Single-molecule FRET Spectroscopy Research Articles

Measurement of Average Transition-Path Time for Protein Folding in Single Molecule FRET Experiments

The transition-path is the tiny fraction of an equilibrium molecular trajectory when a transition occurs between two states, and appears as an instantaneous jump in the measured signal in single molecule force or fluorescence experiments. Transition-paths are readily observed in atomistic molecular dynamics simulations for systems with fast kinetics, but have never been observed experimentally for any system in the condensed phase. The importance of the transition-path in protein folding is that it contains all the mechanistic information on how a protein folds and unfolds and is predicted from both theory and simulations to be heterogeneous. As a first step toward observing transition-paths in protein folding, we previously estimated an upper bound of ∼200 microseconds for the transition-path time of protein G using single molecule FRET spectroscopy, 10,000 times shorter than the average unfolded-state waiting-time of ∼2 seconds (Chung et al., PNAS 2009). The biggest obstacle to resolving a transition-path is to detect a sufficient number of photons during a single transition-path. To overcome this problem, we employed a fully-automated data acquisition system to collect a very large number of photon trajectories at high illumination intensities, and carried out a collective photon-by-photon analysis of the transitions between the folded and unfolded states using a maximum likelihood method (Chung et al., JPC A 2011). We determined a transition-path time of ∼2 microseconds for a WW domain that folds in ∼100 microseconds and an upper bound of ∼15 microseconds for protein GB1 that folds in ∼2 seconds. The transition-path times for the two proteins differ by less than 10-fold while the folding rates differ by a factor of 20,000. This result shows that a slow-folding protein can fold almost as fast as a fast-folding protein when folding actually occurs!

Solution structure of the ESCRT-I complex by small-angle X-ray scattering, EPR, and FRET spectroscopy.

ESCRT-I is required for the sorting of integral membrane proteins to the lysosome, or vacuole in yeast, for cytokinesis in animal cells, and for the budding of HIV-1 from human macrophages and T lymphocytes. ESCRT-I is a heterotetramer of Vps23, Vps28, Vps37, and Mvb12. The crystal structures of the core complex and the ubiquitin E2 variant and Vps28 C-terminal domains have been determined, but internal flexibility has prevented crystallization of intact ESCRT-I. Here we have characterized the structure of ESCRT-I in solution by simultaneous structural refinement against small-angle X-ray scattering and double electron-electron resonance spectroscopy of spin-labeled complexes. An ensemble of at least six structures, comprising an equally populated mixture of closed and open conformations, was necessary to fit all of the data. This structural ensemble was cross-validated against single-molecule FRET spectroscopy, which suggested the presence of a continuum of open states. ESCRT-I in solution thus appears to consist of an approximately 50% population of one or a few related closed conformations, with the other 50% populating a continuum of open conformations. These conformations provide reference points for the structural pathway by which ESCRT-I induces membrane buds.

Combination of single molecule FRET spectroscopy with optical tweezers: A powerful tool for mechanistic studies of enzymes

Combination of single molecule FRET spectroscopy with optical tweezers: A powerful tool for mechanistic studies of enzymes

Single-Molecule Fluorescence Studies of Nucleosome Dynamics

Single-molecule techniques have transformed dramatically the way we think about biophysics, making it possible to address questions about the dynamics of systems in equilibrium that were practically unthinkable just a decade ago. This review focuses on how single-molecule fluorescence and fluorescence correlation techniques have allowed the investigation of the mechanisms by which nucleosomes allow enzymes and other proteins to access DNA regions that are buried within the nucleosome structure. It has been established that DNA-protein and protein-protein interactions in nucleosomes are very dynamic. The dynamics of the interactions between the DNA and the histone proteins have been investigated by single-molecule FRET and fluorescence correlation spectroscopy. Results are consistent with the so-called site exposure model, in which DNA transiently and spontaneously unwraps from the histone core. DNA accessibility is greatest for sites close to the DNA termini, and decreases towards the nucleosome dyad. Evidence also suggests that DNA sequence plays an important role. The dynamics of the H2A-H2B dimers within the nucleosome has also been addressed by several groups in terms of their implications in determining nucleosome stability and DNA dynamics.

Dramatic effect of single-base mutation on the conformational dynamics of human telomeric G-quadruplex

Guanine-rich DNA sequences can form G-quadruplexes. These four-stranded structures are known to form in several genomic regions and to influence certain biological activities. Sometimes, the instability of G-quadruplexes causes the abnormal biological processes. Mutation is a culprit for the destabilization of G-quadruplexes, but the details of mutated G-quadruplexes are poorly understood. In this article, we investigated the conformational dynamics of single-base mutated human telomeric G-quadruplexes in the presence of K+ with single-molecule FRET spectroscopy. We observed that the replacement of single guanine by thymine in a G-track induces various folded structures, i.e. structural polymorphism. Moreover, direct observation of their dynamics revealed that a single-base mutation causes fast unfolding of folded states under physiological conditions. Furthermore, we found that the degree of destabilization varies according to mutation positions. When the central guanine of a G-track is replaced, the G-quadruplexes unfold quickly at any K+ concentrations and temperature. Meanwhile, outer-quartet mutated G-quadruplexes have heterogeneous dynamics at intermediate K+ concentrations and longstanding folded states at high K+ concentrations. Several factors such as base-stacking interaction and K+ coordination are responsible for the different dynamics according to the mutation position.

Characterizing the unfolded states of proteins using single-molecule FRET spectroscopy and molecular simulations

To obtain quantitative information on the size and dynamics of unfolded proteins we combined single-molecule lifetime and intensity FRET measurements with molecular simulations. We compared the unfolded states of the 64-residue, alpha/beta protein L and the 66-residue, all-beta cold-shock protein CspTm. The average radius of gyration (Rg) calculated from FRET data on freely diffusing molecules was identical for the two unfolded proteins at guanidinium chloride concentrations >3 M, and the FRET-derived Rg of protein L agreed well with the Rg previously measured by equilibrium small-angle x-ray scattering. As the denaturant concentration was lowered, the mean FRET efficiency of the unfolded subpopulation increased, signaling collapse of the polypeptide chain, with protein L being slightly more compact than CspTm. A decrease in Rg with decreasing denaturant was also observed in all-atom molecular dynamics calculations in explicit water/urea solvent, and Langevin simulations of a simplified representation of the polypeptide suggest that collapse can result from either increased interresidue attraction or decreased excluded volume. In contrast to both the FRET and simulation results, previous time-resolved small-angle x-ray scattering experiments showed no collapse for protein L. Analysis of the donor fluorescence decay of the unfolded subpopulation of both proteins gives information about the end-to-end chain distribution and suggests that chain dynamics is slow compared with the donor life-time of approximately 2 ns, whereas the bin-size independence of the small excess width above the shot noise for the FRET efficiency distributions may result from incomplete conformational averaging on even the 1-ms time scale.