Single-molecule Fluorescence Imaging Research Articles

Intraflagellar Transport Inhomogeneity in Chlamydomonas IMP3 Mutant

Genetic disorders that affect the development or function of flagella and their associated signalizing pathways are collectively known as ciliopathies. Intraflagellar transport (IFT) is the process that is responsible for the regulation of flagellar growth and signaling. In this study, we perform a single-molecule fluorescence imaging investigation of IFT in a Chlamydomonas mutant (IMP3) that exhibits unexplained phenotypes of slower flagellar regeneration and anterograde IFT speed. Using TIRF microscopy and two-color imaging, we show that the loading and unloading of flagellar membrane signaling proteins is compromised in the IMP3 mutant. We first use BBS4-GFP to quantify IFT speed changes in Chlamydomonas, we then use two-color imaging of IFT20-mCherry and PKD2-GFP to verify that these speed changes correspond to the loading and unloading of cargo membrane signaling proteins onto and from IFT trains, respectively. Preliminary results suggest that the IMP3 mutant is less efficient at the loading of transmembrane cargo proteins onto IFT trains, thus consequently generating a signaling defect.

3P161 リニアモータータンパク質キチナーゼの蛍光一分子観察(分子モーター,ポスター,第52回日本生物物理学会年会(2014年度))

3P161 リニアモータータンパク質キチナーゼの蛍光一分子観察(分子モーター,ポスター,第52回日本生物物理学会年会(2014年度))

Mutagenesis Study of Retinal Entry Pathway of Rhodopsin

The visual photoreceptor rhodopsin binds a photosensitive ligand 11-cis-retinal to respond to light stimulation. The regeneration of rhodopsin with 11-cis-retinal completes the photocycle of visual signaling. The molecular determinants of retinal entry can be assessed by measuring the retinal uptake kinetics of site-directed rhodopsin mutants. Here we report an assay for this purpose based on the energy transfer between 11-cis-retinal and a fluorescent probe covalently attached to the receptor. Previously, we developed an approach for site-specific labeling of G protein-coupled receptors by combining amber codon suppression technology and strain-promoted alkyne-azide cycloaddition reaction[1]. We have demonstrated robust fluorescent labeling of receptors without generating a cysteine-free background. We utilized this approach to label rhodopsin with Alexa488 as the FRET donor. Compared to tryptophan fluorescence spectroscopy, our assay exhibits a greater sensitivity and enables the characterization of mutant with slow retinal uptake kinetics. We showed that the heterologously expressed rhodopsin labeled at the second intracellular loop retains the wild-type retinal uptake kinetics. We further introduced a series of substitutions for the residues located in proximity of the retinal β-ionone binding pocket. We observed three orders of magnitude changes in retinal uptake kinetics. By varying the residue substitution we further studied the effect of hydrogen bonding and sterical hindrance. The insights into retinal entry not only shed light on a physiologically relevant process, but also facilitate understanding of retinal diseases.[1] H Tian, TP Sakmar, T Huber. Site-specific labeling of genetically encoded azido groups for multicolor, single-molecule fluorescence imaging of GPCRs. Methods in Cell Biology. In press.

Understanding the Pathogenicity of Vibrio Cholerae via Two-Color Live-Cell Super-Resolution Microscopy

Cholera afflicts more than 5 million people annually. Here, we investigate the virulence pathway of this epidemic disease with live-cell single-molecule fluorescence imaging in Vibrio cholerae cells, the bacterium responsible for producing the cholera toxin. In the Gram-negative pathogen V. cholerae, virulence gene expression is under control of an unusual set of membrane proteins. Here, a membrane complex including two activators, ToxR and TcpP, binds the toxT promoter, recruits RNA polymerase, and activates toxT gene expression leading to activation of ToxT-controlled virulence genes. To circumvent the diffraction limit of light, which bounds the resolution of optical microscopy to ∼250 nm, we use single-molecule tracking and super-resolution techniques like Photoactivated Localization Microscopy (PALM) to achieve resolutions more than an order of magnitude better than the diffraction limit. We have created fusions of the membrane-bound transcription activators TcpP and ToxR with orthogonal photo-(re)activatable fluorescent proteins, and in this study, we examine the dynamics and co-localization patterns of single PAmCherry-TcpP and mCitrine-ToxR molecules in the virulence pathway. We also image V. cholerae cells that have knockouts of ToxR and/or TcpP to determine if the protein dynamics change in the absence of the binding partner. This work aims to identify characteristics of TcpP and ToxR motion to understand their regulatory behavior in the transcriptional activation of the gene toxT and subsequent activation of downstream virulence genes, and to establish a model for the formation of the ToxR/TcpP/toxT protein-DNA complex important in early pathogenesis. In addition to elucidating the regulatory pathway of V. cholerae, the impact of this work will be to further provide a general model for outer-membrane-bound transcription control in bacteria and nuclear-membrane-bound transcription in eukaryotic cells.

Polyarginine induces an antitumor immune response through binding to toll-like receptor 4.

A novel function of polyarginine as an activator of the immune system is reported. Single-molecule fluorescence imaging and single-molecule force measurements demonstrate that polyarginine binds specifically to the toll-like receptor 4 (TLR4), inducing receptor dimerization and activation. Moreover, polyarginine induced immune activation inhibits tumor growth. These results suggest the potential use ofpolyarginine for cancer immunotherapy.

TRF1 and TRF2 use different mechanisms to find telomeric DNA but share a novel mechanism to search for protein partners at telomeres

Human telomeres are maintained by the shelterin protein complex in which TRF1 and TRF2 bind directly to duplex telomeric DNA. How these proteins find telomeric sequences among a genome of billions of base pairs and how they find protein partners to form the shelterin complex remains uncertain. Using single-molecule fluorescence imaging of quantum dot-labeled TRF1 and TRF2, we study how these proteins locate TTAGGG repeats on DNA tightropes. By virtue of its basic domain TRF2 performs an extensive 1D search on nontelomeric DNA, whereas TRF1’s 1D search is limited. Unlike the stable and static associations observed for other proteins at specific binding sites, TRF proteins possess reduced binding stability marked by transient binding (∼9–17 s) and slow 1D diffusion on specific telomeric regions. These slow diffusion constants yield activation energy barriers to sliding ∼2.8–3.6 κBT greater than those for nontelomeric DNA. We propose that the TRF proteins use 1D sliding to find protein partners and assemble the shelterin complex, which in turn stabilizes the interaction with specific telomeric DNA. This ‘tag-team proofreading’ represents a more general mechanism to ensure a specific set of proteins interact with each other on long repetitive specific DNA sequences without requiring external energy sources.

Single-Molecule Observation of Long Jumps in Polymer Adsorption

Single-molecule fluorescence imaging of adsorption onto initially bare surfaces shows that polymer chains need not localize immediately after arrival. In a system optimized to present limited adsorption sites (quartz surface to which polyethylene glycol (PEG) chains adsorb from aqueous solution at pH 8.2), we find that some chains diffuse back into bulk solution and readsorb at some distance away, sometimes multiple times before they either localize at a stable position or diffuse away into bulk solution. This mechanism of surface diffusion is considerably more rapid than the classical model in which adsorbed polymers crawl on surfaces while the entire molecule remains adsorbed, suggesting the conceptual generality of a recent report ( Phys. Rev. Lett. 2013 , 110 , 256101 ) but in a new experimental system and with comparison of different chain lengths. We find the trajectories with jumps to follow a truncated Lévy distribution of step size with limiting slope -2.5, consistent with a well-defined, rapid surface diffusion coefficient over the times we observe. The broad waiting time distribution appears to reflect that polymer chains possess a broad distribution of bound fraction: the smaller the bound fraction of a given chain, the shorter the surface residence time before executing the next surface jump.

Single-Molecule Dynamics and Mechanisms of Metalloregulators and Metallochaperones

Understanding how cells regulate and transport metal ions is an important goal in the field of bioinorganic chemistry, a frontier research area that resides at the interface of chemistry and biology. This Current Topic reviews recent advances from the authors' group in using single-molecule fluorescence imaging techniques to identify the mechanisms of metal homeostatic proteins, including metalloregulators and metallochaperones. It emphasizes the novel mechanistic insights into how dynamic protein-DNA and protein-protein interactions offer efficient pathways via which MerR-family metalloregulators and copper chaperones can fulfill their functions. This work also summarizes other related single-molecule studies of bioinorganic systems and provides an outlook toward single-molecule imaging of metalloprotein functions in living cells.

Real-time single-molecule coimmunoprecipitation of weak protein-protein interactions

Coimmunoprecipitation (co-IP) analysis is a useful method for studying protein-protein interactions. It currently involves electrophoresis and western blotting, which are not optimized for detecting weak and transient interactions. In this protocol we describe an advanced version of co-IP analysis that uses real-time, single-molecule fluorescence imaging as its detection scheme. Bait proteins are pulled down onto the imaging plane of a total internal reflection (TIR) microscope. With unpurified cells or tissue extracts kept in reaction chambers, we observe single protein-protein interactions between the surface-immobilized bait and the fluorescent protein-labeled prey proteins in real time. Such direct recording provides an improvement of five orders of magnitude in the time resolution of co-IP analysis. With the single-molecule sensitivity and millisecond time resolution, which distinguish our method from other methods for measuring weak protein-protein interactions, it is possible to quantify the interaction kinetics and active fraction of native, unlabeled bait proteins. Real-time single-molecule co-IP analysis, which takes ∼4 h to complete from lysate preparation to kinetic analysis, provides a general avenue for revealing the rich kinetic picture of target protein-protein interactions, and it can be used, for example, to investigate the molecular lesions that drive individual cancers at the level of protein-protein interactions.

Suspended Lipid Bilayer for Optical and Electrical Measurements of Single Ion Channel Proteins

Making and holding an artificial lipid bilayer horizontally in an aqueous solution within the microscopic working distance of ~100 μm are essential for simultaneous single molecule imaging and single ion-channel electrical current recording. However, preparation of such a lipid bilayer without a solid support is technically challenging. In a typical supported lipid bilayer, the asymmetric local environments and the strong perturbation of the underneath solid or dense surface can diverge the normal behavior of membrane proteins and lipids. On the other hand, the suspended lipid bilayers can provide a native local environment for the membrane proteins and lipids by having fluids on both sides. In this technical report, we present a simple and novel methodology for making a suspended lipid bilayer that can be used for recording the single-molecule diffusion and single ion-channel electrical measurements of ion-channel proteins. Our approach has a higher validity for studying the molecular diffusions and conformational fluctuations of membrane proteins without having perturbations from supporting layers. We demonstrate the feasibility of such an approach on simultaneous single-molecule fluorescence imaging and electric current measurements of ion channel proteins.

Fluorescence Imaging of Single-Molecule Retention Trajectories in Reversed-Phase Chromatographic Particles

Due to its high specific surface area and chemical stability, porous silica is used as a support structure in numerous applications, including heterogeneous catalysis, biomolecule immobilization, sensors, and liquid chromatography. Reversed-phase liquid chromatography (RPLC), which uses porous silica support particles, has become an indispensable separations tool in quality control, pharmaceutics, and environmental analysis requiring identification of compounds in mixtures. For complex samples, the need for higher resolution separations requires an understanding of the time scale of processes responsible for analyte retention in the stationary phase. In the present work, single-molecule fluorescence imaging is used to observe transport of individual molecules within RPLC porous silica particles. This technique allows direct measurement of intraparticle molecular residence times, intraparticle diffusion rates, and the spatial distribution of molecules within the particle. On the basis of the localization uncertainty and characteristic measured diffusion rates, statistical criteria were developed to resolve the frame-to-frame behavior of molecules into moving and stuck events. The measured diffusion coefficient of moving molecules was used in a Monte Carlo simulation of a random-walk model within the cylindrical geometry of the particle diameter and microscope depth-of-field. The simulated molecular transport is in good agreement with the experimental data, indicating transport of moving molecules in the porous particle is described by a random-walk. Histograms of stuck-molecule event times, locations, and their contributions to intraparticle residence times were also characterized.

Binding and Movement of Individual Cel7A Cellobiohydrolases on Crystalline Cellulose Surfaces Revealed by Single-molecule Fluorescence Imaging

The efficient catalytic conversion of biomass to bioenergy would meet a large portion of energy requirements in the near future. A crucial step in this process is the enzyme-catalyzed hydrolysis of cellulose to glucose that is then converted into fuel such as ethanol by fermentation. Here we use single-molecule fluorescence imaging to directly monitor the movement of individual Cel7A cellobiohydrolases from Trichoderma reesei (TrCel7A) on the surface of insoluble cellulose fibrils to elucidate molecular level details of cellulase activity. The motion of multiple, individual TrCel7A cellobiohydrolases was simultaneously recorded with ∼15-nm spatial resolution. Time-resolved localization microscopy provides insights on the activity of TrCel7A on cellulose and informs on nonproductive binding and diffusion. We measured single-molecule residency time distributions of TrCel7A bound to cellulose both in the presence of and absence of cellobiose the major product and a potent inhibitor of Cel7A activity. Combining these results with a kinetic model of TrCel7A binding provides microscopic insight into interactions between TrCel7A and the cellulose substrate.

Improving zero-mode waveguide structure for enhancing signal-to-noise ratio of real-time single-molecule fluorescence imaging: A computational study

We investigated the signal-to-noise ratio (S/N) of real-time single-molecule fluorescence imaging (SMFI) using zero-mode waveguides (ZMWs). The excitation light and the fluorescence propagating from a molecule in the ZMW were analyzed by computational optics simulation. The dependence of the S/N on the ZMW structure was investigated with the diameter and etching depth as the simulation parameters. We found that the SMFI using a conventional ZMW was near the critical level for detecting binding and dissociation events. We show that etching the glass surface of the ZMW by 60 nm enhances the S/N six times the conventional nonetched ZMWs. The enhanced S/N improves the temporal resolution of the SMFI at physiological concentrations.

Single-Molecule Study on Polymer Diffusion in a Melt State: Effect of Chain Topology

We report a new methodology for studying diffusion of individual polymer chains in a melt state, with special emphasis on the effect of chain topology. A perylene diimide fluorophore was incorporated into the linear and cyclic poly(THF)s, and real-time diffusion behavior of individual chains in a melt of linear poly(THF) was measured by means of a single-molecule fluorescence imaging technique. The combination of mean squared displacement (MSD) and cumulative distribution function (CDF) analysis demonstrated the broad distribution of diffusion coefficient of both the linear and cyclic polymer chains in the melt state. This indicates the presence of spatiotemporal heterogeneity of the polymer diffusion which occurs at much larger time and length scales than those expected from the current polymer physics theory. We further demonstrated that the cyclic chains showed marginally slower diffusion in comparison with the linear counterparts, to suggest the effective suppression of the translocation through the threading-entanglement with the linear matrix chains. This coincides with the higher activation energy for the diffusion of the cyclic chains than of the linear chains. These results suggest that the single-molecule imaging technique provides a powerful tool to analyze complicated polymer dynamics and contributes to the molecular level understanding of the chain interaction.

Squeezing at Entrance of Proton Transport Pathway in Proton-translocating Pyrophosphatase upon Substrate Binding

Homodimeric proton-translocating pyrophosphatase (H(+)-PPase; EC 3.6.1.1) is indispensable for many organisms in maintaining organellar pH homeostasis. This unique proton pump couples the hydrolysis of PPi to proton translocation across the membrane. H(+)-PPase consists of 14-16 relatively hydrophobic transmembrane domains presumably for proton translocation and hydrophilic loops primarily embedding a catalytic site. Several highly conserved polar residues located at or near the entrance of the transport pathway in H(+)-PPase are essential for proton pumping activity. In this investigation single molecule FRET was employed to dissect the action at the pathway entrance in homodimeric Clostridium tetani H(+)-PPase upon ligand binding. The presence of the substrate analog, imidodiphosphate mediated two sites at the pathway entrance moving toward each other. Moreover, single molecule FRET analyses after the mutation at the first proton-carrying residue (Arg-169) demonstrated that conformational changes at the entrance are conceivably essential for the initial step of H(+)-PPase proton translocation. A working model is accordingly proposed to illustrate the squeeze at the entrance of the transport pathway in H(+)-PPase upon substrate binding.

Single-Molecule Fluorescence Imaging of DNA at a Potential-Controlled Interface

Many interfacial chemical phenomena are governed in part by electrostatic interactions between polyelectrolytes and charged surfaces; these phenomena can influence the performance of biosensors, adsorption of natural polyelectrolytes (humic substances) on soils, and production of polyelectrolyte multilayer films. In order to understand electrostatic interactions that govern these phenomena, we have investigated the behavior of a model polyelectrolyte, 15 kbp fluorescently labeled plasmid DNA, near a polarized indium tin oxide (ITO) electrode surface. The interfacial population of DNA was monitored in situ by imaging individual molecules through the transparent electrode using total-internal-reflection fluorescence microscopy. At applied potentials of +0.8 V versus Ag/AgCl, the DNA interfacial population near the ITO surface can be increased by 2 orders of magnitude relative to bulk solution. The DNA molecules attracted to the interface do not adsorb to ITO, but rather they remain mobile with a diffusion coefficient comparable to free solution. Ionic strength strongly influences the sensitivity of the interfacial population to applied potential, where the increase in the interfacial population over a +300 mV change in potential varies from 20% in 30 mM ionic strength to over 25-fold in 300 μM electrolyte. The DNA accumulation with applied potential was interpreted using a simple Boltzmann model to predict average ion concentrations in the electrical double layer and the fraction of interfacial detection volume that is influenced by applied potential. A Gouy-Chapman model was also applied to the data to account for the dependence of the ion population on distance from the electrode surface, which indicates that the net charge on DNA responsible for interactions with the polarized surface is low, on the order of one excess electron. The results are consistent with a small fraction of the DNA plasmid being resident in the double-layer and with counterions screening much of the DNA excess charge.

Identification of an Inhibitory Mechanism of Luteolin on the Insulin‐Like Growth Factor‐1 Ligand–Receptor Interaction

Using single-molecule force measurement and fluorescence imaging, we have demonstrated that luteolin has an inhibitory effect on IGF-1 ligand-receptor binding, the initial step in IGF-1 signaling. This inhibition mechanism, which was confirmed by flow cytometry and molecular docking, could play a role in cancer therapy.

Single-molecule imaging at high hydrostatic pressure

Direct microscopic fluorescence imaging of single molecules can provide a wealth of mechanistic information, but up to now, it has not been possible under high pressure conditions, due to limitations in microscope pressure cell design. We describe a pressure cell window design that makes it possible to image directly single molecules at high hydrostatic pressure. We demonstrate our design by imaging single molecules of Alexa Fluor 647 dye bound to DNA, at 120 and 210 bar, and following their fluorescence photodynamics. We further show that the failure pressure of this type of pressure cell window can be in excess of 1 kbar.

Observation of structural relaxations in disordered solid media via spectral histories of single impurity molecules

This paper presents the technique and results of the investigation of the structural relaxation in disordered solid media (polyisobutylene, toluene, ortho-dichlorobenzene) at temperatures below the glass transition point via the spectra and fluorescence images of single impurity fluorescent molecules (terrylene, tetra-tert-butylterrylene). Application of the thermal-cycling method has made it possible to significantly extend the temperature range of investigation (from 4.5 K to the glass transition temperature). The changes observed in individual parameters of low-energy elementary excitations of the tunneling and vibrational types due to structural relaxation processes have been studied. It has been found that there is a spatial inhomogeneity in the distribution of the activation temperatures of local relaxation processes.

Mechanical stability of a microscope setup working at a few kelvins for single-molecule localization

A great advantage of single-molecule fluorescence imaging is the localization precision of molecule beyond the diffraction limit. Although longer signal-acquisition yields higher precision, acquisition time at room temperature is normally limited by photobleaching, thermal diffusion, and so on. At low temperature of a few kelvins, much longer acquisition is possible and will improve precision if the sample and the objective are held stably enough. The present work examined holding stability of the sample and objective at 1.5K in superfluid helium in the helium bath. The stability was evaluated by localization precision of a point scattering source of a polymer bead. Scattered light was collected by the objective, and imaged by a home-built rigid imaging unit. The standard deviation of the centroid position determined for 800 images taken continuously in 17min was 0.5nm in the horizontal and 0.9nm in the vertical directions.