Single-molecule folding
Current Opinion in Structural BiologyPublished 1 February 2003
Xiaowei Zhuang, Matthias Rief
Citations230
SJR quartileQ1
SJR score2.91
SNIP1.48
Generate an AI Snapshot to get a quick, structured summary of this paper.
Study Snapshot
ObjectiveStudy objective
MethodsResearch methodology
PopulationPopulation studied
Sample sizeSample sizes
OutcomesStudy outcomes here
ResultsStudy results comes here
LimitationsResearch study limitations comes here
A concise AI-generated summary of the paper will appear here once you click Generate AI Snapshot.
TL;DR
Fluorescence and force spectroscopy can directly resolve transient intermediate states and multiple reaction pathways, and thus are uniquely powerful in characterizing the complex dynamics of biological processes.
Abstract
Recent developments in fluorescence and force spectroscopy enable us to go beyond the ensemble average and measure the behavior of individual biomacromolecules. These single-molecule approaches can directly resolve transient intermediate states and multiple reaction pathways, and thus are uniquely powerful in characterizing the complex dynamics of biological processes. Recent applications of these two techniques to the protein and RNA folding problems have led to exciting new results.
Keywords
Biochemistry, Genetics and Molecular BiologyEngineeringPhysics and Astronomy
ScienceModels for the Specific Adhesion of Cells to Cells
4,382 Citations1978George I. Bell
The force required to separate two cells is shown to be greater than the expected electrical forces between cells, and of the same order of magnitude as the forces required to pull gangliosides and perhaps some integral membrane proteins out of the cell membrane.
ScienceReversible Unfolding of Individual Titin Immunoglobulin Domains by AFM
3,080 Citations1997Matthias Rief, Mathias Gautel +3 more
Single-molecule atomic force microscopy was used to investigate the mechanical properties of titin, the giant sarcomeric protein of striated muscle, and refolding of immunoglobulin domains was observed.
Biophysical JournalDynamic strength of molecular adhesion bonds
2,542 Citations1997E. Evans, Ken Ritchie
How Brownian dynamics can help bridge the gap between molecular dynamics and probe tests is described, which shows that bond strength progresses through three dynamic regimes of loading rate.
Nature Structural & Molecular BiologyFrom Levinthal to pathways to funnels
2,317 Citations1997Ken A. Dill, Hue Sun Chan
The general energy landscape picture provides a conceptual framework for understanding both two-state and multi-state folding kinetics and hopes to learn much more about the real shapes of protein folding landscapes.
Annual Review of Physical ChemistryTHEORY OF PROTEIN FOLDING: The Energy Landscape Perspective
2,230 Citations1997José N. Onuchic, Zaida Luthey‐Schulten +1 more
The energy landscape theory of protein folding suggests that the most realistic model of a protein is a minimally frustrated heteropolymer with a rugged funnel-like landscape biased toward the native structure.
Proceedings of the National Academy of SciencesEnergy transfer: a spectroscopic ruler.
1,938 Citations1967Lubert Stryer, R P Haugland
Electronic excitation energy transfer as function of distance measured, noting energy transfer process use as spectroscopic ruler as well as the use of spectroscopy ruler for measuring distance.
Proceedings of the National Academy of SciencesProbing the interaction between two single molecules: fluorescence resonance energy transfer between a single donor and a single acceptor.
1,266 Citations1996Taekjip Ha, Th. Enderle +4 more
Near-field scanning optical microscopy was used to obtain simultaneous dual color imaging and emission spectra from a single pair of donor and acceptor fluorophores linked by a short (10 or 20 bases long) DNA molecule.
ScienceEquilibrium Information from Nonequilibrium Measurements in an Experimental Test of Jarzynski's Equality
1,252 Citations2002Jan Liphardt, Sophie Dumont +3 more
The implementation and test of Jarzynski's equality provides the first example of its use as a bridge between the statistical mechanics of equilibrium and nonequilibrium systems, and extends the thermodynamic analysis of single molecule manipulation data beyond the context of equilibrium experiments.
ScienceFolding-Unfolding Transitions in Single Titin Molecules Characterized with Laser Tweezers
1,223 Citations1997Miklós Kellermayer, Steven B. Smith +2 more
Scaling the molecular data up to sarcomeric dimensions reproduced many features of the passive force versus extension curve of muscle fibers, including force hysteresis arises from a difference between the unfolding and refolding kinetics of the molecule relative to the stretch and release rates in the experiments.
NatureMolecular mechanistic origin of the toughness of natural adhesives, fibres and composites
1,218 Citations1999Bettye L. Smith, Tilman E. Schäffer +8 more
ScienceIlluminating Single Molecules in Condensed Matter
1,129 Citations1999W. E. Moerner, Michel Orrit
Efficient collection and detection of fluorescence coupled with careful minimization of background from impurities and Raman scattering now enable routine optical microscopy and study of single molecules in complex condensed matter environments.
Current Opinion in Structural BiologySteered molecular dynamics and mechanical functions of proteins
1,077 Citations2001Barry Isralewitz, Mu Gao +1 more
The combination of atomic force microscopy of single molecules, steered molecular dynamics and the theory of stochastic processes yields information on the energy landscape that controls mechanical function and on the force-bearing components of proteins, as well as on the underlying physical mechanisms.
Proceedings of the National Academy of SciencesMechanical and chemical unfolding of a single protein: A comparison
1,035 Citations1999Mariano Carrión‐Vázquez, Andrés F. Oberhauser +5 more
The results indicate that mechanical unfolding of a single protein by AFM does indeed reflect the same event that is observed in traditional unfolding experiments, and the way is now open for the extensive use of AFM to measure folding reactions at the single-molecule level.
Nature Structural BiologyThe renaissance of fluorescence resonance energy transfer.
977 Citations2000Paul R. Selvin
Improvements in fluorescence resonance energy transfer have led to qualitative and quantitative improvements in the technique, including increased spatial resolution, distance range, and sensitivity.
ScienceReversible Unfolding of Single RNA Molecules by Mechanical Force
942 Citations2001Jan Liphardt, Bibiana Onoa +3 more
The force-dependent equilibrium constants for folding/unfolding these single RNA molecules and the positions of their transition states along the reaction coordinate are determined.
NatureProbing the free-energy surface for protein folding with single-molecule fluorescence spectroscopy
935 Citations2002Benjamin Schuler, Everett A. Lipman +1 more
It is shown that single-molecule FRET measurements of a small cold-shock protein expose equilibrium collapse of the unfolded polypeptide and allow us to calculate limits on the polyPEptide reconfiguration time.
Nature Cell BiologySingle-molecule imaging of EGFR signalling on the surface of living cells
895 Citations2000Yasushi Sako, Shigeru Minoghchi +1 more
Single-molecule tracking reveals that the predominant mechanism of dimerization involves the formation of a cell-surface complex of one EGF molecules and an EGFR dimer, followed by the direct arrest of a second EGF molecule, indicating that the EG FR dimers were probably preformed before the binding of the second E GF molecule.
NatureThe molecular elasticity of the extracellular matrix protein tenascin
841 Citations1998Andrés F. Oberhauser, Piotr E. Marszałek +2 more
It is suggested that the extensibility of the modular fibronectin type III region may be important in allowing tenascin–ligand bonds to persist over long extensions, and of widespread use in extracellular proteins containing such domain.
NatureMechanical unfolding intermediates in titin modules
808 Citations1999Piotr E. Marszałek, Hui Lü +5 more
NatureElasticity and unfolding of single molecules of the giant muscle protein titin
745 Citations1997Larissa Tskhovrebova, John Trinick +2 more
Mechanical experiments on single molecules of titin are done to determine their visco-elastic properties, showing that there are two main sources of elasticity: one deriving from the entropy of straightening the molecule; the other consistent with extension of the polypeptide chain in the PEVK region.
ScienceA Single-Molecule Study of RNA Catalysis and Folding
738 Citations2000Xiaowei Zhuang, Laura Bartley +5 more
Results establish single-molecule fluorescence as a powerful tool for examining RNA folding by observing previously established folding pathways and a pathway with an observed folding rate constant of 1 per second was discovered.
Nature Structural BiologyMeasuring conformational dynamics of biomolecules by single molecule fluorescence spectroscopy.
714 Citations2000Shimon Weiss
Dynamic structural changes of macromolecules undergoing biochemical reactions can be studied using novel single molecule spectroscopy tools using distance and orientation molecular rulers.
ScienceUnfolding Pathways of Individual Bacteriorhodopsins
688 Citations2000Filipp Oesterhelt, Dieter Oesterhelt +4 more
Atomic force microscopy and single-molecule force spectroscopy were combined to image and manipulate purple membrane patches from Halobacterium salinarum, revealing the individuality of the unfolding pathways.
Annual Review of Physical ChemistryOPTICAL STUDIES OF SINGLE MOLECULES AT ROOM TEMPERATURE
621 Citations1998Xiaohui Xie, J. K. Trautman
Recent developments in optical studies of single molecules at room temperature are reviewed, with an emphasis on the underlying principles and the potential of single-molecule experiments.
Journal of Molecular BiologySingle molecule force spectroscopy of spectrin repeats: low unfolding forces in helix bundles
563 Citations1999Matthias Rief, Jaime Pascual +2 more
The measured force required to mechanically unfold spectrin repeats shows that the forces stabilizing the coiled-coil lead to a mechanically much weaker structure than multiple hydrogen-bonded beta-sheets.
Proceedings of the National Academy of SciencesSingle-pair fluorescence resonance energy transfer on freely diffusing molecules: Observation of Förster distance dependence and subpopulations
557 Citations1999Ashok A. Deniz, Maxime Dahan +6 more
The denaturation of a DNA hairpin was examined by using single-pair FRET to measure intramolecular distances and identify subpopulations of freely diffusing macromolecules in a heterogeneous ensemble.
NatureReverse engineering of the giant muscle protein titin
529 Citations2002Hongbin Li, Wolfgang A. Linke +6 more
This work uses protein engineering and single-molecule atomic force microscopy to examine the mechanical components that form the elastic region of human cardiac titin and shows the functional reconstitution of a protein from the sum of its parts.
ScienceCorrelating Structural Dynamics and Function in Single Ribozyme Molecules
517 Citations2002Xiaowei Zhuang, Harold Kim +4 more
The complex structural dynamics quantitatively explain the heterogeneous cleavage kinetics common to many catalytic RNAs and the intimate coupling of structural dynamics and function is likely a general phenomenon for RNA.
Physical Review LettersElastically Coupled Two-Level Systems as a Model for Biopolymer Extensibility
484 Citations1998Matthias Rief, Julio M. Fernández +1 more
NatureBone indentation recovery time correlates with bond reforming time
469 Citations2001James B. Thompson, Johannes H. Kindt +4 more
Proceedings of the National Academy of SciencesSingle-molecule protein folding: Diffusion fluorescence resonance energy transfer studies of the denaturation of chymotrypsin inhibitor 2
467 Citations2000Ashok A. Deniz, Ted A. Laurence +7 more
It is shown that new information about different aspects of the protein folding reaction can be extracted from such subpopulation properties, and shifts in the mean transfer efficiencies, FRET efficiency distributions, and denaturation curves are discussed.
Annual Review of Biophysics and Biomolecular StructureOPTICAL DETECTION OF SINGLE MOLECULES
406 Citations1997Shuming Nie, Richard N. Zare
This review focuses on the methodologies and biological applications of single-molecule detection based on laser-induced fluorescence.
Journal of Molecular BiologyThe Mechanical Hierarchies of Fibronectin Observed with Single-molecule AFM
395 Citations2002Andrés F. Oberhauser, Carmelu Badilla-Fernandez +2 more
It is found that fibronectin is highly extensible due to the unfolding of its FNIII domains and that the first FN III domain can acquire multiple, partially folded conformations, and that their incidence is modulated strongly by its neighbor FNIII domain.
Current Opinion in Chemical BiologyForce spectroscopy with single bio-molecules
386 Citations2000Hauke Clausen‐Schaumann, Markus Seitz +2 more
Detailed insights into binding potentials of receptor ligand pairs, protein folding pathways, molecular motors, DNA mechanics and the functioning of DNA-binding agents (such as proteins and drugs), as well as the function of molecular motors have been obtained.
Proceedings of the National Academy of SciencesAtomic force microscopy reveals the mechanical design of a modular protein
284 Citations2000Hongbin Li, Andrés F. Oberhauser +3 more
The experiments reveal the simple mechanical design of modular proteins and open the way for the engineering of elastic proteins with defined mechanical properties, which can be used in tissue and fiber engineering.
Proceedings of the National Academy of SciencesLigand-induced conformational changes observed in single RNA molecules
263 Citations1999Taekjip Ha, Xiaowei Zhuang +4 more
It is presented the first demonstration that fluorescence resonance energy transfer can be used to track the motion of a single molecule undergoing conformational changes, and it is shown that individual RNA molecules can measure the instantaneous Mg(2+) concentration with 20-ms time resolution, making it the world's smallest Mg (2+) meter.
Proceedings of the National Academy of SciencesDynamics and folding of single two-stranded coiled-coil peptides studied by fluorescent energy transfer confocal microscopy
253 Citations2000David S. Talaga, Wai Leung Lau +5 more
End-to-end distance distributions have been characterized under conditions where the peptide is nearly fully folded, unfolded, and in dynamic exchange between folded and unfolded states, where the molecules are undergoing millisecond conformational fluctuations.
Nature MaterialsThe myosin coiled-coil is a truly elastic protein structure
246 Citations2002Ingo Schwaiger, Clara Sattler +2 more
This work has studied the elastic properties of the myosin coiled-coil at the single molecule level and found that this protein undergoes a massive structural transition at forces between 20 and 25 pN where the coil extends to about 2.5 times its original length.
Proceedings of the National Academy of SciencesExploring the folding landscape of a structured RNA
242 Citations2001Rick Russell, Xiaowei Zhuang +5 more
An unprecedented view is provided of the topology of an RNA folding landscape and the RNA structural features that underlie this multidimensional landscape: a specific long-range tertiary contact can either help or hinder folding, depending on when it is formed during the process.
Biophysical JournalCan Non-Mechanical Proteins Withstand Force? Stretching Barnase by Atomic Force Microscopy and Molecular Dynamics Simulation
232 Citations2001Robert B. Best, Bin Li +3 more
The results of AFM experiments on the forced unfolding of barnase in a chimeric construct with I27 suggest that proteins that are not selected for tensile strength may not resist force in the same way as those that are, and that proteins with similar unfolding rates in solution need not have comparable unfolding properties under force.
Proceedings of the National Academy of SciencesSolid-state synthesis and mechanical unfolding of polymers of T4 lysozyme
229 Citations2000Guoliang Yang, Ciro Cecconi +7 more
A method of synthesizing polymers of protein molecules in the solid state by introducing cysteines at locations where bacteriophage T4 lysozyme molecules contact each other in a crystal and taking advantage of the alignment provided by the lattice is developed.
Nature Structural BiologyPoint mutations alter the mechanical stability of immunoglobulin modules.
216 Citations2000Julio M. Fernández, Hongbin Li +3 more
It is demonstrated that point mutations in two β-strands of an immunoglobulin module in human cardiac titin alter the mechanical stability of the protein, resulting in mechanical phenotypes, a previously unrecognized class of phenotypes that may be common in cell adhesion and muscle proteins.
Annual Review of Physical ChemistryE<scp>ARLY</scp> E<scp>VENTS IN</scp> RNA F<scp>OLDING</scp>
212 Citations2001D. Thirumalai, Nam-Kyung Lee +2 more
A conceptual framework for understanding the way large RNA molecules fold based on the notion that their free-energy landscape is rugged is described, which provides a unified description of the way RNA and proteins fold.
Journal of Molecular BiologyMechanical Unfolding of a Titin Ig Domain: Structure of Unfolding Intermediate Revealed by Combining AFM, Molecular Dynamics Simulations, NMR and Protein Engineering
208 Citations2002Susan B. Fowler, Robert B. Best +6 more
The mechanical unfolding of an immunoglobulin domain from the human muscle protein titin has been shown to proceed via a metastable intermediate in which the A-strand is detached, which has a structure very similar to the native state, and is surprisingly stable.
StructureMapping the Folding Pathway of an Immunoglobulin Domain
201 Citations2001Susan A. Fowler, Jane Clarke
A detailed protein engineering phi value analysis of the folding pathway of TI I27, an immunoglobulin domain from human cardiac titin, shows that it is highly structured, and supports the hypothesis that interactions essential for defining the structure of these beta sandwich proteins are also important in nucleation of folding.
Physical Review LettersDynamic Force Spectroscopy of Molecular Adhesion Bonds
162 Citations2000Berthold Heymann, Helmut Grubmüller
A theory is developed that allows one to reconstruct force profiles from force spectra obtained from measurements at varying loading rates, without requiring increased resolution, and it is shown that spectra obtaining from measurements with different spring constants contain complementary information.
Biophysical JournalStability of Bacteriorhodopsin α-Helices and Loops Analyzed by Single-Molecule Force Spectroscopy
158 Citations2002Daniel J. Müller, Max Kessler +4 more
It is concluded that the covalent linkage of the retinal to helix G stabilizes the structure of BR, and polypeptide loops potentially act as a barrier to unfolding and contribute significantly to the structural stability of BR.
Chemical PhysicsFolding dynamics of single GCN-4 peptides by fluorescence resonant energy transfer confocal microscopy
153 Citations1999Yiwei Jia, David S. Talaga +4 more
The distributions indicate that single molecule GCN4-Pf is in dynamic folding equilibrium with the position of the equilibrium being altered by the concentration of urea.
Biophysical JournalThe Effect of Core Destabilization on the Mechanical Resistance of I27
135 Citations2002David J. Brockwell, Godfrey S. Beddard +7 more
A concatamer of five mutant I27 domains (denoted (I27)(5)*) is constructed and it is shown that although the observed forces are considerably lower, core destabilization has little effect on determining the mechanical sensitivity of this domain.
Current Opinion in Structural BiologySingle-molecule fluorescence methods for the study of nucleic acids
135 Citations2001Taekjip Ha
Single-molecule fluorescence methods and biomechanical tools provide exciting new opportunities to probe biochemical processes in unprecedented detail to study the structural changes and functions of enzymes that participate in nucleic acid metabolism.
FEBS LettersStates and transitions during forced unfolding of a single spectrin repeat
118 Citations2000Pierre‐François Lenne, Arnt J. Raae +3 more
It is demonstrated that the unfolding of spectrin domains can occur in a stepwise fashion during stretching, and single molecule force spectroscopy appears to open a new window for the analysis of transition probabilities between different conformational states.
The Journal of Physical Chemistry BSingle-Molecule Fluorescence Resonant Energy Transfer in Calcium Concentration Dependent Cameleon
112 Citations2000Sophie Brasselet, Erwin J.G. Peterman +2 more
This work exemplifies the issues involved in the observation of binding kinetics at the single-molecule level, using fluorescence resonant energy transfer as a signature of the response of the system to the presence of Ca2+ ions.
Biophysical JournalDirect Observation of Ligand Colocalization on Individual Receptor Molecules
105 Citations1998Gerhard J. Schütz, W. Trabesinger +1 more
The use of dual-wavelength single molecule imaging allows discrimination between isolated and colocalized ligands with an accuracy of 40 nm and unequivocally demonstrates colocalization of two ligands on an individual receptor.
Proceedings of the National Academy of SciencesA simple method for probing the mechanical unfolding pathway of proteins in detail
96 Citations2002Robert B. Best, Susan A. Fowler +2 more
This work describes how protein engineering Φ value analysis can be adapted to characterize the transition states for mechanical unfolding of proteins, and shows that unfolding rate constants derived in the standard way by using Monte Carlo simulations are not reliable because of the errors involved.
StructurePathways and Intermediates in Forced Unfolding of Spectrin Repeats
78 Citations2002Stephan Altmann, Raik Grünberg +7 more
The experiments indicate that spectrin repeats can form stable unfolding intermediates when subjected to external forces, and a mutant stabilizing the central helix showed no intermediates in experiments, in agreement with simulation.
LangmuirConformational Analysis of Native Fibronectin by Means of Force Spectroscopy
74 Citations2000York Oberdörfer, Harald Fuchs +1 more
This study focused on the unfolding of native fibronectin, a modular extracellular matrix protein comprising different types of repeating units exhibiting a large variety of functions.