Theoretical formalism for kinesin motility I. Bead movement powered by single one-headed kinesins

The directional movement on a microtubule of a plastic bead connected elastically to a single one-headed kinesin motor is studied theoretically. The kinesin motor can bind and unbind to periodic binding sites on the microtubule and undergo conformational changes while catalyzing the hydrolysis of ATP. An analytic formalism relating the dynamics of the bead and the ATP hydrolysis cycle of the motor is derived so that the calculation of the average velocity of the bead can be easily carried out. The formalism was applied to a simple three-state biochemical model to investigate how the velocity of the bead movement is affected by the external load, the diffusion coefficient of the bead, and the stiffness of the elastic element connecting the bead and the motor. The bead velocity was found to be critically dependent on the diffusion coefficient of the bead and the stiffness of the elastic element. A linear force-velocity relation was found for the model no matter whether the bead velocity was modulated by the diffusion coefficient of the bead or by the externally applied load. The formalism should be useful in modeling the mechanisms of chemimechanical coupling in kinesin motors based on in vitro motility data.     

Fluctuations and randomness of movement of the bead powered by a single kinesin molecule in a force-clamped motility assay: Monte Carlo simulations

The motility assay of K. Visscher, M. J. Schnitzer, and S. M. Block (Nature, 400:184-189, 1999) in which the movement of a bead powered by a single kinesin motor can be measured is a very useful tool in characterizing the force-dependent steps of the mechanochemical cycle of kinesin motors, because in this assay the external force applied to the bead can be controlled (clamped) arbitrarily. However, because the bead is elastically attached to the motor and the response of the clamp is not fast enough to compensate the Brownian motion of the bead, interpretation or analysis of the data obtained from the assay is not trivial. In a recent paper (Y. Chen and B. Yan, Biophys. Chem. 91:79-91, 2001), we showed how to evaluate the mean velocity of the bead and the motor in the motility assay for a given mechanochemical cycle. In this paper we extend the study to the evaluation of the fluctuation or the randomness of the velocity using a Monte Carlo simulation method. Similar to the mean, we found that the randomness of the velocity of the motor is also influenced by the parameters that affect the dynamic behavior of the bead, such as the viscosity of the medium, the size of the bead, the stiffness of the elastic element connecting the bead and the motor, etc. The method presented in this paper should be useful in modeling the kinetic mechanism of any processive motor (such as conventional kinesin and myosin V) based on measured force-clamp motility data.     

Gliding movement in Peranema trichophorum is powered by flagellar surface motility

A colorless euglenoid flagellate Peranema trichophorum shows unique unidirectional gliding cell locomotion on the substratum at velocities up to 30 micro m/s by an as yet unexplained mechanism. In this study, we found that (1) treatment with NiCl(2) inhibited flagellar beating without any effect on gliding movement; (2) water currents applied to a gliding cell from opposite sides caused detachment of the cell body from the substratum. With only the anterior flagellum adhering to the substratum, gliding movement continued along the direction of the anterior flagellum; (3) gentle pipetting induced flagellar severance into various lengths. In these cells, gliding velocity was proportional to the flagellar length; and (4) Polystyrene beads were translocated along the surface of the anterior flagellum. All of these results indicate that a cell surface motility system is present on the anterior flagellum, which is responsible for cell gliding in P. trichophorum.     

Up-and-down movement of a sliding actin filament in the in vitro motility assay

We observed a three-dimensional up-and-down movement of an actin filament sliding on heavy mero-myosin (HMM) molecules in an in vitro motility assay. The up-and-down movement occurred along the direction perpendicular to the planar glass plane on which the filament demonstrated a sliding movement. The height length of the up-and-down movement was measured by monitoring the extent of diminishing fluorescent emission from the marker attached to the filament in the evanescent field of attenuation. The height lengths whose distribution exhibits a local maximum were found around the two values, 150 nm and 90 nm, separately. This undulating three-dimensional movement of an actin filament suggests that the interactions between myosin (HMM) molecules and the actin filament may temporally be modulated during its sliding movement.     

Step length measurement--theory and simulation for tethered bead constant-force single molecule assay

Linear molecular motors translocate along polymeric tracks using discrete steps. The step length is usually measured using constant-force single molecule experiments in which the polymer is tethered to a force-clamped microsphere. During the enzymatic cycle the motor shortens the tether contour length. Experimental conditions influence the achievable step length resolution, and ideally experiments should be conducted with high clamp-force using slow motors linked to small beads via stiff short tethers. We focus on the limitations that the polymer-track flexibility, the thermal motion of the microsphere, and the motor kinetics pose for step-length measurement in a typical optical tweezers experiment. An expression for the signal/noise ratio in a constant-force, worm-like chain tethered particle, single-molecule experiment is developed. The signal/noise ratio is related to the Fourier transform of the pairwise distance distribution, commonly used to determine step length from a time-series. Monte Carlo simulations verify the proposed theory for experimental parameter values typically encountered with molecular motors (polymerases and helicases) translocating along single- or double-stranded nucleic acids. The predictions are consistent with recent experimental results for double-stranded DNA tethers. Our results map favorable experimental conditions for observing single motor steps on various substrates but indicate that principal resolution limits are set by thermal fluctuations.     

Calcium regulation of thin filament movement in an in vitro motility assay.

The ability of calcium to regulate thin filament sliding velocity was studied in an in vitro motility assay system using cardiac troponin and tropomyosin and rhodamine-phalloidin-labeled skeletal actin and skeletal heavy meromyosin to propel the filaments. Measurements showed that both the number of thin filaments sliding and their sliding speed (Sf) were dependent on the calcium concentration in the range of pCa 5 to 9. Thin filament motility was completely inhibited only if troponin and tropomyosin were added at a concentration of 100 nM to the motility assay solution and the pCa was more than 8. The filament sliding speed was dependent on the pCa in a noncooperative fashion (Hill coefficient = 1) and reached maximum at 5 microns/s at a pCa of 5. The number of filaments moving uniformly decreased from > 90% at pCa 5-6 to near zero in less than 1 pCa unit. This behavior may be explained by a hypothesis in which the regulatory proteins control the number of cross-bridge heads interacting with the thin filaments rather than the rate at which they individually hydrolyze ATP or translocate the thin filaments.     

Velocity of movement of actin filaments in in vitro motility assay. Measured by fluorescence correlation spectroscopy.

We have measured the velocity of actin filaments in in vitro motility assay by fluorescence correlation spectroscopy. In this method, one measures fluctuations in the number of filaments in an open sample volume. The number of filaments was calculated from measurements of fluorescence of rhodamine-phalloidin bound to F-actin. Sample volume was defined by a diaphragm placed in front of the photomultiplier. Fluctuations arise when actin filaments enter and leave the sample volume due to translations driven by mechanochemical interactions with myosin heads which are immobilized on a glass surface. The average velocity of the translation of filaments determined by the correlation method, (Vc), was equal to the diameter of the diaphragm divided by the half-time of the relaxation of fluctuations. The average number of moving filaments determined by correlation method, (Nc), was inversely proportional to the relative fluctuations. By the fluctuation method it was possible to determine the average velocity of over 800 moving filaments in less than 4 min. There was good agreement between (Vc) and (Nc) and the average velocity and the average number of moving filaments determined manually. To be able to apply correlation measurements to an experimental problem, neither (Vc) nor (Nc) must depend on the position of observation of filaments. We first confirmed that this was indeed the case. We then applied the method to investigate the dependence of motility on the ATPase activity of myosin heads. ATPase activity was varied by mixing intact heads with heads which were labeled with different thiol reagents. It was found that the motion was drastically influenced by the reagent used for modification. When the reagent was N-ethyl-maleimide, 1.5% modification was sufficient to completely inhibit the motion. When the reagent was 5-iodoacetamidofluorescein, motion declined hyperbolically with the fraction of modified heads.     

ATPase kinetic characterization and single molecule behavior of mutant human kinesin motors defective in microtubule-based motility

Conventional kinesin is a microtubule-based motor protein that is an important model system for understanding mechanochemical transduction. To identify regions of the kinesin protein that participate in microtubule binding and force production, Woehlke et al. [(1997) Cell 90, 207-216] generated 35 alanine mutations in solvent-exposed residues. Here, we have performed presteady-state kinetic and single molecule motility analyses on three of these mutants [Y138A, loop 11 triple (L248A/D249A/E250A), and E311A] that exhibited a similar approximately 3-fold reduction in both microtubule gliding velocity and microtubule-stimulated ATPase activity. All mutants showed normal second-order ATP binding kinetics, indicating correct folding of the active site. The Y138A and loop 11 triple mutants were defective both in nucleotide hydrolysis and in microtubule-stimulated ADP release rates, the latter suggesting a defect in allosteric communication between the microtubule and the active site. A single molecule fluorescence assay further revealed that the loop 11 mutant is defective in initiating processive motion, suggesting that this loop is important for the initial contact between kinesin and the microtubule. Y138A, on the other hand, can bind to the microtubule normally but cannot move processively. For E311A, neither the rate of nucleotide hydrolysis nor ADP release could account for its slower ATPase and gliding velocity, which suggests that either phosphate release or a conformational transition is rate-limiting in this mutant. The single molecule assay showed that E311A has a reduced velocity of movement, but is not defective in processivity. Thus, while these mutants behave similarly in solution ATPase and multiple motor gliding assays, kinetic and single molecule analyses reveal defects in distinct processes in kinesin's mechanochemical cycle.     

A reliable multiplex genotyping assay for HCV using a suspension bead array

The genotyping of the hepatitis C virus (HCV) plays an important role in the treatment of HCV because genotype determination has recently been incorporated into the treatment guidelines for HCV infections. Most current genotyping methods are unable to detect mixed genotypes from two or more HCV infections. We therefore developed a multiplex genotyping assay to determine HCV genotypes using a bead array. Synthetic plasmids, genotype panels and standards were used to verify the target‐specific primer (TSP) design in the assay, and the results indicated that discrimination efforts using 10 TSPs in a single reaction were extremely successful. Thirty‐five specimens were then tested to evaluate the assay performance, and the results were highly consistent with those of direct sequencing, supporting the reliability of the assay. Moreover, the results from samples with mixed HCV genotypes revealed that the method is capable of detecting two different genotypes within a sample. Furthermore, the specificity evaluation results suggested that the assay could correctly identify HCV in HCV/human immunodeficiency virus (HIV) co‐infected patients. This genotyping platform enables the simultaneous detection and identification of more than one genotype in a same sample and is able to test 96 samples simultaneously. It could therefore provide a rapid, efficient and reliable method of determining HCV genotypes in the future.     

Use of a computer to assay motility in bacteria

An assay was developed to study the movement of free-swimming Escherichia coli. Cells were videotaped through a microscope, and the videotape images were then digitized and analyzed with a computer. Angular and linear speeds were measured for wild-type E. coli and for a smooth and a tumbly mutant. The average angular and linear speeds of a population were directly and inversely proportional, respectively, to the time spent tumbling. Changes in angular and linear speeds were followed during the response of wild-type E. coli to attractant or repellent.     

Effect of multiple phosphorylations of smooth muscle and cytoplasmic myosins on movement in an in vitro motility assay

The Nitella-based in vitro motility assay developed by Sheetz and Spudich (Sheetz, M.P., and Spudich, J. A. (1983) Nature 303, 31-35) is a quantitative assay for measuring the velocity of myosin-coated beads over an organized substratum of actin. We have used this assay to analyze the effect of phosphorylation of various sites on the 20,000-Da light chain of smooth muscle and cytoplasmic myosins. Phosphorylation by myosin light chain kinase at serine 19 on the 20,000-Da light chain subunit of smooth muscle myosin from turkey gizzard, bovine trachea and aorta, and of cytoplasmic myosin from human platelets was required for bead movement. The individual phosphorylated myosin-coated beads moved at characteristic rates under the same conditions (turkey gizzard myosin, 0.2 micron/s; aorta or trachea myosin, 0.12 micron/s; and platelet myosin, 0.04 micron/s; in contrast, rabbit skeletal muscle myosin, 2 micron/s). Myosin light chain kinase can also phosphorylate threonine 18 in addition to serine 19, and this phosphorylation resulted in an increase in the actin-activated MgATPase activity (Ikebe, M., and Hartshorne, D.J. (1985) J. Biol. Chem. 260, 10027-10031). Phosphorylation at this site had no effect on the velocity of smooth muscle myosin-coated beads. Protein kinase C (Ca2+/phospholipid-dependent enzyme) can also phosphorylate two to three sites on the 20,000-Da light chain, and this phosphorylation alone did not result in the movement of myosin-coated beads. When myosin that had been previously phosphorylated by myosin light chain kinase at serine 19 was also phosphorylated by protein kinase C, myosin-coated beads moved at the same velocity as beads coated with myosin phosphorylated by myosin light chain kinase alone. Tropomyosin binding to actin also had an activating effect on the actin-activated MgATPase activity through an effect on the Vmax and also resulted in an increase in the velocity of myosin-coated beads.     

A simple and safe method for single HLA-antigen-typing by a solid phase assay

A rapid solid phase assay for detection of single HLA-antigens on platelets was developed. The platelets were attached to the surface of polystyrene microtitre plate wells by means of a sodium carbonate buffer and centrifugation. Uncovered areas were blocked by a gelatin blocking buffer. After incubation with commercially available anti-HLA-sera the bound anti-HLA-specific antibodies directed against HLA-antigens present on the platelets were made visible by anti-IgG-coated indicator red cells and a brief centrifugation. A positive result, meaning the presence of an HLA-antigen, was indicated by a slight red cell adherence over the reaction surface. In the absence of the HLA-antigen no binding occurred and the indicator red cells formed a small red disc-like pellet.     

Rapid and simple detection of food poisoning bacteria by bead assay with a microfluidic chip-based system

A rapid bead assay for detecting pathogenic bacteria with a simple microfluidic chip-based system was developed. Five oligonucleotide probes corresponding to the 16S rRNA of the targeted bacteria were coupled covalently to fluorescent beads. Four species of bacteria (Escherichia coli, Salmonella enterica subsp. enterica serovar Enteritidis, Yersinia enterocolitica, and Bacillus cereus) were used as representative food-borne pathogenic bacteria. The RNAs extracted from pure cultures of these microorganisms were fluorescently labeled and hybridized to the oligonucleotide probes-immobilized fluorescent beads (Bead assay). The duplexes of RNAs and the probes-immobilized beads were analyzed with the commercially available microfluidic chip-based system. This bead assay provided results within 3 h following RNA extraction from bacterial cells.     

A new in vitro assay for cell motility and proliferation

Abstract. We have described and characterized a new micropore membrane assay for migration and proliferation of cells of various tumourigenic potential. The assay was developed to facilitate analysis of some aspects of cancer invasion and metastasis. Tumorigenic and non-tumorigenic C3H/10 T1/2 cells grow in and migrate out of a culture chamber during a 1–11 day period, the shorter periods are used for chambers with 6 μ m thick polycarbonate membranes, the longer ones for 140 μ m thick cellulose nitrate membranes. Cell growth within the chambers, in their micropore membranes and on the outside of the membranes, was assessed with microscopy, electronic cell counting, flow cytometry of propidium iodide (PI) stained cells, and ³H-thymidine ([³H]TdR) incorporation. A complete retrieval of intact cells that have traversed the membraneous chamber wall is possible, and these cells can be recultured or used in other studies. The tumorigenic cells had a steeper growth curve in vitro than the non transformed cells, but the relative sizes of the emigrated subpopulations were not significantly different. The subpopulation of tumorigenic cells that emigrated spontaneously from the chambers was less able than the subpopulation retained to populate secondary chamber cultures, suggesting that the clonogenic (stem) tumour cells are 'slow movers'.     

A new in vitro assay for cell motility and proliferation

We have described and characterized a new micropore membrane assay for migration and proliferation of cells of various tumourigenic potential. The assay was developed to facilitate analysis of some aspects of cancer invasion and metastasis. Tumorigenic and non-tumorigenic C3H/10 T 1/2 cells grow in and migrate out of a culture chamber during a 1-11 day period, the shorter periods are used for chambers with 6 micron thick polycarbonate membranes, the longer ones for 140 micron thick cellulose nitrate membranes. Cell growth within the chambers, in their micropore membranes and on the outside of the membranes, was assessed with microscopy, electronic cell counting, flow cytometry of propidium iodide (PI) stained cells, and 3H-thymidine [( 3H]TdR) incorporation. A complete retrieval of intact cells that have traversed the membraneous chamber wall is possible, and these cells can be recultured or used in other studies. The tumorigenic cells had a steeper growth curve in vitro than the non transformed cells, but the relative sizes of the emigrated subpopulations were not significantly different. The subpopulation of tumorigenic cells that emigrated spontaneously from the chambers was less able than the subpopulation retained to populate secondary chamber cultures, suggesting that the clonogenic (stem) tumour cells are 'slow movers'.     

Metabolic cooperation studied by a quantitative enzyme assay of single cells

A new method making use of a radiochemical enzyme assay at the single cell level is presented to investigate metabolic cooperation, a widely studied form of cellular communication. In this case metabolic cooperation between normal human fibroblasts and fibroblasts derived from a patient deficient for the enzyme hypoxanthine-guanine phosphoribosyl transferase has been studied.A mixture of an equal number of both cell types was cultured in close physical contact and after trypsinisation, replating and culturing the cells for several hours in a high dilution, quantitative enzyme measurements with individual cells isolated from the mixture were carried out. From the distribution curve of the enzyme activities of the individual cells the conclusion could be drawn that a macromolecule, either the enzyme itself or DNA or mRNA, coding for that enzyme, is transferred from normal to mutant cells.     

Mechanochemical coupling in actomyosin energy transduction studied by in vitro movement assay

In order to study the mechanochemical coupling in actomyosin energy transduction, the sliding distance of an actin filament induced by one ATP hydrolysis cycle was obtained by using an in vitro movement assay that permitted quantitative and simultaneous measurements of (1) the movements of single fluorescently labeled actin filaments on myosin bound to coverslip surfaces and (2) the ATPase rates. The sliding distance was determined as (the working stroke time in one ATPase cycle, tws) x (the filament velocity, v). tws was obtained from the ATPase turnover rate of myosin during the sliding (kt), the ATP hydrolysis time (delta t) and the ON-rate at which myosin heads enter into the working stroke state when they encounter actin (kON); tws approximately 1/kt-delta t-1/kON. kt was estimated from the ATPase rates of the myosin-coated surface during the sliding of actin filaments. delta t has been determined as less than 1/100 per second, kON was estimated by analyzing the movements of very short (40 nm) filaments. The resulting sliding distance during one ATP hydrolysis cycle near zero load was greater than 100 nm, which is about ten times longer than that expected for a single attachment-detachment cycle between an actin and a myosin head. This leads to the conclusion that the coupling between the ATPase and attachment-detachment cycles is not determined rigidly in a one-to-one fashion.     

Real-time analysis of the role of Ca(2+) in flagellar movement and motility in single sea urchin sperm

Eggs of many marine and mammalian species attract sperm by releasing chemoattractants that modify the bending properties of flagella to redirect sperm paths toward the egg. This process, called chemotaxis, is dependent on extracellular Ca(2+). We used stroboscopic fluorescence imaging to measure intracellular Ca(2+) concentration ([Ca(2+)]i) in the flagella of swimming sea urchin sperm. Uncaging of cyclic GMP induced Ca(2+) entry via at least two distinct pathways, and we identified a nimodipine-sensitive pathway, compartmentalized in the flagella, as a key regulator of flagellar bending and directed motility changes. We found that, contrary to current models, the degree of flagellar bending does not vary in proportion to the overall [Ca(2+)]i. Instead we propose a new model whereby flagella bending is increased by Ca(2+) flux through the nimodipine-sensitive pathway, and is unaffected by [Ca(2+)]i increases through alternative pathways.     

High-throughput screening for antimicrobial compounds using a 96-well format bacterial motility absorbance assay

There is a pressing need to develop new antimicrobial drugs because of the increasing resistance of pathogenic bacteria to existing antibiotics. The preliminary development and validation of a novel methodology for the high-throughput screening of antimicrobial compounds and inhibitors of bacterial motility is described. This method uses a bacterial motility swarming agar assay, combined with the use of offset inoculation of the wells in a standard, clear, 96-well plate, to enable rapid screening of compounds for potential antibiotic and antimotility properties with a standard absorbance microplate reader. Thus, the methodology should be compatible with 96-well laboratory automation technology used in drug discovery and chemical biology studies. To validate the screening method, the Genesis Plus structurally diverse library of 960 biologically active compounds was screened against a motile strain of the gram-negative bacterial pathogen Salmonella typhimurium. The average Z' value for the positive and negative motility controls on all 12 compound plates was 0.67 +/- 0.14, and the signal-to-baseline ratio calculated from the positive and negative controls was 5.9 +/- 1.1. A collection of 70 compounds with well-known antimicrobial properties was successfully identified using this assay.