Optical traps to study properties of molecular motors

Optical Tweezers Apparatus Based on a Cost-Effective IR Laser-Hardware and Software Description

Optical tweezers (OT), or optical traps, are a device for manipulating microscopic objects through a focused laser beam. They are used in various fields of physical and biophysical chemistry to identify the interactions between individual molecules and measure single-molecule forces. In this work, we describe the development of a homemade optical tweezers device based on a cost-effective IR diode laser, the hardware, and, in particular, the software controlling it. It allows us to control the instrument, calibrate it, and record and process the measured data. It includes the user interface design, peripherals control, recording, A/D conversion of the detector signals, evaluation of the calibration constants, and visualization of the results. Particular stress is put on the signal filtration from noise, where several methods were tested. The calibration experiments indicate a good sensitivity of the instrument that is thus ready to be used for various single-molecule measurements.

Optical trapping of Rayleigh particles based on four-petal Gaussian vortex beams

The intensity distribution of four-petal Gaussian vortex (FPGV) beams through a focused optical system and the radiation force acting on a Rayleigh dielectric sphere is obtained based on the extended Huygens-Fresnel principle and the Rayleigh scattering theory. We mainly study the trapping of high and low refractive index Rayleigh particles by FPGV beams and the effect of the topological charge m on the radiation force. The results show that the specific distribution of the incident beam can be controlled by a reasonable choice of topological charge m. The multiple locations in a beam of light where particles of different refractive indices can be captured will be found. On the other hand, when m changes, the number of particles captured and the locations where they can be captured change accordingly. Therefore, the flexibility to simultaneously capture multiple Rayleigh particles with different refractive indices with a single beam at different locations in the focal plane can be achieved using the FPGV beam.

Dynamic Light Scattering Study of a Laser-Induced Phase-Separated Droplet of Aqueous Glycine

Tightly focusing a continuous-wave, near-infrared laser beam at the air/solution interface of a millimeter-thick layer of glycine in D₂O forms a crystal through a polymorphically and spatially controlled nucleation process known as gradient-force laser-induced nucleation or optical-tweezer laser-induced nucleation. However, when this same beam is focused at the glass/solution interface of a film of aqueous glycine, a highly concentrated laser-induced phase-separated (LIPS) solution droplet is formed that does not nucleate while the focusing beam remains on. Two competing theories have emerged about the nature of the LIPS droplet: one proposes that it is a merger of prenucleation metastable nanodroplets and clusters into one large homogeneous "dense liquid droplet", and the other stipulates that it is the result of the partitioning of larger droplets into the new phase, but not a merging of droplets, around the focal point of the beam. In order to determine the nature of the LIPS droplet, dynamic light scattering was used to detect the presence of nanodroplets undergoing Brownian motion within the droplet and to measure their relative size following a range of laser exposure times. The observation of nanodroplets in motion in the center of the LIPS droplet revealed that the application of optical tweezers at the glass/solution interface forms a relatively monodisperse collection of large nanodroplets (>700 nm) concentrated around the focal point of the beam with smaller particles (<100 nm) depleted within the first 2 min of laser exposure. The LIPS droplet quickly reaches a steady state and is not affected by increasing focusing times. These findings allow for a better understanding of the interactions of optical tweezers with aqueous glycine nanodroplets. This understanding will help in studying the fundamental nature of metastable nanodroplets. More practically, laser-induced phase separation makes possible the nucleation-free separation of large nanodroplets from small clusters, facilitating materials technologies such as high purity, polymorphically selective nucleation of crystals and co-crystals used for pharmaceuticals, dyes, and photovoltaics.

From folding to function: complex macromolecular reactions unraveled one-by-one with optical tweezers

Single-molecule manipulation with optical tweezers has uncovered macromolecular behaviour hidden to other experimental techniques. Recent instrumental improvements have made it possible to expand the range of systems accessible to optical tweezers. Beyond focusing on the folding and structural changes of isolated single molecules, optical tweezers studies have evolved into unraveling the basic principles of complex molecular processes such as co-translational folding on the ribosome, kinase activation dynamics, ligand-receptor binding, chaperone-assisted protein folding, and even dynamics of intrinsically disordered proteins (IDPs). In this mini-review, we illustrate the methodological principles of optical tweezers before highlighting recent advances in studying complex protein conformational dynamics - from protein synthesis to physiological function - as well as emerging future issues that are beginning to be addressed with novel approaches.

Optical tweezers in single-molecule biophysics

Optical tweezers have become the method of choice in single-molecule manipulation studies. In this Primer, we first review the physical principles of optical tweezers and the characteristics that make them a powerful tool to investigate single molecules. We then introduce the modifications of the method to extend the measurement of forces and displacements to torques and angles, and to develop optical tweezers with single-molecule fluorescence detection capabilities. We discuss force and torque calibration of these instruments, their various modes of operation and most common experimental geometries. We describe the type of data obtained in each experimental design and their analyses. This description is followed by a survey of applications of these methods to the studies of protein-nucleic acid interactions, protein/RNA folding and molecular motors. We also discuss data reproducibility, the factors that lead to the data variability among different laboratories and the need to develop field standards. We cover the current limitations of the methods and possible ways to optimize instrument operation, data extraction and analysis, before suggesting likely areas of future growth.

Applications of Optically Controlled Gold Nanostructures in Biomedical Engineering

Since their inception, optical tweezers have proven to be a useful tool for improving human understanding of the microscopic world with wide-ranging applications across science. In recent years, they have found many particularly appealing applications in the field of biomedical engineering which harnesses the knowledge and skills in engineering to tackle problems in biology and medicine. Notably, metallic nanostructures like gold nanoparticles have proven to be an excellent tool for OT-based micromanipulation due to their large polarizability and relatively low cytotoxicity. In this article, we review the progress made in the application of optically trapped gold nanomaterials to problems in bioengineering. After an introduction to the basic methods of optical trapping, we give an overview of potential applications to bioengineering specifically: nano/biomaterials, microfluidics, drug delivery, biosensing, biophotonics and imaging, and mechanobiology/single-molecule biophysics. We highlight the recent research progress, discuss challenges, and provide possible future directions in this field.

Effective behavior of cooperative and nonidentical molecular motors

Analytical formulas for effective drift, diffusivity, run times, and run lengths are derived for an intracellular transport system consisting of a cargo attached to two cooperative but not identical molecular motors (for example, kinesin-1 and kinesin-2) which can each attach and detach from a microtubule. The dynamics of the motor and cargo in each phase are governed by stochastic differential equations, and the switching rates depend on the spatial configuration of the motor and cargo. This system is analyzed in a limit where the detached motors have faster dynamics than the cargo, which in turn has faster dynamics than the attached motors. The attachment and detachment rates are also taken to be slow relative to the spatial dynamics. Through an application of iterated stochastic averaging to this system, and the use of renewal-reward theory to stitch together the progress within each switching phase, we obtain explicit analytical expressions for the effective drift, diffusivity, and processivity of the motor-cargo system. Our approach accounts in particular for jumps in motor-cargo position that occur during attachment and detachment events, as the cargo tracking variable makes a rapid adjustment due to the averaged fast scales. The asymptotic formulas are in generally good agreement with direct stochastic simulations of the detailed model based on experimental parameters for various pairings of kinesin-1 and kinesin-2 under assisting, hindering, or no load.

An optical trapping system for particle probes in plasma diagnostics

We present one of the first experiments for optically trapping of single microparticles as probes for low temperature plasma diagnostics. Based on the dual laser beam, counter-propagating technique, SiO₂ microparticles are optically trapped at very large distances in low-temperature, low-pressure rf plasma. External forces on the particle are measured by means of the displacement of the probe particle in the trap. Measurements can be performed during plasma operation as well as without plasma. The paper focuses on the optical setup and the verification of the system and its principle. Three examples for the particle behavior in the trapping system are presented: First, we measured the neutral gas damping as a verification of the technique. Second, an experiment without a plasma studies the changing particle charge by UV light radiation, and third, by moving the probe particle in the vertical direction into the sheath or into the plasma bulk, respectively, the acting forces on the probe particle are measured.

Single Molecule Studies Enabled by Model-Based Controller Design

Optical tweezers have enabled important insights into intracellular transport through the investigation of motor proteins, with their ability to manipulate particles at the microscale, affording femto newton force resolution. Its use to realize a constant force clamp has enabled vital insights into the behavior of motor proteins under different load conditions. However, the varying nature of disturbances and the effect of thermal noise pose key challenges to force regulation. Furthermore, often the main aim of many studies is to determine the motion of the motor and the statistics related to the motion, which can be at odds with the force regulation objective. In this article, we propose a mixed objective H ₂ /H _∞ optimization framework using a model-based design, that achieves the dual goals of force regulation and real time motion estimation with quantifiable guarantees. Here, we minimize the H _∞ norm for the force regulation and error in step estimation while maintaining the H ₂ norm of the noise on step estimate within user specified bounds. We demonstrate the efficacy of the framework through extensive simulations and an experimental implementation using an optical tweezer setup with live samples of the motor protein 'kinesin'; where regulation of forces below 1 piconewton with errors below 10% is obtained while simultaneously providing real time estimates of motor motion.

Estimation of actomyosin active force maintained by tropomyosin and troponin complex under vertical forces in the in vitro motility assay system

The interaction between actin filaments and myosin molecular motors is a power source of a variety of cellular functions including cell division, cell motility, and muscular contraction. In vitro motility assay examines actin filaments interacting with myosin molecules that are adhered to a substrate (e.g., glass surface). This assay has been the standard method of studying the molecular mechanisms of contraction under an optical microscope. While the force generation has been measured through an optically trapped bead to which an actin filament is attached, a force vector vertical to the glass surface has been largely ignored with the in vitro motility assay. The vertical vector is created by the gap (distance) between the trapped bead and the glass surface. In this report, we propose a method to estimate the angle between the actin filament and the glass surface by optically determining the gap size. This determination requires a motorized stage in a standard epi-fluorescence microscope equipped with optical tweezers. This facile method is applied to force measurements using both pure actin filaments, and thin filaments reconstituted from actin, tropomyosin and troponin. We find that the angle-corrected force per unit filament length in the active condition (pCa = 5.0) decreases as the angle between the filament and the glass surface increases; i.e. as the force in the vertical direction increases. At the same time, we demonstrate that the force on reconstituted thin filaments is approximately 1.5 times larger than that on pure actin filaments. The range of angles we tested was between 11° and 36° with the estimated measurement error less than 6°. These results suggest the ability of cytoplasmic tropomyosin isoforms maintaining actomyosin active force to stabilize cytoskeletal architecture.

Modulating Beta-Cardiac Myosin Function at the Molecular and Tissue Levels

Inherited cardiomyopathies are a common form of heart disease that are caused by mutations in sarcomeric proteins with beta cardiac myosin (MYH7) being one of the most frequently affected genes. Since the discovery of the first cardiomyopathy associated mutation in beta-cardiac myosin, a major goal has been to correlate the in vitro myosin motor properties with the contractile performance of cardiac muscle. There has been substantial progress in developing assays to measure the force and velocity properties of purified cardiac muscle myosin but it is still challenging to correlate results from molecular and tissue-level experiments. Mutations that cause hypertrophic cardiomyopathy are more common than mutations that lead to dilated cardiomyopathy and are also often associated with increased isometric force and hyper-contractility. Therefore, the development of drugs designed to decrease isometric force by reducing the duty ratio (the proportion of time myosin spends bound to actin during its ATPase cycle) has been proposed for the treatment of hypertrophic cardiomyopathy. Para-Nitroblebbistatin is a small molecule drug proposed to decrease the duty ratio of class II myosins. We examined the impact of this drug on human beta cardiac myosin using purified myosin motor assays and studies of permeabilized muscle fiber mechanics. We find that with purified human beta-cardiac myosin para-Nitroblebbistatin slows actin-activated ATPase and in vitro motility without altering the ADP release rate constant. In permeabilized human myocardium, para-Nitroblebbistatin reduces isometric force, power, and calcium sensitivity while not changing shortening velocity or the rate of force development (k_tr). Therefore, designing a drug that reduces the myosin duty ratio by inhibiting strong attachment to actin while not changing detachment can cause a reduction in force without changing shortening velocity or relaxation.

Enzyme Catalysis To Power Micro/Nanomachines

Enzymes play a crucial role in many biological processes which require harnessing and converting free chemical energy into kinetic forces in order to accomplish tasks. Enzymes are considered to be molecular machines, not only because of their capability of energy conversion in biological systems but also because enzymatic catalysis can result in enhanced diffusion of enzymes at a molecular level. Enlightened by nature's design of biological machinery, researchers have investigated various types of synthetic micro/nanomachines by using enzymatic reactions to achieve self-propulsion of micro/nanoarchitectures. Yet, the mechanism of motion is still under debate in current literature. Versatile proof-of-concept applications of these enzyme-powered micro/nanodevices have been recently demonstrated. In this review, we focus on discussing enzymes not only as stochastic swimmers but also as nanoengines to power self-propelled synthetic motors. We present an overview on different enzyme-powered micro/nanomachines, the current debate on their motion mechanism, methods to provide motion and speed control, and an outlook of the future potentials of this multidisciplinary field.

Kinetic Adaptations of Myosins for Their Diverse Cellular Functions

Members of the myosin superfamily are involved in all aspects of eukaryotic life. Their function ranges from the transport of organelles and cargos to the generation of membrane tension, and the contraction of muscle. The diversity of physiological functions is remarkable, given that all enzymatically active myosins follow a conserved mechanoenzymatic cycle in which the hydrolysis of ATP to ADP and inorganic phosphate is coupled to either actin-based transport or tethering of actin to defined cellular compartments. Kinetic capacities and limitations of a myosin are determined by the extent to which actin can accelerate the hydrolysis of ATP and the release of the hydrolysis products and are indispensably linked to its physiological tasks. This review focuses on kinetic competencies that - together with structural adaptations - result in myosins with unique mechanoenzymatic properties targeted to their diverse cellular functions.

Impulsive Enzymes: A New Force in Mechanobiology

We review studies that quantify newly discovered forces from single enzymatic reactions. These forces arise from the conversion of chemical energy to kinetic energy, which can be harnessed to direct diffusion of the enzyme up a concentration gradient of substrate, a novel phenomenon of molecular chemotaxis. When immobilized, enzymes can move fluid around them and perform directional pumping in microfluidic chambers. Because of the extensive array of enzymes in biological cells, we also develop three new hypotheses: that enzymatic self diffusion can assist in organizing signaling pathways in cells, can assist in pumping of fluid in cells, and can impose biologically significant forces on organelles, which will be manifested as stochastic motion not explained by thermal forces or myosin II. Such mechanochemical phenomena open up new directions in research in mechanobiology in which all enzymes, in addition to their primary function as catalysts for reactions, may have secondary functions as initiators of mechanosensitive transduction pathways.

Estimating Velocity for Processive Motor Proteins with Random Detachment

We show that, for a wide range of models, the empirical velocity of processive motor proteins has a limiting Pearson type VII distribution with finite mean but infinite variance. We develop maximum likelihood inference for this Pearson type VII distribution. In two simulation studies, we compare the performance of our MLE with the performance of standard Student's t-based inference. The studies show that incorrectly assuming normality (1) can lead to imprecise inference regarding motor velocity in the one-sample case, and (2) can significantly reduce power in the two-sample case. These results should be of interest to experimentalists who wish to engineer motors possessing specific functional characteristics.

Construction of a high resolution microscope with conventional and holographic optical trapping capabilities

High resolution microscope systems with optical traps allow for precise manipulation of various refractive objects, such as dielectric beads (1) or cellular organelles (2,3), as well as for high spatial and temporal resolution readout of their position relative to the center of the trap. The system described herein has one such "traditional" trap operating at 980 nm. It additionally provides a second optical trapping system that uses a commercially available holographic package to simultaneously create and manipulate complex trapping patterns in the field of view of the microscope (4,5) at a wavelength of 1,064 nm. The combination of the two systems allows for the manipulation of multiple refractive objects at the same time while simultaneously conducting high speed and high resolution measurements of motion and force production at nanometer and piconewton scale.

Attachment of anti-GFP antibodies to microspheres for optical trapping experiments

In vitro motility assays enabled the analysis of coupling between ATP hydrolysis and movement of myosin along actin filaments or kinesin along microtubules. Single-molecule assays using laser trapping have been used to obtain more detailed information about kinesins, myosins, and processive DNA enzymes. The combination of in vitro motility assays with laser-trap measurements has revealed detailed dynamic structural changes associated with the ATPase cycle. This protocol describes a method for attaching anti-GFP (green fluorescent protein) antibodies to microspheres. GFP-motor fusion proteins can then be adsorbed to the microspheres for use in single-molecule motility studies and optical trapping experiments.

The optical trapping dumbbell assay for nonprocessive motors or motors that turn around filaments

In vitro motility assays enabled the analysis of coupling between ATP hydrolysis and movement of myosin along actin filaments or kinesin along microtubules. Single-molecule assays using laser trapping have been used to obtain more detailed information about kinesins, myosins, and processive DNA enzymes. The combination of in vitro motility assays with laser-trap measurements has revealed detailed dynamic structural changes associated with the ATPase cycle. This protocol describes the preparation of biotin-actin filaments and coverslips coated with polystyrene beads. These are then used in optical trapping dumbbell assays to study interactions between motors and filaments.

Dynamic charge interactions create surprising rigidity in the ER/K alpha-helical protein motif

Protein alpha-helices are ubiquitous secondary structural elements, seldom considered to be stable without tertiary contacts. However, amino acid sequences in proteins that are based on alternating repeats of four glutamic acid (E) residues and four positively charged residues, a combination of arginine (R) and lysine (K), have been shown to form stable alpha-helices in a few proteins, in the absence of tertiary interactions. Here, we find that this ER/K motif is more prevalent than previously reported, being represented in proteins of diverse function from archaea to humans. By using molecular dynamics (MD) simulations, we characterize a dynamic pattern of side-chain interactions that extends along the backbone of ER/K alpha-helices. A simplified model predicts that side-chain interactions alone contribute substantial bending rigidity (0.5 pN/nm) to ER/K alpha-helices. Results of small-angle x-ray scattering (SAXS) and single-molecule optical-trap analyses are consistent with the high bending rigidity predicted by our model. Thus, the ER/K alpha-helix is an isolated secondary structural element that can efficiently span long distances in proteins, making it a promising tool in designing synthetic proteins. We propose that the significant rigidity of the ER/K alpha-helix can help regulate protein function, as a force transducer between protein subdomains.