotides regulate the mechanical hierarchy between subdomains of the nucleotide binding domain of the Hsp70 chaperone DnaK. Proc Natl Acad Sci U S A (2015) 0.78

Fluctuating Nonlinear Spring Model of Mechanical Deformation of Biological Particles. PLoS Comput Biol (2016) 0.77

Structural basis of fluorescence quenching in caspase activatable-GFP. Protein Sci (2013) 0.77

GFP's mechanical intermediate states. PLoS One (2012) 0.77

Temperature and chemical denaturant dependence of forced unfolding of titin I27. J Phys Chem B (2009) 0.77

Experimental and computational characterization of biological liquid crystals: a review of single-molecule bioassays. Int J Mol Sci (2009) 0.76

Molecular investigations into the mechanics of a muscle anchoring complex. Biophys J (2015) 0.76

Mechanically unfolding protein L using a laser-feedback-controlled cantilever. Biophys J (2011) 0.76

Structural Basis of Interfacial Flexibility in Fibrin Oligomers. Structure (2016) 0.75

A fusion tag to fold on: the S-layer protein SgsE confers improved folding kinetics to translationally fused enhanced green fluorescent protein. J Microbiol Biotechnol (2012) 0.75

Kinetic Ductility and Force-Spike Resistance of Proteins from Single-Molecule Force Spectroscopy. Biophys J (2016) 0.75

The mechanochemistry of copper reports on the directionality of unfolding in model cupredoxin proteins. Nat Commun (2015) 0.75

SOP-GPU: influence of solvent-induced hydrodynamic interactions on dynamic structural transitions in protein assemblies. J Comput Chem (2016) 0.75

Capsid deformations reveal complex mechano-chemistry. Biophys J (2013) 0.75

Decoding Single Molecule Time Traces with Dynamic Disorder. PLoS Comput Biol (2016) 0.75

The role of binding site on the mechanical unfolding mechanism of ubiquitin. Sci Rep (2015) 0.75

Native structure-based modeling and simulation of biomolecular systems per mouse click. BMC Bioinformatics (2014) 0.75

Articles cited by this

Entropic elasticity of lambda-phage DNA. Science (1994) 15.40

The molecular structure of green fluorescent protein. Nat Biotechnol (1996) 9.63

Mechanical and chemical unfolding of a single protein: a comparison. Proc Natl Acad Sci U S A (1999) 7.74

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

Steered molecular dynamics and mechanical functions of proteins. Curr Opin Struct Biol (2001) 5.97

Unfolding pathways of individual bacteriorhodopsins. Science (2000) 5.08

The mechanical stability of ubiquitin is linkage dependent. Nat Struct Biol (2003) 4.66

Fast kinetics and mechanisms in protein folding. Annu Rev Biophys Biomol Struct (2000) 3.90

Protein folding and unfolding at atomic resolution. Cell (2002) 3.57

Green fluorescent protein (GFP): applications, structure, and related photophysical behavior. Chem Rev (2002) 3.46

The key event in force-induced unfolding of Titin's immunoglobulin domains. Biophys J (2000) 3.40

Identifying kinetic barriers to mechanical unfolding of the T. thermophila ribozyme. Science (2003) 3.32

Pulling geometry defines the mechanical resistance of a beta-sheet protein. Nat Struct Biol (2003) 3.21

Protein folding kinetics: timescales, pathways and energy landscapes in terms of sequence-dependent properties. Fold Des (1997) 3.14

Exploring the energy landscape of GFP by single-molecule mechanical experiments. Proc Natl Acad Sci U S A (2004) 2.65

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

Is protein folding hierarchic? II. Folding intermediates and transition states. Trends Biochem Sci (1999) 2.36

Anisotropic deformation response of single protein molecules. Proc Natl Acad Sci U S A (2006) 2.28

Unfolding proteins by external forces and temperature: the importance of topology and energetics. Proc Natl Acad Sci U S A (2000) 2.24

A mechanical unfolding intermediate in an actin-crosslinking protein. Nat Struct Mol Biol (2003) 2.12

Native topology determines force-induced unfolding pathways in globular proteins. Proc Natl Acad Sci U S A (2000) 2.09

Contour length and refolding rate of a small protein controlled by engineered disulfide bonds. Biophys J (2006) 1.82

Mechanically induced titin kinase activation studied by force-probe molecular dynamics simulations. Biophys J (2004) 1.70

Pathways and kinetic barriers in mechanical unfolding and refolding of RNA and proteins. Structure (2006) 1.58

Acid denaturation and refolding of green fluorescent protein. Biochemistry (2004) 1.46

Mechanical unfolding of proteins: insights into biology, structure and folding. Curr Opin Struct Biol (2007) 1.43

Forced-unfolding and force-quench refolding of RNA hairpins. Biophys J (2006) 1.42

Stretching single-domain proteins: phase diagram and kinetics of force-induced unfolding. Proc Natl Acad Sci U S A (1999) 1.41

Mechanical unfolding of TNfn3: the unfolding pathway of a fnIII domain probed by protein engineering, AFM and MD simulation. J Mol Biol (2005) 1.37

Mechanical unfolding pathways of the enhanced yellow fluorescent protein revealed by single molecule force spectroscopy. J Biol Chem (2006) 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

Mechanical unfolding of RNA: from hairpins to structures with internal multiloops. Biophys J (2006) 1.27

Signatures of hydrophobic collapse in extended proteins captured with force spectroscopy. Proc Natl Acad Sci U S A (2007) 1.24

Single-molecule force spectroscopy reveals a mechanically stable protein fold and the rational tuning of its mechanical stability. Proc Natl Acad Sci U S A (2007) 1.22

Real-time control of the energy landscape by force directs the folding of RNA molecules. Proc Natl Acad Sci U S A (2007) 1.15

Articles by these authors

Navigating the folding routes. Science (1995) 7.34

Self-assembly of DNA into nanoscale three-dimensional shapes. Nature (2009) 6.53

Metastability of the folded states of globular proteins. Proc Natl Acad Sci U S A (1990) 3.79

Synthetic lipid membrane channels formed by designed DNA nanostructures. Science (2012) 3.36

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

Exploring the energy landscape of GFP by single-molecule mechanical experiments. Proc Natl Acad Sci U S A (2004) 2.65

RNA and protein folding: common themes and variations. Biochemistry (2005) 2.47

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

The myosin coiled-coil is a truly elastic protein structure. Nat Mater (2002) 2.38

The complex folding network of single calmodulin molecules. Science (2011) 2.37

Can tyrosine kinase inhibitors be discontinued in patients with metastatic renal cell carcinoma and a complete response to treatment? A multicentre, retrospective analysis. Eur Urol (2008) 2.29

Single-molecule folding. Curr Opin Struct Biol (2003) 2.28

Anisotropic deformation response of single protein molecules. Proc Natl Acad Sci U S A (2006) 2.28

Folding of RNA involves parallel pathways. J Mol Biol (1997) 2.22

A primer to scaffolded DNA origami. Nat Methods (2011) 2.18

A mechanical unfolding intermediate in an actin-crosslinking protein. Nat Struct Mol Biol (2003) 2.12

Native topology determines force-induced unfolding pathways in globular proteins. Proc Natl Acad Sci U S A (2000) 2.09

Ligand-dependent equilibrium fluctuations of single calmodulin molecules. Science (2009) 2.05

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

Force-dependent stepping kinetics of myosin-V. Biophys J (2005) 1.88

Exploring the kinetic requirements for enhancement of protein folding rates in the GroEL cavity. J Mol Biol (1999) 1.85

Full distance-resolved folding energy landscape of one single protein molecule. Proc Natl Acad Sci U S A (2010) 1.85

Myosin-V is a mechanical ratchet. Proc Natl Acad Sci U S A (2006) 1.83

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

Dynamic Ca2+-dependent stimulation of vesicle fusion by membrane-anchored synaptotagmin 1. Science (2010) 1.77

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

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

Mechanism of fibrin(ogen) forced unfolding. Structure (2011) 1.72

Protein structure by mechanical triangulation. Proc Natl Acad Sci U S A (2006) 1.65

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

Temperature softening of a protein in single-molecule experiments. J Mol Biol (2005) 1.59

Dynamics of unbinding of cell adhesion molecules: transition from catch to slip bonds. Proc Natl Acad Sci U S A (2005) 1.59

Single-molecule unfolding force distributions reveal a funnel-shaped energy landscape. Biophys J (2005) 1.58

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

Theoretical perspectives on protein folding. Annu Rev Biophys (2010) 1.53

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

Comparison of non-gated vs. electrocardiogram-gated 64-detector-row computed tomography for integrated electroanatomic mapping in patients undergoing pulmonary vein isolation. Europace (2010) 1.50

DNA origami gatekeepers for solid-state nanopores. Angew Chem Int Ed Engl (2012) 1.48

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

The titin-telethonin complex is a directed, superstable molecular bond in the muscle Z-disk. Proc Natl Acad Sci U S A (2009) 1.40

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

Rapid folding of DNA into nanoscale shapes at constant temperature. Science (2012) 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

Direct observation of active protein folding using lock-in force spectroscopy. Biophys J (2007) 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

Quantitative prediction of 3D solution shape and flexibility of nucleic acid nanostructures. Nucleic Acids Res (2011) 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

The folding pathway of a fast-folding immunoglobulin domain revealed by single-molecule mechanical experiments. EMBO Rep (2005) 1.21

Metal ion dependence of cooperative collapse transitions in RNA. J Mol Biol (2009) 1.20

Cryo-EM structure of a 3D DNA-origami object. Proc Natl Acad Sci U S A (2012) 1.20

Effects of crowding and confinement on the structures of the transition state ensemble in proteins. J Phys Chem B (2007) 1.20