Single-molecule Behavior Research Articles

Multiple kinesins induce tension for smooth cargo transport.

How cargoes move within a crowded cell-over long distances and at speeds nearly the same as when moving on unimpeded pathway-has long been mysterious. Through an in vitro force-gliding assay, which involves measuring nanometer displacement and piconewtons of force, we show that multiple mammalian kinesin-1 (from 2 to 8) communicate in a team by inducing tension (up to 4 pN) on the cargo. Kinesins adopt two distinct states, with one-third slowing down the microtubule and two-thirds speeding it up. Resisting kinesins tend to come off more rapidly than, and speed up when pulled by driving kinesins, implying an asymmetric tug-of-war. Furthermore, kinesins dynamically interact to overcome roadblocks, occasionally combining their forces. Consequently, multiple kinesins acting as a team may play a significant role in facilitating smooth cargo motion in a dense environment. This is one of few cases in which single molecule behavior can be connected to ensemble behavior of multiple motors.

How Nanoparticles Transform Single Molecule Measurements into Quantitative Sensors.

Single molecule measurements are revolutionizing the understanding of the stochastics of behavior of single molecules. There is a common theme referred to as a near-field approach, in how many single molecule measurements are being performed in assays. The term near field is used because the measurement volume is typically very small such that a single molecule, or a single molecule binding pair, within that volume is of an appreciable concentration. The next development in detection will be performing many single molecule measurements at one time such that single molecule measurements can be used as the basis for quantitative analysis. There have already been some notable developments in this direction. Again, all have a common theme in that nanoparticles are used to create many near-field volumes that can be measured simultaneously. Herein, the coupled developments in nanoparticles and measurement strategies that allow nanoparticles to be the backbone of the next generation of sensing technologies are discussed.

Multimerization and Retention of the Scavenger Receptor SR-B1 in the Plasma Membrane

Scavenger receptor B1 (SR-B1), the main receptor for high-density lipoprotein (HDL), is key in preventing atherosclerosis. It removes cholesterol from HDL, returning the lipid-poor lipoprotein to the circulation. To study the mechanisms controlling SR-B1 dynamics at the plasma membrane and its internalization rate, we developed a single-chain variable fragment (ScFv) antibody to image the receptor in live cells and track the behavior of single SR-B1 molecules. Unlike transferrin receptors, cholera-toxin-binding gangliosides, and bulk membrane markers, SR-B1 was internalized only marginally over hours. Plasmalemmal retention was not attributable to its C-terminal PDZ-binding domain or to attachment to the cortical cytoskeleton. Instead, SR-B1 undergoes multimerization into large metastable clusters that, despite being mobile in the membrane, fail to enter endocytic pathways. SR-B1 multimerization was impaired by mutating its C-terminal leucine zipper and by disrupting actin polymerization, causing rapid receptor internalization. Multimerization and plasmalemmal retention are critical for SR-B1 function.

Raftophilic rhodopsin-clusters offer stochastic platforms for G protein signalling in retinal discs

Rhodopsin is a G protein-coupled receptor (GPCR) that initiates the phototransduction cascade in retinal disc membrane. Recent studies have suggested that rhodopsin forms highly ordered rows of dimers responsible for single-photon detection by rod photoreceptors. Dimerization is also known to confer to rhodopsin a high affinity for ordered lipids (raftophilicity). However, the role of rhodopsin organization and its raftophilicity in phototransduction remains obscure, owing to the lack of direct observation of rhodopsin dynamics and distribution in native discs. Here, we explore the single-molecule and semi-multimolecule behaviour of rhodopsin in native discs. Rhodopsin forms transient meso-scale clusters, even in darkness, which are loosely confined to the disc centre. Cognate G protein transducin co-distributes with rhodopsin, and exhibits lateral translocation to the disc periphery upon activation. We demonstrate that rhodopsin offers inherently distributed and stochastic platforms for G protein signalling by self-organizing raftophilic clusters, which continually repeat generation/extinction in the disc membrane.

Differentiating between Inactive and Active States of Rhodopsin by Atomic Force Microscopy in Native Membranes.

Membrane proteins, including G protein-coupled receptors (GPCRs), present a challenge in studying their structural properties under physiological conditions. Moreover, to better understand the activity of proteins requires examination of single molecule behaviors rather than ensemble averaged behaviors. Force-distance curve-based AFM (FD-AFM) was utilized to directly probe and localize the conformational states of a GPCR within the membrane at nanoscale resolution based on the mechanical properties of the receptor. FD-AFM was applied to rhodopsin, the light receptor and a prototypical GPCR, embedded in native rod outer segment disc membranes from photoreceptor cells of the retina in mice. Both FD-AFM and computational studies on coarse-grained models of rhodopsin revealed that the active state of the receptor has a higher Young's modulus compared to the inactive state of the receptor. Thus, the inactive and active states of rhodopsin could be differentiated based on the stiffness of the receptor. Differentiating the states based on the Young's modulus allowed for the mapping of the different states within the membrane. Quantifying the active states present in the membrane containing the constitutively active G90D rhodopsin mutant or apoprotein opsin revealed that most receptors adopt an active state. Traditionally, constitutive activity of GPCRs has been described in terms of two-state models where the receptor can achieve only a single active state. FD-AFM data are inconsistent with a two-state model but instead require models that incorporate multiple active states.

Anticooperative Binding Governs the Mechanics of Ethidium-Complexed DNA

DNA intercalators bind nucleic acids by stacking between adjacent basepairs. This causes a considerable elongation of the DNA backbone as well as untwisting of the double helix. In the past few years, single-molecule mechanical experiments have become a common tool to characterize these deformations and to quantify important parameters of the intercalation process. Parameter extraction typically relies on the neighbor-exclusion model, in which a bound intercalator prevents intercalation into adjacent sites. Here, we challenge the neighbor-exclusion model by carefully quantifying and modeling the force-extension and twisting behavior of single ethidium-complexed DNA molecules. We show that only an anticooperative ethidium binding that allows for a disfavored but nonetheless possible intercalation into nearest-neighbor sites can consistently describe the mechanical behavior of intercalator-bound DNA. At high ethidium concentrations and elevated mechanical stress, this causes an almost complete occupation of nearest-neighbor sites and almost a doubling of the DNA contour length. We furthermore show that intercalation into nearest-neighbor sites needs to be considered when estimating intercalator parameters from zero-stress elongation and twisting data. We think that the proposed anticooperative binding mechanism may also be applicable to other intercalating molecules.

Transition from stochastic events to deterministic ensemble average in electron transfer reactions revealed by single-molecule conductance measurement

Electron transfer reactions can now be followed at the single-molecule level, but the connection between the microscopic and macroscopic data remains to be understood. By monitoring the conductance of a single molecule, we show that the individual electron transfer reaction events are stochastic and manifested as large conductance fluctuations. The fluctuation probability follows first-order kinetics with potential dependent rate constants described by the Butler-Volmer relation. Ensemble averaging of many individual reaction events leads to a deterministic dependence of the conductance on the external electrochemical potential that follows the Nernst equation. This study discloses a systematic transition from stochastic kinetics of individual reaction events to deterministic thermodynamics of ensemble averages and provides insights into electron transfer processes of small systems, consisting of a single molecule or a small number of molecules.

Synthesis, Structures, and Magnetic Properties of Two Coordination Assemblies of Mn(III) Single Molecule Magnets Bridged via Photochromic Diarylethene Ligands.

Two new coordination assemblies were prepared by combining the open and close forms of 1,2-bis(5-carboxyl-2-methyl-3-thienyl)perfluorocyclopentene (H2dae) with [Mn2(saltmen)2(H2O)2](PF6)2, where H2saltmen = 2,2'-((1 E,1' E)-((2,3-dimethylbutane-2,3-diyl)bis(azaneylylidene)) bis(methaneylylidene))diphenol. From X-ray diffraction analyses, the complexes had the following formula: [Mn2(saltmen)2(dae-open)] (1open) and [Mn(saltmen)(dae-close)]·H2O·Et3N (1close). Both complexes crystallized in the C2/ c monoclinic space group. In 1open, dae-o2- behaves as a bidentate ligand attached to the outer Mn-saltmen monomer via the oxygen atom of carboxylato groups, whereas in 1close, the dae-c2- ligand behaves as a monodentate ligand attached to the external Mn-saltmen dimer by only one carboxylato group of the photochromic ligand. The complexes showed reversible photochromic responses to UV/vis light and showed single-molecule magnet-like behavior. The relaxation times and energy barriers of the metal complexes are clearly affected by UV/vis irradiation.

One-Dimensional Assemblies of a DNA Tetrahedron: Manipulations on the Structural Conformation and Single-Molecule Behaviors.

DNA nanotechnology can construct various nanostructures with diverse functionalities. However, conformation fluctuations due to the structural flexibility of duplex DNA compromise the efficiency to realize the functionality and reactivity of DNA nanostructures. To understand and control the structural deviation from the design represents a major challenge as well as an opportunity for DNA nanotechnology. In the present work, two series of one-dimensional assemblies of DNA tetrahedrons (DTHs) were fabricated and applied to demonstrate the manipulations of conformation dynamics of a one-dimensional DTH assembly by simple variation on linkage styles at single-molecule resolution. A stepwise strategy allows both nanoassembly with a high fidelity in the number and sequence of DTH units to be assembled with a minimum number of linkage sequences. The characterization for these nanostructures with atomic force microscope (AFM) and a solid-state nanopore technique indicates the difference in conformation dynamics and bending stiffness between two analogous nanoassemblies both in the immobilized state on the surface and free state in solution. This work showed the power of fine-tuning the dynamic conformation of the nanostructures and could see the applications in single-molecule biosensing and functionalization of DNA nanostructures.

Lessons from (pre-)mRNA Imaging.

Cells are complex assemblies of molecules organized into organelles and membraneless compartments, each playing important roles in ensuring cellular homeostasis. The different steps of the gene expression pathway take place within these various cellular compartments, and studying gene regulation and RNA metabolism requires incorporating the spatial as well as temporal separation and progression of these processes. Microscopy has been a valuable tool to study RNA metabolism, as it allows the study of biomolecules in the context of intact individual cells, embryos or tissues, preserving cellular context often lost in experimental approaches that require the collection and lysis of cells in large numbers to obtain sufficient material for different types of assays. Indeed, from the first detection of RNAs and ribosomes in cells to today's ability to study the behaviour of single RNA molecules in living cells, or the expression profile and localization of hundreds of mRNA simultaneously in cells, constant effort in developing tools for microscopy has extensively contributed to our understanding of gene regulation. In this chapter, we will describe the role various microscopy approaches have played in shaping our current understanding of mRNA metabolism and outline how continuous development of new approaches might help in finding answers to outstanding questions or help to look at old dogmas through a new lens.

Probing molecule-like isolated octahedra via phase stabilization of zero-dimensional cesium lead halide nanocrystals

Zero-dimensional (0D) inorganic perovskites have recently emerged as an interesting class of material owing to their intrinsic Pb2+ emission, polaron formation, and large exciton binding energy. They have a unique quantum-confined structure, originating from the complete isolation of octahedra exhibiting single-molecule behavior. Herein, we probe the optical behavior of single-molecule-like isolated octahedra in 0D Cesium lead halide (Cs4PbX6, X = Cl, Br/Cl, Br) nanocrystals through isovalent manganese doping at lead sites. The incorporation of manganese induced phase stabilization of 0D Cs4PbX6 over CsPbX3 by lowering the symmetry of PbX6 via enhanced octahedral distortion. This approach enables the synthesis of CsPbX3 free Cs4PbX6 nanocrystals. A high photoluminescence quantum yield for manganese emission was obtained in colloidal (29%) and solid (21%, powder) forms. These performances can be attributed to structure-induced confinement effects, which enhance the energy transfer from localized host exciton states to Mn2+ dopant within the isolated octahedra.

Stress Dissipation in Cucurbit[8]uril Ternary Complex Small Molecule Adhesives.

The ability to control supramolecular and macroscopic self-assembly and disassembly holds great potential for responsive, reversible adhesives that can efficiently broker stresses accumulated between two surfaces. Here, cucurbit[8]uril is used to directly adhere two functionalized mica substrates creating surface-surface interactions that are held together through photoreversible CB[8] heteroternary complexes. Comparison of single-molecule, bulk, and macroscopic adhesion behavior give insight into cooperativity and stress dissipation in dynamic adhesive systems.

Revealing Compartmentalized Diffusion in Living Cells with Interferometric Scattering Microscopy

The spatiotemporal organization and dynamics of the plasma membrane and its constituents are central to cellular function. Fluorescence-based single-particle tracking has emerged as a powerful approach for studying the single molecule behavior of plasma-membrane-associated events because of its excellent background suppression, at the expense of imaging speed and observation time. Here, we show that interferometric scattering microscopy combined with 40 nm gold nanoparticle labeling can be used to follow the motion of membrane proteins in the plasma membrane of live cultured mammalian cell lines and hippocampal neurons with up to 3 nm precision and 25 μs temporal resolution. The achievable spatiotemporal precision enabled us to reveal signatures of compartmentalization in neurons likely caused by the actin cytoskeleton.

Ultra-small dye-doped silica nanoparticles via modified sol-gel technique

In modern biosensing and imaging, fluorescence-based methods constitute the most diffused approach to achieve optimal detection of analytes, both in solution and on the single-particle level. Despite the huge progresses made in recent decades in the development of plasmonic biosensors and label-free sensing techniques, fluorescent molecules remain the most commonly used contrast agents to date for commercial imaging and detection methods. However, they exhibit low stability, can be difficult to functionalise, and often result in a low signal-to-noise ratio. Thus, embedding fluorescent probes into robust and bio-compatible materials, such as silica nanoparticles, can substantially enhance the detection limit and dramatically increase the sensitivity. In this work, ultra-small fluorescent silica nanoparticles (NPs) for optical biosensing applications were doped with a fluorescent dye, using simple water-based sol-gel approaches based on the classical Stöber procedure. By systematically modulating reaction parameters, controllable size tuning of particle diameters as low as 10 nm was achieved. Particles morphology and optical response were evaluated showing a possible single-molecule behaviour, without employing microemulsion methods to achieve similar results.Graphical abstractWe report a simple, cheap, reliable protocol for the synthesis and systematic tuning of ultra-small (< 10 nm) dye-doped luminescent silica nanoparticles.

Molecular and dissociative adsorption of a single water molecule on a β‐dicalcium silicate (100) surface explored by a DFT approach

AbstractThe adsorption of water on a C2S surface initiates belite to hydrate. In the present work, the adsorption behavior of single water molecule on a β‐C2S (100) surface is explored using density functional theory (DFT) due to the lack of alternative approaches for direct observation. Four possible calcium atom sites on the β‐C2S (100) surface slab are considered in our calculations. The results show that water can adsorb on the 2 five‐coordinated calcium sites only via molecular adsorption with adsorption energies of 0.59 and 0.85 eV, respectively, but can dissociate on the other 2 six‐coordinated calcium sites with higher adsorption energies of 0.96 and 0.99 eV, respectively. The energy barriers to the dissociative adsorption of water at the Ca(III) site(0.10 eV) is much lower than that at the Ca(IV) site, indicating that water prefers to adsorb and dissociate on Ca(III) sites. The dissociative adsorption of water causes more obvious surface calcium shifts and Si–O bond length increases than molecular adsorption. The dissociative adsorption of a water molecule changes the electron distribution, and the overlap between Ca 2p and O 2s orbitals leads to new Ca–O bond formations.

Nanopore confinement for electrochemical sensing at the single-molecule level

Summary Single-molecule sensing opens avenues of studying the population heterogeneities and the conformational dynamics of system ranging from single DNAs to single proteins. Nanopores providing the electrochemically confined space for accommodation of single analytes, directly convert the single-molecule behaviors into the measurable electrochemical read-outs with high signal-to-noise ratio. A good volume of researches exists on nanopore-based electrochemical detection ranging from nucleic acids, peptides, proteins, and biomolecular complexes to organic polymers and small molecules. Due to the advantage of nanopore confinement, new sensing mechanisms have been reported to shed light on single-molecule structure and activity correlation. In this review, we provide an overview of the electrochemically confined effects in a nanopore on the aspects ranging from single-molecule volume exclusion, redox process confinement, and electromagnetic field enhancement. The electrochemically confined effects would provide nanopore a series of vivid and exciting discoveries in single-molecule analysis of biological processes and chemical reactions.

A multiplexed magnetic tweezer with precision particle tracking and bi-directional force control

BackgroundIn the past two decades, methods have been developed to measure the mechanical properties of single biomolecules. One of these methods, Magnetic tweezers, is amenable to acquisition of data on many single molecules simultaneously, but to take full advantage of this "multiplexing" ability, it is necessary to simultaneously incorporate many capabilities that have been only demonstrated separately.MethodsOur custom built magnetic tweezer combines high multiplexing, precision bead tracking, and bi-directional force control into a flexible and stable platform for examining single molecule behavior. This was accomplished using electromagnets, which provide high temporal control of force while achieving force levels similar to permanent magnets via large paramagnetic beads.ResultsHere we describe the instrument and its ability to apply 2–260 pN of force on up to 120 beads simultaneously, with a maximum spatial precision of 12 nm using a variety of bead sizes and experimental techniques. We also demonstrate a novel method for increasing the precision of force estimations on heterogeneous paramagnetic beads using a combination of density separation and bi-directional force correlation which reduces the coefficient of variation of force from 27% to 6%. We then use the instrument to examine the force dependence of uncoiling and recoiling velocity of type 1 fimbriae from Eschericia coli (E. coli) bacteria, and see similar results to previous studies.ConclusionThis platform provides a simple, effective, and flexible method for efficiently gathering single molecule force spectroscopy measurements.

Visualizing endocytic recycling and trafficking in live neurons by subdiffractional tracking of internalized molecules.

Our understanding of endocytic pathway dynamics is restricted by the diffraction limit of light microscopy. Although super-resolution techniques can overcome this issue, highly crowded cellular environments, such as nerve terminals, can also dramatically limit the tracking of multiple endocytic vesicles such as synaptic vesicles (SVs), which in turn restricts the analytical dissection of their discrete diffusional and transport states. We recently introduced a pulse-chase technique for subdiffractional tracking of internalized molecules (sdTIM) that allows the visualization of fluorescently tagged molecules trapped in individual signaling endosomes and SVs in presynapses or axons with 30- to 50-nm localization precision. We originally developed this approach for tracking single molecules of botulinum neurotoxin type A, which undergoes activity-dependent internalization and retrograde transport in autophagosomes. This method was then adapted to localize the signaling endosomes containing cholera toxin subunit-B that undergo retrograde transport in axons and to track SVs in the crowded environment of hippocampal presynapses. We describe (i) the construction of a custom-made microfluidic device that enables control over neuronal orientation; (ii) the 3D printing of a perfusion system for sdTIM experiments performed on glass-bottom dishes; (iii) the dissection, culturing and transfection of hippocampal neurons in microfluidic devices; and (iv) guidance on how to perform the pulse-chase experiments and data analysis. In addition, we describe the use of single-molecule-tracking analytical tools to reveal the average and the heterogeneous single-molecule mobility behaviors. We also discuss alternative reagents and equipment that can, in principle, be used for sdTIM experiments and describe how to adapt sdTIM to image nanocluster formation and/or tubulation in early endosomes during sorting events. The procedures described in this protocol take ∼1 week.

Single-molecule study of full-length NaChBac by planar lipid bilayer recording.

Planar lipid bilayer device, alternatively known as BLM, is a powerful tool to study functional properties of conducting membrane proteins such as ion channels and porins. In this work, we used BLM to study the prokaryotic voltage-gated sodium channel (Nav) NaChBac in a well-defined membrane environment. Navs are an essential component for the generation and propagation of electric signals in excitable cells. The successes in the biochemical, biophysical and crystallographic studies on prokaryotic Navs in recent years has greatly promoted the understanding of the molecular mechanism that underlies these proteins and their eukaryotic counterparts. In this work, we investigated the single-molecule conductance and ionic selectivity behavior of NaChBac. Purified NaChBac protein was first reconstituted into lipid vesicles, which is subsequently incorporated into planar lipid bilayer by fusion. At single-molecule level, we were able to observe three distinct long-lived conductance sub-states of NaChBac. Change in the membrane potential switches on the channel mainly by increasing its opening probability. In addition, we found that individual NaChBac has similar permeability for Na+, K+, and Ca2+. The single-molecule behavior of the full-length protein is essentially highly stochastic. Our results show that planar lipid bilayer device can be used to study purified ion channels at single-molecule level in an artificial environment, and such studies can reveal new protein properties that are otherwise not observable in in vivo ensemble studies.

Electron-donating effect dominated 5,6-dimethoxy-2-(2,2,2-trifluoroethyl)-1-indone dysprosium SMM

A series of three β-diketone mononuclear lanthanide complexes, namely, Dy(5,6-DTFI)3(H2O)2·H2O2CH2Cl2 (1), Tb(5,6-DTFI)3(H2O)2·H2O2CH2Cl2 (2) and Ho(5,6-DTFI)3(H2O)2·H2O2CH2Cl2 (3) (5,6-DTFI=5,6-dimethoxy-2-(2,2,2-trifluoroethyl)-1-indone) have been isolated by reactions of 5,6-DTFI and LnCl3·6H2O (Ln=Dy, Tb, Ho). X-ray crystallographic analysis reveals that complexes 1–3 are all eight-coordinated mononuclear structures. Magnetic studies indicate that complex 1 is of single-molecule magnetic behaviors under 0 Oe. Notably, the ligands play essential role on regulating their magnetism. The corresponding structural and magnetic parameters have been discussed in details.