WorldWideScience

Sample records for depolymerizing molecular motors

  1. Crowding of molecular motors determines microtubule depolymerization

    CERN Document Server

    Reese, Louis; Frey, Erwin

    2011-01-01

    Assembly and disassembly dynamics of microtubules (MTs) is tightly controlled by MT associated proteins. Here, we investigate how plus-end-directed depolymerases of the kinesin-8 family regulate MT depolymerization dynamics. Employing an individual-based model, we reproduce experimental findings. Moreover, crowding is identified as the key regulatory mechanism of depolymerization dynamics. Our analysis gives two qualitatively distinct regimes. For motor densities above a particular threshold, a macroscopic traffic jam emerges at the plus-end and the MT dynamics become independent of the motor concentration. Below this threshold, microscopic traffic jams at the tip arise which cancel out the effect of the depolymerization kinetics such that the depolymerization speed is solely determined by the motor density. Because this density changes over the MT length, length-dependent regulation is possible. Remarkably, motor cooperativity does not affect the depolymerization speed but only the end-residence time of depo...

  2. Motility and microtubule depolymerization mechanisms of the Kinesin-8 motor, KIF19A

    Science.gov (United States)

    Wang, Doudou; Nitta, Ryo; Morikawa, Manatsu; Yajima, Hiroaki; Inoue, Shigeyuki; Shigematsu, Hideki; Kikkawa, Masahide; Hirokawa, Nobutaka

    2016-01-01

    The kinesin-8 motor, KIF19A, accumulates at cilia tips and controls cilium length. Defective KIF19A leads to hydrocephalus and female infertility because of abnormally elongated cilia. Uniquely among kinesins, KIF19A possesses the dual functions of motility along ciliary microtubules and depolymerization of microtubules. To elucidate the molecular mechanisms of these functions we solved the crystal structure of its motor domain and determined its cryo-electron microscopy structure complexed with a microtubule. The features of KIF19A that enable its dual function are clustered on its microtubule-binding side. Unexpectedly, a destabilized switch II coordinates with a destabilized L8 to enable KIF19A to adjust to both straight and curved microtubule protofilaments. The basic clusters of L2 and L12 tether the microtubule. The long L2 with a characteristic acidic-hydrophobic-basic sequence effectively stabilizes the curved conformation of microtubule ends. Hence, KIF19A utilizes multiple strategies to accomplish the dual functions of motility and microtubule depolymerization by ATP hydrolysis. DOI: http://dx.doi.org/10.7554/eLife.18101.001 PMID:27690357

  3. Length regulation of active biopolymers by molecular motors.

    Science.gov (United States)

    Johann, Denis; Erlenkämper, Christoph; Kruse, Karsten

    2012-06-22

    For biopolymers like cytoskeletal actin filaments and microtubules, assembly and disassembly are inherently dissipative processes. Molecular motors can affect the rates of subunit removal at filament ends. We introduce a driven lattice-gas model to study the effects of motor-induced depolymerization on the length of active biopolymers and find that increasing motor activity sharpens unimodal steady-state length distributions. Furthermore, for sufficiently fast moving motors, the relative width of the length distribution is determined only by the attachment rate of motors. Our results show how established molecular processes can be used to robustly regulate the size of cytoskeletal structures like mitotic spindles.

  4. Immune-enhancing activities of low molecular weight {beta}-glucan depolymerized by gamma irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Sung, Nak-Yun [Team for Radiation Food Science and Biotechnology, Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 580-185 (Korea, Republic of); Byun, Eui-Hong [Team for Radiation Food Science and Biotechnology, Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 580-185 (Korea, Republic of); Laboratory of Food Chemistry, Division of Applied Biological Chemistry, Department of Bioscience and Biotechnology, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, 812-8581 (Japan); Kwon, Sun-Kyu; Song, Beom-Seok; Choi, Jong-il; Kim, Jae-Hun; Byun, Myung-Woo [Team for Radiation Food Science and Biotechnology, Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 580-185 (Korea, Republic of); Yoo, Young-Choon [Department of Microbiology, College of Medicine, Konyang University, Daejeon 302-718 (Korea, Republic of); Kim, Mee-Ree [Department of Food and Nutrition, Chungnam National University, Daejeon 305-764 (Korea, Republic of); Lee, Ju-Woon [Team for Radiation Food Science and Biotechnology, Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 580-185 (Korea, Republic of)], E-mail: sjwlee@kaeri.re.kr

    2009-07-15

    {beta}-glucans are structural cell wall polymers of many microorganisms and cereals which possess immunomodulatory properties and have been used in the food, cosmetic and medical industry. In our previous study, {beta}-glucan was depolymerized by gamma irradiation and leads to improve the solubility and viscosity. This study was carried out to evaluate the functional properties, mainly immune-enhancing activities of low molecular weight {beta}-glucan fragmented by gamma irradiation. The results showed that RAW 264.7 macrophage cell stimulation activities of irradiated {beta}-glucan were higher than that of non-irradiated {beta}-glucan. In addition, the oral administration of gamma-irradiated {beta}-glucan significantly increased the proliferation and cytokine (IFN-{gamma} and IL-2) release of spleen and Peyer's patch cells compared with non-irradiated {beta}-glucan. In conclusion, gamma irradiation could be used as an effective method for the production of depolymerized {beta}-glucan improved functional property such as immunomodulatory activity.

  5. Molecular simulation evidence for processive motion of Trichoderma reesei Cel7A during cellulose depolymerization

    Science.gov (United States)

    Zhao, Xiongce; Rignall, Tauna R.; McCabe, Clare; Adney, William S.; Himmel, Michael E.

    2008-07-01

    We present free energy calculations for the Trichoderma reesei Cel7A (cellobiohydrolase I) linker peptide from molecular dynamics simulations directed towards understanding the linker role in cellulose hydrolysis. The calculations predict an energy storage mechanism of the linker under stretching/compression that is consistent with processive depolymerization. The linker exhibits two stable states at lengths of 2.5 nm and 5.5 nm during extension/compression, with a free energy difference of 10.5 kcal/mol between the two states separated by an energy barrier. The switching between stable states supports the hypothesis that the linker peptide has the capacity to store energy in a manner similar to a spring.

  6. Engineering Nanoscale Biological Molecular Motors

    OpenAIRE

    Korosec, Chapin; Forde, Nancy R.

    2017-01-01

    Understanding the operation of biological molecular motors, nanoscale machines that transduce electrochemical energy into mechanical work, is enhanced by bottom-up strategies to synthesize novel motors.

  7. Light-driven molecular motors

    OpenAIRE

    van Delden, RA; FERINGA, BL; Kuzmany, H.; Fink, J.; Mehring, M.; Roth, S.

    2004-01-01

    Molecular motors can be defined as molecules that are able to convert any type of energy input (a fuel) into controlled motion. These systems can be categorized into linear and rotary motors, depending on the motion induced. This brief account will discuss the state of affairs of the research on light-driven rotary molecular motors.

  8. Molecular Cloning and Characterization of the Actin-depolymerizing Factor Gene in Gossypium barbadense

    Institute of Scientific and Technical Information of China (English)

    MA Zhi-ying; CHI Ji-na; WANG Xing fen; ZHOU Hong-mei; ZHANG Gui-yin

    2008-01-01

    @@ Sea Island cotton (Gossypium barbadense L.) has been highly valued in Verticillium wilt resistance and many fiber qualities including fiber length,strength,and fineness.To identify whether it had some special genes in fiber development in comparison with the upland cotton (G.hirsutum L.),an actin-depolymerizing factor (ADF) gene was cloned and characterized in this research.A 420 bp open reading frame of the cloned gene,termed GbADF1,encoded a protein of 139 amino acids,which included39.57% nonpolar amino acids,17.27% acidic amino acids,15.83% basic amino acids,and 31.92% hydrophobic amino aids.

  9. Depolymerization of sulfated polysaccharides under hydrothermal conditions.

    Science.gov (United States)

    Morimoto, Minoru; Takatori, Masaki; Hayashi, Tetsuya; Mori, Daiki; Takashima, Osamu; Yoshida, Shinichi; Sato, Kimihiko; Kawamoto, Hitoshi; Tamura, Jun-ichi; Izawa, Hironori; Ifuku, Shinsuke; Saimoto, Hiroyuki

    2014-01-30

    Fucoidan and chondroitin sulfate, which are well known sulfated polysaccharides, were depolymerized under hydrothermal conditions (120-180°C, 5-60min) as a method for the preparation of sulfated polysaccharides with controlled molecular weights. Fucoidan was easily depolymerized, and the change of the molecular weight values depended on the reaction temperature and time. The degree of sulfation and IR spectra of the depolymerized fucoidan did not change compared with those of untreated fucoidan at reaction temperatures below 140°C. However, fucoidan was partially degraded during depolymerization above 160°C. Nearly the same depolymerization was observed for chondroitin sulfate. These results indicate that hydrothermal treatment is applicable for the depolymerization of sulfated polysaccharides, and that low molecular weight products without desulfation and deformation of the initial glycan structures can be obtained under mild hydrothermal conditions.

  10. Fluctuation Relations for Molecular Motors

    Science.gov (United States)

    Lacoste, David; Mallick, Kirone

    This review is focused on the application of specific fluctuation relations, such as the Gallavotti-Cohen relation, to ratchet models of a molecular motor. A special emphasis is placed on two-state models such as the flashing ratchet model. We derive the Gallavotti-Cohen fluctuation relation for these models and we discuss some of its implications.

  11. [Depolymerization of high-molecular-weight chitosan by the enzyme preparation Celloviridine G20x].

    Science.gov (United States)

    Il'ina, A V; Tkacheva, Iu V; Varlamov, V P

    2002-01-01

    A low-molecular-weight water-soluble chitosan was obtained from high-molecular-weight crab chitosan using the enzyme preparation Celloviridine G20x. Optimum conditions for the enzymatic hydrolysis were designed. The reaction should be performed for 4 h in a sodium-acetate buffer (pH 5.2) at 55 degrees C and the enzyme to substrate ratio of 1:400. Fractional extraction of chitosan hydrolysate by aqueous ethanol (ethanol: distilled water) yielded fractions with molecular weights in the range 3.2-26.4 kDa.

  12. Biophysics of filament length regulation by molecular motors

    CERN Document Server

    Kuan, Hui-Shun

    2013-01-01

    Regulating physical size is an essential problem that biological organisms must solve from the subcellular to the organismal scales, but it is not well understood what physical principles and mechanisms organisms use to sense and regulate their size. Any biophysical size-regulation scheme operates in a noisy environment and must be robust to other cellular dynamics and fluctuations. This work develops theory of filament length regulation inspired by recent experiments on kinesin-8 motor proteins, which move with directional bias on microtubule filaments and alter microtubule dynamics. Purified kinesin-8 motors can depolymerize chemically-stabilized microtubules. In the length-dependent depolymerization model, the rate of depolymerization tends to increase with filament length, because long filaments accumulate more motors at their tips and therefore shorten more quickly. When balanced with a constant filament growth rate, this mechanism can lead to a fixed polymer length. However, the mechanism by which kines...

  13. Nanotechnology Review: Molecular Electronics to Molecular Motors

    Science.gov (United States)

    Srivastava, Deepak; Saini, Subhash (Technical Monitor)

    1998-01-01

    Reviewing the status of current approaches and future projections, as already published in scientific journals and books, the talk will summarize the direction in which computational and experimental nanotechnologies are progressing. Examples of nanotechnological approaches to the concepts of design and simulation of carbon nanotube based molecular electronic and mechanical devices will be presented. The concepts of nanotube based gears and motors will be discussed. The above is a non-technical review talk which covers long term precompetitive basic research in already published material that has been presented before many US scientific meeting audiences.

  14. Fucosylated high molecular mass but not non-fucosylated low molecular mass xyloglucans undergo an extensive depolymerization in cell walls of azuki bean epicotyls.

    Science.gov (United States)

    Arai, Kuninori; Wakabayashi, Kazuyuki; Soga, Kouichi; Hoson, Takayuki

    2010-07-01

    Epicotyl cuttings of azuki bean were incubated with [14C]-glucose (Glc) or [3H]-fucose (Fuc), and the metabolism of radiolabeled polymers in the 24% KOH-extractable cell wall fraction was investigated. Applied 14C-Glc and (3)H-Fuc were predominantly incorporated into the glucan backbone and Fuc residue of xyloglucan molecules, respectively. On gel permeation chromatography, 14C-polymers consisted of a main peak (0.7-1.0 MDa) and shoulder peak (30 kDa). The pattern was similar to that of iodine-reactive xyloglucans in the fraction. On the other hand, 3H-polymers consisted of a single peak eluted around 0.7-1.0 MDa. The elution patterns of 14C- and 3H-polymers were constant during the incubation period, although incorporated radioactivity increased with time. In the pulse-chase experiment, the high molecular mass peaks (0.7-1.0 MDa) of both 14C- and 3H-polymers showed an extensive molecular mass downshift, but not the shoulder peak of 14C-polymers. These results indicate that xyloglucans in the fraction consist of two types of molecules; fucosylated high molecular mass polymers and non-fucosylated low molecular mass polymers. Azuki bean epicotyls may synthesize both types of xyloglucans independently, but only fucosylated xyloglucans undergo an active depolymerization in the cell wall.

  15. Active fluidization of polymer networks through molecular motors.

    Science.gov (United States)

    Humphrey, D; Duggan, C; Saha, D; Smith, D; Käs, J

    2002-03-28

    Entangled polymer solutions and melts exhibit elastic, solid-like resistance to quick deformations and a viscous, fluid-like response to slow deformations. This viscoelastic behaviour reflects the dynamics of individual polymer chains driven by brownian motion: since individual chains can only move in a snake-like fashion through the mesh of surrounding polymer molecules, their diffusive transport, described by reptation, is so slow that the relaxation of suddenly imposed stress is delayed. Entangled polymer solutions and melts therefore elastically resist deforming motions that occur faster than the stress relaxation time. Here we show that the protein myosin II permits active control over the viscoelastic behaviour of actin filament solutions. We find that when each actin filament in a polymerized actin solution interacts with at least one myosin minifilament, the stress relaxation time of the polymer solution is significantly shortened. We attribute this effect to myosin's action as a 'molecular motor', which allows it to interact with randomly oriented actin filaments and push them through the solution, thus enhancing longitudinal filament motion. By superseding reptation with sliding motion, the molecular motors thus overcome a fundamental principle of complex fluids: that only depolymerization makes an entangled, isotropic polymer solution fluid for quick deformations.

  16. Duty ratio of cooperative molecular motors.

    Science.gov (United States)

    Dharan, Nadiv; Farago, Oded

    2012-02-01

    Molecular motors are found throughout the cells of the human body and have many different and important roles. These micromachines move along filament tracks and have the ability to convert chemical energy into mechanical work that powers cellular motility. Different types of motors are characterized by different duty ratios, which is the fraction of time that a motor is attached to its filament. In the case of myosin II (a nonprocessive molecular machine with a low duty ratio), cooperativity between several motors is essential to induce motion along its actin filament track. In this work we use statistical mechanical tools to calculate the duty ratio of cooperative molecular motors. The model suggests that the effective duty ratio of nonprocessive motors that work in cooperation is lower than the duty ratio of the individual motors. The origin of this effect is the elastic tension that develops in the filament which is relieved when motors detach from the track.

  17. Molecular motors and their functions in plants

    Science.gov (United States)

    Reddy, A. S.

    2001-01-01

    Molecular motors that hydrolyze ATP and use the derived energy to generate force are involved in a variety of diverse cellular functions. Genetic, biochemical, and cellular localization data have implicated motors in a variety of functions such as vesicle and organelle transport, cytoskeleton dynamics, morphogenesis, polarized growth, cell movements, spindle formation, chromosome movement, nuclear fusion, and signal transduction. In non-plant systems three families of molecular motors (kinesins, dyneins, and myosins) have been well characterized. These motors use microtubules (in the case of kinesines and dyneins) or actin filaments (in the case of myosins) as tracks to transport cargo materials intracellularly. During the last decade tremendous progress has been made in understanding the structure and function of various motors in animals. These studies are yielding interesting insights into the functions of molecular motors and the origin of different families of motors. Furthermore, the paradigm that motors bind cargo and move along cytoskeletal tracks does not explain the functions of some of the motors. Relatively little is known about the molecular motors and their roles in plants. In recent years, by using biochemical, cell biological, molecular, and genetic approaches a few molecular motors have been isolated and characterized from plants. These studies indicate that some of the motors in plants have novel features and regulatory mechanisms. The role of molecular motors in plant cell division, cell expansion, cytoplasmic streaming, cell-to-cell communication, membrane trafficking, and morphogenesis is beginning to be understood. Analyses of the Arabidopsis genome sequence database (51% of genome) with conserved motor domains of kinesin and myosin families indicates the presence of a large number (about 40) of molecular motors and the functions of many of these motors remain to be discovered. It is likely that many more motors with novel regulatory

  18. Molecular Motors: Power Strokes Outperform Brownian Ratchets.

    Science.gov (United States)

    Wagoner, Jason A; Dill, Ken A

    2016-07-07

    Molecular motors convert chemical energy (typically from ATP hydrolysis) to directed motion and mechanical work. Their actions are often described in terms of "Power Stroke" (PS) and "Brownian Ratchet" (BR) mechanisms. Here, we use a transition-state model and stochastic thermodynamics to describe a range of mechanisms ranging from PS to BR. We incorporate this model into Hill's diagrammatic method to develop a comprehensive model of motor processivity that is simple but sufficiently general to capture the full range of behavior observed for molecular motors. We demonstrate that, under all conditions, PS motors are faster, more powerful, and more efficient at constant velocity than BR motors. We show that these differences are very large for simple motors but become inconsequential for complex motors with additional kinetic barrier steps.

  19. Molecular switches and motors on surfaces.

    Science.gov (United States)

    Pathem, Bala Krishna; Claridge, Shelley A; Zheng, Yue Bing; Weiss, Paul S

    2013-01-01

    Molecular switches and motors respond structurally, electronically, optically, and/or mechanically to external stimuli, testing and potentially enabling extreme miniaturization of optoelectronic devices, nanoelectromechanical systems, and medical devices. The assembly of motors and switches on surfaces makes it possible both to measure the properties of individual molecules as they relate to their environment and to couple function between assembled molecules. In this review, we discuss recent progress in assembling molecular switches and motors on surfaces, measuring static and dynamic structures, understanding switching mechanisms, and constructing functional molecular materials and devices. As demonstrative examples, we choose a representative molecule from three commonly studied classes including molecular switches, photochromic molecules, and mechanically interlocked molecules. We conclude by offering perspectives on the future of molecular switches and motors on surfaces.

  20. Loose mechanochemical coupling of molecular motors

    CERN Document Server

    Zhang, Yunxin

    2011-01-01

    In living cells, molecular motors convert chemical energy into mechanical work. Its thermodynamic energy efficiency, i.e. the ratio of output mechanical work to input chemical energy, is usually high. However, using two-state models, we found the motion of molecular motors is loosely coupled to the chemical cycle. Only part of the input energy can be converted into mechanical work. Others is dissipated into environment during substeps without contributions to the macro scale unidirectional movement.

  1. Duty-ratio of cooperative molecular motors

    CERN Document Server

    Dharan, Nadiv

    2012-01-01

    Molecular motors are found throughout the cells of the human body, and have many different and important roles. These micro-machines move along filament tracks, and have the ability to convert chemical energy into mechanical work that powers cellular motility. Different types of motors are characterized by different duty-ratios, which is the fraction of time that a motor is attached to its filament. In the case of myosin II - a non-processive molecular machine with a low duty ratio - cooperativity between several motors is essential to induce motion along its actin filament track. In this work we use statistical mechanical tools to calculate the duty ratio of cooperative molecular motors. The model suggests that the effective duty ratio of non-processive motors that work in cooperation is lower than the duty ratio of the individual motors. The origin of this effect is the elastic tension that develops in the filament which is relieved when motors detach from the track.

  2. Bio-inspired novel design principles for artificial molecular motors.

    Science.gov (United States)

    Hugel, Thorsten; Lumme, Christina

    2010-10-01

    Since we have learned that biological organisms like ourselves are driven by tiny biological molecular motors we try to design and produce artificial molecular motors. However, despite the huge efforts since decades, man-made artificial molecular motors are still far from biological molecular motors or macroscopic motors with regard to performance, especially with respect to energy efficiency. This review highlights recent progress towards artificial molecular motors and discusses how their design and development can be guided by the design concepts of biological molecular motors or macroscopic motors.

  3. Depolymerization-driven flow and the crawling of nematode sperm

    Science.gov (United States)

    Wolgemuth, Charles

    2008-03-01

    Cell crawling motility is integral in many biological and biomedical processes, such as wound healing, cancer metastasis, and morphogenesis. A complete understanding of the mechanisms by which cells crawl is still lacking, but it is known to entail at least three separate physical processes: (i) cytoskeletal extension at the front of the cell; (ii) adhesion to the substrate at the cell front and release at the rear; and (iii) advance of the cell body. In most cells, the cytoskeletal network is composed of actin. The mechanism by which force is generated to drive translocation of the cell body is still debated. Originally, this force was attributed to an actomyosin system similar to muscle. However, nematode sperm utilize a cytoskeleton composed of a network of Major Sperm Protein (MSP) that forms non-polar filaments for which molecular motors have not been identified. The motility of these cells still exhibits all three fundamental processes required for standard crawling motility. Experiments suggest that depolymerization of the cytoskeletal network is the force-producing mechanism for pulling up the rear. In this talk I will present a mechanical model that describes how depolymerization of the cytoskeleton can drive motility. This model accounts for both cytoskeletal displacements and cytsolic (the fluid component of the cell) flow. The model accurately fits in vitro data using nematode sperm extracts where depolymerization induces contraction of MSP polymer bundles. Application of this model to cell crawling produces testable predictions about how the size and shape of a cell affect crawling speed. Experiments using Caenorhabditis elegans sperm show good agreement with the model predictions. Interestingly, the model requires that cells are anisotropically elastic, being more stiff in the direction of motion than perpendicular to it. A simple physical picture can account for this anisotropy. The model also predicts that cell speed increases with anisotropy and

  4. Unidirectional rotary motion in achiral molecular motors.

    Science.gov (United States)

    Kistemaker, Jos C M; Štacko, Peter; Visser, Johan; Feringa, Ben L

    2015-11-01

    Control of the direction of motion is an essential feature of biological rotary motors and results from the intrinsic chirality of the amino acids from which the motors are made. In synthetic autonomous light-driven rotary motors, point chirality is transferred to helical chirality, and this governs their unidirectional rotation. However, achieving directional rotary motion in an achiral molecular system in an autonomous fashion remains a fundamental challenge. Here, we report an achiral molecular motor in which the presence of a pseudo-asymmetric carbon atom proved to be sufficient for exclusive autonomous disrotary motion of two appended rotor moieties. Isomerization around the two double bonds enables both rotors to move in the same direction with respect to their surroundings--like wheels on an axle--demonstrating that autonomous unidirectional rotary motion can be achieved in a symmetric system.

  5. Molecular Motor Proteins and Amyotrophic Lateral Sclerosis

    Directory of Open Access Journals (Sweden)

    Manal Farg

    2011-12-01

    Full Text Available Amyotrophic lateral sclerosis (ALS is a neurodegenerative disorder affecting motor neurons in the brain, brainstem and spinal cord, which is characterized by motor dysfunction, muscle dystrophy and progressive paralysis. Both inherited and sporadic forms of ALS share common pathological features, however, the initial trigger of neurodegeneration remains unknown. Motor neurons are uniquely targeted by ubiquitously expressed proteins in ALS but the reason for this selectively vulnerability is unclear. However motor neurons have unique characteristics such as very long axons, large cell bodies and high energetic metabolism, therefore placing high demands on cellular transport processes. Defects in cellular trafficking are now widely reported in ALS, including dysfunction to the molecular motors dynein and kinesin. Abnormalities to dynein in particular are linked to ALS, and defects in dynein-mediated axonal transport processes have been reported as one of the earliest pathologies in transgenic SOD1 mice. Furthermore, dynein is very highly expressed in neurons and neurons are particularly sensitive to dynein dysfunction. Hence, unravelling cellular transport processes mediated by molecular motor proteins may help shed light on motor neuron loss in ALS.

  6. Universal optimal working cycles of molecular motors.

    Science.gov (United States)

    Efremov, Artem; Wang, Zhisong

    2011-04-07

    Molecular motors capable of directional track-walking or rotation are abundant in living cells, and inspire the emerging field of artificial nanomotors. Some biomotors can convert 90% of free energy from chemical fuels into usable mechanical work, and the same motors still maintain a speed sufficient for cellular functions. This study exposed a new regime of universal optimization that amounts to a thermodynamically best working regime for molecular motors but is unfamiliar in macroscopic engines. For the ideal case of zero energy dissipation, the universally optimized working cycle for molecular motors is infinitely slow like Carnot cycle for heat engines. But when a small amount of energy dissipation reduces energy efficiency linearly from 100%, the speed is recovered exponentially due to Boltzmann's law. Experimental data on a major biomotor (kinesin) suggest that the regime of universal optimization has been largely approached in living cells, underpinning the extreme efficiency-speed trade-off in biomotors. The universal optimization and its practical approachability are unique thermodynamic advantages of molecular systems over macroscopic engines in facilitating motor functions. The findings have important implications for the natural evolution of biomotors as well as the development of artificial counterparts.

  7. Thermally driven molecular linear motors - A molecular dynamics study

    DEFF Research Database (Denmark)

    Zambrano, Harvey A; Walther, Jens Honore; Jaffe, Richard Lawrence

    2009-01-01

    We conduct molecular dynamics simulations of a molecular linear motor consisting of coaxial carbon nanotubes with a long outer carbon nanotube confining and guiding the motion of an inner short, capsule-like nanotube. The simulations indicate that the motion of the capsule can be controlled...

  8. Development of an electrically driven molecular motor.

    Science.gov (United States)

    Murphy, Colin J; Sykes, E Charles H

    2014-10-01

    For molecules to be used as components in molecular machinery, methods are required that couple individual molecules to external energy sources in order to selectively excite motion in a given direction. While significant progress has been made in the construction of synthetic molecular motors powered by light and by chemical reactions, there are few experimental examples of electrically driven molecular motors. To this end, we pioneered the use of a new, stable and tunable molecular rotor system based on surface-bound thioethers to comprehensively study many aspects of molecular rotation. As biological molecular motors often operate at interfaces, our synthetic system is especially amenable to microscopic interrogation as compared to solution-based systems. Using scanning tunneling microscopy (STM) and density functional theory, we studied the rotation of surface-bound thioethers, which can be induced either thermally or by electrons from the STM tip in a two-terminal setup. Moreover, the temperature and electron flux can be adjusted to allow each rotational event to be monitored at the molecular scale in real time. This work culminated in the first experimental demonstration of a single-molecule electric motor, where the electrically driven rotation of a butyl methyl sulfide molecule adsorbed on a copper surface could be directionally biased. The direction and rate of the rotation are related to the chirality of both the molecule and the STM tip (which serves as the electrode), illustrating the importance of the symmetry of the metal contacts in atomic-scale electrical devices. Copyright © 2014 The Chemical Society of Japan and Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Cooperative transport by small teams of molecular motors

    OpenAIRE

    Klumpp, Stefan; Muller, Melanie J. I.; Lipowsky, Reinhard

    2006-01-01

    Molecular motors power directed transport of cargoes within cells. Even if a single motor is sufficient to transport a cargo, motors often cooperate in small teams. We discuss the cooperative cargo transport by several motors theoretically and explore some of its properties. In particular we emphasize how motor teams can drag cargoes through a viscous environment.

  10. Thermodynamics and kinetics of molecular motors.

    Science.gov (United States)

    Astumian, R Dean

    2010-06-02

    Molecular motors are first and foremost molecules, governed by the laws of chemistry rather than of mechanics. The dynamical behavior of motors based on chemical principles can be described as a random walk on a network of states. A key insight is that any molecular motor in solution explores all possible motions and configurations at thermodynamic equilibrium. By using input energy and chemical design to prevent motion that is not wanted, what is left behind is the motion that is desired. This review is focused on two-headed motors such as kinesin and Myosin V that move on a polymeric track. By use of microscopic reversibility, it is shown that the ratio between the number of forward steps and the number of backward steps in any sufficiently long time period does not directly depend on the mechanical properties of the linker between the two heads. Instead, this ratio is governed by the relative chemical specificity of the heads in the front-versus-rear position for the fuel, adenosine triphosphate and its products, adenosine diphosphate and inorganic phosphate. These insights have been key factors in the design of biologically inspired synthetic molecular walkers constructed out of DNA or out of small organic molecules.

  11. A model for processivity of molecular motors

    Institute of Scientific and Technical Information of China (English)

    Xie Ping; Dou Shuo-Xing; Wang Peng-Ye

    2004-01-01

    We propose a two-dimensional model for a complete description of the dynamics of molecular motors, including both the processive movement along track filaments and the dissociation from the filaments. Theoretical results on the distributions of the run length and dwell time at a given adenosine triphosphate (ATP) concentration, the dependences of mean run length, mean dwell time and mean velocity on ATP concentration and load are in good agreement with the previous experimental results.

  12. Molecular genetics of distal hereditary motor neuropathies.

    Science.gov (United States)

    Irobi, Joy; De Jonghe, Peter; Timmerman, Vincent

    2004-10-01

    Inherited peripheral neuropathies comprise a wide variety of diseases primarily affecting the peripheral nervous system. The best-known peripheral neuropathy is Charcot-Marie-Tooth disease (CMT) described in 1886 by J.-M. Charcot, P. Marie and H.H. Tooth. In 1980, A.E. Harding and P.K. Thomas showed that in a large group of individuals with CMT, several only had motor abnormalities on clinical and electrophysiological examination, whereas sensory abnormalities were absent. This exclusively motor variant of CMT was designated as spinal CMT or hereditary distal spinal muscular atrophy, and included in the distal hereditary motor neuropathies (distal HMN). The distal HMN are clinically and genetically heterogeneous and are subdivided according to the mode of inheritance, age at onset and clinical evolution. Since the introduction of positional cloning, 12 chromosomal loci and seven disease-causing genes have been identified for autosomal dominant and recessive distal HMN. Most of the genes involved have housekeeping functions, as in RNA processing, translation synthesis, glycosylation, stress response, apoptosis, but also axonal trafficking and editing. Functional characterization of the mutations will help to unravel the cellular processes that underlie the specificity of motor neuropathies leading to neurogenic muscular atrophy of distal limb muscles. Here we review the recent progress of the molecular genetics of distal HMN and discuss the genes implicated.

  13. Light-driven rotary molecular motors : an ultrafast optical study

    NARCIS (Netherlands)

    Augulis, Ramunas; Klok, Martin; Loosdrecht, Paul H.M. van; Feringa, Bernard

    2009-01-01

    Molecular rotary motors, though common in nature, were first synthesized rather recently. One of the most promising categories of light-driven rotary molecular motors which allow for optical control is based on helical overcrowded alkenes. In this category of motors, the rotation of the motor’s roto

  14. Noninvasive probes of mitochondrial molecular motors

    Science.gov (United States)

    Nawarathna, Dharmakeerthna; Claycomb, James

    2005-03-01

    We report on a noninvasive method of probing mitochondrial molecular motors using nonlinear dielectric spectroscopy. It has been found previously that enzymes in the plasma membrane, particularly H+ ATPase, result in a strong low frequency (less than 100 Hz) nonlinear harmonic response. In this study, we find evidence that molecular motors located in the inner membranes of mitochondria cause the generation of harmonics at relatively high frequencies (1 - 30 kHz). In particular, we find that potassium cyanide (KCN), a respiratory inhibitor that binds to cytochrome c oxidase and thus prevents transport of protons across the mitochondrial inner membrane, suppresses the harmonic response. We observe this behavior in yeast (S. cerevisiae), a eucaryote that typically contains about 300 mitochondria, and B. indicas, a procaryote believed to be related to the ancient ancestor of mitochondria. Our current modeling efforts are focusing on a Brownian ratchet model of the F0 unit of ATP synthase, a remarkable molecular turbine driven by the proton gradient across the mitochondrial inner membrane.

  15. Stokes Efficiency of Molecular Motor-Cargo Systems

    Directory of Open Access Journals (Sweden)

    Hongyun Wang

    2008-01-01

    Full Text Available A molecular motor utilizes chemical free energy to generate a unidirectional motion through the viscous fluid. In many experimental settings and biological settings, a molecular motor is elastically linked to a cargo. The stochastic motion of a molecular motor-cargo system is governed by a set of Langevin equations, each corresponding to an individual chemical occupancy state. The change of chemical occupancy state is modeled by a continuous time discrete space Markov process. The probability density of a motor-cargo system is governed by a two-dimensional Fokker-Planck equation. The operation of a molecular motor is dominated by high viscous friction and large thermal fluctuations from surrounding fluid. The instantaneous velocity of a molecular motor is highly stochastic: the past velocity is quickly damped by the viscous friction and the new velocity is quickly excited by bombardments of surrounding fluid molecules. Thus, the theory for macroscopic motors should not be applied directly to molecular motors without close examination. In particular, a molecular motor behaves differently working against a viscous drag than working against a conservative force. The Stokes efficiency was introduced to measure how efficiently a motor uses chemical free energy to drive against viscous drag. For a motor without cargo, it was proved that the Stokes efficiency is bounded by 100% [H. Wang and G. Oster, (2002]. Here, we present a proof for the general motor-cargo system.

  16. Propagation Modeling and Analysis of Molecular Motors in Molecular Communication.

    Science.gov (United States)

    Chahibi, Youssef; Akyildiz, Ian F; Balasingham, Ilangko

    2016-12-01

    Molecular motor networks (MMNs) are networks constructed from molecular motors to enable nanomachines to perform coordinated tasks of sensing, computing, and actuation at the nano- and micro- scales. Living cells are naturally enabled with this same mechanism to establish point-to-point communication between different locations inside the cell. Similar to a railway system, the cytoplasm contains an intricate infrastructure of tracks, named microtubules, interconnecting different internal components of the cell. Motor proteins, such as kinesin and dynein, are able to travel along these tracks directionally, carrying with them large molecules that would otherwise be unreliably transported across the cytoplasm using free diffusion. Molecular communication has been previously proposed for the design and study of MMNs. However, the topological aspects of MMNs, including the effects of branches, have been ignored in the existing studies. In this paper, a physical end-to-end model for MMNs is developed, considering the location of the transmitter node, the network topology, and the receiver nodes. The end-to-end gain and group delay are considered as the performance measures, and analytical expressions for them are derived. The analytical model is validated by Monte-Carlo simulations and the performance of MMNs is analyzed numerically. It is shown that, depending on their nature and position, MMN nodes create impedance effects that are critical for the overall performance. This model could be applied to assist the design of artificial MMNs and to study cargo transport in neurofilaments to elucidate brain diseases related to microtubule jamming.

  17. Statistical kinetics of processive molecular motors

    Science.gov (United States)

    Schnitzer, Mark Jacob

    1999-10-01

    We describe new theoretical and experimental tools for studying biological motor proteins at the single molecule scale. These tools enable measurements of molecular fuel economies, thereby providing insight into the pathways for conversion of biochemical energy into mechanical work. Kinesin is an ATP-dependent motor that moves processively along microtubules in discrete steps of 8 nm. How many molecules of ATP are hydrolysed per step? To determine this coupling ratio, we develop a fluctuation analysis, which relates the variance in records of mechanical displacement to the number of rate-limiting biochemical transitions in the engine cycle. Using fluctuation analysis and optical trapping interferometry, we determine that near zero load, single molecules of kinesin hydrolyse one ATP nucleotide per 8-nm step. To study kinesin behavior under load, we use a molecular force clamp, capable of maintaining constant loads on single kinesin motors moving processively. Analysis of records of motion under variable ATP concentrations and loads reveals that kinesin is a `tightly- coupled' motor, maintaining the 1:1 coupling ratio up to loads of ~ 5 pN. Moreover, a Michaelis-Menten analysis of velocity shows that the kinesin cycle contains at least two load- dependent transitions. The rate of one of these transitions affects ATP affinity, while the other does not. Therefore, the kinesin stall force must depend on the ATP concentration, as is demonstrated experimentally. These findings rule out existing theoretical models of kinesin motility. We develop a simple theoretical formalism describing a tightly-coupled mechanism for movement. This `energy-landscape' formalism quantitatively accounts for motile properties of RNA polymerase (RNAP), the enzyme that transcribes DNA into RNA. The shapes of RNAP force-velocity curves indicate that biochemical steps limiting transcription rates at low loads do not generate movement. Modeling suggests that high loads may halt RNAP by promoting a

  18. High-Pressure Microscopy for Studying Molecular Motors.

    Science.gov (United States)

    Nishiyama, Masayoshi

    2015-01-01

    Movement is a fundamental characteristic of all living things. This biogenic function is carried out by various nanometer-sized molecular machines. Molecular motor is a typical molecular machinery in which the characteristic features of proteins are integrated; these include enzymatic activity, energy conversion, molecular recognition and self-assembly. These biologically important reactions occur with the association of water molecules that surround the motors. Applied pressures can alter the intermolecular interactions between the motors and water. In this chapter we describe the development of a high-pressure microscope and a new motility assay that enables the visualization of the motility of molecular motors under conditions of high-pressure. Our results demonstrate that applied pressure dynamically changes the motility of molecular motors such as kinesin, F1-ATPase and bacterial flagellar motors.

  19. Theoretical Analysis of Dynamic Processes for Interacting Molecular Motors.

    Science.gov (United States)

    Teimouri, Hamid; Kolomeisky, Anatoly B; Mehrabiani, Kareem

    2015-02-13

    Biological transport is supported by collective dynamics of enzymatic molecules that are called motor proteins or molecular motors. Experiments suggest that motor proteins interact locally via short-range potentials. We investigate the fundamental role of these interactions by analyzing a new class of totally asymmetric exclusion processes where interactions are accounted for in a thermodynamically consistent fashion. It allows us to connect explicitly microscopic features of motor proteins with their collective dynamic properties. Theoretical analysis that combines various mean-field calculations and computer simulations suggests that dynamic properties of molecular motors strongly depend on interactions, and correlations are stronger for interacting motor proteins. Surprisingly, it is found that there is an optimal strength of interactions (weak repulsion) that leads to a maximal particle flux. It is also argued that molecular motors transport is more sensitive to attractive interactions. Applications of these results for kinesin motor proteins are discussed.

  20. Thermodynamics and kinetics of a molecular motor ensemble.

    Science.gov (United States)

    Baker, J E; Thomas, D D

    2000-10-01

    If, contrary to conventional models of muscle, it is assumed that molecular forces equilibrate among rather than within molecular motors, an equation of state and an expression for energy output can be obtained for a near-equilibrium, coworking ensemble of molecular motors. These equations predict clear, testable relationships between motor structure, motor biochemistry, and ensemble motor function, and we discuss these relationships in the context of various experimental studies. In this model, net work by molecular motors is performed with the relaxation of a near-equilibrium intermediate step in a motor-catalyzed reaction. The free energy available for work is localized to this step, and the rate at which this free energy is transferred to work is accelerated by the free energy of a motor-catalyzed reaction. This thermodynamic model implicitly deals with a motile cell system as a dynamic network (not a rigid lattice) of molecular motors within which the mechanochemistry of one motor influences and is influenced by the mechanochemistry of other motors in the ensemble.

  1. Cytoskeleton Molecular Motors: Structures and Their Functions in Neuron.

    Science.gov (United States)

    Xiao, Qingpin; Hu, Xiaohui; Wei, Zhiyi; Tam, Kin Yip

    2016-01-01

    Cells make use of molecular motors to transport small molecules, macromolecules and cellular organelles to target region to execute biological functions, which is utmost important for polarized cells, such as neurons. In particular, cytoskeleton motors play fundamental roles in neuron polarization, extension, shape and neurotransmission. Cytoskeleton motors comprise of myosin, kinesin and cytoplasmic dynein. F-actin filaments act as myosin track, while kinesin and cytoplasmic dynein move on microtubules. Cytoskeleton motors work together to build a highly polarized and regulated system in neuronal cells via different molecular mechanisms and functional regulations. This review discusses the structures and working mechanisms of the cytoskeleton motors in neurons.

  2. Lignin depolymerization by fungal secretomes and a microbial sink

    Energy Technology Data Exchange (ETDEWEB)

    Salvachúa, Davinia; Katahira, Rui; Cleveland, Nicholas S.; Khanna, Payal; Resch, Michael G.; Black, Brenna A.; Purvine, Samuel O.; Zink, Erika M.; Prieto, Alicia; Martínez, María J.; Martínez, Angel T.; Simmons, Blake A.; Gladden, John M.; Beckham, Gregg T.

    2016-08-25

    In Nature, powerful oxidative enzymes secreted by white rot fungi and some bacteria catalyze lignin depolymerization and some microbes are able to catabolize the resulting aromatic compounds as carbon and energy sources. Taken together, these two processes offer a potential route for microbial valorization of lignin. However, many challenges remain in realizing this concept, including that oxidative enzymes responsible for lignin depolymerization also catalyze polymerization of low molecular weight (LMW) lignin. Here, multiple basidiomycete secretomes were screened for ligninolytic enzyme activities in the presence of a residual lignin solid stream from a corn stover biorefinery, dubbed DMR-EH (Deacetylation, Mechanical Refining, and Enzymatic Hydrolysis) lignin. Two selected fungal secretomes, with high levels of laccases and peroxidases, were utilized for DMR-EH lignin depolymerization assays. The secretome from Pleurotus eryngii, which exhibited the highest laccase activity, reduced the lignin average molecular weight by 63% and 75% at pH 7 compared to the Mw of the control treated at the same conditions and the initial DMR-EH lignin, respectively, and was applied in further depolymerization assays as a function of time. As repolymerization was observed after 3 days of incubation, an aromatic-catabolic microbe (Pseudomonas putida KT2440) was incubated with the fungal secretome and DMR-EH lignin. These experiments demonstrated that the presence of the bacterium enhances lignin depolymerization, likely due to bacterial catabolism of LMW lignin, which may partially prevent repolymerization. In addition, proteomics was also applied to the P. eryngii secretome to identify the enzymes present in the fungal cocktail utilized for the depolymerization assays, which highlighted a significant number of glucose/ methanol/choline (GMC) oxidoreductases and laccases. Overall, this study demonstrates that ligninolytic enzymes can be used to partially depolymerize a solid, high

  3. Lignin Depolymerization by Fungal Secretomes and a Microbial Sink

    Energy Technology Data Exchange (ETDEWEB)

    Salvachua, Davinia; Katahira, Rui; Cleveland, Nicholas S.; Khanna, Payal; Resch, Michael G.; Black, Brenna A.; Purvine, Samuel O.; Zink, Erika M.; Prieto, Alicia; Martinez, Maria J.; Martinez, Angel T.; Simmons, Blake A.; Gladden, John M.; Beckham, Gregg T.

    2016-11-21

    In Nature, powerful oxidative enzymes secreted by white rot fungi and some bacteria catalyze lignin depolymerization and some microbes are able to catabolize the resulting aromatic compounds as carbon and energy sources. Taken together, these two processes offer a potential route for microbial valorization of lignin. However, many challenges remain in realizing this concept, including that oxidative enzymes responsible for lignin depolymerization also catalyze polymerization of low molecular weight (LMW) lignin. Here, multiple basidiomycete secretomes were screened for ligninolytic enzyme activities in the presence of a residual lignin solid stream from a corn stover biorefinery, dubbed DMR-EH (Deacetylation, Mechanical Refining, and Enzymatic Hydrolysis) lignin. Two selected fungal secretomes, with high levels of laccases and peroxidases, were utilized for DMR-EH lignin depolymerization assays. The secretome from Pleurotus eryngii, which exhibited the highest laccase activity, reduced the lignin average molecular weight (Mw) by 63% and 75% at pH 7 compared to the Mw of the control treated at the same conditions and the initial DMR-EH lignin, respectively, and was applied in further depolymerization assays as a function of time. As repolymerization was observed after 3 days of incubation, an aromatic-catabolic microbe (Pseudomonas putida KT2440) was incubated with the fungal secretome and DMR-EH lignin. These experiments demonstrated that the presence of the bacterium enhances lignin depolymerization, likely due to bacterial catabolism of LMW lignin, which may partially prevent repolymerization. In addition, proteomics was also applied to the P. eryngii secretome to identify the enzymes present in the fungal cocktail utilized for the depolymerization assays, which highlighted a significant number of glucose/methanol/choline (GMC) oxidoreductases and laccases. Overall, this study demonstrates that ligninolytic enzymes can be used to partially depolymerize a solid

  4. Distinct transport regimes for two elastically coupled molecular motors.

    Science.gov (United States)

    Berger, Florian; Keller, Corina; Klumpp, Stefan; Lipowsky, Reinhard

    2012-05-18

    Cooperative cargo transport by two molecular motors involves an elastic motor-motor coupling, which can reduce the motors' velocity and/or enhance their unbinding from the filament. We show theoretically that these interference effects lead, in general, to four distinct transport regimes. In addition to a weak coupling regime, kinesin and dynein motors are found to exhibit a strong coupling and an enhanced unbinding regime, whereas myosin motors are predicted to attain a reduced velocity regime. All of these regimes, which we derive by explicit calculations and general time scale arguments, can be explored experimentally by varying the elastic coupling strength.

  5. Unidirectional light-driven molecular motors based on overcrowded alkenes.

    Science.gov (United States)

    Cnossen, Arjen; Browne, Wesley R; Feringa, Ben L

    2014-01-01

    Over the last two decades, interest in nanotechnology has led to the design and synthesis of a toolbox of nanoscale versions of macroscopic devices and components. In molecular nanotechnology, linear motors based on rotaxanes and rotary motors based on overcrowded alkenes are particularly promising for performing work at the nanoscale. In this chapter, progress on light-driven molecular motors based on overcrowded alkenes is reviewed. Both the so-called first and second generation molecular motors are discussed, as well as their potential applications.

  6. Light-driven altitudinal molecular motors on surfaces

    NARCIS (Netherlands)

    London, Gabor; Carroll, Gregory T.; Fernández Landaluce, Tatiana; Pollard, Michael M.; Rudolf, Petra; Feringa, Ben L.

    2009-01-01

    A Cu(I)-catalyzed 1,3-dipolar cycloaddition was used to construct a monolayer of an altitudinal molecular motor on quartz and silicon substrates, which represents the fastest light-driven molecular motor, to date, grafted to a solid surface.

  7. Control of rotor function in light-driven molecular motors

    NARCIS (Netherlands)

    Lubbe, Anouk S.; Ruangsupapichat, Nopporn; Caroli, Giuseppe; Feringa, Ben L.

    2011-01-01

    A study is presented on the control of rotary motion of an appending rotor unit in a light-driven molecular motor. Two new light driven molecular motors were synthesized that contain aryl groups connected to the stereogenic centers. The aryl groups behave as bidirectional free rotors in three of the

  8. Distribution of lifetimes of kinetochore-microtubule attachments:interplay of energy landscape, molecular motors and microtubule (de-)polymerization

    CERN Document Server

    Sharma, Ajeet K; Chowdhury, Debashish

    2013-01-01

    Before a cell divides into two daughter cells, the chromosomes are replicated resulting in two sister chromosomes embracing each other. Each sister chromosome is bound to a separate proteinous structure, called kinetochore (kt), that captures the tip of a filamentous protein, called microtubule (MT). Two oppositely oriented MTs pull the two kts attached to two sister chromosomes thereby pulling the two sisters away from each other. Here we theoretically study an even simpler system, namely an isolated kt coupled to a single MT; this system mimics an {\\it in-vitro} experiment where a single kt-MT attachment is reconstituted using purified extracts from budding yeast. Our models not only account for the experimentally observed "catch-bond-like" behavior of the kt-MT coupling, but also make new predictions on the probability distribution of the lifetimes of the attachments. In principle, our new predictions can be tested by analyzing the data collected in the {\\it in-vitro} experiments provided the experiment is...

  9. A General Random Walk Model of Molecular Motor

    Institute of Scientific and Technical Information of China (English)

    WANG Xian-Ju; AI Bao-Quan; LIU Guo-Tao; LIU Liang-Gang

    2003-01-01

    A general random walk model framework is presented which can be used to statistically describe the internaldynamics and external mechanical movement of molecular motors along filament track. The motion of molecular motorin a periodic potential and a constant force is considered. We show that the molecular motor's movement becomesslower with the potential barrier increasing, but if the forceis increased, the molecular motor's movement becomesfaster. The relation between the effective rate constant and the potential barrier's height, and that between the effectiverate constant and the value of the force are discussed. Our results are consistent with the experiments and relevanttheoretical consideration, and can be used to explain some physiological phenomena.

  10. Linking molecular motors to membrane cargo

    NARCIS (Netherlands)

    A.S. Akhmanova (Anna); J.A. Hammer (John)

    2010-01-01

    textabstractThree types of motors, myosins, kinesins, and cytoplasmic dynein, cooperate to transport intracellular membrane organelles. Transport of each cargo is determined by recruitment of specific sets of motors and their regulation. Targeting of motors to membranes often depends on the formatio

  11. Maximum power operation of interacting molecular motors

    DEFF Research Database (Denmark)

    Golubeva, Natalia; Imparato, Alberto

    2013-01-01

    We study the mechanical and thermodynamic properties of different traffic models for kinesin which are relevant in biological and experimental contexts. We find that motor-motor interactions play a fundamental role by enhancing the thermodynamic efficiency at maximum power of the motors......, as compared to the non-interacting system, in a wide range of biologically compatible scenarios. We furthermore consider the case where the motor-motor interaction directly affects the internal chemical cycle and investigate the effect on the system dynamics and thermodynamics....

  12. Motor proteins and molecular motors: how to operate machines at the nanoscale.

    Science.gov (United States)

    Kolomeisky, Anatoly B

    2013-11-20

    Several classes of biological molecules that transform chemical energy into mechanical work are known as motor proteins or molecular motors. These nanometer-sized machines operate in noisy stochastic isothermal environments, strongly supporting fundamental cellular processes such as the transfer of genetic information, transport, organization and functioning. In the past two decades motor proteins have become a subject of intense research efforts, aimed at uncovering the fundamental principles and mechanisms of molecular motor dynamics. In this review, we critically discuss recent progress in experimental and theoretical studies on motor proteins. Our focus is on analyzing fundamental concepts and ideas that have been utilized to explain the non-equilibrium nature and mechanisms of molecular motors.

  13. A General Random Walk Model of Molecular Motor

    Institute of Scientific and Technical Information of China (English)

    WANGXian-Ju; AIBao-Quan; LIUGuo-Tao; LIULiang-Gang

    2003-01-01

    A general random walk model framework is presented which can be used to statistically describe the internal dynamics and external mechanical movement of molecular motors along filament track. The motion of molecular motor in a periodic potential and a constant force is considered. We show that the molecular motor's movement becomes slower with the potential barrier increasing, but if the force is increased, the molecular motor''s movement becomes faster. The relation between the effective rate constant and the potential battler's height, and that between the effective rate constant and the value of the force are discussed. Our results are consistent with the experiments and relevant theoretical consideration, and can be used to explain some physiological phenomena.

  14. Collective alignment of polar filaments by molecular motors.

    Science.gov (United States)

    Ziebert, F; Vershinin, M; Gross, S P; Aranson, I S

    2009-04-01

    We study the alignment of polar biofilaments, such as microtubules and actin, subject to the action of multiple molecular motors attached simultaneously to more than one filament. Focusing on a paradigm model of only two filaments interacting with multiple motors, we were able to investigate in detail the alignment dynamics. While almost no alignment occurs in the case of a single motor, the filaments become rapidly aligned due to the collective action of the motors. Our analysis shows that the alignment time is governed by the number of bound motors and the magnitude of the motors' stepping fluctuations. We predict that the time scale of alignment is in the order of seconds, much faster than that reported for passive crosslink-induced bundling. In vitro experiments on the alignment of microtubules by multiple-motor covered beads are in qualitative agreement. We also discuss another mode of fast alignment of filaments, namely the cooperation between motors and passive crosslinks.

  15. Exploiting molecular motors as nanomachines: the mechanisms of de novo and re-engineered cytoskeletal motors.

    Science.gov (United States)

    DelRosso, Nicole V; Derr, Nathan D

    2017-01-11

    Cytoskeletal molecular motors provide exciting proof that nanoscale transporters can be highly efficient, moving for microns along filamentous tracks by hydrolyzing ATP to fuel nanometer-size steps. For nanotechnology, such conversion of chemical energy into productive work serves as an enticing platform for re-purposing and re-engineering. It also provides a roadmap for successful molecular mechanisms that can be mimicked to create de novo molecular motors for nanotechnology applications. Here we focus specifically on how the mechanisms of molecular motors are being re-engineered for greater control over their transport parameters. We then discuss mechanistic work to create fully synthetic motors de novo and conclude with future directions in creating novel motor systems.

  16. The Art of Building Small : From Molecular Switches to Molecular Motors

    NARCIS (Netherlands)

    Feringa, Bernard

    2007-01-01

    Molecular switches and motors are essential components of artificial molecular machines. In this perspective, we discuss progress in our design, synthesis, and functioning of photochemical and electrochemical switches and chemical and light-driven molecular motors. Special emphasis is given to the c

  17. The art of building small : From molecular switches to molecular motors

    NARCIS (Netherlands)

    Feringa, Ben L.

    2007-01-01

    Molecular switches and motors are essential components of artificial molecular machines. In this perspective, we discuss progress in our design, synthesis, and functioning of photochemical and electrochemical switches and chemical and light-driven molecular motors. Special emphasis is given to the c

  18. The art of building small : From molecular switches to molecular motors

    NARCIS (Netherlands)

    Feringa, Ben L.

    2007-01-01

    Molecular switches and motors are essential components of artificial molecular machines. In this perspective, we discuss progress in our design, synthesis, and functioning of photochemical and electrochemical switches and chemical and light-driven molecular motors. Special emphasis is given to the

  19. The Art of Building Small : From Molecular Switches to Molecular Motors

    NARCIS (Netherlands)

    Feringa, Bernard

    2007-01-01

    Molecular switches and motors are essential components of artificial molecular machines. In this perspective, we discuss progress in our design, synthesis, and functioning of photochemical and electrochemical switches and chemical and light-driven molecular motors. Special emphasis is given to the

  20. Monte Carlo simulations of single and coupled synthetic molecular motors.

    Science.gov (United States)

    Chen, C-M; Zuckermann, M

    2012-11-01

    We use a minimal model to study the processive motion of coupled synthetic molecular motors along a DNA track and we present data from Monte Carlo (MC) computer simulations based on this model. The model was originally proposed by Bromley et al. [HFSP J. 3, 204 (2009)] for studying the properties of a synthetic protein motor, the "Tumbleweed" (TW), and involves rigid Y-shaped motors diffusively rotating along the track while controlled by a series of periodically injected ligand pulses into the solution. The advantage of the model is that it mimics the mechanical properties of the TW motor in detail. Both the average first passage time which measures the diffusive motion of the motors, and the average dwell time on the track which measures their processivity are investigated by varying the parameters of the model. The latter includes ligand concentration and the range and strength of the binding interaction between motors and the track. In particular, it is of experimental interest to study the dependence of these dynamic time scales of the motors on the ligand concentration. Single rigid TW motors were first studied since no previous MC simulations of these motors have been performed. We first studied single motors for which we found a logarithmic decrease of the average first passage time and a logarithmic increase of the average dwell time with increasing ligand concentration. For two coupled motors, the dependence on ligand concentration is still logarithmic for the average first passage time but becomes linear for the average dwell time. This suggests a much greater stability in the processive motion of coupled motors as compared to single motors in the limit of large ligand concentration. By increasing the number of coupled motors, m, it was found that the average first passage time of the coupled motors only increases slowly with m while the average dwell time increases exponentially with m. Thus the stability of coupled motors on the track can be

  1. Ultrafast ignition of a uni-directional molecular motor

    Directory of Open Access Journals (Sweden)

    Feringa Ben L.

    2013-03-01

    Full Text Available Light-driven molecular motors convert light into mechanical energy via excited state reactions. In this work we follow sub-picosecond primary events in the cycle of a two-stroke unidirectional motor by fluorescence up-conversion and transient absorption.

  2. Unidirectional Light-Driven Molecular Motors Based on Overcrowded Alkenes

    NARCIS (Netherlands)

    Cnossen, Arjen; Browne, Wesley R.; Feringa, Ben L.; Credi, Alberto; Silvi, Serena; Venturi, Margherita

    2014-01-01

    Over the last two decades, interest in nanotechnology has led to the design and synthesis of a toolbox of nanoscale versions of macroscopic devices and components. In molecular nanotechnology, linear motors based on rotaxanes and rotary motors based on overcrowded alkenes are particularly promising

  3. Light-Driven Rotary Molecular Motors on Gold Nanoparticles

    NARCIS (Netherlands)

    Pollard, Michael M.; ter Wiel, Matthijs K. J.; van Delden, Richard A.; Vicario, Javier; Koumura, Nagatoshi; van den Brom, Coenraad R.; Meetsma, Auke; Feringa, Ben L.

    2008-01-01

    We report the synthesis of unidirectional light-driven rotary molecular motors based oil chiral overcrowded alkenes and their immobilisation on the surface of gold nanoparticles through two anchors. Using a combination of (1)H and (13)C NMR, UV/Vis and CD spectroscopy, we show that these motors pres

  4. Rotation of artificial rotor axles in rotary molecular motors

    National Research Council Canada - National Science Library

    Baba, Mihori; Iwamoto, Kousuke; Iino, Ryota; Ueno, Hiroshi; Hara, Mayu; Nakanishi, Atsuko; Kishikawa, Jun-ichi; Noji, Hiroyuki; Yokoyama, Ken

    2016-01-01

    [F.sub.1]- and [V.sub.1]-ATPase are rotary molecular motors that convert chemical energy released upon ATP hydrolysis into torque to rotate a central rotor axle against the surrounding catalytic stator cylinder with high efficiency...

  5. Fluctuation theorem for the flashing ratchet model of molecular motors

    Science.gov (United States)

    Lacoste, D.; Mallick, K.

    2009-08-01

    Molecular motors convert chemical energy derived from the hydrolysis of adenosine triphosphate (ATP) into mechanical energy. A well-studied model of a molecular motor is the flashing ratchet model. We show that this model exhibits a fluctuation relation known as the Gallavotti-Cohen symmetry. Our study highlights the fact that the symmetry is present only if the chemical and mechanical degrees of freedom are both included in the description.

  6. Molecular motor traffic: From biological nanomachines to macroscopic transport

    Science.gov (United States)

    Lipowsky, Reinhard; Chai, Yan; Klumpp, Stefan; Liepelt, Steffen; Müller, Melanie J. I.

    2006-12-01

    All cells of animals and plants contain complex transport systems based on molecular motors which walk along cytoskeletal filaments. These motors are rather small and have a size of 20-100 nm but are able to pull vesicles, organelles and other types of cargo over large distances, from micrometers up to meters. There are several families of motors: kinesins, dyneins, and myosins. Most of these motors have two heads which are used as legs and perform discrete steps along the filaments. Several aspects of the motor behavior will be discussed: motor cycles of two-headed motors; walks of single motors or cargo particles which consist of directed movements interrupted by random, diffusive motion; cargo transport through tube-like compartments; active diffusion of cargo particles in slab-like compartments; cooperative transport of cargo by several motors which may be uni- or bi-directional; and systems with many interacting motors that exhibit traffic jams, self-organized density and flux patterns, and traffic phase transitions far from equilibrium. It is necessary to understand these traffic phenomena in a quantitative manner in order to construct and optimize biomimetic transport systems based on motors and filaments with many possible applications in bioengineering, pharmacology, and medicine.

  7. Towards synthetic molecular motors: a model elastic-network study

    Science.gov (United States)

    Sarkar, Amartya; Flechsig, Holger; Mikhailov, Alexander S.

    2016-04-01

    Protein molecular motors play a fundamental role in biological cells and development of their synthetic counterparts is a major challenge. Here, we show how a model motor system with the operation mechanism resembling that of muscle myosin can be designed at the concept level, without addressing the implementation aspects. The model is constructed as an elastic network, similar to the coarse-grained descriptions used for real proteins. We show by numerical simulations that the designed synthetic motor can operate as a deterministic or Brownian ratchet and that there is a continuous transition between such two regimes. The motor operation under external load, approaching the stall condition, is also analysed.

  8. Cooperative behavior of molecular motors: Cargo transport and traffic phenomena

    Science.gov (United States)

    Lipowsky, Reinhard; Beeg, Janina; Dimova, Rumiana; Klumpp, Stefan; Müller, Melanie J. I.

    2010-01-01

    All eukaryotic cells including those of our own body contain complex transport systems based on molecular motors which walk along cytoskeletal filaments. These motors are rather small and make discrete mechanical steps with a step size of the order of 10 nm but are able to pull cargo particles over much larger distances, from micrometers up to meters. In vivo, the intracellular cargos include large membrane-bounded organelles, smaller vesicles, a subset of mRNAs, cytoskeletal filaments, and various protein building blocks, which are transported between different cell compartments. This cargo transport is usually performed by teams of motors. If all motors belong to the same molecular species, the cooperative action of the motors leads to uni-directional transport with a strongly increased run length and with a characteristic force dependence of the velocity distributions. If two antagonistic teams of motors pull on the same cargo particle, they perform a stochastic tug-of-war, which is characterized by a subtle force balance between the two motor teams and leads to several distinct patterns of bi-directional transport. So far, all experimental observations on bi-directional transport are consistent with such a tug-of-war. If many motors and/or cargo particles are transported along the filaments, one encounters various traffic phenomena. Depending on their mutual interactions and the compartment geometry, the motors form various spatio-temporal patterns such as traffic jams, and undergo nonequilibrium phase transitions between different patterns of transport.

  9. Ultrasonic depolymerization of aqueous polyvinyl alcohol.

    Science.gov (United States)

    Grönroos, A; Pirkonen, P; Heikkinen, J; Ihalainen, J; Mursunen, H; Sekki, H

    2001-07-01

    Ultrasonication has proved to be a highly advantageous method for depolymerizing macromolecules because it reduces their molecular weight simply by splitting the most susceptible chemical bond without causing any changes in the chemical nature of the polymer. Most of the effects involved in controlling molecular weight can be attributed to the large shear gradients and shock waves generated around collapsing cavitation bubbles. In general, for any polymer degradation process to become acceptable to industry, it is necessary to be able to specify the sonication conditions which lead to a particular relative molar mass distribution. This necessitates the identification of the appropriate irradiation power, temperature, concentration and irradiation time. According to the results of this study the reactors constructed worked well in depolymerization and it was possible to degrade aqueous polyvinyl alcohol (PVA) polymer with ultrasound. The most extensive degradation took place at the lowest frequency used in this study, i.e. 23 kHz, when the input power was above the cavitation threshold and at the lowest test concentration of PVA, i.e. 1% (w/w). Thus this study confirms the general assumption that the shear forces generated by the rapid motion of the solvent following cavitational collapse are responsible for the breakage of the chemical bonds within the polymer. The effect of polymer concentration can be interpreted in terms of the increase in viscosity with concentration, causing the molecules to become less mobile in solution and the velocity gradients around the collapsing bubbles to therefore become smaller.

  10. Control of rotor motion in a light-driven molecular motor : Towards a molecular gearbox

    NARCIS (Netherlands)

    Wiel, Matthijs K.J. ter; Delden, Richard A. van; Meetsma, Auke; Feringa, Bernard

    2005-01-01

    Controlled intramolecular movement and coupling of motor and rotor functions is exerted by this new molecular device. The rate of rotation of the rotor part of the molecule can be adjusted by alteration of the conformation of the motor part of the molecule. For all states of the motor part, differen

  11. Tetrapodal molecular switches and motors: synthesis and photochemistry.

    Science.gov (United States)

    Chen, Kuang-Yen; Wezenberg, Sander J; Carroll, Gregory T; London, Gábor; Kistemaker, Jos C M; Pijper, Thomas C; Feringa, Ben L

    2014-08-01

    The design, synthesis, and dynamic behavior of a series of novel tetrapodal molecular switches and motors containing common functional groups for attachment to various inorganic and organic surfaces are presented. Using a Diels-Alder reaction, an anthracene unit with four functionalized alkyl substituents ("legs") was coupled to maleimide-functionalized molecular switches or motors under ambient conditions. Terminal functional groups at the "legs" include thioacetates and azides, making these switches and motors ideal candidates for attachment to metallic or alkyne-functionalized surfaces. UV/vis absorption spectroscopy shows that the molecular switches and motors retain their ability to undergo reversible photoinduced and/or thermally induced structural changes after attachment to the tetrapodal anthracene.

  12. A Stochastic Markov Model for Coordinated Molecular Motors

    CERN Document Server

    Materassi, Donatello; Salapaka, Murti V

    2010-01-01

    Many cell functions are accomplished thanks to intracellular transport mechanisms of macromolecules along filaments. Molecular motors such as dynein or kinesin are proteins playing a primary role in these processes. The behavior of such proteins is quite well understood when there is only one of them moving a cargo particle. Indeed, numerous in vitro experiments have been performed to derive accurate models for a single molecular motor. However, in vivo macromolecules are often carried by multiple motors. The main focus of this paper is to provide an analysis of the behavior of more molecular motors interacting together in order to improve the understanding of their actual physiological behavior. Previous studies provide analyses based on results obtained from Monte Carlo simulations. Different from these studies, we derive an equipollent probabilistic model to describe the dynamics of multiple proteins coupled together and provide an exact theoretical analysis. We are capable of obtaining the probability den...

  13. How molecular motors work - insights from the molecular machinist's toolbox: the Nobel prize in Chemistry 2016.

    Science.gov (United States)

    Astumian, R D

    2017-02-01

    The Nobel prize in Chemistry for 2016 was awarded to Jean Pierre Sauvage, Sir James Fraser Stoddart, and Bernard (Ben) Feringa for their contributions to the design and synthesis of molecular machines. While this field is still in its infancy, and at present there are no commercial applications, many observers have stressed the tremendous potential of molecular machines to revolutionize technology. However, perhaps the most important result so far accruing from the synthesis of molecular machines is the insight provided into the fundamental mechanisms by which molecular motors, including biological motors such as kinesin, myosin, FoF1 ATPase, and the flagellar motor, function. The ability to "tinker" with separate components of molecular motors allows asking, and answering, specific questions about mechanism, particularly with regard to light driven vs. chemistry driven molecular motors.

  14. Molecular motor transport through hollow nanowires

    DEFF Research Database (Denmark)

    Lard, Mercy; Ten Siethoff, Lasse; Generosi, Johanna;

    2014-01-01

    Biomolecular motors offer self-propelled, directed transport in designed microscale networks and can potentially replace pump-driven nanofluidics. However, in existing systems, transportation is limited to the two-dimensional plane. Here we demonstrate fully one-dimensional (1D) myosin-driven mot......Biomolecular motors offer self-propelled, directed transport in designed microscale networks and can potentially replace pump-driven nanofluidics. However, in existing systems, transportation is limited to the two-dimensional plane. Here we demonstrate fully one-dimensional (1D) myosin......-driven motion of fluorescent probes (actin filaments) through 80 nm wide, Al2O 3 hollow nanowires of micrometer length. The motor-driven transport is orders of magnitude faster than would be possible by passive diffusion. The system represents a necessary element for advanced devices based on gliding assays...

  15. Chemically Optimizing Operational Efficiency of Molecular Rotary Motors

    NARCIS (Netherlands)

    Conyard, Jamie; Cnossen, Arjen; Browne, Wesley R.; Feringa, Ben L.; Meech, Stephen R.

    2014-01-01

    Unidirectional molecular rotary motors that harness photoinduced cis-trans (E-Z) isomerization are promising tools for the conversion of light energy to mechanical motion in nanoscale molecular machines. Considerable progress has been made in optimizing the frequency of ground-state rotation, but le

  16. Synthetic light-activated molecular switches and motors on surfaces

    NARCIS (Netherlands)

    Katsonis, Nathalie; Lubomska, Monika; Pollard, Michael M.; Feringa, Ben L.; Rudolf, Petra

    2007-01-01

    Recent advances in synthetic methods and analysis techniques provide a basis for the construction and characterization of organized arrays of molecular switches and motors on surfaces. Among them, molecular systems that can be controlled by light are particularly promising because of their ease of a

  17. Engineering controllable bidirectional molecular motors based on myosin.

    Science.gov (United States)

    Chen, Lu; Nakamura, Muneaki; Schindler, Tony D; Parker, David; Bryant, Zev

    2012-02-19

    Cytoskeletal motors drive the transport of organelles and molecular cargoes within cells and have potential applications in molecular detection and diagnostic devices. Engineering molecular motors with controllable properties will allow selective perturbation of mechanical processes in living cells and provide optimized device components for tasks such as molecular sorting and directed assembly. Biological motors have previously been modified by introducing activation/deactivation switches that respond to metal ions and other signals. Here, we show that myosin motors can be engineered to reversibly change their direction of motion in response to a calcium signal. Building on previous protein engineering studies and guided by a structural model for the redirected power stroke of myosin VI, we have constructed bidirectional myosins through the rigid recombination of structural modules. The performance of the motors was confirmed using gliding filament assays and single fluorophore tracking. Our strategy, in which external signals trigger changes in the geometry and mechanics of myosin lever arms, should make it possible to achieve spatiotemporal control over a range of motor properties including processivity, stride size and branchpoint turning.

  18. Embedding dual function into molecular motors through collective motion.

    Science.gov (United States)

    Saito, Nen; Kaneko, Kunihiko

    2017-03-10

    Protein motors, such as kinesins and dyneins, bind to a microtubule and travel along it in a specific direction. Previously, it was thought that the directionality for a given motor was constant in the absence of an external force. However, the directionality of the kinesin-5 Cin8 was recently found to change as the number of motors that bind to the same microtubule is increased. Here, we introduce a simple mechanical model of a microtubule-sliding assay in which multiple motors interact with the filament. We show that, due to the collective phenomenon, the directionality of the motor changes (e.g., from minus- to plus- end directionality), depending on the number of motors. This is induced by a large diffusive component in the directional walk and by the subsequent frustrated motor configuration, in which multiple motors pull the filament in opposite directions, similar to a game of tug-of-war. A possible role of the dual-directional motors for the mitotic spindle formation is also discussed. Our framework provides a general mechanism to embed two conflicting tasks into a single molecular machine, which works context-dependently.

  19. Stochastic simulations of cargo transport by processive molecular motors.

    Science.gov (United States)

    Korn, Christian B; Klumpp, Stefan; Lipowsky, Reinhard; Schwarz, Ulrich S

    2009-12-28

    We use stochastic computer simulations to study the transport of a spherical cargo particle along a microtubule-like track on a planar substrate by several kinesin-like processive motors. Our newly developed adhesive motor dynamics algorithm combines the numerical integration of a Langevin equation for the motion of a sphere with kinetic rules for the molecular motors. The Langevin part includes diffusive motion, the action of the pulling motors, and hydrodynamic interactions between sphere and wall. The kinetic rules for the motors include binding to and unbinding from the filament as well as active motor steps. We find that the simulated mean transport length increases exponentially with the number of bound motors, in good agreement with earlier results. The number of motors in binding range to the motor track fluctuates in time with a Poissonian distribution, both for springs and cables being used as models for the linker mechanics. Cooperativity in the sense of equal load sharing only occurs for high values for viscosity and attachment time.

  20. Single rotating molecule-machines: nanovehicles and molecular motors.

    Science.gov (United States)

    Rapenne, Gwénaël; Joachim, Christian

    2014-01-01

    In the last decade many molecular machines with controlled molecular motions have been synthesized. In the present review chapter we will present and discuss our contribution to the field, in particular through some examples of rotating molecular machines that have been designed, synthesized, and studied in our group. After starting by explaining why it is so important to study such machines as single molecules, we will focus on two families of molecular machines, nanovehicles and molecular motors. The first members of the nanovehicle family are molecules with two triptycenes as wheels: the axle and the wheelbarrow. Then come the four-wheel nanocars. Since triptycene wheels are not very mobile on metallic surfaces, alternative wheels with a bowl-shape structure have also been synthesized and studied on surfaces. The molecular motors are built around ruthenium organometallic centers and have a piano-stool geometry with peripheric ferrocenyl groups.

  1. Controlled Rotation and Manipulation of Individual Molecular Motors

    Science.gov (United States)

    Kersell, Heath; Perera, U. G. E.; Ample, F.; Zhang, Y.; Vives, G.; Echeverria, J.; Grisolia, M.; Rapenne, G.; Joachim, C.; Hla, S.-W.

    2015-03-01

    The design of artificial molecular machines often takes inspiration from macroscopic machines, but the parallels between the two are frequently only superficial because many molecular machines are governed by quantum processes. Previously, chemically and light driven rotary molecular motors have been developed. For electrically driven motors, tunneling electrons from the tip of a scanning tunneling microscope (STM) have been used to drive rotation in a simple rotor into a single direction and to move a wheeled molecule across a surface. Here, we show that a single standalone molecular motor adsorbed on a gold surface can be made to rotate in a clockwise or counterclockwise direction [1] by selective inelastic electron tunneling through different sub-units of the motor. Our motor is composed of a tripodal stator for vertical positioning, a five-arm rotator for controlled rotations, and a Ru atomic ball bearing connecting the static and rotational parts. The directional rotation originates from saw-tooth-like rotational potentials, which are determined by the internal molecular structure and are independent of the surface adsorption site. This project is supported by the US DOE, BES grant: DE-FG02-02ER46012.

  2. Energetics and efficiency of a molecular motor model

    DEFF Research Database (Denmark)

    C. Fogedby, Hans; Svane, Axel

    2013-01-01

    The energetics and efficiency of a linear molecular motor model proposed by Mogilner et al. (Phys. Lett. 237, 297 (1998)) is analyzed from an analytical point of view. The model which is based on protein friction with a track is described by coupled Langevin equations for the motion in combination...... with coupled master equations for the ATP hydrolysis. Here the energetics and efficiency of the motor is addressed using a many body scheme with focus on the efficiency at maximum power (EMP). It is found that the EMP is reduced from about 10 pct in a heuristic description of the motor to about 1 per mille...... when incorporating the full motor dynamics, owing to the strong dissipation associated with the motor action....

  3. Biasing the random walk of a molecular motor

    Energy Technology Data Exchange (ETDEWEB)

    Astumian, R Dean [Department of Physics, University of Maine, Orono, ME 04469-5709 (United States)

    2005-11-30

    Biomolecular motors are often described in mechanical terms, with analogy to cars, turbines, judo throws, levers, etc. It is important to remember however that because of their small size, and because of the aqueous environment in which molecular motors move, viscous drag and thermal noise dominate the inertial forces that drive macroscopic machines. The sequence of motions-conformational changes-by which a motor protein moves can best be described as a random walk, with transitions from one state to another occurring by thermal activation over energy barriers. In this paper I will address the question of how this random walk is biased by a non-equilibrium chemical reaction (ATP hydrolysis) so that the motor molecule moves preferentially (with almost unit certainty) in one direction, even when an external force is applied to drive it in the opposite direction. I will also discuss how these 'soft matter' motors can achieve thermodynamic efficiencies of nearly 100%.

  4. Stochastic modeling of cargo transport by teams of molecular motors

    CERN Document Server

    Klein, Sarah; Santen, Ludger

    2014-01-01

    Many different types of cellular cargos are transported bidirectionally along microtubules by teams of molecular motors. The motion of this cargo-motors system has been experimentally characterized in vivo as processive with rather persistent directionality. Different theoretical approaches have been suggested in order to explore the origin of this kind of motion. An effective theoretical approach, introduced by M\\"uller et al., describes the cargo dynamics as a tug-of-war between different kinds of motors. An alternative approach has been suggested recently by Kunwar et al., who considered the coupling between motor and cargo in more detail. Based on this framework we introduce a model considering single motor positions which we propagate in continuous time. Furthermore, we analyze the possible influence of the discrete time update schemes used in previous publications on the system's dynamic.

  5. Traffic of molecular motors: from theory to experiments

    CERN Document Server

    Pierobon, Paolo

    2007-01-01

    Intracellular transport along microtubules or actin filaments, powered by molecular motors such as kinesins, dyneins or myosins, has been recently modeled using one-dimensional driven lattice gases. We discuss some generalizations of these models, that include extended particles and defects. We investigate the feasibility of single molecule experiments aiming to measure the average motor density and to locate the position of traffic jams by mean of a tracer particle. Finally, we comment on preliminary single molecule experiments performed in living cells.

  6. Symposium FF: Molecular Motors, Nanomachines, and Active Nanostructures

    Science.gov (United States)

    2008-06-23

    long and thin tubal heart called “dorsal vessel DV.” Lepidoptera larvae, Ctenoplusia agnata were used in this study. Resulting from culture examinations...motors. It is difficult to systematically vary parameters in studies of biological molecular motors and using a model system can help understand the...were generated by systematically varying the conditions of assembly: (1) mobile linear composites, (2) rotating circular composites, and (3) immobile

  7. Coiled coils and SAH domains in cytoskeletal molecular motors.

    Science.gov (United States)

    Peckham, Michelle

    2011-10-01

    Cytoskeletal motors include myosins, kinesins and dyneins. Myosins move along tracks of actin filaments, whereas kinesins and dyneins move along microtubules. Many of these motors are involved in trafficking cargo in cells. However, myosins are mostly monomeric, whereas kinesins are mostly dimeric, owing to the presence of a coiled coil. Some myosins (myosins 6, 7 and 10) contain an SAH (single α-helical) domain, which was originally thought to be a coiled coil. These myosins are now known to be monomers, not dimers. The differences between SAH domains and coiled coils are described and the potential roles of SAH domains in molecular motors are discussed.

  8. Ultrasound assisted enzymatic depolymerization of aqueous guar gum solution.

    Science.gov (United States)

    Prajapat, Amrutlal L; Subhedar, Preeti B; Gogate, Parag R

    2016-03-01

    The present work investigates the effectiveness of application of low intensity ultrasonic irradiation for the intensification of enzymatic depolymerization of aqueous guar gum solution. The extent of depolymerization of guar gum has been analyzed in terms of intrinsic viscosity reduction. The effect of ultrasonic irradiation on the kinetic and thermodynamic parameters related to the enzyme activity as well as the intrinsic viscosity reduction of guar gum using enzymatic approach has been evaluated. The kinetic rate constant has been found to increase with an increase in the temperature and cellulase loading. It has been observed that application of ultrasound not only enhances the extent of depolymerization but also reduces the time of depolymerization as compared to conventional enzymatic degradation technique. In the presence of cellulase enzyme, the maximum extent of depolymerization of guar gum has been observed at 60 W of ultrasonic rated power and ultrasonic treatment time of 30 min. The effect of ultrasound on the kinetic and thermodynamic parameters as well as the molecular structure of cellulase enzyme was evaluated with the help of the chemical reaction kinetics model and fluorescence spectroscopy. Application of ultrasound resulted in a reduction in the thermodynamic parameters of activation energy (Ea), enthalpy (ΔH), entropy (ΔS) and free energy (ΔG) by 47%, 50%, 65% and 1.97%, respectively. The changes in the chemical structure of guar gum treated using ultrasound assisted enzymatic approach in comparison to the native guar gum were also characterized by FTIR. The results revealed that enzymatic depolymerization of guar gum resulted in a polysaccharide with low degree of polymerization, viscosity and consistency index without any change in the core chemical structure which could make it useful for incorporation in food products.

  9. Characterization of anaerobic consortia coupled lignin depolymerization with biomethane generation.

    Science.gov (United States)

    Wu, Yi-Rui; He, Jianzhong

    2013-07-01

    Two sediment-free microbial consortia (LI3 and LP3) were established to depolymerize lignin under anaerobic conditions. During depolymerizing high molecular weight lignin to low molecular weight molecules, the two cultures produced biomethane up to 151.7 and 113.0 mL g(-1) total lignin. Furthermore, LI3 and LP3 could also utilize the biomass - oil palm empty fruit bunch fiber (OPEFB) to produce 190.6 and 195.6 mL methaneg(-1) total lignin in OPEFB, and at the same time improve the bioavailability of lignocellulosic matters for further enzymatic hydrolysis. The microbial community analysis by denature gradient gel electrophoresis (DGGE) and the high-density 16S rDNA gene microarray (PhyloChip) exhibited that Methanomethylovorans sp. (LI3) and Methanoculleus sp. (LP3) were the main methanogens present, and phylum Firmicutes and Bacteroidetes were mainly involved in the lignin depolymerization. The established microbial consortia with both lignin depolymerization and biomethane production provide profound application on the environmental friendly pretreatment of lignocellulosic materials.

  10. Molecular motor assembly of a biomimetic system

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    @@ Active biological molecules and functional structures can be fabricated into a bio-mimetic system by using molecular assembly method. Such materials can be used for the drug delivery, disease diagnosis and therapy, and new nanodevice construction.

  11. Collective transport of weakly interacting molecular motors with Langmuir kinetics

    Science.gov (United States)

    Chandel, Sameep; Chaudhuri, Abhishek; Muhuri, Sudipto

    2015-04-01

    Filament-based intracellular transport involves the collective action of molecular motor proteins. Experimental evidences suggest that microtubule (MT) filament bound motor proteins such as kinesins weakly interact among themselves during transport and with the surrounding cellular environment. Motivated by these observations we study a driven lattice gas model for collective unidirectional transport of molecular motors on open filament. This model incorporates short-range next-nearest-neighbour (NNN) interactions between the motors and couples the transport process on filament with surrounding cellular environment through adsorption-desorption Langmuir kinetics (LK) of the motors. We analyse this model within the framework of a mean-field (MF) theory in the limit of weak interactions between the motors. We point to the mapping of this model with the non-conserved version of the Katz-Lebowitz-Spohn (KLS) model. The system exhibits rich phase behavior with a variety of inhomogeneous phases including localized shocks in the bulk of the filament. We obtain the steady-state density and current profiles, analyse their variation as a function of the strength of interaction and construct the non-equilibrium MF phase diagram. We compare these MF results with Monte Carlo simulations and find that the MF analysis shows reasonably good agreement with simulation results as long as the motors are weakly interacting. For sufficently strong NNN interaction between the motors, the mean-field results deviate significantly, and for very strong NNN interaction in the absence of LK, the current in the lattice is determined solely by the NNN interaction parameter and it becomes independent of entry and exit rates of motors at the filament boundaries.

  12. "Cargo-mooring" as an operating principle for molecular motors.

    Science.gov (United States)

    Lisowski, Bartosz; Kuśmierz, Łukasz; Żabicki, Michał; Bier, Martin

    2015-06-07

    Navigating through an ever-changing and unsteady environment, and utilizing chemical energy, molecular motors transport the cell׳s crucial components, such as organelles and vesicles filled with neurotransmitter. They generate force and pull cargo, as they literally walk along the polymeric tracks, e.g. microtubules. What we suggest in this paper is that the motor protein is not really pulling its load. The load is subject to diffusion and the motor may be doing little else than rectifying the fluctuations, i.e. ratcheting the load׳s diffusion. Below we present a detailed model to show how such ratcheting can quantitatively account for observed data. The consequence of such a mechanism is the dependence of the transport׳s speed and efficacy not only on the motor, but also on the cargo (especially its size) and on the environment (i.e. its viscosity and structure). Current experimental works rarely provide this type of information for in vivo studies. We suggest that even small differences between assays can impact the outcome. Our results agree with those obtained in wet laboratories and provide novel insight in a molecular motor׳s functioning.

  13. Patterns of molecular motors that guide and sort filaments.

    Science.gov (United States)

    Rupp, Beat; Nédélec, François

    2012-11-21

    Molecular motors can be immobilized to transport filaments and loads that are attached to these filaments inside a nano-device. However, if motors are distributed uniformly over a flat surface, the motility is undirected, and the filaments move equally in all directions. For many applications it is important to control the direction in which the filaments move, and two strategies have been explored to achieve this: applying external forces and confining the filaments inside channels. In this article, we discuss a third strategy in which the topography of the sample remains flat, but the motors are distributed non-uniformly over the surface. Systems of filaments and patterned molecular motors were simulated using a stochastic engine that included Brownian motion and filament bending elasticity. Using an evolutionary algorithm, patterns were optimized for their capacity to precisely control the paths of the filaments. We identified patterns of motors that could either direct the filaments in a particular direction, or separate short and long filaments. These functionalities already exceed what has been achieved with confinement. The patterns are composed of one or two types of motors positioned in lines or along arcs and should be easy to manufacture. Finally, these patterns can be easily combined into larger designs, allowing one to precisely control the motion of microscopic objects inside a device.

  14. Redox Catalysis Facilitates Lignin Depolymerization.

    Science.gov (United States)

    Bosque, Irene; Magallanes, Gabriel; Rigoulet, Mathilde; Kärkäs, Markus D; Stephenson, Corey R J

    2017-06-28

    Lignin is a recalcitrant and underexploited natural feedstock for aromatic commodity chemicals, and its degradation generally requires the use of high temperatures and harsh reaction conditions. Herein we present an ambient temperature one-pot process for the controlled oxidation and depolymerization of this potent resource. Harnessing the potential of electrocatalytic oxidation in conjugation with our photocatalytic cleavage methodology, we have developed an operationally simple procedure for selective fragmentation of β-O-4 bonds with excellent mass recovery, which provides a unique opportunity to expand the existing lignin usage from energy source to commodity chemicals and synthetic building block source.

  15. The depolymerization of sodium alginate by oxidative degradation.

    Science.gov (United States)

    Mao, Shirui; Zhang, Tingting; Sun, Wei; Ren, Xuhong

    2012-01-01

    Alginate has been extensively used as a carrier for macromolecules and as gene delivery vehicle. Both properties are molecular weight (Mw) dependent. Herein, we investigated factors affecting the oxidative depolymerization of alginate. The depolymerization process occurred mainly in the first 1 h. The Mw of the depolymerized alginate was influenced by the reaction temperature. At temperature 20 and 30°C, Mw of the alginate fragment kept constant and further Mw decrease was observed at 40°C. Along with the increase of hydrogen peroxide concentration, the Mw of the fragments decreased gradually. Influence of alginate initial concentration was marginal. A linear decrease of Mw was observed when the system pH was in the range of 5-7, whereas no further change was found when the system pH decreased from 7 to 8. Fourier transformed infrared spectroscopy spectra revealed that degradation undergoes by the breakage of the glycosidic bonds of polymers. No structural change was observed during the depolymerization process by UV spectroscopy. Cloud point pH increase was found for alginate 30 k. In summary, this method is an effective and convenient approach for preparing low Mw oligosaccharides from sodium alginate and may be potentially useful for the drug delivery system design with alginate.

  16. In Control of Motion : From Molecular Switches to Molecular Motors

    NARCIS (Netherlands)

    Feringa, Bernard

    2001-01-01

    The design of molecular systems in which controlled linear and rotary motion can be achieved under the influence of an external signal is a major endeavor toward future nanoscale machinery. In this Account we describe the development of molecular switches and the discoveries that culminated in the

  17. Rotation of artificial rotor axles in rotary molecular motors.

    Science.gov (United States)

    Baba, Mihori; Iwamoto, Kousuke; Iino, Ryota; Ueno, Hiroshi; Hara, Mayu; Nakanishi, Atsuko; Kishikawa, Jun-Ichi; Noji, Hiroyuki; Yokoyama, Ken

    2016-10-04

    F1- and V1-ATPase are rotary molecular motors that convert chemical energy released upon ATP hydrolysis into torque to rotate a central rotor axle against the surrounding catalytic stator cylinder with high efficiency. How conformational change occurring in the stator is coupled to the rotary motion of the axle is the key unknown in the mechanism of rotary motors. Here, we generated chimeric motor proteins by inserting an exogenous rod protein, FliJ, into the stator ring of F1 or of V1 and tested the rotation properties of these chimeric motors. Both motors showed unidirectional and continuous rotation, despite no obvious homology in amino acid sequence between FliJ and the intrinsic rotor subunit of F1 or V1 These results showed that any residue-specific interactions between the stator and rotor are not a prerequisite for unidirectional rotation of both F1 and V1 The torque of chimeric motors estimated from viscous friction of the rotation probe against medium revealed that whereas the F1-FliJ chimera generates only 10% of WT F1, the V1-FliJ chimera generates torque comparable to that of V1 with the native axle protein that is structurally more similar to FliJ than the native rotor of F1 This suggests that the gross structural mismatch hinders smooth rotation of FliJ accompanied with the stator ring of F1.

  18. Myosin-I molecular motors at a glance.

    Science.gov (United States)

    McIntosh, Betsy B; Ostap, E Michael

    2016-07-15

    Myosin-I molecular motors are proposed to play various cellular roles related to membrane dynamics and trafficking. In this Cell Science at a Glance article and the accompanying poster, we review and illustrate the proposed cellular functions of metazoan myosin-I molecular motors by examining the structural, biochemical, mechanical and cell biological evidence for their proposed molecular roles. We highlight evidence for the roles of myosin-I isoforms in regulating membrane tension and actin architecture, powering plasma membrane and organelle deformation, participating in membrane trafficking, and functioning as a tension-sensitive dock or tether. Collectively, myosin-I motors have been implicated in increasingly complex cellular phenomena, yet how a single isoform accomplishes multiple types of molecular functions is still an active area of investigation. To fully understand the underlying physiology, it is now essential to piece together different approaches of biological investigation. This article will appeal to investigators who study immunology, metabolic diseases, endosomal trafficking, cell motility, cancer and kidney disease, and to those who are interested in how cellular membranes are coupled to the underlying actin cytoskeleton in a variety of different applications.

  19. [Depolymerization of chitosan by chinolytic complex from Bacillus sp. 739].

    Science.gov (United States)

    Il'ina, A V; Varlamov, V P; Melent'ev, A I; Aktuganov, G E

    2001-01-01

    Low-molecular-weight (3-6 kDa) water-soluble chitosan was obtained by enzymatic depolymerization. Hydrolysis of crab chitosan was induced by O-glycoside hydrolase (EC 3.2.1), an extracellular chitinolytic complex from Bacillus sp. 739. The optimum conditions for hydrolysis were found (sodium-acetate buffer, pH 5.2; 55 degrees C; an enzyme/substrate ratio 4 U/g chitosan; 1 h).

  20. Interferometric Scattering Microscopy for the Study of Molecular Motors.

    Science.gov (United States)

    Andrecka, J; Takagi, Y; Mickolajczyk, K J; Lippert, L G; Sellers, J R; Hancock, W O; Goldman, Y E; Kukura, P

    2016-01-01

    Our understanding of molecular motor function has been greatly improved by the development of imaging modalities, which enable real-time observation of their motion at the single-molecule level. Here, we describe the use of a new method, interferometric scattering microscopy, for the investigation of motor protein dynamics by attaching and tracking the motion of metallic nanoparticle labels as small as 20nm diameter. Using myosin-5, kinesin-1, and dynein as examples, we describe the basic assays, labeling strategies, and principles of data analysis. Our approach is relevant not only for motor protein dynamics but also provides a general tool for single-particle tracking with high spatiotemporal precision, which overcomes the limitations of single-molecule fluorescence methods.

  1. Universal bound on the efficiency of molecular motors

    Science.gov (United States)

    Pietzonka, Patrick; Barato, Andre C.; Seifert, Udo

    2016-12-01

    The thermodynamic uncertainty relation provides an inequality relating any mean current, the associated dispersion and the entropy production rate for arbitrary non-equilibrium steady states. Applying it here to a general model of a molecular motor running against an external force or torque, we show that the thermodynamic efficiency of such motors is universally bounded by an expression involving only experimentally accessible quantities. For motors pulling cargo through a viscous fluid, a universal bound for the corresponding Stokes efficiency follows as a variant. A similar result holds if mechanical force is used to synthesize molecules of high chemical potential. Crucially, no knowledge of the detailed underlying mechano-chemical mechanism is required for applying these bounds.

  2. 分子马达与布朗马达%MOLECULAR MOTORS AND BROWNIAN MOTORS

    Institute of Scientific and Technical Information of China (English)

    卓益忠; 赵同军; 展永

    2000-01-01

    综述了有关分子马达,主要是肌球蛋白马达和动 蛋白马达的实验研究进展情况,并对理论模型,特别是近年来广为流行的布朗马达模型作了 介绍和评论.最后展望了这一领域的发展前景及其所面临的挑战性问题.%Experimental studies on molecular motors,in parti cular myosin and kinesin motors are reviewed.Theoretical models,such as the Brow nian motor models are described and evaluated.Finally,the prospects and challen ges in this field are discussed.

  3. Advanced molecular devices based on light-driven molecular motors

    NARCIS (Netherlands)

    Chen, Jiawen

    2015-01-01

    Nature has provided a large collection of molecular machines and devices that are among the most amazing nanostructures on this planet. These machines are able to operate complex biological processes which are of great importance in our organisms. Inspired by these natural devices, artificial molecu

  4. Advanced molecular devices based on light-driven molecular motors

    NARCIS (Netherlands)

    Chen, Jiawen

    2015-01-01

    Nature has provided a large collection of molecular machines and devices that are among the most amazing nanostructures on this planet. These machines are able to operate complex biological processes which are of great importance in our organisms. Inspired by these natural devices, artificial

  5. Master Equation Approach to Molecular Motor's Directed Motion

    Institute of Scientific and Technical Information of China (English)

    FENG Juan; ZHUO Yi-Zhong

    2005-01-01

    @@ The master equation approach based on the periodic one-dimensional three-state hopping model is developed to study the molecular motor's directed motion. An explicit solution Px ( t ) is obtained for the probability distribution as a function of the time for any initial distribution Px(0) with all the transients included. We introduce dj to represent the sub-step lengths, which can reflect how the external load affects the individual rate via load distribution factors θ+j and θ-j. A wide variety of molecular motor behaviour under external load f can readily be obtained by the unequal-distance transition model with load-dependent transition rates. By comparison with the experiments, namely of the drift velocity v and the randomness parameter r versus adenosine triphosphate concentration and external load f, it is shown that the model presented here can rather satisfactorily explain the available data.

  6. Two-dimensional model of elastically coupled molecular motors

    Institute of Scientific and Technical Information of China (English)

    Zhang Hong-Wei; Wen Shu-Tang; Chen Gai-Rong; Li Yu-Xiao; Cao Zhong-Xing; Li Wei

    2012-01-01

    A flashing ratchet model of a two-headed molecular motor in a two-dimensional potential is proposed to simulate the hand-over-hand motion of kinesins.Extensive Langevin simulations of the model are performed.We discuss the dependences of motion and efficiency on the model parameters,including the external force and the temperature.A good qualitative agreement with the expected behavior is observed.

  7. Chemically optimizing operational efficiency of molecular rotary motors.

    Science.gov (United States)

    Conyard, Jamie; Cnossen, Arjen; Browne, Wesley R; Feringa, Ben L; Meech, Stephen R

    2014-07-09

    Unidirectional molecular rotary motors that harness photoinduced cis-trans (E-Z) isomerization are promising tools for the conversion of light energy to mechanical motion in nanoscale molecular machines. Considerable progress has been made in optimizing the frequency of ground-state rotation, but less attention has been focused on excited-state processes. Here the excited-state dynamics of a molecular motor with electron donor and acceptor substituents located to modify the excited-state reaction coordinate, without altering its stereochemistry, are studied. The substituents are shown to modify the photochemical yield of the isomerization without altering the motor frequency. By combining 50 fs resolution time-resolved fluorescence with ultrafast transient absorption spectroscopy the underlying excited-state dynamics are characterized. The Franck-Condon excited state relaxes in a few hundred femtoseconds to populate a lower energy dark state by a pathway that utilizes a volume conserving structural change. This is assigned to pyramidalization at a carbon atom of the isomerizing bridging double bond. The structure and energy of the dark state thus reached are a function of the substituent, with electron-withdrawing groups yielding a lower energy longer lived dark state. The dark state is coupled to the Franck-Condon state and decays on a picosecond time scale via a coordinate that is sensitive to solvent friction, such as rotation about the bridging bond. Neither subpicosecond nor picosecond dynamics are sensitive to solvent polarity, suggesting that intramolecular charge transfer and solvation are not key driving forces for the rate of the reaction. Instead steric factors and medium friction determine the reaction pathway, with the sterically remote substitution primarily influencing the energetics. Thus, these data indicate a chemical method of optimizing the efficiency of operation of these molecular motors without modifying their overall rotational frequency.

  8. Stokes Efficiency of Molecular Motor-Cargo Systems

    Science.gov (United States)

    2008-01-01

    2655, 1994. 11 F. Reif , Fundamentals of Statistical and Thermal Physics, McGraw-Hill, New York, NY, USA, 1985. 12 H. Kleinert, Path Integrals in...Quantum Mechanics , Statistics , Polymer Physics, and Financial Markets, World Scientific, River Edge, NJ, USA, 3rd edition, 2004. 13 A. Einstein...Efficiency of Molecular Motor-Cargo Systems Hongyun Wang1 and Hong Zhou2 1Department of Applied Mathematics and Statistics , University of California

  9. Periodic thermodynamics of laser-driven molecular motor

    Institute of Scientific and Technical Information of China (English)

    Li Dan; Zheng Wen-Wei; Wang Zhi-Song

    2008-01-01

    Operation of a laser-driven nano-motor inevitably generates a non-trivial amount of heat,which can possibly lead to instability or even hinder the motor's continual running.This work quantitatively examines the overheating problem for a recently proposed laser-operated molecular locomotive.We present a single-molecule cooling theory,in which molecular details of the locomotive system are explicitly treated.This theory is able to quantitatively predict cooling efficiency for various candidates of molecular systems for the locomotive,and also suggests concrete strategies for improving the locomotive's cooling.It is found that water environment is able to cool the hot locomotive down to room temperature within 100 picoseconds after photon absorption.This cooling time is a few orders of magnitude shorter than the typical time for laser operation,effectively preventing any overheating for the nano-locomotive.However,when the cooling is less effective in non-aqueous environment,residual heat may build up.A continuous running of the motor will then lead to a periodic thermodynamics,which is a common character of many laser-operated nano-devices.

  10. Mechanical transduction mechanisms of RecA-like molecular motors.

    Science.gov (United States)

    Liao, Jung-Chi

    2011-12-01

    A majority of ATP-dependent molecular motors are RecA-like proteins, performing diverse functions in biology. These RecA-like molecular motors consist of a highly conserved core containing the ATP-binding site. Here I examined how ATP binding within this core is coupled to the conformational changes of different RecA-like molecular motors. Conserved hydrogen bond networks and conformational changes revealed two major mechanical transduction mechanisms: (1) intra-domain conformational changes and (2) inter-domain conformational changes. The intra-domain mechanism has a significant hydrogen bond rearrangement within the domain containing the P-loop, causing relative motion between two parts of the protein. The inter-domain mechanism exhibits little conformational change in the P-loop domain. Instead, the major conformational change is observed between the P-loop domain and an adjacent domain or subunit containing the arginine finger. These differences in the mechanical transduction mechanisms may link to the underlying energy surface governing a Brownian ratchet or a power stroke.

  11. Operating principles of rotary molecular motors: differences between F1 and V1 motors.

    Science.gov (United States)

    Yamato, Ichiro; Kakinuma, Yoshimi; Murata, Takeshi

    2016-01-01

    Among the many types of bioenergy-transducing machineries, F- and V-ATPases are unique bio- and nano-molecular rotary motors. The rotational catalysis of F1-ATPase has been investigated in detail, and molecular mechanisms have been proposed based on the crystal structures of the complex and on extensive single-molecule rotational observations. Recently, we obtained crystal structures of bacterial V1-ATPase (A3B3 and A3B3DF complexes) in the presence and absence of nucleotides. Based on these new structures, we present a novel model for the rotational catalysis mechanism of V1-ATPase, which is different from that of F1-ATPases.

  12. Ultrafast Excited State Dynamics in Molecular Motors: Coupling of Motor Length to Medium Viscosity.

    Science.gov (United States)

    Conyard, Jamie; Stacko, Peter; Chen, Jiawen; McDonagh, Sophie; Hall, Christopher R; Laptenok, Sergey P; Browne, Wesley R; Feringa, Ben L; Meech, Stephen R

    2017-03-07

    Photochemically driven molecular motors convert the energy of incident radiation to intramolecular rotational motion. The motor molecules considered here execute four step unidirectional rotational motion. This comprises a pair of successive light induced isomerizations to a metastable state followed by thermal helix inversions. The internal rotation of a large molecular unit required in these steps is expected to be sensitive to both the viscosity of the medium and the volume of the rotating unit. In this work, we describe a study of motor motion in both ground and excited states as a function of the size of the rotating units. The excited state decay is ultrafast, highly non-single exponential, and is best described by a sum of three exponential relaxation components. The average excited state decay time observed for a series of motors with substituents of increasing volume was determined. While substitution does affect the lifetime, the size of the substituent has only a minor effect. The solvent polarity dependence is also slight, but there is a significant solvent viscosity effect. Increasing the viscosity has no effect on the fastest of the three decay components, but it does lengthen the two slower decay times, consistent with them being associated with motion along an intramolecular coordinate displacing a large solvent volume. However, these slower relaxation times are again not a function of the size of the substituent. We conclude that excited state decay arises from motion along a coordinate which does not necessarily require complete rotation of the substituents through the solvent, but is instead more localized in the core structure of the motor. The decay of the metastable state to the ground state through a helix inversion occurs 14 orders of magnitude more slowly than the excited state decay, and was measured as a function of substituent size, solvent viscosity and temperature. In this case neither substituent size nor solvent viscosity influences

  13. Microtubules and associated molecular motors in Neurospora crassa.

    Science.gov (United States)

    Mouriño-Pérez, Rosa Reyna; Riquelme, Meritxell; Callejas-Negrete, Olga Alicia; Galván-Mendoza, José Iván

    2016-01-01

    The cytoskeleton provides structure, shape and movement to various cells. Microtubules (MTs) are tubular structures made of α and β-tubulin heterodimers organized in 13 protofilaments, forming a hollow cylinder. A vast group of MT-associated proteins determines the function, behavior and interaction of the MTs with other cellular components. Among these proteins, molecular motors such as the dynein-dynactin complex and kinesin superfamily play roles in MT organization and organelle transport. This article focuses on the MT cytoskeleton and associated molecular motors in the filamentous fungus Neurospora crassa In addition to reviewing current available information for this fungus and contrasting it with knowledge of other fungal species, we present new experimental results that support the role of dynein, dynactin and conventional kinesin in MT organization, dynamics and transport of subcellular structures (nuclei and secretory vesicles). In wild type hyphae of N. crassa, cytoplasmic MTs are arranged longitudinally along hyphae and display a helical curvature. They interlace with one another to form a network throughout the cytoplasm. N. crassa dynein and dynactin mutants have a scant and disorganized MT cytoskeleton, an erratic and reduced Spitzenkörper (Spk) and distorted hyphal morphology. In contrast, hyphae of mutants with defective conventional kinesin exhibit only minor disruptions in MT and Spk organization. Although nuclear positioning is affected in all mutants, the MT-associated motor proteins are not major contributors to nuclear movement during hyphal growth. Cytoplasmic bulk flow is the vehicle for nuclear displacement in growing hyphal regions of N. crassa Motors are involved in nuclei saltatory movements in both retrograde or anterograde direction. In the dynein and kinesin mutants, micro and macrovesicles can reach the Spk, although growth is slightly impaired and the Spk displays an erratic path. Hyphal growth requires MTs, and their associated

  14. Stochastic mechano-chemical kinetics of molecular motors: a multidisciplinary enterprise from a physicist's perspective

    CERN Document Server

    Chowdhury, Debashish

    2013-01-01

    A molecular motor is made of either a single macromolecule or a macromolecular complex. Just like their macroscopic counterparts, molecular motors "transduce" input energy into mechanical work. All the nano-motors considered here operate under isothermal conditions far from equilibrium. Moreover, one of the possible mechanisms of energy transduction, called Brownian ratchet, does not even have any macroscopic counterpart. But, molecular motor is not synonymous with Brownian ratchet; a large number of molecular motors execute a noisy power stroke, rather than operating as Brownian ratchet. We review not only the structural design and stochastic kinetics of individual single motors, but also their coordination, cooperation and competition as well as the assembly of multi-module motors in various intracellular kinetic processes. Although all the motors considered here execute mechanical movements, efficiency and power output are not necessarily good measures of performance of some motors. Among the intracellular...

  15. Formic-acid-induced depolymerization of oxidized lignin to aromatics.

    Science.gov (United States)

    Rahimi, Alireza; Ulbrich, Arne; Coon, Joshua J; Stahl, Shannon S

    2014-11-13

    Lignin is a heterogeneous aromatic biopolymer that accounts for nearly 30% of the organic carbon on Earth and is one of the few renewable sources of aromatic chemicals. As the most recalcitrant of the three components of lignocellulosic biomass (cellulose, hemicellulose and lignin), lignin has been treated as a waste product in the pulp and paper industry, where it is burned to supply energy and recover pulping chemicals in the operation of paper mills. Extraction of higher value from lignin is increasingly recognized as being crucial to the economic viability of integrated biorefineries. Depolymerization is an important starting point for many lignin valorization strategies, because it could generate valuable aromatic chemicals and/or provide a source of low-molecular-mass feedstocks suitable for downstream processing. Commercial precedents show that certain types of lignin (lignosulphonates) may be converted into vanillin and other marketable products, but new technologies are needed to enhance the lignin value chain. The complex, irregular structure of lignin complicates chemical conversion efforts, and known depolymerization methods typically afford ill-defined products in low yields (that is, less than 10-20wt%). Here we describe a method for the depolymerization of oxidized lignin under mild conditions in aqueous formic acid that results in more than 60wt% yield of low-molecular-mass aromatics. We present the discovery of this facile C-O cleavage method, its application to aspen lignin depolymerization, and mechanistic insights into the reaction. The broader implications of these results for lignin conversion and biomass refining are also considered.

  16. Formic-acid-induced depolymerization of oxidized lignin to aromatics

    Science.gov (United States)

    Rahimi, Alireza; Ulbrich, Arne; Coon, Joshua J.; Stahl, Shannon S.

    2014-11-01

    Lignin is a heterogeneous aromatic biopolymer that accounts for nearly 30% of the organic carbon on Earth and is one of the few renewable sources of aromatic chemicals. As the most recalcitrant of the three components of lignocellulosic biomass (cellulose, hemicellulose and lignin), lignin has been treated as a waste product in the pulp and paper industry, where it is burned to supply energy and recover pulping chemicals in the operation of paper mills. Extraction of higher value from lignin is increasingly recognized as being crucial to the economic viability of integrated biorefineries. Depolymerization is an important starting point for many lignin valorization strategies, because it could generate valuable aromatic chemicals and/or provide a source of low-molecular-mass feedstocks suitable for downstream processing. Commercial precedents show that certain types of lignin (lignosulphonates) may be converted into vanillin and other marketable products, but new technologies are needed to enhance the lignin value chain. The complex, irregular structure of lignin complicates chemical conversion efforts, and known depolymerization methods typically afford ill-defined products in low yields (that is, less than 10-20wt%). Here we describe a method for the depolymerization of oxidized lignin under mild conditions in aqueous formic acid that results in more than 60wt% yield of low-molecular-mass aromatics. We present the discovery of this facile C-O cleavage method, its application to aspen lignin depolymerization, and mechanistic insights into the reaction. The broader implications of these results for lignin conversion and biomass refining are also considered.

  17. Traffic jams and shocks of molecular motors inside cellular protrusions.

    Science.gov (United States)

    Pinkoviezky, I; Gov, N S

    2014-05-01

    Molecular motors are involved in key transport processes inside actin-based cellular protrusions. The motors carry cargo proteins to the protrusion tip which participate in regulating the actin polymerization and play a key role in facilitating the growth and formation of such protrusions. It is observed that the motors accumulate at the tips of cellular protrusions and form aggregates that are found to drift towards the protrusion base at the rate of actin treadmilling. We present a one-dimensional driven lattice model, where motors become inactive after delivering their cargo at the tip, or by loosing their cargo to a cargoless neighbor. The results suggest that the experimental observations may be explained by the formation of traffic jams that form at the tip. The model is solved using a novel application of mean-field and shock analysis. We find a new class of shocks that undergo intermittent collapses. Extensions with attachment and detachment events and relevance to experiments are briefly described.

  18. Traffic Jams and Shocks of Molecular Motors inside Cellular Protrusions

    CERN Document Server

    Pinkoviezky, Itai

    2013-01-01

    Molecular motors are involved in key transport processes inside actin-based cellular protrusions. The motors carry cargo proteins to the protrusion tip which participate in regulating the actin polymerization, and play a key role in facilitating the growth and formation of such protrusions. It is observed that the motors accumulate at the tips of cellular protrusions, and in addition form aggregates that are found to drift towards the protrusion base at the rate of actin treadmilling. We present a one-dimensional driven lattice model, where motors become inactive after delivering their cargo at the tip, or by loosing their cargo to a cargo-less neighbor. The results suggest that the experimental observations may be explained by the formation of traffic jams that form at the tip. The model is solved using a novel application of mean-field and shock analysis. We find a new class of shocks that undergo intermittent collapses, and on average do not obey the Rankine-Hugoniot relation.

  19. Facile assembly of light-driven molecular motors onto a solid surface.

    Science.gov (United States)

    Chen, Jiawen; Chen, Kuang-Yen; Carroll, Gregory T; Feringa, Ben L

    2014-10-28

    In order to improve the rotary motion of surface assembled light-driven molecular motors, tetra-acid-functionalized motors were bound to an amine-coated quartz surface without prior activation of the acid groups. In contrast to earlier bipodal motors, the tetravalent motor showed no significant reduction in the rotation speed when attached to a surface.

  20. Facile assembly of light-driven molecular motors onto a solid surface

    NARCIS (Netherlands)

    Chen, Jiawen; Chen, Kuang-Yen; Carroll, Gregory T; Feringa, Ben L

    2014-01-01

    In order to improve the rotary motion of surface assembled light-driven molecular motors, tetra-acid-functionalized motors were bound to an amine-coated quartz surface without prior activation of the acid groups. In contrast to earlier bipodal motors, the tetravalent motor showed no significant redu

  1. Statistical determination of the step size of molecular motors

    Energy Technology Data Exchange (ETDEWEB)

    Neuman, K C; Saleh, O A; Lionnet, T; Lia, G; Allemand, J-F; Bensimon, D; Croquette, V [Laboratoire de Physique Statistique, Ecole Normale Superieure, 24 rue Lhomond, Paris 75005 (France)

    2005-11-30

    Molecular motors are enzymatic proteins that couple the consumption of chemical energy to mechanical displacement. In order to elucidate the translocation mechanisms of these enzymes, it is of fundamental importance to measure the physical step size. The step size can, in certain instances, be directly measured with single-molecule techniques; however, in the majority of cases individual steps are masked by noise. The step size can nevertheless be obtained from noisy single-molecule records through statistical methods. This analysis is analogous to determining the charge of the electron from current shot noise. We review methods for obtaining the step size based on analysing, in both the time and frequency domains, the variance in position from noisy single-molecule records of motor displacement. Additionally, we demonstrate how similar methods may be applied to measure the step size in bulk kinetic experiments.

  2. The role of molecular motor HKLP2 in spindle assembly

    OpenAIRE

    Vanneste, David

    2010-01-01

    Durante la división celular, tiene lugar el ensamblaje de la maquinaria macromolecular encargada de segregar los dos conjuntos de cromosomas en las dos células hijas. Esta maquinaria, el huso mitótico, es una matriz bipolar compuesta de microtúbulos y de proteínas que controlan la dinámica y la organización. Las quinesinas son motores moleculares que pueden ejercer fuerzas sobre los microtúbulos y organizarlos en el espacio para dar lugar al huso bipolar. Este estudio aporta evidencias del...

  3. Actin-based motility propelled by molecular motors

    Science.gov (United States)

    Upadyayula, Sai Pramod; Rangarajan, Murali

    2012-09-01

    Actin-based motility of Listeria monocytogenes propelled by filament end-tracking molecular motors has been simulated. Such systems may act as potential nanoscale actuators and shuttles useful in sorting and sensing biomolecules. Filaments are modeled as three-dimensional elastic springs distributed on one end of the capsule and persistently attached to the motile bacterial surface through an end-tracking motor complex. Filament distribution is random, and monomer concentration decreases linearly as a function of position on the bacterial surface. Filament growth rate increases with monomer concentration but decreases with the extent of compression. The growing filaments exert push-pull forces on the bacterial surface. In addition to forces, torques arise due to two factors—distribution of motors on the bacterial surface, and coupling of torsion upon growth due to the right-handed helicity of F-actin—causing the motile object to undergo simultaneous translation and rotation. The trajectory of the bacterium is simulated by performing a force and torque balance on the bacterium. All simulations use a fixed value of torsion. Simulations show strong alignment of the filaments and the long axis of the bacterium along the direction of motion. In the absence of torsion, the bacterial surface essentially moves along the direction of the long axis. When a small amount of the torsion is applied to the bacterial surface, the bacterium is seen to move in right-handed helical trajectories, consistent with experimental observations.

  4. Mesoscopic non-equilibrium thermodynamic analysis of molecular motors.

    Science.gov (United States)

    Kjelstrup, S; Rubi, J M; Pagonabarraga, I; Bedeaux, D

    2013-11-28

    We show that the kinetics of a molecular motor fueled by ATP and operating between a deactivated and an activated state can be derived from the principles of non-equilibrium thermodynamics applied to the mesoscopic domain. The activation by ATP, the possible slip of the motor, as well as the forward stepping carrying a load are viewed as slow diffusion along a reaction coordinate. Local equilibrium is assumed in the reaction coordinate spaces, making it possible to derive the non-equilibrium thermodynamic description. Using this scheme, we find expressions for the velocity of the motor, in terms of the driving force along the spacial coordinate, and for the chemical reaction that brings about activation, in terms of the chemical potentials of the reactants and products which maintain the cycle. The second law efficiency is defined, and the velocity corresponding to maximum power is obtained for myosin movement on actin. Experimental results fitting with the description are reviewed, giving a maximum efficiency of 0.45 at a myosin headgroup velocity of 5 × 10(-7) m s(-1). The formalism allows the introduction and test of meso-level models, which may be needed to explain experiments.

  5. Coexistence and efficiency of normal and anomalous transport by molecular motors in living cells

    CERN Document Server

    Goychuk, Igor; Metzler, R

    2013-01-01

    Recent experiments reveal both passive subdiffusion of various nanoparticles and anomalous active transport of such particles by molecular motors in the molecularly crowded environment of living biological cells. Passive and active microrheology reveals that the origin of this anomalous dynamics is due to the viscoelasticity of the intracellular fluid. How do molecular motors perform in such a highly viscous, dissipative environment? Can we explain the observed co-existence of the anomalous transport of relatively large particles of 100 to 500 nm in size by kinesin motors with the normal transport of smaller particles by the same molecular motors? What is the efficiency of molecular motors in the anomalous transport regime? Here we answer these seemingly conflicting questions and consistently explain experimental findings in a generalization of the well-known continuous diffusion model for molecular motors with two conformational states in which viscoelastic effects are included.

  6. Stochastic thermodynamics of single enzymes and molecular motors.

    Science.gov (United States)

    Seifert, U

    2011-03-01

    For a single enzyme or molecular motor operating in an aqueous solution of non-equilibrated solute concentrations, a thermodynamic description is developed on the level of an individual trajectory of transitions between states. The concept of internal energy, intrinsic entropy and free energy for states follows from a microscopic description using one assumption on time scale separation. A first-law energy balance then allows the unique identification of the heat dissipated in one transition. Consistency with the second law on the ensemble level enforces both stochastic entropy as third contribution to the entropy change involved in one transition and the local detailed balance condition for the ratio between forward and backward rates for any transition. These results follow without assuming weak coupling between the enzyme and the solutes, ideal solution behavior or mass action law kinetics. The present approach highlights both the crucial role of the intrinsic entropy of each state and the physically questionable role of chemiostats for deriving the first law for molecular motors subject to an external force under realistic conditions.

  7. Influence of Random Potentials on the Current of the Molecular Motor Model

    Institute of Scientific and Technical Information of China (English)

    贾亚; 李家荣

    2001-01-01

    The current of the molecular motor model disturbed by random potentials, which involve the dichotomous and Ornstein-Uhlenbeck potentials, is studied using a finite-space correlation function. It is found that: (i) the amplitude and the correlation length of random potentials play opposing roles in the transport of the molecular motor model; (ii) a random potential with small amplitude and large correlation length is very useful in the molecular motor system.

  8. Traffic phenomena in biology: from molecular motors to organisms

    CERN Document Server

    Chowdhury, D; Nishinari, K; Chowdhury, Debashish; Schadschneider, Andreas; Nishinari, Katsuhiro

    2007-01-01

    Traffic-like collective movements are observed at almost all levels of biological systems. Molecular motor proteins like, for example, kinesin and dynein, which are the vehicles of almost all intra-cellular transport in eukayotic cells, sometimes encounter traffic jam that manifests as a disease of the organism. Similarly, traffic jam of collagenase MMP-1, which moves on the collagen fibrils of the extracellular matrix of vertebrates, has also been observed in recent experiments. Traffic-like movements of social insects like ants and termites on trails are, perhaps, more familiar in our everyday life. Experimental, theoretical and computational investigations in the last few years have led to a deeper understanding of the generic or common physical principles involved in these phenomena. In particular, some of the methods of non-equilibrium statistical mechanics, pioneered almost a hundred years ago by Einstein, Langevin and others, turned out to be powerful theoretical tools for quantitative analysis of mode...

  9. Control of Surface Wettability Using Tripodal Light-Activated Molecular Motors

    NARCIS (Netherlands)

    Chen, Kuang-Yen; Ivashenko, Oleksii; Carroll, Gregory T.; Robertus, Jort; Kistemaker, Jos C. M.; London, Gabor; Browne, Wesley R.; Rudolf, Petra; Feringa, Ben L.

    2014-01-01

    Monolayers of fluorinated light-driven molecular motors were synthesized and immobilized on gold films in an altitudinal orientation via tripodal stators. In this design the fimctionalized molecular motors are not interfering and preserve their rotary function on gold. The wettability of the

  10. Reprogrammable Assembly of Molecular Motor on Solid Surfaces via Dynamic Bonds.

    Science.gov (United States)

    Yu, Li; Sun, Jian; Wang, Qian; Guan, Yan; Zhou, Le; Zhang, Jingxuan; Zhang, Lanying; Yang, Huai

    2017-06-01

    Controllable assembly of molecular motors on solid surfaces is a fundamental issue for providing them to perform physical tasks. However, it can hardly be achieved by most previous methods due to their inherent limitations. Here, a general strategy is designed for the reprogrammable assembly of molecular motors on solid surfaces based on dynamic bonds. In this method, molecular motors with disulfide bonds can be remotely, reversibly, and precisely attached to solid surfaces with disulfide bonds, regardless of their chemical composition and microstructure. More importantly, it not only allows encoding geometric information referring to a pattern of molecular motors, but also enables erasing and re-encoding of geometric information via hemolytic photocleavage and recombination of disulfide bonds. Thus, solid surfaces can be regarded as "computer hardware", where molecular motors can be reformatted and reprogramed as geometric information. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. External forces influence the elastic coupling effects during cargo transport by molecular motors.

    Science.gov (United States)

    Berger, Florian; Keller, Corina; Klumpp, Stefan; Lipowsky, Reinhard

    2015-02-01

    Cellular transport is achieved by the cooperative action of molecular motors which are elastically linked to a common cargo. When the motors pull on the cargo at the same time, they experience fluctuating elastic strain forces induced by the stepping of the other motors. These elastic coupling forces can influence the motors' stepping and unbinding behavior and thereby the ability to transport cargos. Based on a generic single motor description, we introduce a framework that explains the response of two identical molecular motors to a constant external force. In particular, we relate the single motor parameters, the coupling strength and the external load force to the dynamics of the motor pair. We derive four distinct transport regimes and determine how the crossover lines between the regimes depend on the load force. Our description of the overall cargo dynamics takes into account relaxational displacements of the cargo caused by the unbinding of one motor. For large forces and weak elastic coupling these back-shifts dominate the displacements. To develop an intuitive understanding about motor cooperativity during cargo transport, we introduce a time scale for load sharing. This time scale allows us to predict how the regulation of single motor parameters influences the cooperativity. As an example, we show that up-regulating the single motor processivity enhances load sharing of the motor pair.

  12. Kinetics and Thermodynamics of Ultrasound-Assisted Depolymerization of κ-Carrageenan

    Directory of Open Access Journals (Sweden)

    Ratnawati Ratnawati

    2016-03-01

    Full Text Available The ultrasound-assisted depolymerization of κ-carrageenan has been studied at various temperatures and times. The κ-carrageenan with initial molecular weight of 545 kDa was dispersed in water to form a 5 g/L solution, which was then depolymerized in an ultrasound device at various temperatures and times. The viscosity of the solution was measured using Brookfield viscometer, which was then used to find the number-average molecular weight by Mark-Houwink equation. To obtain the kinetics of κ-carrageenan depolymerization, the number-average molecular weight data was treated using midpoint-chain scission kinetics model. The pre-exponential factor and activation energies for the reaction are 2.683×10-7 mol g-1 min-1 and 6.43 kJ mol-1, respectively. The limiting molecular weight varies from 160 kDa to 240 kDa, and it is linearly correlated to temperature. The results are compared to the result of thermal depolymerization by calculating the half life. It is revealed that ultrasound assisted depolymerization of κ-carrageenan is faster than thermal depolymerization at temperatures below 72.2°C. Compared to thermal depolymerization, the ultrasound-assisted process has lower values of Ea, ΔG‡, ΔH‡, and ΔS‡, which can be attributed to the ultrasonically induced breakage of non-covalent bonds in κ-carrageenan molecules. Copyright © 2016 BCREC GROUP. All rights reserved Received: 10th November 2015; Revised: 18th January 2016; Accepted: 19th January 2016 How to Cite: Ratnawati, R., Prasetyaningrum, A., Wardhani, D.H. (2016. Kinetics and Thermodynamics of Ultrasound-Assisted Depolymerization of κ-Carrageenan. Bulletin of Chemical Reaction Engineering & Catalysis, 11(1: 48-58. (doi:10.9767/bcrec.11.1.415.48-58 Permalink/DOI: http://dx.doi.org/10.9767/bcrec.11.1.415.48-58

  13. Collective effects in intra-cellular molecular motor transport: coordination, cooperation and competetion

    CERN Document Server

    Chowdhury, D

    2006-01-01

    Molecular motors do not work in isolation {\\it in-vivo}. We highlight some of the coordinations, cooperations and competitions that determine the collective properties of molecular motors in eukaryotic cells. In the context of traffic-like movement of motors on a track, we emphasize the importance of single-motor bio-chemical cycle and enzymatic activity on their collective spatio-temporal organisation. Our modelling strategy is based on a synthesis- the same model describes the single-motor mechano-chemistry at sufficiently low densities whereas at higher densities it accounts for the collective flow properties and the density profiles of the motors. We consider two specific examples, namely, traffic of single-headed kinesin motors KIF1A on a microtubule track and ribosome traffic on a messenger RNA track.

  14. The reciprocal coordination and mechanics of molecular motors in living cells.

    Science.gov (United States)

    Laib, Jeneva A; Marin, John A; Bloodgood, Robert A; Guilford, William H

    2009-03-03

    Molecular motors in living cells are involved in whole-cell locomotion, contractility, developmental shape changes, and organelle movement and positioning. Whether motors of different directionality are functionally coordinated in cells or operate in a semirandom "tug of war" is unclear. We show here that anterograde and retrograde microtubule-based motors in the flagella of Chlamydomonas are regulated such that only motors of a common directionality are engaged at any single time. A laser trap was used to position microspheres on the plasma membrane of immobilized paralyzed Chlamydomonas flagella. The anterograde and retrograde movements of the microsphere were measured with nanometer resolution as microtubule-based motors engaged the transmembrane protein FMG-1. An average of 10 motors acted to move the microsphere in either direction. Reversal of direction during a transport event was uncommon, and quiescent periods separated every transport event, suggesting the coordinated and exclusive action of only a single motor type. After a jump to 32 degrees C, temperature-sensitive mutants of kinesin-2 (fla10) showed exclusively retrograde transport events, driven by 7 motors on average. These data suggest that molecular motors in living cells can be reciprocally coordinated to engage simultaneously in large numbers and for exclusive transport in a single direction, even when a mixed population of motors is present. This offers a unique model for studying the mechanics, regulation, and directional coordination of molecular motors in a living intracellular environment.

  15. Enantiopure Functional Molecular Motors Obtained by a Switchable Chiral-Resolution Process.

    Science.gov (United States)

    van Leeuwen, Thomas; Gan, Jefri; Kistemaker, Jos C M; Pizzolato, Stefano F; Chang, Mu-Chieh; Feringa, Ben L

    2016-05-17

    Molecular switches, rotors, and motors play an important role in the development of nano-machines and devices, as well as responsive and adaptive functional materials. For unidirectional rotors based on chiral overcrowded alkenes, their stereochemical homogeneity is of crucial importance. Herein, a method to obtain new and functionalizable overcrowded alkenes in enantiopure form is presented. The procedure involves a short synthesis of three steps and a solvent-switchable chiral resolution by using a readily available resolving agent. X-ray crystallography revealed the mode of binding of the motor with the resolving agent, as well as the absolute configuration of the motor. (1) H NMR and UV/Vis spectroscopy techniques were used to determine the dynamic behavior of this molecular motor. This method provides rapid access to ample amounts of enantiopure molecular motors, which will greatly facilitate the further development of responsive molecular systems based on chiral overcrowded alkenes.

  16. Fluctuation theorems for discrete kinetic models of molecular motors

    Science.gov (United States)

    Faggionato, Alessandra; Silvestri, Vittoria

    2017-04-01

    Motivated by discrete kinetic models for non-cooperative molecular motors on periodic tracks, we consider random walks (also not Markov) on quasi one dimensional (1d) lattices, obtained by gluing several copies of a fundamental graph in a linear fashion. We show that, for a suitable class of quasi-1d lattices, the large deviation rate function associated to the position of the walker satisfies a Gallavotti-Cohen symmetry for any choice of the dynamical parameters defining the stochastic walk. This class includes the linear model considered in Lacoste et al (2008 Phys. Rev. E 78 011915). We also derive fluctuation theorems for the time-integrated cycle currents and discuss how the matrix approach of Lacoste et al (2008 Phys. Rev. E 78 011915) can be extended to derive the above Gallavotti-Cohen symmetry for any Markov random walk on {Z} with periodic jump rates. Finally, we review in the present context some large deviation results of Faggionato and Silvestri (2017 Ann. Inst. Henri Poincaré 53 46-78) and give some specific examples with explicit computations.

  17. Molecular motors robustly drive active gels to a critically connected state

    CERN Document Server

    Alvarado, Jose; Sharma, Abhinav; MacKintosh, Fred C; Koenderink, Gijsje H

    2013-01-01

    Living systems often exhibit internal driving: active, molecular processes drive nonequilibrium phenomena such as metabolism or migration. Active gels constitute a fascinating class of internally driven matter, where molecular motors exert localized stresses inside polymer networks. There is evidence that network crosslinking is required to allow motors to induce macroscopic contraction. Yet a quantitative understanding of how network connectivity enables contraction is lacking. Here we show experimentally that myosin motors contract crosslinked actin polymer networks to clusters with a scale-free size distribution. This critical behavior occurs over an unexpectedly broad range of crosslink concentrations. To understand this robustness, we develop a quantitative model of contractile networks that takes into account network restructuring: motors reduce connectivity by forcing crosslinks to unbind. Paradoxically, to coordinate global contractions, motor activity should be low. Otherwise, motors drive initially ...

  18. Correlations and Symmetry of Interactions Influence Collective Dynamics of Molecular Motors

    CERN Document Server

    Celis-Garza, Daniel; Kolomeisky, Anatoly B

    2015-01-01

    Enzymatic molecules that actively support many cellular processes, including transport, cell division and cell motility, are known as motor proteins or molecular motors. Experimental studies indicate that they interact with each other and they frequently work together in large groups. To understand the mechanisms of collective behavior of motor proteins we study the effect of interactions in the transport of molecular motors along linear filaments. It is done by analyzing a recently introduced class of totally asymmetric exclusion processes that takes into account the intermolecular interactions via thermodynamically consistent approach. We develop a new theoretical method that allows us to compute analytically all dynamic properties of the system. Our analysis shows that correlations play important role in dynamics of interacting molecular motors. Surprisingly, we find that the correlations for repulsive interactions are weaker and more short-range than the correlations for the attractive interactions. In ad...

  19. Crossing the Border: Molecular Control of Motor Axon Exit

    Directory of Open Access Journals (Sweden)

    Arlene Bravo-Ambrosio

    2011-11-01

    Full Text Available Living organisms heavily rely on the function of motor circuits for their survival and for adapting to ever-changing environments. Unique among central nervous system (CNS neurons, motor neurons (MNs project their axons out of the CNS. Once in the periphery, motor axons navigate along highly stereotyped trajectories, often at considerable distances from their cell bodies, to innervate appropriate muscle targets. A key decision made by pathfinding motor axons is whether to exit the CNS through dorsal or ventral motor exit points (MEPs. In contrast to the major advances made in understanding the mechanisms that regulate the specification of MN subtypes and the innervation of limb muscles, remarkably little is known about how MN axons project out of the CNS. Nevertheless, a limited number of studies, mainly in Drosophila, have identified transcription factors, and in some cases candidate downstream effector molecules, that are required for motor axons to exit the spinal cord. Notably, specialized neural crest cell derivatives, referred to as Boundary Cap (BC cells, pre-figure and demarcate MEPs in vertebrates. Surprisingly, however, BC cells are not required for MN axon exit, but rather restrict MN cell bodies from ectopically migrating along their axons out of the CNS. Here, we describe the small set of studies that have addressed motor axon exit in Drosophila and vertebrates, and discuss our fragmentary knowledge of the mechanisms, which guide motor axons out of the CNS.

  20. How molecular motors are arranged on a cargo is important for vesicular transport.

    Science.gov (United States)

    Erickson, Robert P; Jia, Zhiyuan; Gross, Steven P; Yu, Clare C

    2011-05-01

    The spatial organization of the cell depends upon intracellular trafficking of cargos hauled along microtubules and actin filaments by the molecular motor proteins kinesin, dynein, and myosin. Although much is known about how single motors function, there is significant evidence that cargos in vivo are carried by multiple motors. While some aspects of multiple motor function have received attention, how the cargo itself--and motor organization on the cargo--affects transport has not been considered. To address this, we have developed a three-dimensional Monte Carlo simulation of motors transporting a spherical cargo, subject to thermal fluctuations that produce both rotational and translational diffusion. We found that these fluctuations could exert a load on the motor(s), significantly decreasing the mean travel distance and velocity of large cargos, especially at large viscosities. In addition, the presence of the cargo could dramatically help the motor to bind productively to the microtubule: the relatively slow translational and rotational diffusion of moderately sized cargos gave the motors ample opportunity to bind to a microtubule before the motor/cargo ensemble diffuses out of range of that microtubule. For rapidly diffusing cargos, the probability of their binding to a microtubule was high if there were nearby microtubules that they could easily reach by translational diffusion. Our simulations found that one reason why motors may be approximately 100 nm long is to improve their 'on' rates when attached to comparably sized cargos. Finally, our results suggested that to efficiently regulate the number of active motors, motors should be clustered together rather than spread randomly over the surface of the cargo. While our simulation uses the specific parameters for kinesin, these effects result from generic properties of the motors, cargos, and filaments, so they should apply to other motors as well.

  1. How molecular motors are arranged on a cargo is important for vesicular transport.

    Directory of Open Access Journals (Sweden)

    Robert P Erickson

    2011-05-01

    Full Text Available The spatial organization of the cell depends upon intracellular trafficking of cargos hauled along microtubules and actin filaments by the molecular motor proteins kinesin, dynein, and myosin. Although much is known about how single motors function, there is significant evidence that cargos in vivo are carried by multiple motors. While some aspects of multiple motor function have received attention, how the cargo itself--and motor organization on the cargo--affects transport has not been considered. To address this, we have developed a three-dimensional Monte Carlo simulation of motors transporting a spherical cargo, subject to thermal fluctuations that produce both rotational and translational diffusion. We found that these fluctuations could exert a load on the motor(s, significantly decreasing the mean travel distance and velocity of large cargos, especially at large viscosities. In addition, the presence of the cargo could dramatically help the motor to bind productively to the microtubule: the relatively slow translational and rotational diffusion of moderately sized cargos gave the motors ample opportunity to bind to a microtubule before the motor/cargo ensemble diffuses out of range of that microtubule. For rapidly diffusing cargos, the probability of their binding to a microtubule was high if there were nearby microtubules that they could easily reach by translational diffusion. Our simulations found that one reason why motors may be approximately 100 nm long is to improve their 'on' rates when attached to comparably sized cargos. Finally, our results suggested that to efficiently regulate the number of active motors, motors should be clustered together rather than spread randomly over the surface of the cargo. While our simulation uses the specific parameters for kinesin, these effects result from generic properties of the motors, cargos, and filaments, so they should apply to other motors as well.

  2. Can molecular motors drive distance measurements in injured neurons?

    Directory of Open Access Journals (Sweden)

    Naaman Kam

    2009-08-01

    Full Text Available Injury to nerve axons induces diverse responses in neuronal cell bodies, some of which are influenced by the distance from the site of injury. This suggests that neurons have the capacity to estimate the distance of the injury site from their cell body. Recent work has shown that the molecular motor dynein transports importin-mediated retrograde signaling complexes from axonal lesion sites to cell bodies, raising the question whether dynein-based mechanisms enable axonal distance estimations in injured neurons? We used computer simulations to examine mechanisms that may provide nerve cells with dynein-dependent distance assessment capabilities. A multiple-signals model was postulated based on the time delay between the arrival of two or more signals produced at the site of injury-a rapid signal carried by action potentials or similar mechanisms and slower signals carried by dynein. The time delay between the arrivals of these two types of signals should reflect the distance traversed, and simulations of this model show that it can indeed provide a basis for distance measurements in the context of nerve injuries. The analyses indicate that the suggested mechanism can allow nerve cells to discriminate between distances differing by 10% or more of their total axon length, and suggest that dynein-based retrograde signaling in neurons can be utilized for this purpose over different scales of nerves and organisms. Moreover, such a mechanism might also function in synapse to nucleus signaling in uninjured neurons. This could potentially allow a neuron to dynamically sense the relative lengths of its processes on an ongoing basis, enabling appropriate metabolic output from cell body to processes.

  3. Chiral Hydrogen Bond Environment Providing Unidirectional Rotation in Photoactive Molecular Motors.

    Science.gov (United States)

    García-Iriepa, Cristina; Marazzi, Marco; Zapata, Felipe; Valentini, Alessio; Sampedro, Diego; Frutos, Luis Manuel

    2013-05-02

    Generation of a chiral hydrogen bond environment in efficient molecular photoswitches is proposed as a novel strategy for the design of photoactive molecular motors. Here, the following strategy is used to design a retinal-based motor presenting singular properties: (i) a single excitation wavelength is needed to complete the unidirectional rotation process (360°); (ii) the absence of any thermal step permits the process to take place at low temperatures; and (iii) the ultrafast process permits high rotational frequencies.

  4. Recovery of state-specific potential of molecular motor from single-molecule trajectory

    CERN Document Server

    Toyabe, Shoichi; Muneyuki, Eiro

    2011-01-01

    We have developed a novel method to evaluate the potential profile of a molecular motor at each chemical state from only the probe's trajectory and applied it to a rotary molecular motor F$_1$-ATPase. By using this method, we could also obtain the information regarding the mechanochemical coupling and energetics. We demonstrate that the position-dependent transition of the chemical states is the key feature for the highly efficient free-energy transduction by F$_1$-ATPase.

  5. From the Cover: Cooperative extraction of membrane nanotubes by molecular motors

    Science.gov (United States)

    Leduc, Cécile; Campàs, Otger; Zeldovich, Konstantin B.; Roux, Aurélien; Jolimaitre, Pascale; Bourel-Bonnet, Line; Goud, Bruno; Joanny, Jean-François; Bassereau, Patricia; Prost, Jacques

    2004-12-01

    In eukaryotic cells, nanotubes represent a substantial fraction of transport intermediates between organelles. They are extracted from membranes by molecular motors walking along microtubules. We previously showed that kinesins fixed on giant unilamellar vesicles in contact with microtubules are sufficient to form nanotubes in vitro. Motors were attached to the membrane through beads, thus facilitating cooperative effects. Koster et al. [Koster, G., VanDuijn, M., Hofs, B. & Dogterom, M. (2003) Proc. Natl. Acad. Sci. USA 100, 15583-15588] proposed that motors could dynamically cluster at the tip of tubes when they are individually attached to the membrane. We demonstrate, in a recently designed experimental system, the existence of an accumulation of motors allowing tube extraction. We determine the motor density along a tube by using fluorescence intensity measurements. We also perform a theoretical analysis describing the dynamics of motors and tube growth. The only adjustable parameter is the motor binding rate onto microtubules, which we measure to be 4.7 ± 2.4 s-1. In addition, we quantitatively determine, for a given membrane tension, the existence of a threshold in motor density on the vesicle above which nanotubes can be formed. We find that the number of motors pulling a tube can range from four at threshold to a few tens away from it. The threshold in motor density (or in membrane tension at constant motor density) could be important for the understanding of membrane traffic regulation in cells. giant unilamellar vesicle | intracellular transport | kinesin | membrane tubule | traffic jam

  6. Enhanced Diffusion of Molecular Motors in the Presence of Adenosine Triphosphate and External Force

    Science.gov (United States)

    Shinagawa, Ryota; Sasaki, Kazuo

    2016-06-01

    The diffusion of a molecular motor in the presence of a constant external force is considered on the basis of a simple theoretical model. The motor is represented by a Brownian particle moving in a series of parabolic potentials placed periodically on a line, and the potential is switched stochastically from one parabola to another by a chemical reaction, which corresponds to the hydrolysis or synthesis of adenosine triphosphate (ATP) in motor proteins. It is found that the diffusion coefficient as a function of the force exhibits peaks. The mechanism of this diffusion enhancement and the possibility of observing it in F1-ATPase, a biological rotary motor, are discussed.

  7. Transport dynamics of molecular motors that switch between an active and inactive state.

    Science.gov (United States)

    Pinkoviezky, I; Gov, N S

    2013-08-01

    Molecular motors are involved in key transport processes in the cell. Many of these motors can switch from an active to a nonactive state, either spontaneously or depending on their interaction with other molecules. When active, the motors move processively along the filaments, while when inactive they are stationary. We treat here the simple case of spontaneously switching motors, between the active and inactive states, along an open linear track. We use our recent analogy with vehicular traffic, where we go beyond the mean-field description. We map the phase diagram of this system, and find that it clearly breaks the symmetry between the different phases, as compared to the standard total asymmetric exclusion process. We make several predictions that may be testable using molecular motors in vitro and in living cells.

  8. Computational Design of a Family of Light-Driven Rotary Molecular Motors with Improved Quantum Efficiency.

    Science.gov (United States)

    Nikiforov, Alexander; Gamez, Jose A; Thiel, Walter; Filatov, Michael

    2016-01-07

    Two new light-driven molecular rotary motors based on the N-alkylated indanylidene benzopyrrole frameworks are proposed and studied using quantum chemical calculations and nonadiabatic molecular dynamics simulations. These new motors perform pure axial rotation, and the photochemical steps of the rotary cycle are dominated by the fast bond-length-alternation motion that enables ultrafast access to the S1/S0 intersection. The new motors are predicted to display a quantum efficiency higher than that of the currently available synthetic all-hydrocarbon motors. Remarkably, the quantum efficiency is not governed by the topography (peaked versus sloped) of the minimum-energy conical intersection, whereas the S1 decay time depends on the topography as well as on the energy of the intersection relative to the S1 minimum. It is the axial chirality (helicity), rather than the point chirality, that controls the sense of rotation of the motor.

  9. Towards dynamic control of wettability by using functionalized altitudinal molecular motors on solid surfaces.

    Science.gov (United States)

    London, Gábor; Chen, Kuang-Yen; Carroll, Gregory T; Feringa, Ben L

    2013-08-05

    We report the synthesis of altitudinal molecular motors that contain functional groups in their rotor part. In an approach to achieve dynamic control over the properties of solid surfaces, a hydrophobic perfluorobutyl chain and a relatively hydrophilic cyano group were introduced to the rotor part of the motors. Molecular motors were attached to quartz surfaces by using interfacial 1,3-dipolar cycloadditions. To test the effect of the functional groups on the rotary motion, photochemical and thermal isomerization studies of the motors were performed both in solution and when attached to the surface. We found that the substituents have no significant effect on the thermal and photochemical processes, and the functionalized motors preserved their rotary function both in solution and on a quartz surface. Preliminary results on the influence of the functional groups on surface wettability are also described.

  10. Enzymatic depolymerization of low-rank coal (lignite)

    Energy Technology Data Exchange (ETDEWEB)

    Hofrichter, M.; Ziegenhagen, D.; Sorge, S.; Bublitz, F.; Fritsche, W. [Jena Univ. (Germany). Inst. fuer Mikrobiologie

    1997-12-31

    Ligninolytic basidiomycetes (wood and litter decaying fungi) have the ability to degrade low-rank coal (lignite). Extracellular manganese peroxidase (MnP) is the decisive enzyme in the depolymerization process both of coal derived humic substances and native coal. The depolymerization of coal occurred via Mn{sup 3+}-ions acting as primary mediator and can be considerably enhanced by certain thiols acting as secondary mediators. The depolymerization process leads finally to complex mixtures of fulvic acid-like compounds. (orig.)

  11. Exclusion and Hierarchy of Time Scales Lead to Spatial Segregation of Molecular Motors in Cellular Protrusions

    Science.gov (United States)

    Pinkoviezky, I.; Gov, N. S.

    2017-01-01

    Molecular motors that carry cargo along biopolymer filaments within cells play a crucial role in the functioning of the cell. In particular, these motors are essential for the formation and maintenance of the cellular protrusions that play key roles in motility and specific functionalities, such as the stereocilia in hair cells. Typically, there are several species of motors, carrying different cargos, that share the same track. Furthermore, it was observed that in the mature stereocilia, the different motors occupy well-segregated bands as a function of distance from the tip. We use a totally asymmetric exclusion process model with two- and three-motor species, to study the conditions that give rise to such spatial patterns. We find that the well-segregated bands appear for motors with a strong hierarchy of attachment or detachment rates. This is a striking example of pattern formation in nonequilibrium, low-dimensional systems.

  12. Mechanism of cooperative behaviour in systems of slow and fast molecular motors.

    Science.gov (United States)

    Larson, Adam G; Landahl, Eric C; Rice, Sarah E

    2009-06-28

    Two recent theoretical advances have described cargo transport by multiple identical motors and by multiple oppositely directed, but otherwise identical motors [M. J. Muller, S. Klumpp and R. Lipowsky, Proc. Natl. Acad. Sci. U. S. A., 2008, 105(12), 4609-4614; S. Klumpp and R. Lipowsky, Proc. Natl. Acad. Sci. U. S. A., 2005, 102(48), 17284-17289]. Here, we combine a similar theoretical approach with a simple experiment to describe the behaviour of a system comprised of slow and fast molecular motors having the same directionality. We observed the movement of microtubules by mixtures of slow and fast kinesin motors attached to a glass coverslip in a classic sliding filament assay. The motors are identical, except that the slow ones contain five point mutations that collectively reduce their velocity approximately 15-fold without compromising maximal ATPase activity. Our results indicate that a small fraction of fast motors are able to accelerate the dissociation of slow motors from microtubules. Because of this, a sharp, highly cooperative transition occurs from slow to fast microtubule movement as the relative number of fast motors in the assay is increased. Microtubules move at half-maximal velocity when only 15% of the motors in the assay are fast. Our model indicates that this behaviour depends primarily on the relative motor velocities and the asymmetry between their forward and backward dissociation forces. It weakly depends on the number of motors and their processivity. We predict that movement of cargoes bound to two types of motors having very different velocities will be dominated by one or the other motor. Therefore, cargoes can potentially undergo abrupt changes in movement in response to regulatory mechanisms acting on only a small fraction of motors.

  13. Kinetic mechanism of DNA translocation by the RSC molecular motor.

    Science.gov (United States)

    Eastlund, Allen; Malik, Shuja Shafi; Fischer, Christopher J

    2013-04-15

    ATP-dependent nucleosome repositioning by chromatin remodeling enzymes requires the translocation of these enzymes along the nucleosomal DNA. Using a fluorescence stopped-flow assay we monitored DNA translocation by a minimal RSC motor and through global analysis of these time courses we have determined that this motor has a macroscopic translocation rate of 2.9 bp/s with a step size of 1.24 bp. From the complementary quantitative analysis of the associated time courses of ATP consumption during DNA translocation we have determined that this motor has an efficiency of 3.0 ATP/bp, which is slightly less that the efficiency observed for several genetically related DNA helicases and which likely results from random pausing by the motor during translocation. Nevertheless, this motor is able to exert enough force during translocation to displace streptavidin from biotinylated DNA. Taken together these results are the necessary first step for quantifying both the role of DNA translocation in nucleosome repositioning by RSC and the efficiency at which RSC couples ATP binding and hydrolysis to nucleosome repositioning.

  14. Increased speed of rotation for the smallest light-driven molecular motor

    NARCIS (Netherlands)

    ter Wiel, MKJ; van Delden, RA; Meetsma, A; Feringa, BL; Delden, Richard A. van; Feringa, Bernard

    2003-01-01

    In this paper we present the smallest artificial light-driven molecular motor consisting of only 28 carbon and 24 hydrogen atoms. The concept of controlling directionality of rotary movement at the molecular level by introduction of a stereogenic center next to the central olefinic bond of a sterica

  15. Molecular motors: how to make models that can be used to convey the concept of molecular ratchets and thermal capture.

    Science.gov (United States)

    DoHarris, Lindsay; Giesler, Amanda; Humber, Brent; Sukumar, Aravin; Janssen, Luke J

    2011-06-01

    A wide variety of cellular processes use molecular motors, including processive motors that move along some form of track (e.g., myosin with actin, kinesin or dynein with tubulin) and polymerases that move along a template (e.g., DNA and RNA polymerases, ribosomes). In trying to understand how these molecular motors actually move, many apply their understanding of how man-made motors work: the latter use some form of energy to exert a force or torque on its load. However, quite a different mechanism has been proposed to possibly account for the movement of molecular motors. Rather than hydrolyzing ATP to push or pull their load, they might use their own thermal vibrational energy as well as that of their load and their environment to move the load, capturing those movements that occur along a desired vector or axis and resisting others; ATP hydrolysis is required to make backward movements impossible. This intriguing thermal capture or Brownian ratchet model is relatively more difficult to convey to students. In this report, we describe several teaching aids that are very easily constructed using widely available household materials to convey the concept of a molecular ratchet.

  16. Intrinsic irreversibility limits the efficiency of multidimensional molecular motors

    Science.gov (United States)

    Jack, M. W.; Tumlin, C.

    2016-05-01

    We consider the efficiency limits of Brownian motors able to extract work from the temperature difference between reservoirs or from external thermodynamic forces. These systems can operate in a variety of modes, including as isothermal engines, heat engines, refrigerators, and heat pumps. We derive analytical results showing that certain classes of multidimensional Brownian motor, including the Smoluchowski-Feynman ratchet, are unable to attain perfect efficiency (Carnot efficiency for heat engines). This demonstrates the presence of intrinsic irreversibilities in their operating mechanism. We present numerical simulations showing that in some cases the loss process that limits efficiency is associated with vortices in the probability current.

  17. Intrinsic irreversibility limits the efficiency of multidimensional molecular motors.

    Science.gov (United States)

    Jack, M W; Tumlin, C

    2016-05-01

    We consider the efficiency limits of Brownian motors able to extract work from the temperature difference between reservoirs or from external thermodynamic forces. These systems can operate in a variety of modes, including as isothermal engines, heat engines, refrigerators, and heat pumps. We derive analytical results showing that certain classes of multidimensional Brownian motor, including the Smoluchowski-Feynman ratchet, are unable to attain perfect efficiency (Carnot efficiency for heat engines). This demonstrates the presence of intrinsic irreversibilities in their operating mechanism. We present numerical simulations showing that in some cases the loss process that limits efficiency is associated with vortices in the probability current.

  18. Molecular motors pulling cargos in the viscoelastic cytosol: how power strokes beat subdiffusion.

    Science.gov (United States)

    Goychuk, Igor; Kharchenko, Vasyl O; Metzler, Ralf

    2014-08-21

    The discovery of anomalous diffusion of larger biopolymers and submicron tracers such as endogenous granules, organelles, or virus capsids in living cells, attributed to the viscoelastic nature of the cytoplasm, provokes the question whether this complex environment equally impacts the active intracellular transport of submicron cargos by molecular motors such as kinesins: does the passive anomalous diffusion of free cargo always imply its anomalously slow active transport by motors, the mean transport distance along microtubule growing sublinearly rather than linearly in time? Here we analyze this question within the widely used two-state Brownian ratchet model of kinesin motors based on the continuous-state diffusion along microtubules driven by a flashing binding potential, where the cargo particle is elastically attached to the motor. Depending on the cargo size, the loading force, the amplitude of the binding potential, the turnover frequency of the molecular motor enzyme, and the linker stiffness we demonstrate that the motor transport may turn out either normal or anomalous, as indeed measured experimentally. We show how a highly efficient normal active transport mediated by motors may emerge despite the passive anomalous diffusion of the cargo, and study the intricate effects of the elastic linker. Under different, well specified conditions the microtubule-based motor transport becomes anomalously slow and thus significantly less efficient.

  19. Tuning the Rotation Rate of Light-Driven Molecular Motors

    NARCIS (Netherlands)

    Bauer, Jurica; Hou, Lili; Kistemaker, Jos C. M.; Feringa, Bernard

    2014-01-01

    Overcrowded alkenes are among the most promising artificial mol. motors because of their ability to undergo repetitive light-driven unidirectional rotary motion around the central C=C bond. The exceptional features of these mols. render them highly useful for a no. of applications in nanotechnol. Ma

  20. Improved postharvest quality in patagonian squash (Cucurbita moschata) coated with radiation depolymerized chitosan

    Energy Technology Data Exchange (ETDEWEB)

    Pugliese, Maria Alicia; Goitia, Maria Teresa [Laboratorio de Investigaciones Basicas Aplicadas en Quitina, Departamento de Quimica, Universidad Nacional del Sur. Avenida Alem 1253, B8000CPB Bahia Blanca (Argentina); Yossen, Mariana [Instituto de Desarrollo Tecnologico para la Industria Quimica (INTEC), CONICET-Universidad Nacional del Litoral, Ruta Nacional 168-Paraje ' El Pozo' , 3000 Santa Fe (Argentina); Cifone, Norma; Agullo, Enrique [Laboratorio de Investigaciones Basicas Aplicadas en Quitina, Departamento de Quimica, Universidad Nacional del Sur. Avenida Alem 1253, B8000CPB Bahia Blanca (Argentina); Andreucetti, Noemi, E-mail: andreuce@criba.edu.ar [Laboratorio de Radioisotopos, Departamento de Quimica, Universidad Nacional del Sur, Avenida Alem 1253, B8000CPB Bahia Blanca (Argentina)

    2011-12-15

    Different molecular weight chitosans were evaluated on the decay of coated Anquito squashes (Cucurbita moschata) as well as the maintenance of the fruit quality along five storage months. The original chitosan (Mw=391 kDa, 83% DD), was depolymerized by gamma radiation. Apart from chain scission, other chemical changes were not detected by FTIR or UV-vis analyses. The molecular weight characterization of chitosans was done by size exclusion chromatography with dual light scattering and concentration detection (SEC-MALLS-RI). The coating effectiveness was evaluated on the following parameters: fungal decay incidence, weight loss, firmness, total reducing sugar, soluble solid, flesh color, carotene content, pH and titratable acidity. No sign of fungal decay was observed in squashes coated with 122 and 56 kDa chitosans, which were also the most effective treatments in reducing the weight loss. The chitosan with Mw=122 kDa was also the best treatment considering firmness, internal aspect, sugar and carotene content. Then, radiation degraded chitosan was better in C. moschata preservation than the original chitosan. - Highlights: > Original Chitosan was radiation depolymerized producing chitosans with lower molecular weights. > Gamma-irradiated chitosans only exhibit chain scission. > SEC-MALLS-RI chromatography is a useful tool in molecular weight analysis. > Depolymerized chitosans were the best in maintaining the quality and the storage life of coated squashes.

  1. How molecular motors work in the crowded environment of living cells: coexistence and efficiency of normal and anomalous transport.

    Science.gov (United States)

    Goychuk, Igor; Kharchenko, Vasyl O; Metzler, Ralf

    2014-01-01

    Recent experiments reveal both passive subdiffusion of various nanoparticles and anomalous active transport of such particles by molecular motors in the molecularly crowded environment of living biological cells. Passive and active microrheology reveals that the origin of this anomalous dynamics is due to the viscoelasticity of the intracellular fluid. How do molecular motors perform in such a highly viscous, dissipative environment? Can we explain the observed co-existence of the anomalous transport of relatively large particles of 100 to 500 nm in size by kinesin motors with the normal transport of smaller particles by the same molecular motors? What is the efficiency of molecular motors in the anomalous transport regime? Here we answer these seemingly conflicting questions and consistently explain experimental findings in a generalization of the well-known continuous diffusion model for molecular motors with two conformational states in which viscoelastic effects are included.

  2. How molecular motors work in the crowded environment of living cells: coexistence and efficiency of normal and anomalous transport.

    Directory of Open Access Journals (Sweden)

    Igor Goychuk

    Full Text Available Recent experiments reveal both passive subdiffusion of various nanoparticles and anomalous active transport of such particles by molecular motors in the molecularly crowded environment of living biological cells. Passive and active microrheology reveals that the origin of this anomalous dynamics is due to the viscoelasticity of the intracellular fluid. How do molecular motors perform in such a highly viscous, dissipative environment? Can we explain the observed co-existence of the anomalous transport of relatively large particles of 100 to 500 nm in size by kinesin motors with the normal transport of smaller particles by the same molecular motors? What is the efficiency of molecular motors in the anomalous transport regime? Here we answer these seemingly conflicting questions and consistently explain experimental findings in a generalization of the well-known continuous diffusion model for molecular motors with two conformational states in which viscoelastic effects are included.

  3. Increased speed of rotation for the smallest light-driven molecular motor.

    Science.gov (United States)

    ter Wiel, Matthijs K J; van Delden, Richard A; Meetsma, Auke; Feringa, Ben L

    2003-12-10

    In this paper we present the smallest artificial light-driven molecular motor consisting of only 28 carbon and 24 hydrogen atoms. The concept of controlling directionality of rotary movement at the molecular level by introduction of a stereogenic center next to the central olefinic bond of a sterically overcrowded alkene does not only hold for molecular motors with six-membered rings, but is also applicable to achieve the unidirectional movement for molecular motors having five-membered rings. Although X-ray analyses show that the five-membered rings in the cis- and trans-isomer of the new molecular motor are nearly flat, the energy differences between the (pseudo-)diaxial and (pseudo-)diequatorial conformations of the methyl substituents in both isomers are still large enough to direct the rotation of one-half of the molecule with respect to the other half in a clockwise fashion. The full rotary cycle comprises four consecutive steps: two photochemical isomerizations each followed by a thermal helix inversion. Both photochemical cis-trans isomerizations proceed with a preference for the unstable diequatorial isomers over the stable diaxial isomers. The thermal barriers for helix inversion of this motor molecule have decreased dramatically compared to its six-membered ring analogue, the half-life of the fastest step being only 18 s at room temperature.

  4. Tug-of-war between opposing molecular motors explains chromosomal oscillation during mitosis.

    Science.gov (United States)

    Sutradhar, S; Paul, R

    2014-03-07

    Chromosomes move towards and away from the centrosomes during the mitosis. This oscillation is observed when the kinetochore, a specific protein structure on the chromosome is captured by centrosome-nucleated polymer called microtubules. We present a computational model, incorporating activities of various molecular motors and microtubule dynamics, to demonstrate the observed oscillation. The model is robust and is not restricted to any particular cell type. Quantifying the average velocity, amplitude and periodicity of the chromosomal oscillation, we compare numerical results with the available experimental data. Our analysis supports a tug-of-war like mechanism between opposing motors that changes the course of chromosomal oscillation. It turns out that, various modes of oscillation can be fully understood by assembling the dynamics of molecular motors. Near the stall regime, when opposing motors are engaged in a tug-of-war, sufficiently large kinetochore-microtubule generated force may prolong the stall durations.

  5. Highly sensitive detection of NT-proBNP by molecular motor

    Directory of Open Access Journals (Sweden)

    Jie Zhang

    2017-03-01

    Full Text Available FoF1-ATPase is an active rotary motor, and generates three-ATP for each rotation. At saturated substrate concentration, the motor can achieve about 103 r.p.m, which means one motor can generate about 105 ATP molecules during 30 min. Here, we constituted a novel nanodevice with a molecular rotary motor and a “battery”, FoF1-ATPase and chromatophore, and presented a novel method of sandwich type rotary biosensor based on ε subunit with one target-to-one motor, in which one target corresponds 105 ATP molecules as detection signals during 30 min. The target such as NT-proBNP detection demonstrated that this novel nanodevice has potential to be developed into an ultrasensitive biosensor to detect low expressed targets.

  6. Review on Modeling Molecular Motor%分子马达模型综述

    Institute of Scientific and Technical Information of China (English)

    王先菊; 艾保全; 刘良钢

    2001-01-01

    The structure and function of three kinds of motor proteins are introduced. The fundamental importance on studying molecular motor in living systems is also discribed. With detailed review on several archetype theoretical models, the progress and application on modeling molecule motor are presented.%介绍三类马达酶的结构,功能和生命体内分子马达的研究状况,并详细介绍几类典型分子马达的理论模型,同时展望了分子马达的发展前景和应用.

  7. Future challenges in single-molecule fluorescence and laser trap approaches to studies of molecular motors.

    Science.gov (United States)

    Elting, Mary Williard; Spudich, James A

    2012-12-11

    Single-molecule analysis is a powerful modern form of biochemistry, in which individual kinetic steps of a catalytic cycle of an enzyme can be explored in exquisite detail. Both single-molecule fluorescence and single-molecule force techniques have been widely used to characterize a number of protein systems. We focus here on molecular motors as a paradigm. We describe two areas where we expect to see exciting developments in the near future: first, characterizing the coupling of force production to chemical and mechanical changes in motors, and second, understanding how multiple motors work together in the environment of the cell.

  8. Molecular and Functional Characterization of the Developing Respiratory Motor Circuit

    OpenAIRE

    2015-01-01

    The faithful and sophisticated control of motor neurons (MNs) allows for our ability to walk, chew, breathe, and speak. This dissertation is focused on the characterization of MNs and the intricate circuitry that are involved in the control of these MNs that surround the airways. The relevance of this study goes beyond satisfying our curiosity of the physiology of breathing. This knowledge is critical in their application in respiratory medicine and speech rehabilitation – as the same set of ...

  9. Stepping and crowding of molecular motors: statistical kinetics from an exclusion process perspective.

    Science.gov (United States)

    Ciandrini, Luca; Romano, M Carmen; Parmeggiani, Andrea

    2014-09-02

    Motor enzymes are remarkable molecular machines that use the energy derived from the hydrolysis of a nucleoside triphosphate to generate mechanical movement, achieved through different steps that constitute their kinetic cycle. These macromolecules, nowadays investigated with advanced experimental techniques to unveil their molecular mechanisms and the properties of their kinetic cycles, are implicated in many biological processes, ranging from biopolymerization (e.g., RNA polymerases and ribosomes) to intracellular transport (motor proteins such as kinesins or dyneins). Although the kinetics of individual motors is well studied on both theoretical and experimental grounds, the repercussions of their stepping cycle on the collective dynamics still remains unclear. Advances in this direction will improve our comprehension of transport process in the natural intracellular medium, where processive motor enzymes might operate in crowded conditions. In this work, we therefore extend contemporary statistical kinetic analysis to study collective transport phenomena of motors in terms of lattice gas models belonging to the exclusion process class. Via numerical simulations, we show how to interpret and use the randomness calculated from single particle trajectories in crowded conditions. Importantly, we also show that time fluctuations and non-Poissonian behavior are intrinsically related to spatial correlations and the emergence of large, but finite, clusters of comoving motors. The properties unveiled by our analysis have important biological implications on the collective transport characteristics of processive motor enzymes in crowded conditions.

  10. Muscle activation described with a differential equation model for large ensembles of locally coupled molecular motors.

    Science.gov (United States)

    Walcott, Sam

    2014-10-01

    Molecular motors, by turning chemical energy into mechanical work, are responsible for active cellular processes. Often groups of these motors work together to perform their biological role. Motors in an ensemble are coupled and exhibit complex emergent behavior. Although large motor ensembles can be modeled with partial differential equations (PDEs) by assuming that molecules function independently of their neighbors, this assumption is violated when motors are coupled locally. It is therefore unclear how to describe the ensemble behavior of the locally coupled motors responsible for biological processes such as calcium-dependent skeletal muscle activation. Here we develop a theory to describe locally coupled motor ensembles and apply the theory to skeletal muscle activation. The central idea is that a muscle filament can be divided into two phases: an active and an inactive phase. Dynamic changes in the relative size of these phases are described by a set of linear ordinary differential equations (ODEs). As the dynamics of the active phase are described by PDEs, muscle activation is governed by a set of coupled ODEs and PDEs, building on previous PDE models. With comparison to Monte Carlo simulations, we demonstrate that the theory captures the behavior of locally coupled ensembles. The theory also plausibly describes and predicts muscle experiments from molecular to whole muscle scales, suggesting that a micro- to macroscale muscle model is within reach.

  11. Self-organization of waves and pulse trains by molecular motors in cellular protrusions.

    Science.gov (United States)

    Yochelis, A; Ebrahim, S; Millis, B; Cui, R; Kachar, B; Naoz, M; Gov, N S

    2015-09-03

    Actin-based cellular protrusions are an ubiquitous feature of cells, performing a variety of critical functions ranging from cell-cell communication to cell motility. The formation and maintenance of these protrusions relies on the transport of proteins via myosin motors, to the protrusion tip. While tip-directed motion leads to accumulation of motors (and their molecular cargo) at the protrusion tip, it is observed that motors also form rearward moving, periodic and isolated aggregates. The origins and mechanisms of these aggregates, and whether they are important for the recycling of motors, remain open puzzles. Motivated by novel myosin-XV experiments, a mass conserving reaction-diffusion-advection model is proposed. The model incorporates a non-linear cooperative interaction between motors, which converts them between an active and an inactive state. Specifically, the type of aggregate formed (traveling waves or pulse-trains) is linked to the kinetics of motors at the protrusion tip which is introduced by a boundary condition. These pattern selection mechanisms are found not only to qualitatively agree with empirical observations but open new vistas to the transport phenomena by molecular motors in general.

  12. Influence of molecular motors on the motion of particles in viscoelastic media.

    Science.gov (United States)

    Bouzat, Sebastián

    2014-06-01

    We study theoretically and by numerical simulations the motion of particles driven by molecular motors in a viscoelastic medium representing the cell cytoplasm. For this, we consider a generalized Langevin equation coupled to a stochastic stepping dynamics for the motors that takes into account the action of each motor separately. In the absence of motors, the model produces subdiffusive motion of particles characterized by a power-law scaling of the mean square displacement versus the lag time as t^{α}, with 0motors can induce a transition to a superdiffusive regime at large lag times with the characteristics of those found in experiments reported in the literature. We also show that at small lag times, the motors can act as static crosslinkers that slow down the natural subdiffusive transport. An analysis of previously reported experimental data in the relevant time scales provides evidence of this phenomenon. Finally, we study the effect of a harmonic potential representing an optical trap, and we show a way to approach to a macroscopic description of the active transport in cells. This last point stresses the relevance of the molecular motors for generating not only directed motion to specific targets, but also fast diffusivelike random motion.

  13. A Molecular Motor, KIF13A, Controls Anxiety by Transporting the Serotonin Type 1A Receptor

    Directory of Open Access Journals (Sweden)

    Ruyun Zhou

    2013-02-01

    Full Text Available Molecular motors are fundamental to neuronal morphogenesis and function. However, the extent to which molecular motors are involved in higher brain functions remains largely unknown. In this study, we show that mice deficient in the kinesin family motor protein KIF13A (Kif13a−/− mice exhibit elevated anxiety-related behavioral phenotypes, probably because of a reduction in 5HT1A receptor (5HT1AR transport. The cell-surface expression level of the 5HT1AR was reduced in KIF13A-knockdown neuroblastoma cells and Kif13a−/− hippocampal neurons. Biochemical analysis showed that the forkhead-associated (FHA domain of KIF13A and an intracellular loop of the 5HT1AR are the interface between the motor and cargo vesicles. A minimotor consisting of the motor and FHA domains is able to transport 5HT1AR-carrying organelles in in vitro reconstitution assays. Collectively, our results suggest a role for this molecular motor in anxiety control.

  14. Metathesis depolymerization for removable surfactant templates.

    Energy Technology Data Exchange (ETDEWEB)

    Zifer, Thomas (Sandia National Laboratories, Livermore, CA); Wheeler, David Roger; Rahimian, Kamayar; McElhanon, James Ross (Sandia National Laboratories, Livermore, CA); Long, Timothy Michael; Jamison, Gregory Marks; Loy, Douglas Anson (Los Alamos National Laboratories, Los Alamos, NM); Kline, Steven R. (National Institute of Standards and Technology, Gaithersburg, MD); Simmons, Blake Alexander (Sandia National Laboratories, Livermore, CA)

    2005-03-01

    Current methodologies for the production of meso- and nanoporous materials include the use of a surfactant to produce a self-assembled template around which the material is formed. However, post-production surfactant removal often requires centrifugation, calcination, and/or solvent washing which can damage the initially formed material architecture(s). Surfactants that can be disassembled into easily removable fragments following material preparation would minimize processing damage to the material structure, facilitating formation of templated hybrid architectures. Herein, we describe the design and synthesis of novel cationic and anionic surfactants with regularly spaced unsaturation in their hydrophobic hydrocarbon tails and the first application of ring closing metathesis depolymerization to surfactant degradation resulting in the mild, facile decomposition of these new compounds to produce relatively volatile nonsurface active remnants.

  15. An enantioselective synthetic route toward second-generation light-driven rotary molecular motors.

    Science.gov (United States)

    Pijper, Thomas C; Pijper, Dirk; Pollard, Michael M; Dumur, Frédéric; Davey, Stephen G; Meetsma, Auke; Feringa, Ben L

    2010-02-05

    Controlling the unidirectional rotary process of second-generation molecular motors demands access to these motors in their enantiomerically pure form. In this paper, we describe an enantioselective route to three new second-generation light-driven molecular motors. Their synthesis starts with the preparation of an optically active alpha-methoxy-substituted upper-half ketone involving an enzymatic resolution. The subsequent conversion of this ketone to the corresponding hydrazone by treatment with hydrazine led to full racemization. However, conversion to a TBDMS-protected hydrazone by treatment with bis-TBDMS hydrazine, prepared according to a new procedure, proceeds with nearly full retention of the stereochemical integrity. Oxidation of the TBDMS-protected hydrazone and subsequent coupling to a lower-half thioketone followed by recrystallization provided the molecular motors with >99% ee. As these are the first molecular motors that have a methoxy substituent at the stereogenic center, the photochemical and thermal isomerization steps involved in the rotary cycle of one of these new molecules were studied in detail with various spectroscopic techniques.

  16. Mechanical properties of organelles driven by microtubule-dependent molecular motors in living cells.

    Directory of Open Access Journals (Sweden)

    Luciana Bruno

    Full Text Available The organization of the cytoplasm is regulated by molecular motors which transport organelles and other cargoes along cytoskeleton tracks. Melanophores have pigment organelles or melanosomes that move along microtubules toward their minus and plus end by the action of cytoplasmic dynein and kinesin-2, respectively. In this work, we used single particle tracking to characterize the mechanical properties of motor-driven organelles during transport along microtubules. We tracked organelles with high temporal and spatial resolutions and characterized their dynamics perpendicular to the cytoskeleton track. The quantitative analysis of these data showed that the dynamics is due to a spring-like interaction between melanosomes and microtubules in a viscoelastic microenvironment. A model based on a generalized Langevin equation explained these observations and predicted that the stiffness measured for the motor complex acting as a linker between organelles and microtubules is ∼ one order smaller than that determined for motor proteins in vitro. This result suggests that other biomolecules involved in the interaction between motors and organelles contribute to the mechanical properties of the motor complex. We hypothesise that the high flexibility observed for the motor linker may be required to improve the efficiency of the transport driven by multiple copies of motor molecules.

  17. Directed Motion of a Molecular Motor Based Qn the Four-State Model with Unequal Substeps

    Institute of Scientific and Technical Information of China (English)

    WUWei-Xia; ZHANYong; ZHAOTong-Jun; MEIJumPing

    2003-01-01

    A periodic one-dimensional four-state hopping model is proposed. In the model, the substeps between arbitrary adjacent states are unequal, and an explicit solution of the master equation is first obtained for the probability distribution as a function of the time and position for any initial distribution with all the transients included. Next, the transient behaviors in the initial period of time and the characteristic time to reach the steady state for the molecular motor are discussed. Finally, we compare the steady state results to experiments and illustrate qualitatively the kinetic behaviors of a molecular motor under external load F.

  18. O demônio de Maxwell e os motores moleculares

    OpenAIRE

    Goldman, Carla

    2014-01-01

    O transporte ativo nas células é efetuado por certas proteínas, ou motores moleculares como são conhecidas na literatura, capazes de realizar trabalho mecânico em um meio onde predominam forças viscosas. Os mecanismos físicos que regem o movimento dos motores moleculares se inserem no contexto dos processos estocásticos. O modelo padrão introduzido nos anos 90 por Adjari e Prost e por Magnasco para descrever movimento direcionado nesta situação é revisto de maneira pedagógica. Um dos objetivo...

  19. Efficiency bounds of molecular motors under a trade-off figure of merit

    Science.gov (United States)

    Zhang, Yanchao; Huang, Chuankun; Lin, Guoxing; Chen, Jincan

    2017-05-01

    On the basis of the theory of irreversible thermodynamics and an elementary model of the molecular motors converting chemical energy by ATP hydrolysis to mechanical work exerted against an external force, the efficiencies of the molecular motors at two different optimization configurations for trade-off figure of merit representing a best compromise between the useful energy and the lost energy are calculated. The upper and lower bounds for the efficiency at two different optimization configurations are determined. It is found that the optimal efficiencies at the two different optimization configurations are always larger than 1 / 2.

  20. Structured attachment of bacterial molecular motors for defined microflow induction

    Directory of Open Access Journals (Sweden)

    Woerdemann Mike

    2014-01-01

    Full Text Available Bacterial rotational motor complexes that propel flagellated bacteria possess unique properties like their size of a few nanometres and the ability of selfreproduction that have led to various exciting applications including biohybrid nano-machines. One mandatory prerequisite to utilize bacterial nano motors in fluid applications is the ability to transfer force and torque to the fluid, which usually can be achieved by attachment of the bacterial cell to adequate surfaces. Additionally, for optimal transfer of force or torque, precise control of the position down to the single cell level is of utmost importance. Based on a PIV (particle image velocimetry evaluation of the induced flow of single bacteria,we propose and demonstrate attachment of arbitrary patterns of motile bacterial cells in a fast light-based two-step process for the first time to our knowledge. First, these cells are pre-structured by holographic optical tweezers and then attached to a homogeneous, polystyrene-coated surface. In contrast to the few approaches that have been implemented up to now and which rely on pre-structured surfaces, our scheme allows for precise control on a single bacterium level, is versatile, interactive and has low requirements with respect to the surface preparation.

  1. Bounds and phase diagram of efficiency at maximum power for tight-coupling molecular motors.

    Science.gov (United States)

    Tu, Z C

    2013-02-01

    The efficiency at maximum power (EMP) for tight-coupling molecular motors is investigated within the framework of irreversible thermodynamics. It is found that the EMP depends merely on the constitutive relation between the thermodynamic current and force. The motors are classified into four generic types (linear, superlinear, sublinear, and mixed types) according to the characteristics of the constitutive relation, and then the corresponding ranges of the EMP for these four types of molecular motors are obtained. The exact bounds of the EMP are derived and expressed as the explicit functions of the free energy released by the fuel in each motor step. A phase diagram is constructed which clearly shows how the region where the parameters (the load distribution factor and the free energy released by the fuel in each motor step) are located can determine whether the value of the EMP is larger or smaller than 1/2. This phase diagram reveals that motors using ATP as fuel under physiological conditions can work at maximum power with higher efficiency (> 1/2) for a small load distribution factor (< 0.1).

  2. Bidirectional transport by molecular motors: enhanced processivity and response to external forces.

    Science.gov (United States)

    Müller, Melanie J I; Klumpp, Stefan; Lipowsky, Reinhard

    2010-06-02

    Intracellular transport along cytoskeletal filaments is often mediated by two teams of molecular motors that pull on the same cargo and move in opposite directions along the filaments. We have recently shown theoretically that this bidirectional transport can be understood as a stochastic tug-of-war between the two motor teams. Here, we further develop our theory to investigate the experimentally accessible dynamic behavior of cargos transported by strong motors such as kinesin-1 or cytoplasmic dynein. By studying the run and binding times of such a cargo, we show that the properties of biological motors, such as the large ratio of stall/detachment force and the small ratio of superstall backward/forward velocity, are favorable for bidirectional cargo transport, leading to fast motion and enhanced diffusion. In addition, cargo processivity is shown to be strongly enhanced by transport via several molecular motors even if these motors are engaged in a tug-of-war. Finally, we study the motility of a bidirectional cargo under force. Frictional forces arising, e.g., from the viscous cytoplasm, lead to peaks in the velocity distribution, while external forces as exerted, e.g., by an optical trap, lead to hysteresis effects. Our results, in particular our explicit expressions for the cargo binding time and the distance of the peaks in the velocity relation under friction, are directly accessible to in vitro as well as in vivo experiments.

  3. Assembly of bipolar microtubule structures by passive cross-linkers and molecular motors

    Science.gov (United States)

    Johann, D.; Goswami, D.; Kruse, K.

    2016-06-01

    During cell division, sister chromatids are segregated by the mitotic spindle, a bipolar assembly of interdigitating antiparallel polar filaments called microtubules. The spindle contains the midzone, a stable region of overlapping antiparallel microtubules, that is essential for maintaining bipolarity. Although a lot is known about the molecular players involved, the mechanism underlying midzone formation and maintenance is still poorly understood. We study the interaction of polar filaments that are cross-linked by molecular motors moving directionally and by passive cross-linkers diffusing along microtubules. Using a particle-based stochastic model, we find that the interplay of motors and passive cross-linkers can generate a stable finite overlap between a pair of antiparallel polar filaments. We develop a mean-field theory to study this mechanism in detail and investigate the influence of steric interactions between motors and passive cross-linkers on the overlap dynamics. In the presence of interspecies steric interactions, passive cross-linkers mimic the behavior of molecular motors and stable finite overlaps are generated even for non-cross-linking motors. Finally, we develop a mean-field theory for a bundle of aligned polar filaments and show that they can self-organize into a spindlelike pattern. Our work suggests possible ways as to how cells can generate spindle midzones and control their extensions.

  4. Forced desorption of semiflexible polymers, adsorbed and driven by molecular motors

    CERN Document Server

    Chaudhuri, Abhishek

    2014-01-01

    We formulate and characterize a model to describe dynamics of semiflexible polymers in the presence of activity due to motor proteins attached irreversibly to a substrate, and a transverse pulling force acting on one end of the filament. The stochastic binding-unbinding of the motor proteins and their ability to move along the polymer, generates active forces. As the pulling force reaches a threshold value, the polymer eventually desorbs from the substrate. We present a mean field theory that predicts increase in desorption force with polymer bending rigidity, active velocity and processivity of the motor proteins. Performing molecular dynamics simulations of the polymer in presence of a Langevin heat bath, and stochastic motor activity we obtain desorption phase diagrams that show good agreement with theory. With increase in pulling force, the polymer undergoes a first order phase transition from mostly adsorbed to fully desorbed state via a regime of coexistence where the steady state dynamics of the polyme...

  5. Effective rates from thermodynamically consistent coarse-graining of models for molecular motors with probe particles.

    Science.gov (United States)

    Zimmermann, Eva; Seifert, Udo

    2015-02-01

    Many single-molecule experiments for molecular motors comprise not only the motor but also large probe particles coupled to it. The theoretical analysis of these assays, however, often takes into account only the degrees of freedom representing the motor. We present a coarse-graining method that maps a model comprising two coupled degrees of freedom which represent motor and probe particle to such an effective one-particle model by eliminating the dynamics of the probe particle in a thermodynamically and dynamically consistent way. The coarse-grained rates obey a local detailed balance condition and reproduce the net currents. Moreover, the average entropy production as well as the thermodynamic efficiency is invariant under this coarse-graining procedure. Our analysis reveals that only by assuming unrealistically fast probe particles, the coarse-grained transition rates coincide with the transition rates of the traditionally used one-particle motor models. Additionally, we find that for multicyclic motors the stall force can depend on the probe size. We apply this coarse-graining method to specific case studies of the F(1)-ATPase and the kinesin motor.

  6. A hopping mechanism for cargo transport by molecular motors in crowded microtubules

    CERN Document Server

    Goldman, Carla

    2010-01-01

    Most models designed to study the bidirectional movement of cargos as they are driven by molecular motors rely on the idea that motors of different polarities can be coordinated by external agents if arranged into a motor-cargo complex to perform the necessary work [gross04]. Although these models have provided us with important insights into these phenomena, there are still many unanswered questions regarding the mechanisms through which the movement of the complex takes place on crowded microtubules. For example (i) how does cargo-binding affect motor motility? and in connection with that - (ii) how does the presence of other motors (and also other cargos) on the microtubule affect the motility of the motor-cargo complex? We discuss these questions from a different perspective. The movement of a cargo is conceived here as a hopping process resulting from the transference of cargo between neighboring motors. In the light of this, we examine the conditions under which cargo might display bidirectional movemen...

  7. Adhesion of Photon-Driven Molecular Motors to Surfaces via 1,3-Dipolar Cycloadditions : Effect of Interfacial Interactions on Molecular Motion

    NARCIS (Netherlands)

    Carroll, Gregory T.; London, Gabor; Fernández Landaluce, Tatiana; Rudolf, Petra; Feringa, Ben L.

    2011-01-01

    We report the attachment of altitudinal light-driven molecular motors to surfaces using 1,3-dipolar cycloaddition reactions. Molecular motors were designed containing azide or alkyne groups for attachment to alkyne- or azide-modified surfaces. Surface attachment was characterized by UV-vis, IR, XPS,

  8. Towards Dynamic Control of Wettability by Using Functionalized Altitudinal Molecular Motors on Solid Surfaces

    NARCIS (Netherlands)

    London, Gabor; Chen, Kuang-Yen; Carroll, Gregory T.; Feringa, Ben L.

    2013-01-01

    We report the synthesis of altitudinal molecular motors that contain functional groups in their rotor part. In an approach to achieve dynamic control over the properties of solid surfaces, a hydrophobic perfluorobutyl chain and a relatively hydrophilic cyano group were introduced to the rotor part o

  9. Kinetic analysis of the rotation rate of light-driven unidirectional molecular motors

    NARCIS (Netherlands)

    Klok, Martin; Browne, Wesley R.; Feringa, Ben L.

    2009-01-01

    The combination of a photochemical and a thermal equilibrium in overcrowded alkenes, which is the basis for unidirectional rotation of light-driven molecular rotary motors, is analysed in relation to the actual average rotation rates of such structures. Experimental parameters such as temperature, c

  10. Structural Dynamics of Overcrowded Alkene-Based Molecular Motors during Thermal Isomerization

    NARCIS (Netherlands)

    Cnossen, Arjen; Kistemaker, Jos C. M.; Kojima, Tatsuo; Feringa, Ben L.

    2014-01-01

    Synthetic light-driven rotary molecular motors show complicated structural dynamics during the rotation process. A combination of DFT calculations and various spectroscopic techniques is employed to study the effect of the bridging group in the lower half of the molecule on the conformational dynami

  11. Allosteric Regulation of the Rotational Speed in a Light-Driven Molecular Motor

    NARCIS (Netherlands)

    Faulkner, Adele; van Leeuwen, Thomas; Feringa, Ben L; Wezenberg, Sander J

    2016-01-01

    The rotational speed of an overcrowded alkene-based molecular rotary motor, having an integrated 4,5-diazafluorenyl coordination motif, can be regulated allosterically via the binding of metal ions. DFT calculations have been used to predict the relative speed of rotation of three different (i.e. zi

  12. Design and Construction of a One-Dimensional DNA Track for an Artificial Molecular Motor

    Directory of Open Access Journals (Sweden)

    Suzana Kovacic

    2012-01-01

    Full Text Available DNA is a versatile heteropolymer that shows great potential as a building block for a diverse array of nanostructures. We present here a solution to the problem of designing and synthesizing a DNA-based nanostructure that will serve as the track along which an artificial molecular motor processes. This one-dimensional DNA track exhibits periodically repeating elements that provide specific binding sites for the molecular motor. Besides these binding elements, additional sequences are necessary to label specific regions within the DNA track and to facilitate track construction. Designing an ideal DNA track sequence presents a particular challenge because of the many variable elements that greatly expand the number of potential sequences from which the ideal sequence must be chosen. In order to find a suitable DNA sequence, we have adapted a genetic algorithm which is well suited for a large but sparse search space. This algorithm readily identifies long DNA sequences that include all the necessary elements to both facilitate DNA track construction and to present appropriate binding sites for the molecular motor. We have successfully experimentally incorporated the sequence identified by the algorithm into a long DNA track meeting the criteria for observation of the molecular motor's activity.

  13. Fine tuning of the rotary motion by structural modification in light-driven unidirectional molecular motors

    NARCIS (Netherlands)

    Vicario, J; Walko, M; Meetsma, A; Feringa, Ben L.

    2006-01-01

    The introduction of bulky substituents at the stereogenic center of light-driven second-generation molecular motors results in an acceleration of the speed of rotation. This is due to a more strained structure with elongated C=C bonds and a higher energy level of the ground state relative to the tra

  14. In situ control of polymer helicity with a non-covalently bound photoresponsive molecular motor dopant.

    Science.gov (United States)

    van Leeuwen, Thomas; Heideman, G Henrieke; Zhao, Depeng; Wezenberg, Sander J; Feringa, Ben L

    2017-06-13

    The transfer of chirality from a molecular motor to a dynamic helical polymer via ionic interactions was investigated. A dopant with photoswitchable chirality was able to induce a preferred helicity in a poly(phenylacetylene) polymer and the helicity is inverted upon irradiation. The findings described herein will advance the development of functional and responsive polymeric systems.

  15. Photoinduced Reorganization of Motor-Doped Chiral Liquid Crystals : Bridging Molecular Isomerization and Texture Rotation

    NARCIS (Netherlands)

    Bosco, Alessandro; Jongejan, Mahthild G. M.; Eelkema, Rienk; Katsonis, Nathalie; Lacaze, Ernmanuelle; Ferrarini, Alberta; Feringa, Ben L.; Lacaze, Emmanuelle

    2008-01-01

    We recently reported that the photoisomerization of molecular motors used as chiral dopants in a cholesteric liquid crystal film induces a rotational reorganization which can be observed by optical microscopy and produces the motion of microscopic objects placed on top of the film (Feringa, B. L.;

  16. Towards Dynamic Control of Wettability by Using Functionalized Altitudinal Molecular Motors on Solid Surfaces

    NARCIS (Netherlands)

    London, Gabor; Chen, Kuang-Yen; Carroll, Gregory T.; Feringa, Ben L.

    2013-01-01

    We report the synthesis of altitudinal molecular motors that contain functional groups in their rotor part. In an approach to achieve dynamic control over the properties of solid surfaces, a hydrophobic perfluorobutyl chain and a relatively hydrophilic cyano group were introduced to the rotor part

  17. Characterizing the composition of molecular motors on moving axonal cargo using "cargo mapping" analysis.

    Science.gov (United States)

    Neumann, Sylvia; Campbell, George E; Szpankowski, Lukasz; Goldstein, Lawrence S B; Encalada, Sandra E

    2014-10-30

    Understanding the mechanisms by which molecular motors coordinate their activities to transport vesicular cargoes within neurons requires the quantitative analysis of motor/cargo associations at the single vesicle level. The goal of this protocol is to use quantitative fluorescence microscopy to correlate ("map") the position and directionality of movement of live cargo to the composition and relative amounts of motors associated with the same cargo. "Cargo mapping" consists of live imaging of fluorescently labeled cargoes moving in axons cultured on microfluidic devices, followed by chemical fixation during recording of live movement, and subsequent immunofluorescence (IF) staining of the exact same axonal regions with antibodies against motors. Colocalization between cargoes and their associated motors is assessed by assigning sub-pixel position coordinates to motor and cargo channels, by fitting Gaussian functions to the diffraction-limited point spread functions representing individual fluorescent point sources. Fixed cargo and motor images are subsequently superimposed to plots of cargo movement, to "map" them to their tracked trajectories. The strength of this protocol is the combination of live and IF data to record both the transport of vesicular cargoes in live cells and to determine the motors associated to these exact same vesicles. This technique overcomes previous challenges that use biochemical methods to determine the average motor composition of purified heterogeneous bulk vesicle populations, as these methods do not reveal compositions on single moving cargoes. Furthermore, this protocol can be adapted for the analysis of other transport and/or trafficking pathways in other cell types to correlate the movement of individual intracellular structures with their protein composition. Limitations of this protocol are the relatively low throughput due to low transfection efficiencies of cultured primary neurons and a limited field of view available for

  18. Macroscopic contraction of a gel induced by the integrated motion of light-driven molecular motors.

    Science.gov (United States)

    Li, Quan; Fuks, Gad; Moulin, Emilie; Maaloum, Mounir; Rawiso, Michel; Kulic, Igor; Foy, Justin T; Giuseppone, Nicolas

    2015-02-01

    Making molecular machines that can be useful in the macroscopic world is a challenging long-term goal of nanoscience. Inspired by the protein machinery found in biological systems, and based on the theoretical understanding of the physics of motion at the nanoscale, organic chemists have developed a number of molecules that can produce work by contraction or rotation when triggered by various external chemical or physical stimuli. In particular, basic molecular switches that commute between at least two thermodynamic minima and more advanced molecular motors that behave as dissipative units working far from equilibrium when fuelled with external energy have been reported. However, despite recent progress, the ultimate challenge of coordinating individual molecular motors in a continuous mechanical process that can have a measurable effect at the macroscale has remained elusive. Here, we show that by integrating light-driven unidirectional molecular rotors as reticulating units in a polymer gel, it is possible to amplify their individual motions to achieve macroscopic contraction of the material. Our system uses the incoming light to operate under far-from-equilibrium conditions, and the work produced by the motor in the photostationary state is used to twist the entangled polymer chains up to the collapse of the gel. Our design could be a starting point to integrate nanomotors in metastable materials to store energy and eventually to convert it.

  19. Macroscopic contraction of a gel induced by the integrated motion of light-driven molecular motors

    Science.gov (United States)

    Li, Quan; Fuks, Gad; Moulin, Emilie; Maaloum, Mounir; Rawiso, Michel; Kulic, Igor; Foy, Justin T.; Giuseppone, Nicolas

    2015-02-01

    Making molecular machines that can be useful in the macroscopic world is a challenging long-term goal of nanoscience. Inspired by the protein machinery found in biological systems, and based on the theoretical understanding of the physics of motion at the nanoscale, organic chemists have developed a number of molecules that can produce work by contraction or rotation when triggered by various external chemical or physical stimuli. In particular, basic molecular switches that commute between at least two thermodynamic minima and more advanced molecular motors that behave as dissipative units working far from equilibrium when fuelled with external energy have been reported. However, despite recent progress, the ultimate challenge of coordinating individual molecular motors in a continuous mechanical process that can have a measurable effect at the macroscale has remained elusive. Here, we show that by integrating light-driven unidirectional molecular rotors as reticulating units in a polymer gel, it is possible to amplify their individual motions to achieve macroscopic contraction of the material. Our system uses the incoming light to operate under far-from-equilibrium conditions, and the work produced by the motor in the photostationary state is used to twist the entangled polymer chains up to the collapse of the gel. Our design could be a starting point to integrate nanomotors in metastable materials to store energy and eventually to convert it.

  20. Light-driven rotary molecular motors without point chirality: a minimal design.

    Science.gov (United States)

    Wang, Jun; Oruganti, Baswanth; Durbeej, Bo

    2017-03-08

    A fundamental requirement for achieving photoinduced unidirectional rotary motion about an olefinic bond in a molecular motor is that the potential energy surface of the excited state is asymmetric with respect to clockwise and counterclockwise rotations. In most available light-driven rotary molecular motors, such asymmetry is guaranteed by the presence of a stereocenter. Here, we present non-adiabatic molecular dynamics simulations based on multiconfigurational quantum chemistry to demonstrate that this chiral feature is not essential for inducing unidirectional rotary motion in molecules that incorporate a cyclohexenylidene moiety into a protonated Schiff-base framework. Rather, the simulations show that it is possible to exploit the intrinsic asymmetry of the puckered cyclohexenylidene to control the direction of photoinduced rotation.

  1. Extracting the stepping dynamics of molecular motors in living cells from trajectories of single particles.

    Science.gov (United States)

    Bruno, Augusto; Bruno, Luciana; Levi, Valeria

    2013-01-01

    Molecular motors are responsible of transporting a wide variety of cargos in the cytoplasm. Current efforts are oriented to characterize the biophysical properties of motors in cells with the aim of elucidating the mechanisms of these nanomachines in the complex cellular environment. In this study, we present an algorithm designed to extract motor step sizes and dwell times between steps from trajectories of motors or cargoes driven by motors in cells. The algorithm is based on finding patterns in the trajectory compatible with the behavior expected for a motor step, i.e., a region of confined motion followed by a jump in the position to another region of confined motion with similar characteristics to the previous one. We show that this algorithm allows the analysis of 2D trajectories even if they present complex motion patterns such as active transport interspersed with diffusion and does not require the assumption of a given step size or dwell period. The confidence on the step detection can be easily obtained and allows the evaluation of the confidence of the dwell and step size distributions. To illustrate the possible applications of this algorithm, we analyzed trajectories of myosin-V driven organelles in living cells.

  2. Purification, characterization, and coal depolymerizing activity of lignin peroxidase from Gloeophyllum sepiarium MTCC-1170

    Energy Technology Data Exchange (ETDEWEB)

    Yadav, M.; Yadav, P.; Yadav, K.D.S. [DDU Gorakhpur University, Gorakhpur (India). Dept. of Chemistry

    2009-10-15

    Lignin peroxidase from the liquid culture filtrate of Gloeophyllum sepiarium MTCC-1170 has been purified to homogeneity. The molecular weight of the purified enzyme was 42 kDa as determined by SDS-PAGE. The K{sub m} values were 54 and 76 {mu}M for veratryl alcohol and H{sub 2}O{sub 2}, respectively. The pH and temperature optima were 2.5 and 25{sup o}C, respectively. Depolymerization of coal by the fungal strain has been demonstrated using humic acid as a model of coal. Depolymerization of humic acid by the purified lignin peroxidase has been shown by the decrease in absorbance at 450 nm and increase in absorbance at 360 nm in presence of H{sub 2}O{sub 2}. Depolymerization of humic acid by the purified enzyme has also been demonstrated by the decrease in the viscosity with time of the reaction solution containing humic acid, H{sub 2}O{sub 2}, and the purified lignin peroxidase. The influence of NaCl and NaN{sub 3} and inhibitory effects of various metal chelating agents on the lignin peroxidase activity were studied.

  3. Effective Potential of a Two-State Model for Molecular Motor

    Institute of Scientific and Technical Information of China (English)

    HAN Ying-Rong; ZHAO Tong-Jun; ZHAN-Yong; YAN Wei-Li

    2005-01-01

    We study force generation and motion of molecular motors using a simple two-state model in the paper.Asymmetric and periodic potential is adopted to describe the interaction between motor proteins and filaments that are periodic and polar. The current and the slope of the effective potential as functions of the temperature and transition rates are calculated in the two-state model. The ratio of the slope of the effective potential to the current is also calculated. It is shown that the directed motion of motor proteins is relevant to the effective potential. The slope of the effective potential corresponds to an average force. The non-vanishing force therefore implies that detailed balance is broken in the process of transition between different states.

  4. Analysis of persistence during intracellular actin-based transport mediated by molecular motors

    Energy Technology Data Exchange (ETDEWEB)

    Pallavicini, C; Levi, V; Bruno, L [Departamento de Fisica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, 1428 Buenos Aires (Argentina); Desposito, M A, E-mail: lbruno@df.uba.a

    2010-09-01

    The displacement of particles or probes in the cell cytoplasm as a function of time is characterized by different anomalous diffusion regimes. The transport of large cargoes, such as organelles, vesicles or large proteins, involves the action of ATP-consuming molecular motors. We investigate the motion of pigment organelles driven by myosin-V motors in Xenopus laevis melanocytes using a high spatio-temporal resolution tracking technique. By analyzing the turning angles ({phi}) of the obtained 2D trajectories as a function of the time lag, we determine the critical time of the transition between anticorrelated and directed motion as the time when the turning angles begin to concentrate around {phi} = 0. We relate this transition with the crossover from subdiffusive to superdiffusive behavior observed in a previous work [5]. We also assayed the properties of the trajectories in cells with inhibited myosin activity, and we can compare the results in the presence and absence of active motors.

  5. Asymptotic Analysis of Microtubule-Based Transport by Multiple Identical Molecular Motors

    CERN Document Server

    McKinley, Scott A; Fricks, John; Kramer, Peter R

    2011-01-01

    We describe a system of stochastic differential equations (SDEs) which model the interaction between processive molecular motors, such as kinesin and dynein, and the biomolecular cargo they tow as part of microtubule-based intracellular transport. We show that the classical experimental environment fits within a parameter regime which is qualitatively distinct from conditions one expects to find in living cells. Through an asymptotic analysis of our system of SDEs, we develop a means for applying in vitro observations of the nonlinear response by motors to forces induced on the attached cargo to make analytical predictions for two parameter regimes that have thus far eluded direct experimental observation: 1) highly viscous in vivo transport and 2) dynamics when multiple identical motors are attached to the cargo and microtubule.

  6. Operations and thermodynamics of an artificial rotary molecular motor in solution.

    Science.gov (United States)

    Moro, Lorenzo; di Giosia, Matteo; Calvaresi, Matteo; Bakalis, Evangelos; Zerbetto, Francesco

    2014-06-23

    A general framework is provided that makes possible the estimation of time-dependent properties of a stochastic system moving far from equilibrium. The process is investigated and discussed in general terms of nonequilibrium thermodynamics. The approach is simple and can be exploited to gain insight into the dynamics of any molecular-level machine. As a case study, the dynamics of an artificial molecular rotary motor, similar to the inversion of a helix, which drives the motor from a metastable state to equilibrium, are examined. The energy path that the motor walks was obtained from the results of atomistic calculations. The motor undergoes unidirectional rotation and its entropy, internal energy, free energy, and net exerted force are given as a function of time, starting from the solution of Smoluchowski's equation. The rather low value of the organization index, that is, the ratio of the work done by the particle against friction during the unidirectional motion per available free energy, reveals that the motion is mainly subject to randomness, and the amount of energy converted to heat due to the directional motion is very small.

  7. A unified phenomenological analysis of the experimental velocity curves in molecular motors.

    Science.gov (United States)

    Ciudad, Aleix; Sancho, J M

    2008-06-14

    We present a unified phenomenological kinetic framework to analyze the experimental data of several motor proteins (either linear or rotatory). This formalism allows us to discriminate the characteristic times of most relevant subprocesses. Explicitly, internal mechanical as well as chemical times are taken into account and joined together in a full-cycle time where effusion, diffusion and chemical rates, viscoelastic friction, and overdamped motion are considered. This approach clarifies the most relevant mechanisms in a particular motor by using the available experimental data of velocity versus external load and substrate concentration. We apply our analysis to three real molecular motors for which enough experimental data are available: the bacterial flagellar motor [Yoshiyuki et al., J. Mol. Biol. 377, 1043 (2003)], conventional kinesin (kinesin-1) [Block et al., Proc. Natl. Acad. Sci. U.S.A. 100, 2351 (2003)], and a RAN polymerase [Abbondanzieril, Nature (London) 438, 460 (2003)]. Moreover, the mechanism of stalling a motor is revised and split into two different concepts (mechanical and chemical stalling) that shed light to the understanding of backstepping in kinesin-1.

  8. Structural and Molecular Basis for Coordination in a Viral DNA Packaging Motor

    Directory of Open Access Journals (Sweden)

    Huzhang Mao

    2016-03-01

    Full Text Available Ring NTPases are a class of ubiquitous molecular motors involved in basic biological partitioning processes. dsDNA viruses encode ring ATPases that translocate their genomes to near-crystalline densities within pre-assembled viral capsids. Here, X-ray crystallography, cryoEM, and biochemical analyses of the dsDNA packaging motor in bacteriophage phi29 show how individual subunits are arranged in a pentameric ATPase ring and suggest how their activities are coordinated to translocate dsDNA. The resulting pseudo-atomic structure of the motor and accompanying functional analyses show how ATP is bound in the ATPase active site; identify two DNA contacts, including a potential DNA translocating loop; demonstrate that a trans-acting arginine finger is involved in coordinating hydrolysis around the ring; and suggest a functional coupling between the arginine finger and the DNA translocating loop. The ability to visualize the motor in action illuminates how the different motor components interact with each other and with their DNA substrate.

  9. Structural and Molecular Basis for Coordination in a Viral DNA Packaging Motor

    Science.gov (United States)

    Reyes-Aldrete, Emilio; Sherman, Michael B.; Woodson, Michael; Atz, Rockney; Grimes, Shelley; Jardine, Paul J.; Morais, Marc C.

    2016-01-01

    SUMMARY Ring NTPases are a class of ubiquitous molecular motors involved in basic biological partitioning processes. dsDNA viruses encode ring ATPases that translocate their genomes to near-crystalline densities within pre-assembled viral capsids. Here, X-ray crystallography, cryoEM, and biochemical analyses of the dsDNA packaging motor in bacteriophage phi29 show how individual subunits are arranged in a pentameric ATPase ring, and suggest how their activities are coordinated to translocate dsDNA. The resulting pseudo-atomic structure of the motor and accompanying functional analyses show how ATP is bound in the ATPase active site; identify two DNA contacts, including a potential DNA translocating loop; demonstrate that a trans-acting arginine finger is involved in coordinating hydrolysis around the ring; and suggest a functional coupling between the arginine finger and the DNA translocating loop. The ability to visualize the motor in action illuminates how the different motor components interact with each other and with their DNA substrate. PMID:26904950

  10. How molecular motors extract order from chaos (a key issues review)

    Science.gov (United States)

    Hoffmann, Peter M.

    2016-03-01

    Molecular motors are the workhorses of living cells. Seemingly by ‘magic’, these molecules are able to complete purposeful tasks while being immersed in a sea of thermal chaos. Here, we review the current understanding of how these machines work, present simple models based on thermal ratchets, discuss implications for statistical physics, and provide an overview of ongoing research in this important and fascinating field of study.

  11. Recent Development in Chemical Depolymerization of Lignin: A Review

    Directory of Open Access Journals (Sweden)

    Hai Wang

    2013-01-01

    Full Text Available This article reviewed recent development of chemical depolymerization of lignins. There were five types of treatment discussed, including base-catalyzed, acid-catalyzed, metallic catalyzed, ionic liquids-assisted, and supercritical fluids-assisted lignin depolymerizations. The methods employed in this research were described, and the important results were marked. Generally, base-catalyzed and acid-catalyzed methods were straightforward, but the selectivity was low. The severe reaction conditions (high pressure, high temperature, and extreme pH resulted in requirement of specially designed reactors, which led to high costs of facility and handling. Ionic liquids, and supercritical fluids-assisted lignin depolymerizations had high selectivity, but the high costs of ionic liquids recycling and supercritical fluid facility limited their applications on commercial scale biomass treatment. Metallic catalyzed depolymerization had great advantages because of its high selectivity to certain monomeric compounds and much milder reaction condition than base-catalyzed or acid-catalyzed depolymerizations. It would be a great contribution to lignin conversion if appropriate catalysts were synthesized.

  12. Computational Insight to Improve the Thermal Isomerisation Performance of Overcrowded Alkene-Based Molecular Motors through Structural Redesign.

    Science.gov (United States)

    Oruganti, Baswanth; Wang, Jun; Durbeej, Bo

    2016-11-04

    Synthetic overcrowded alkene-based molecular motors achieve 360° unidirectional rotary motion of one motor half (rotator) relative to the other (stator) through sequential photochemical and thermal isomerisation steps. In order to facilitate and expand the use of these motors for various applications, it is important to investigate ways to increase the rates and efficiencies of the reactions governing the rotary motion. Here, we use computational methods to explore whether the thermal isomerisation performance of some of the fastest available motors of this type can be further improved by reducing the sizes of the motor halves. Presenting three new redesigned motors that combine an indanylidene rotator with a cyclohexadiene, pyran or thiopyran stator, we first use multiconfigurational quantum chemical methods to verify that the photoisomerisations of these motors sustain unidirectional rotary motion. Then, by performing density functional calculations, we identify both stepwise and concerted mechanisms for the thermal isomerisations of the motors and show that the rate-determining free-energy barriers of these processes are up to 25 kJ mol(-1) smaller than those of the original motors. Furthermore, the thermal isomerisations of the redesigned motors proceed in fewer steps. Altogether, the results suggest that the redesigned motors are useful templates for improving the thermal isomerisation performance of existing overcrowded alkene-based motors.

  13. A non-Markov ratchet model of molecular motors: processive movement of single-headed kinesin KIF1A

    Institute of Scientific and Technical Information of China (English)

    Xie Ping; Dou Shuo-Xing; Wang Peng-Ye

    2006-01-01

    A fluctuating ratchet model of non-Markov process is presented to describe the processive movement of molecular motors of single-headed kinesin KIF1A, where the fluctuation perturbation to the local potential is introduced and the detailed ATPase pathway of the motor is included. The theoretical results show good quantitative agreement with the previous experimental ones.

  14. Stochastic dynamics of small ensembles of non-processive molecular motors: the parallel cluster model.

    Science.gov (United States)

    Erdmann, Thorsten; Albert, Philipp J; Schwarz, Ulrich S

    2013-11-07

    Non-processive molecular motors have to work together in ensembles in order to generate appreciable levels of force or movement. In skeletal muscle, for example, hundreds of myosin II molecules cooperate in thick filaments. In non-muscle cells, by contrast, small groups with few tens of non-muscle myosin II motors contribute to essential cellular processes such as transport, shape changes, or mechanosensing. Here we introduce a detailed and analytically tractable model for this important situation. Using a three-state crossbridge model for the myosin II motor cycle and exploiting the assumptions of fast power stroke kinetics and equal load sharing between motors in equivalent states, we reduce the stochastic reaction network to a one-step master equation for the binding and unbinding dynamics (parallel cluster model) and derive the rules for ensemble movement. We find that for constant external load, ensemble dynamics is strongly shaped by the catch bond character of myosin II, which leads to an increase of the fraction of bound motors under load and thus to firm attachment even for small ensembles. This adaptation to load results in a concave force-velocity relation described by a Hill relation. For external load provided by a linear spring, myosin II ensembles dynamically adjust themselves towards an isometric state with constant average position and load. The dynamics of the ensembles is now determined mainly by the distribution of motors over the different kinds of bound states. For increasing stiffness of the external spring, there is a sharp transition beyond which myosin II can no longer perform the power stroke. Slow unbinding from the pre-power-stroke state protects the ensembles against detachment.

  15. Stochastic dynamics of small ensembles of non-processive molecular motors: The parallel cluster model

    Science.gov (United States)

    Erdmann, Thorsten; Albert, Philipp J.; Schwarz, Ulrich S.

    2013-11-01

    Non-processive molecular motors have to work together in ensembles in order to generate appreciable levels of force or movement. In skeletal muscle, for example, hundreds of myosin II molecules cooperate in thick filaments. In non-muscle cells, by contrast, small groups with few tens of non-muscle myosin II motors contribute to essential cellular processes such as transport, shape changes, or mechanosensing. Here we introduce a detailed and analytically tractable model for this important situation. Using a three-state crossbridge model for the myosin II motor cycle and exploiting the assumptions of fast power stroke kinetics and equal load sharing between motors in equivalent states, we reduce the stochastic reaction network to a one-step master equation for the binding and unbinding dynamics (parallel cluster model) and derive the rules for ensemble movement. We find that for constant external load, ensemble dynamics is strongly shaped by the catch bond character of myosin II, which leads to an increase of the fraction of bound motors under load and thus to firm attachment even for small ensembles. This adaptation to load results in a concave force-velocity relation described by a Hill relation. For external load provided by a linear spring, myosin II ensembles dynamically adjust themselves towards an isometric state with constant average position and load. The dynamics of the ensembles is now determined mainly by the distribution of motors over the different kinds of bound states. For increasing stiffness of the external spring, there is a sharp transition beyond which myosin II can no longer perform the power stroke. Slow unbinding from the pre-power-stroke state protects the ensembles against detachment.

  16. Molecular interactions and residues involved in force generation in the T4 viral DNA packaging motor.

    Science.gov (United States)

    Migliori, Amy D; Smith, Douglas E; Arya, Gaurav

    2014-12-12

    Many viruses utilize molecular motors to package their genomes into preformed capsids. A striking feature of these motors is their ability to generate large forces to drive DNA translocation against entropic, electrostatic, and bending forces resisting DNA confinement. A model based on recently resolved structures of the bacteriophage T4 motor protein gp17 suggests that this motor generates large forces by undergoing a conformational change from an extended to a compact state. This transition is proposed to be driven by electrostatic interactions between complementarily charged residues across the interface between the N- and C-terminal domains of gp17. Here we use atomistic molecular dynamics simulations to investigate in detail the molecular interactions and residues involved in such a compaction transition of gp17. We find that although electrostatic interactions between charged residues contribute significantly to the overall free energy change of compaction, interactions mediated by the uncharged residues are equally if not more important. We identify five charged residues and six uncharged residues at the interface that play a dominant role in the compaction transition and also reveal salt bridging, van der Waals, and solvent hydrogen-bonding interactions mediated by these residues in stabilizing the compact form of gp17. The formation of a salt bridge between Glu309 and Arg494 is found to be particularly crucial, consistent with experiments showing complete abrogation in packaging upon Glu309Lys mutation. The computed contributions of several other residues are also found to correlate well with single-molecule measurements of impairments in DNA translocation activity caused by site-directed mutations.

  17. Stochastic dynamics of small ensembles of non-processive molecular motors: the parallel cluster model

    CERN Document Server

    Erdmann, Thorsten; Schwarz, Ulrich S

    2013-01-01

    Non-processive molecular motors have to work together in ensembles in order to generate appreciable levels of force or movement. In skeletal muscle, for example, hundreds of myosin II molecules cooperate in thick filaments. In non-muscle cells, by contrast, small groups with few tens of non-muscle myosin II motors contribute to essential cellular processes such as transport, shape changes or mechanosensing. Here we introduce a detailed and analytically tractable model for this important situation. Using a three-state crossbridge model for the myosin II motor cycle and exploiting the assumptions of fast power stroke kinetics and equal load sharing between motors in equivalent states, we reduce the stochastic reaction network to a one-step master equation for the binding and unbinding dynamics (parallel cluster model) and derive the rules for ensemble movement. We find that for constant external load, ensemble dynamics is strongly shaped by the catch bond character of myosin II, which leads to an increase of th...

  18. Discrete Step Sizes of Molecular Motors Lead to Bimodal Non-Gaussian Velocity Distributions under Force

    Science.gov (United States)

    Vu, Huong T.; Chakrabarti, Shaon; Hinczewski, Michael; Thirumalai, D.

    2016-08-01

    Fluctuations in the physical properties of biological machines are inextricably linked to their functions. Distributions of run lengths and velocities of processive molecular motors, like kinesin-1, are accessible through single-molecule techniques, but rigorous theoretical models for these probabilities are lacking. Here, we derive exact analytic results for a kinetic model to predict the resistive force (F )-dependent velocity [P (v )] and run length [P (n )] distribution functions of generic finitely processive molecular motors. Our theory quantitatively explains the zero force kinesin-1 data for both P (n ) and P (v ) using the detachment rate as the only parameter. In addition, we predict the F dependence of these quantities. At nonzero F , P (v ) is non-Gaussian and is bimodal with peaks at positive and negative values of v , which is due to the discrete step size of kinesin-1. Although the predictions are based on analyses of kinesin-1 data, our results are general and should hold for any processive motor, which walks on a track by taking discrete steps.

  19. Molecular motor-induced instabilities and cross linkers determine biopolymer organization.

    Energy Technology Data Exchange (ETDEWEB)

    Smith, D.; Ziebert, F.; Humphrey, D.; Duggan, C.; Steinbeck, M.; Zimmermann, W.; Kas, J.; Materials Science Division; Univ. of Leipzig; Univ. of Texas at Austin; Univ. Bayreuth

    2007-01-01

    All eukaryotic cells rely on the active self-organization of protein filaments to form a responsive intracellular cytoskeleton. The necessity of motility and reaction to stimuli additionally requires pathways that quickly and reversibly change cytoskeletal organization. While thermally driven order-disorder transitions are, from the viewpoint of physics, the most obvious method for controlling states of organization, the timescales necessary for effective cellular dynamics would require temperatures exceeding the physiologically viable temperature range. We report a mechanism whereby the molecular motor myosin II can cause near-instantaneous order-disorder transitions in reconstituted cytoskeletal actin solutions. When motor-induced filament sliding diminishes, the actin network structure rapidly and reversibly self-organizes into various assemblies. Addition of stable cross linkers was found to alter the architectures of ordered assemblies. These isothermal transitions between dynamic disorder and self-assembled ordered states illustrate that the interplay between passive crosslinking and molecular motor activity plays a substantial role in dynamic cellular organization.

  20. Carbon Nanotube Based Molecular Electronics and Motors: A View from Classical and Quantum Dynamics Simulations

    Science.gov (United States)

    Srivastava, Deepak; Saini, Subhash (Technical Monitor)

    1998-01-01

    The tubular forms of fullerenes popularly known as carbon nanotubes are experimentally produced as single-, multiwall, and rope configurations. The nanotubes and nanoropes have shown to exhibit unusual mechanical and electronic properties. The single wall nanotubes exhibit both semiconducting and metallic behavior. In short undefected lengths they are the known strongest fibers which are unbreakable even when bent in half. Grown in ropes their tensile strength is approximately 100 times greater than steel at only one sixth the weight. Employing large scale classical and quantum molecular dynamics simulations we will explore the use of carbon nanotubes and carbon nanotube junctions in 2-, 3-, and 4-point molecular electronic device components, dynamic strength characterization for compressive, bending and torsional strains, and chemical functionalization for possible use in a nanoscale molecular motor. The above is an unclassified material produced for non-competitive basic research in the nanotechnology area.

  1. Silanization of quartz, silicon and mica surfaces with light-driven molecular motors : construction of surface-bound photo-active nanolayers

    NARCIS (Netherlands)

    London, Gabor; Carroll, Gregory T.; Feringa, Ben L.

    2013-01-01

    The attachment of molecular rotary motors containing triethoxysilane functional groups to quartz, silicon and mica surfaces is described. Motors containing silane coupling agents in their structure form stable molecular layers on quartz and silicon surfaces. Motors attached to these surfaces were fo

  2. On the possibility of the in-cell molecular motors working as cargo moorings only

    CERN Document Server

    Lisowski, Bartosz

    2012-01-01

    Although active transport is considered the most efficient way of depositing materials in the appropriate compartments within living cells, free diffusion remains the energetically cheapest and most widespread determinant of the in-cell dynamics. Here we investigate the hypothesis of cargoes - vesicles or organelles - being transported by the means of free diffusion, limited spatially by the molecular motors. Routinely navigating through ever-changing and unsteady environment, utilizing chemical energy (e.g. from hydrolyzing ATP), as the result they transport cell's crucial components, such as neurotransmitters and organelles. In our model the motor, which we identify with kinesin-1 walking along the microtubule, tethers the cargo in the same manner as a mooring rope attached to a bollard holds a ship from drifting toward the open sea. We study the model behavior in the context of optical trap single molecule experiments, mimicking their procedures in our simulations and investigate how the mechanical propert...

  3. Molecular motors transporting cargos in viscoelastic cytosol: how to beat subdiffusion with a power stroke?

    CERN Document Server

    Goychuk, Igor; Metzler, Ralf

    2013-01-01

    Anomalously slow passive diffusion, $\\langle \\delta x^2(t)\\rangle\\simeq t^{\\alpha}$, with $0<\\alpha<1$, of larger tracers such as messenger RNA and endogenous submicron granules in the cytoplasm of living biological cells has been demonstrated in a number of experiments and has been attributed to the viscoelastic physical nature of the cellular cytoplasm. This finding provokes the question to which extent active intracellular transport is affected by this viscoelastic environment: does the subdiffusion of free submicron cargo such as vesicles and organelles always imply anomalously slow transport by molecular motors such as kinesins, that is, directed transport characterized by a sublinear growth of the mean distance, $\\langle x(t)\\rangle\\simeq t^{\\alpha_{\\rm eff}}$, with $0<\\alpha_{\\rm eff}<1$? Here we study a generic model approach combining the commonly accepted two-state Brownian ratchet model of kinesin motors based on the continuous-state diffusion along microtubule driven by a flashing bind...

  4. The Role of Molecular Microtubule Motors and the Microtubule Cytoskeleton in Stress Granule Dynamics

    Directory of Open Access Journals (Sweden)

    Kristen M. Bartoli

    2011-01-01

    Full Text Available Stress granules (SGs are cytoplasmic foci that appear in cells exposed to stress-induced translational inhibition. SGs function as a triage center, where mRNAs are sorted for storage, degradation, and translation reinitiation. The underlying mechanisms of SGs dynamics are still being characterized, although many key players have been identified. The main components of SGs are stalled 48S preinitiation complexes. To date, many other proteins have also been found to localize in SGs and are hypothesized to function in SG dynamics. Most recently, the microtubule cytoskeleton and associated motor proteins have been demonstrated to function in SG dynamics. In this paper, we will discuss current literature examining the function of microtubules and the molecular microtubule motors in SG assembly, coalescence, movement, composition, organization, and disassembly.

  5. Microtubule depolymerization induces traction force increase through two distinct pathways.

    Science.gov (United States)

    Rape, Andrew; Guo, Wei-hui; Wang, Yu-li

    2011-12-15

    Traction forces increase after microtubule depolymerization; however, the signaling mechanisms underlying this, in particular the dependence upon myosin II, remain unclear. We investigated the mechanism of traction force increase after nocodazole-induced microtubule depolymerization by applying traction force microscopy to cells cultured on micropatterned polyacrylamide hydrogels to obtain samples of homogeneous shape and size. Control cells and cells treated with a focal adhesion kinase (FAK) inhibitor showed similar increases in traction forces, indicating that the response is independent of FAK. Surprisingly, pharmacological inhibition of myosin II did not prevent the increase of residual traction forces upon nocodazole treatment. This increase was abolished upon pharmacological inhibition of FAK. These results suggest two distinct pathways for the regulation of traction forces. First, microtubule depolymerization activates a myosin-II-dependent mechanism through a FAK-independent pathway. Second, microtubule depolymerization also enhances traction forces through a myosin-II-independent, FAK-regulated pathway. Traction forces are therefore regulated by a complex network of complementary signals and force-generating mechanisms.

  6. Um modelo simplificado para a dinâmica de motores moleculares

    OpenAIRE

    Ferreira, Luiza Gomes

    2015-01-01

    Dissertação (mestrado) - Universidade Federal de Santa Catarina, Centro de Ciências Físicas e Matermáticas, Programa de Pós-Graduação em Física, Florianópolis, 2015. Neste trabalho desenvolvemos um estudo sobre motores moleculares. Um tema muito pesquisado na última década, e que se mostra cada vez mais amplo e interessante. Trabalhamos com modelos estocásticos a fim de modelar o movimento de proteínas motoras de transporte. Os principais exemplos desse tipo de proteína motora são a cinesi...

  7. Directed Motion of a Molecular Motor Based on the Four-State Model with Unequal Substeps

    Institute of Scientific and Technical Information of China (English)

    WU Wei-Xia; ZHAN Yong; ZHAO Tong-Jun; GUAN Rong-Hua; MEI Jun-Ping

    2003-01-01

    A periodic one-dimensional four-state hopping model is proposed. In the model, the substeps betweenarbitrary adjacent states are unequal, and an explicit solution of the master equation is first obtained for the probabilitydistribution as a function of the time and position for any initial distribution with all the transients included. Next, thetransient behaviors in the initial period of time and the characteristic time to reach the steady state for the molecularmotor are discussed. Finally, we compare the steady state results to experiments and illustrate qualitatively the kineticbehaviors of a molecular motor under external load F.

  8. Identification of enzymes responsible for extracellular alginate depolymerization and alginate metabolism in Vibrio algivorus.

    Science.gov (United States)

    Doi, Hidetaka; Tokura, Yuriko; Mori, Yukiko; Mori, Kenichi; Asakura, Yoko; Usuda, Yoshihiro; Fukuda, Hiroo; Chinen, Akito

    2017-02-01

    Alginate is a marine non-food-competing polysaccharide that has potential applications in biorefinery. Owing to its large size (molecular weight >300,000 Da), alginate cannot pass through the bacterial cell membrane. Therefore, bacteria that utilize alginate are presumed to have an enzyme that degrades extracellular alginate. Recently, Vibrio algivorus sp. SA2(T) was identified as a novel alginate-decomposing and alginate-utilizing species. However, little is known about the mechanism of alginate degradation and metabolism in this species. To address this issue, we screened the V. algivorus genomic DNA library for genes encoding polysaccharide-decomposing enzymes using a novel double-layer plate screening method and identified alyB as a candidate. Most identified alginate-decomposing enzymes (i.e., alginate lyases) must be concentrated and purified before extracellular alginate depolymerization. AlyB of V. algivorus heterologously expressed in Escherichia coli depolymerized extracellular alginate without requiring concentration or purification. We found seven homologues in the V. algivorus genome (alyB, alyD, oalA, oalB, oalC, dehR, and toaA) that are thought to encode enzymes responsible for alginate transport and metabolism. Introducing these genes into E. coli enabled the cells to assimilate soluble alginate depolymerized by V. algivorus AlyB as the sole carbon source. The alginate was bioconverted into L-lysine (43.3 mg/l) in E. coli strain AJIK01. These findings demonstrate a simple and novel screening method for identifying polysaccharide-degrading enzymes in bacteria and provide a simple alginate biocatalyst and fermentation system with potential applications in industrial biorefinery.

  9. Affinity of molecular interactions in the bacteriophage phi29 DNA packaging motor.

    Science.gov (United States)

    Robinson, Mark A; Wood, Jonathan P A; Capaldi, Stephanie A; Baron, Andrew J; Gell, Christopher; Smith, D Alastair; Stonehouse, Nicola J

    2006-01-01

    DNA packaging in the bacteriophage phi29 involves a molecular motor with protein and RNA components, including interactions between the viral connector protein and molecules of pRNA, both of which form multimeric complexes. Data are presented to demonstrate the higher order assembly of pRNA together with the affinity of pRNA:pRNA and pRNA:connector interactions, which are used to propose a model for motor function. In solution, pRNA can form dimeric and trimeric multimers in a magnesium-dependent manner, with dissociation constants for multimerization in the micromolar range. pRNA:connector binding is also facilitated by the presence of magnesium ions, with a nanomolar apparent dissociation constant for the interaction. From studies with a mutant pRNA, it appears that multimerization of pRNA is not essential for connector binding and it is likely that connector protein is involved in the stabilization of higher order RNA multimers. It is proposed that magnesium ions may promote conformational change that facilitate pRNA:connector interactions, essential for motor function.

  10. Affinity of molecular interactions in the bacteriophage φ29 DNA packaging motor

    Science.gov (United States)

    Robinson, Mark A.; Wood, Jonathan P.A.; Capaldi, Stephanie A.; Baron, Andrew J.; Gell, Christopher; Smith, D. Alastair; Stonehouse, Nicola J.

    2006-01-01

    DNA packaging in the bacteriophage φ29 involves a molecular motor with protein and RNA components, including interactions between the viral connector protein and molecules of pRNA, both of which form multimeric complexes. Data are presented to demonstrate the higher order assembly of pRNA together with the affinity of pRNA:pRNA and pRNA:connector interactions, which are used to propose a model for motor function. In solution, pRNA can form dimeric and trimeric multimers in a magnesium-dependent manner, with dissociation constants for multimerization in the micromolar range. pRNA:connector binding is also facilitated by the presence of magnesium ions, with a nanomolar apparent dissociation constant for the interaction. From studies with a mutant pRNA, it appears that multimerization of pRNA is not essential for connector binding and it is likely that connector protein is involved in the stabilization of higher order RNA multimers. It is proposed that magnesium ions may promote conformational change that facilitate pRNA:connector interactions, essential for motor function. PMID:16714447

  11. A chemically powered unidirectional rotary molecular motor based on a palladium redox cycle

    Science.gov (United States)

    Collins, Beatrice S. L.; Kistemaker, Jos C. M.; Otten, Edwin; Feringa, Ben L.

    2016-09-01

    The conversion of chemical energy to drive directional motion at the molecular level allows biological systems, ranging from subcellular components to whole organisms, to perform a myriad of dynamic functions and respond to changes in the environment. Directional movement has been demonstrated in artificial molecular systems, but the fundamental motif of unidirectional rotary motion along a single-bond rotary axle induced by metal-catalysed transformation of chemical fuels has not been realized, and the challenge is to couple the metal-centred redox processes to stepwise changes in conformation to arrive at a full unidirectional rotary cycle. Here, we present the design of an organopalladium-based motor and the experimental demonstration of a 360° unidirectional rotary cycle using simple chemical fuels. Exploiting fundamental reactivity principles in organometallic chemistry enables control of directional rotation and offers the potential of harnessing the wealth of opportunities offered by transition-metal-based catalytic conversions to drive motion and dynamic functions.

  12. A Research on the Depolymerization of Chitosan with the Aid of Papain%木瓜蛋白酶降解甲壳胺的研究

    Institute of Scientific and Technical Information of China (English)

    叶眉; 薛长湖; 方煜; 孙方强

    2000-01-01

    One kind of papain was used to depolymerize chitosan in this paper. Four factors of reactions were studied including concentration of enzyme, pH, temperature and time. The result indicated that temperature influenced the depolymerization of chitosan efficiently, while time had relatively little effect on it with pH from 3.0 to 6.0, temperature from 30℃ to 60℃, and time from 2 to 8 hours. The data revealed that the enzymatic process did not obey a simple kinetic model; chitosan with average molecular weights in the range (5-10)×105 could be easily depolymerized to highly polydisperse chitosans under conditions such as pH 4.0, 40℃, 8 hrs, and papain 1.5 mg/mL.

  13. Are two-station biased random walkers always potential molecular motors?

    Science.gov (United States)

    Bakalis, Evangelos; Zerbetto, Francesco

    2015-01-12

    The short answer to the title question is no. Despite their tremendous complexity, many nanomachines are simply one-dimensional systems undergoing a biased, that is, unidirectional, walk on a two-minima potential energy curve. The initially prepared state, or station, is higher in energy than the final equilibrium state that is reached after overcoming an energy barrier. All chemical reactions comply with this scheme, which does not necessarily imply that a generic chemical reaction is a potential molecular motor. If the barrier is low, the system may walk back and the motion will have a large purely Brownian component. Alternatively, a large distance from the barrier of either of the two stations may introduce a Brownian component. Starting from a general inequality that leverages on the idea that the amount of heat dissipated along the potential energy curve is a good indication of the effectiveness of the biased walk, we provide guidelines for the selection of the features of artificial molecular motors.

  14. The molecular motor Myosin Va interacts with the cilia-centrosomal protein RPGRIP1L

    Science.gov (United States)

    Assis, L. H. P.; Silva-Junior, R. M. P.; Dolce, L. G.; Alborghetti, M. R.; Honorato, R. V.; Nascimento, A. F. Z.; Melo-Hanchuk, T. D.; Trindade, D. M.; Tonoli, C. C. C.; Santos, C. T.; Oliveira, P. S. L.; Larson, R. E.; Kobarg, J.; Espreafico, E. M.; Giuseppe, P. O.; Murakami, M. T.

    2017-01-01

    Myosin Va (MyoVa) is an actin-based molecular motor abundantly found at the centrosome. However, the role of MyoVa at this organelle has been elusive due to the lack of evidence on interacting partners or functional data. Herein, we combined yeast two-hybrid screen, biochemical studies and cellular assays to demonstrate that MyoVa interacts with RPGRIP1L, a cilia-centrosomal protein that controls ciliary signaling and positioning. MyoVa binds to the C2 domains of RPGRIP1L via residues located near or in the Rab11a-binding site, a conserved site in the globular tail domain (GTD) from class V myosins. According to proximity ligation assays, MyoVa and RPGRIP1L can interact near the cilium base in ciliated RPE cells. Furthermore, we showed that RPE cells expressing dominant-negative constructs of MyoVa are mostly unciliated, providing the first experimental evidence about a possible link between this molecular motor and cilia-related processes. PMID:28266547

  15. Silanization of quartz, silicon and mica surfaces with light-driven molecular motors: construction of surface-bound photo-active nanolayers

    OpenAIRE

    London, Gábor; Carroll, Gregory T.; Feringa, Ben L.

    2013-01-01

    The attachment of molecular rotary motors containing triethoxysilane functional groups to quartz, silicon and mica surfaces is described. Motors containing silane coupling agents in their structure form stable molecular layers on quartz and silicon surfaces. Motors attached to these surfaces were found to undergo photochemical and thermal isomerization steps similar to those observed in solution. Additionally, successful formation of molecular "carpets" on atomically flat mica extending micro...

  16. Adhesion of photon-driven molecular motors to surfaces via 1,3-dipolar cycloadditions: effect of interfacial interactions on molecular motion.

    Science.gov (United States)

    Carroll, Gregory T; London, Gábor; Landaluce, Tatiana Fernández; Rudolf, Petra; Feringa, Ben L

    2011-01-25

    We report the attachment of altitudinal light-driven molecular motors to surfaces using 1,3-dipolar cycloaddition reactions. Molecular motors were designed containing azide or alkyne groups for attachment to alkyne- or azide-modified surfaces. Surface attachment was characterized by UV-vis, IR, XPS, and ellipsometry measurements. Surface-bound motors were found to undergo photochemical and thermal isomerizations consistent with unidirectional rotation in solution. Confinement at a surface was found to reduce the rate of the thermal isomerization process. The rate of thermal isomerization was also dependent on the surface coverage of the motors. In solution, changes in the UV-vis signal that accompany thermal isomerization can be fit with a single monoexponential decay. In contrast, thermal isomerization of the surface-bound motors does not follow a single monoexponential decay and was found to fit a biexponential decay. Both one- and two-legged motors were attached to surfaces. The kinetics of thermal isomerization was not affected by the valency of attachment, indicating that the changes in kinetics from solution to surface systems are related to interactions between the surface-bound motors.

  17. Depolymerization of actin cytoskeleton is involved in stomatal closure-induced by extracellular calmodulin in Arabidopsis

    Institute of Scientific and Technical Information of China (English)

    2004-01-01

    Extracellular calmodulin(CaM)plays significant roles in many physiological processes,but little is known about its mechanism of regulating stomatal movements.In this paper,whether CaM exists in the guard cell walls of Arabidopsis and whether depolymerization of actin cytoskeleton is involved in extracellular CaM-induced stomatal closing are investigated.It is found that CaM exists in guard cell walls of Arabidopsis,and its molecular weight is about 17 kD.Bioassay using CaM antagonists W7-agarose and anti-CaM serum shows that the endogenous extracellular CaM promotes stomatal closure and delays stomatal opening.The long radial actin filaments in guard cells undergo disruption in a time-dependent manner during exogenous CaM-induced stomatal closing.Pharmacological experiments show that depolymerization of actin cytoskeleton enhances the effect of exogenous CaM-induced stomatal closing and polymerization reduces the effect.We also find that exogenous CaM triggers an increase in [Ca2+]cyt of guard cells.If [Ca2+]cyt increase is blocked with EGTA,exogenous CaM-induced stomatal closure is inhibited.These results indicate that extracellular CaM causes elevation of [Ca2+]cyt in guard cells,subsequently resulting in disruption of actin filaments and finally leading to guard cells closure.

  18. Depolymerization of polysaccharides from Opuntia ficus indica: Antioxidant and antiglycated activities.

    Science.gov (United States)

    Chaouch, Mohamed Aymen; Hafsa, Jawhar; Rihouey, Christophe; Le Cerf, Didier; Majdoub, Hatem

    2015-08-01

    The extraction, purification and degradation of polysaccharides from Opuntia ficus indica cladodes, as well as the evaluation of their antioxidant and antiglycated activities in vitro were investigated. The optimization of the extraction showed that extraction by ultrasound at 40 °C presented the best carbohydrates yield. The degradation of the extracted polysaccharides was achieved by free radical depolymerization with H2O2 in the presence of copper(II) acetate for various reaction times. Sugar contents were determined by colorimetric assays. The macromolecular characteristics of the different isolated and degraded carbohydrates were carried by size exclusion chromatography (SEC/MALS/VD/DRI). These experiments showed that all samples are polysaccharides, which are probably pectins and that molecular weight (Mw) has decreased from 6,800,000 to 14,000 g/mol after 3 h of depolymerization without changing the structure. Preliminary antioxidant and antiglycated tests indicated that degraded polysaccharides for 2 and 3 h showed even better antioxidant and antiglycated activities.

  19. Base-Catalyzed Depolymerization of Solid Lignin-Rich Streams Enables Microbial Conversion

    Energy Technology Data Exchange (ETDEWEB)

    Beckham, Gregg T [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Salvachua Rodriguez, Davinia [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Katahira, Rui [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Pleitner, Brenna P [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Cleveland, Nicholas S [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Nolker, Michelle L [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Smith, Holly K [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Rodriguez, Alberto [Sandia National Laboratories; Baidoo, Edward E. K. [Lawrence Berkeley National Laboratory; DOE Joint BioEnergy Institute; Keasling, Jay D. [Lawrence Berkeley National Laboratory; DOE Joint BioEnergy InstituteUniversity of California, Berkeley; Technical University of Denmark; Simmons, Blake A. [Sandia National Laboratories; Lawrence Berkeley National Laboratory; DOE Joint BioEnergy Institute; Technical University of Denmark; Gladden, John M. [Sandia National Laboratories; DOE Joint BioEnergy Institute

    2017-08-01

    Lignin valorization offers significant potential to enhance the economic viability of lignocellulosic biorefineries. However, because of its heterogeneous and recalcitrant nature, conversion of lignin to value-added coproducts remains a considerable technical challenge. In this study, we employ base-catalyzed depolymerization (BCD) using a process-relevant solid lignin stream produced via deacetylation, mechanical refining, and enzymatic hydrolysis to enable biological lignin conversion. BCD was conducted with the solid lignin substrate over a range of temperatures at two NaOH concentrations, and the results demonstrate that the lignin can be partially extracted and saponified at temperatures as low as 60 degrees C. At 120 degrees C and 2% NaOH, the high extent of lignin solubility was accompanied by a considerable decrease in the lignin average molecular weight and the release of lignin-derived monomers including hydroxycinnamic acids. BCD liquors were tested for microbial growth using seven aromatic-catabolizing bacteria and two yeasts. Three organisms (Pseudomonas putida KT2440, Rhodotorula mucilaginosa, and Corynebacterium glutamicum) tolerate high BCD liquor concentrations (up to 90% v/v) and rapidly consume the main lignin-derived monomers, resulting in lignin conversion of up to 15%. Furthermore, as a proof of concept, muconic acid production from a representative lignin BCD liquor was demonstrated with an engineered P. putida KT2440 strain. These results highlight the potential for a mild lignin depolymerization process to enhance the microbial conversion of solid lignin-rich biorefinery streams.

  20. Theory for strength and stability of an unusual "ligand-receptor" bond: a microtubule attached to a wall by molecular motor tethers

    CERN Document Server

    Ghanti, Dipanwita

    2016-01-01

    A microtubule (MT) is a tubular stiff filament formed by a hierarchical organization of tubulin proteins. We develop a stochastic kinetic model for studying the strength and stability of a pre-formed attachment of a MT with a rigid wall where the MT is tethered to the wall by a group of motor proteins. Such an attachment, formed by the specific interactions between the MT and the motors, is an analog of ligand-receptor bonds, the MT and the motors anchored on the wall being the counterparts of the ligand and receptors, respectively. However, unlike other ligands, the length of a MT can change with time because of its polymerization-depolymerization kinetics. The simple model developed here is motivated by the MTs linked to the cell cortex by dynein motors. We present the theory for both force-ramp and force-clamp conditions. In the force-ramp protocol we investigate the strength of the attachment by assuming imposition of a time-dependent external load tension that increases linearly with time till the attach...

  1. Study of ion beam induced depolymerization using positron annihilation techniques

    Energy Technology Data Exchange (ETDEWEB)

    Puglisi, O. E-mail: opuglisi@dipchi.unict.it; Fragala, M.E.; Lynn, K.G.; Petkov, M.; Weber, M.; Somoza, A.; Dupasquier, A.; Quasso, F

    2001-04-01

    Ion beam induced depolymerization of polymers is a special class of ion beam induced chemical reaction which gives rise to catastrophic 'unzipping' of macromolecules with production of large amounts of the monomer, of the order of many hundreds monomer molecules per each macromolecule. The possible modification of the density at microscopic level prompted us to undertake a study of this effect utilizing positron annihilation techniques in Poly(methylmethacrylate) (PMMA) before and after bombardment with He{sup +} 300 keV ions at 200 deg. C. Preliminary results shown here indicate that before bombardment there is a reproducible dependence of nano-hole distribution on the sample history. Moreover at 200 deg. C we do not detect formation of new cavities as a consequence of the strong depolymerization that occurs under the ion beam. The possible correlation of these findings with transport properties of PMMA at temperature higher than the glass transition temperature will be discussed.

  2. Formaldehyde stabilization facilitates lignin monomer production during biomass depolymerization.

    Science.gov (United States)

    Shuai, Li; Amiri, Masoud Talebi; Questell-Santiago, Ydna M; Héroguel, Florent; Li, Yanding; Kim, Hoon; Meilan, Richard; Chapple, Clint; Ralph, John; Luterbacher, Jeremy S

    2016-10-21

    Practical, high-yield lignin depolymerization methods could greatly increase biorefinery productivity and profitability. However, development of these methods is limited by the presence of interunit carbon-carbon bonds within native lignin, and further by formation of such linkages during lignin extraction. We report that adding formaldehyde during biomass pretreatment produces a soluble lignin fraction that can be converted to guaiacyl and syringyl monomers at near theoretical yields during subsequent hydrogenolysis (47 mole % of Klason lignin for beech and 78 mole % for a high-syringyl transgenic poplar). These yields were three to seven times those obtained without formaldehyde, which prevented lignin condensation by forming 1,3-dioxane structures with lignin side-chain hydroxyl groups. By depolymerizing cellulose, hemicelluloses, and lignin separately, monomer yields were between 76 and 90 mole % for these three major biomass fractions. Copyright © 2016, American Association for the Advancement of Science.

  3. Depolymerization of polyethylene terephthalate in supercritical methanol

    Science.gov (United States)

    Goto, Motonobu; Koyamoto, Hiroshi; Kodama, Akio; Hirose, Tsutomu; Nagaoka, Shoji

    2002-11-01

    The degradation of polyethylene terephthalate (PET) in supercritical methanol was investigated with the aim of developing a process for chemical recycling of waste plastics. A batch reactor was used at temperatures of 573-623 K under an estimated pressure of 20 MPa for a reaction time of 2-120 min. PET was decomposed to its monomers, dimethyl terephthalate and ethylene glycol, by methanolysis in supercritical methanol. The reaction products were analysed using size-exclusion chromatography, gas chromatography-mass spectrometry, and reversed-phase liquid chromatography. The molecular weight distribution of the products was obtained as a function of reaction time. The yields of monomer components of the decomposition products including by-products were measured. Continuous kinetics analysis was performed on the experimental data.

  4. Synthetic Molecular Motors: Thermal N Inversion and Directional Photoinduced C=N Bond Rotation of Camphorquinone Imines.

    Science.gov (United States)

    Greb, Lutz; Eichhöfer, Andreas; Lehn, Jean-Marie

    2015-11-23

    The thermal and photochemical E/Z isomerization of camphorquinone-derived imines was studied by a combination of kinetic, structural, and computational methods. The thermal isomerization proceeds by linear N inversion, whereas the photoinduced process occurs through C=N bond rotation with preferred directionality as a result of diastereoisomerism. Thereby, these imines are arguably the simplest example of synthetic molecular motors. The generality of the orthogonal trajectories of the thermal and photochemical pathways allows for the postulation that every suitable chiral imine qualifies, in principle, as a molecular motor driven by light or heat.

  5. Filament depolymerization can pull a chromosome during bacterial mitosis

    Science.gov (United States)

    Banigan, Edward; Gelbart, Michael; Gitai, Zemer; Liu, Andrea; Wingreen, Ned

    2011-03-01

    Chromosome segregation is fundamental to all cells, but the force-generating mechanisms underlying chromosome translocation in bacteria remain mysterious. Caulobacter crescentus utilizes a depolymerization-driven process in which a ParA protein structure elongates from the new cell pole and binds to a ParB-decorated chromosome, and then retracts via disassembly, thus pulling the chromosome across the cell. This poses the question of how a depolymerizing structure can robustly pull the chromosome that is disassembling it. We perform Brownian dynamics simulations with a simple and physically consistent model of the ParABS system. The simulations suggest that the mechanism of translocation is ``self-diffusiophoretic'': by disassembling ParA, ParB generates a ParA concentration gradient so that the concentration of ParA is higher in front of the chromosome than behind it. Since the chromosome is attracted to ParA via ParB, it moves up the ParA gradient and across the cell. We find that translocation is controlled by the product of an effective relaxation time for the chromosome and the rate of ParA disassembly. Our results provide a physical explanation of the mechanism of depolymerization-driven translocation and suggest physical explanations for recent experimental observations.

  6. Drug Transport Microdevice Mimicking an Idealized Nanoscale Bio-molecular Motor

    Institute of Scientific and Technical Information of China (English)

    Jae Hwan Lee; Ramana M. Pidaparti

    2011-01-01

    Molecular motors are nature's nano-devices and the essential agents of movement that are an integral part of many living organisms.The supramolecular motor,called Nuclear Pore Complex (NPC),controls the transport of all cellular material between the cytoplasm and the nucleus that occurs naturally in biological cells of many organisms.In order to understand the design characteristics of the NPC,we developed a microdevice for drug/fluidic transport mimicking the coarse-grained representation of the NPC geometry through computational fluid dynamic analysis and optimization.Specifically,the role of the central plug in active fluidic/particle transport and passive transport (without central plug) was investigated.Results of flow rate,pressure and velocity profiles obtained from the models indicate that the central plug plays a major role in transport through this biomolecular machine.The results of this investigation show that fluidic transport and flow passages are important factors in designing NPC based nano- and micro-devices for drug delivery.

  7. The Survival of Motor Neuron Protein Acts as a Molecular Chaperone for mRNP Assembly

    Directory of Open Access Journals (Sweden)

    Paul G. Donlin-Asp

    2017-02-01

    Full Text Available Spinal muscular atrophy (SMA is a motor neuron disease caused by reduced levels of the survival of motor neuron (SMN protein. SMN is part of a multiprotein complex that facilitates the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs. SMN has also been found to associate with mRNA-binding proteins, but the nature of this association was unknown. Here, we have employed a combination of biochemical and advanced imaging methods to demonstrate that SMN promotes the molecular interaction between IMP1 protein and the 3′ UTR zipcode region of β-actin mRNA, leading to assembly of messenger ribonucleoprotein (mRNP complexes that associate with the cytoskeleton to facilitate trafficking. We have identified defects in mRNP assembly in cells and tissues from SMA disease models and patients that depend on the SMN Tudor domain and explain the observed deficiency in mRNA localization and local translation, providing insight into SMA pathogenesis as a ribonucleoprotein (RNP-assembly disorder.

  8. Lattice-gas model for active vesicle transport by molecular motors with opposite polarities

    Science.gov (United States)

    Muhuri, Sudipto; Pagonabarraga, Ignacio

    2010-08-01

    We introduce a multispecies lattice-gas model for motor protein driven collective cargo transport on cellular filaments. We use this model to describe and analyze the collective motion of interacting vesicle cargos being carried by oppositely directed molecular motors, moving on a single biofilament. Building on a totally asymmetric exclusion process to characterize the motion of the interacting cargos, we allow for mass exchange with the environment, input, and output at filament boundaries and focus on the role of interconversion rates and how they affect the directionality of the net cargo transport. We quantify the effect of the various different competing processes in terms of nonequilibrium phase diagrams. The interplay of interconversion rates, which allow for flux reversal and evaporation-deposition processes, introduces qualitatively unique features in the phase diagrams. We observe regimes of three-phase coexistence, the possibility of phase re-entrance, and a significant flexibility in how the different phase boundaries shift in response to changes in control parameters. The moving steady-state solutions of this model allows for different possibilities for the spatial distribution of cargo vesicles, ranging from homogeneous distribution of vesicles to polarized distributions, characterized by inhomogeneities or shocks. Current reversals due to internal regulation emerge naturally within the framework of this model. We believe that this minimal model will clarify the understanding of many features of collective vesicle transport, apart from serving as the basis for building more exact quantitative models for vesicle transport relevant to various in vivo situations.

  9. Reaction-diffusion-advection approach to spatially localized treadmilling aggregates of molecular motors

    Science.gov (United States)

    Yochelis, Arik; Bar-On, Tomer; Gov, Nir S.

    2016-04-01

    Unconventional myosins belong to a class of molecular motors that walk processively inside cellular protrusions towards the tips, on top of actin filament. Surprisingly, in addition, they also form retrograde moving self-organized aggregates. The qualitative properties of these aggregates are recapitulated by a mass conserving reaction-diffusion-advection model and admit two distinct families of modes: traveling waves and pulse trains. Unlike the traveling waves that are generated by a linear instability, pulses are nonlinear structures that propagate on top of linearly stable uniform backgrounds. Asymptotic analysis of isolated pulses via a simplified reaction-diffusion-advection variant on large periodic domains, allows to draw qualitative trends for pulse properties, such as the amplitude, width, and propagation speed. The results agree well with numerical integrations and are related to available empirical observations.

  10. Physics of Transport and Traffic Phenomena in Biology: from molecular motors and cells to organisms

    CERN Document Server

    Chowdhury, D; Nishinari, K; Chowdhury, Debashish; Schadschneider, Andreas; Nishinari, Katsuhiro

    2005-01-01

    Traffic-like collective movements are observed at almost all levels of biological systems. Molecular motor proteins like, for example, kinesin and dynein, which are the vehicles of almost all intra-cellular transport in eukayotic cells, sometimes encounter traffic jam that manifests as a disease of the organism. Similarly, traffic jam of collagenase MMP-1, which moves on the collagen fibrils of the extracellular matrix of vertebrates, has also been observed in recent experiments. Traffic-like movements of social insects like ants and termites on trails are, perhaps, more familiar in our everyday life. Experimental, theoretical and computational investigations in the last few years have led to a deeper understanding of the generic or common physical principles involved in these phenomena. In particular, some of the methods of non-equilibrium statistical mechanics, pioneered almost a hundred years ago by Einstein, Langevin and others, turned out to be powerful theoretical tools for quantitaive analysis of model...

  11. Advanced Model Compounds for Understanding Acid-Catalyzed Lignin Depolymerization: Identification of Renewable Aromatics and a Lignin-Derived Solvent.

    Science.gov (United States)

    Lahive, Ciaran W; Deuss, Peter J; Lancefield, Christopher S; Sun, Zhuohua; Cordes, David B; Young, Claire M; Tran, Fanny; Slawin, Alexandra M Z; de Vries, Johannes G; Kamer, Paul C J; Westwood, Nicholas J; Barta, Katalin

    2016-07-20

    The development of fundamentally new approaches for lignin depolymerization is challenged by the complexity of this aromatic biopolymer. While overly simplified model compounds often lack relevance to the chemistry of lignin, the direct use of lignin streams poses significant analytical challenges to methodology development. Ideally, new methods should be tested on model compounds that are complex enough to mirror the structural diversity in lignin but still of sufficiently low molecular weight to enable facile analysis. In this contribution, we present a new class of advanced (β-O-4)-(β-5) dilinkage models that are highly realistic representations of a lignin fragment. Together with selected β-O-4, β-5, and β-β structures, these compounds provide a detailed understanding of the reactivity of various types of lignin linkages in acid catalysis in conjunction with stabilization of reactive intermediates using ethylene glycol. The use of these new models has allowed for identification of novel reaction pathways and intermediates and led to the characterization of new dimeric products in subsequent lignin depolymerization studies. The excellent correlation between model and lignin experiments highlights the relevance of this new class of model compounds for broader use in catalysis studies. Only by understanding the reactivity of the linkages in lignin at this level of detail can fully optimized lignin depolymerization strategies be developed.

  12. Depolymerization of Fucosylated Chondroitin Sulfate with a Modified Fenton-System and Anticoagulant Activity of the Resulting Fragments

    Science.gov (United States)

    Li, Jun-hui; Li, Shan; Zhi, Zi-jian; Yan, Lu-feng; Ye, Xing-qian; Ding, Tian; Yan, Lei; Linhardt, Robert John; Chen, Shi-guo

    2016-01-01

    Fucosylated chondroitin sulfate (fCS) from sea cucumber Isostichopus badionotus (fCS-Ib) with a chondroitin sulfate type E (CSE) backbone and 2,4-O-sulfo fucose branches has shown excellent anticoagulant activity although has also show severe adverse effects. Depolymerization represents an effective method to diminish this polysaccharide’s side effects. The present study reports a modified controlled Fenton system for degradation of fCS-Ib and the anticoagulant activity of the resulting fragments. Monosaccharides and nuclear magnetic resonance (NMR) analysis of the resulting fragments indicate that no significant chemical changes in the backbone of fCS-Ib and no loss of sulfate groups take place during depolymerization. A reduction in the molecular weight of fCS-Ib should result in a dramatic decrease in prolonging activated partial thromboplastin time and thrombin time. A decrease in the inhibition of thrombin (FIIa) by antithromin III (AT III) and heparin cofactor II (HCII), and the slight decrease of the inhibition of factor X activity, results in a significant increase of anti-factor Xa (FXa)/anti-FIIa activity ratio. The modified free-radical depolymerization method enables preparation of glycosaminoglycan (GAG) oligosaccharides suitable for investigation of clinical anticoagulant application. PMID:27657094

  13. The Utilization of Sensori-motor Experiences for Introducing Young Pupils to Molecular Motion: A Report of a Pilot Study.

    Science.gov (United States)

    Hadzigeorgiou, Yannis

    2002-01-01

    Does a sensori-motor experience help a physics student understand the movement of molecules in solids, liquids, and gases? Students aged 9-10 were given either traditional demonstrations of solids, liquids, and gases and the variation of molecular motion with temperature (iconic presentation), or they were involved in physical activities as they…

  14. Driving Unidirectional Molecular Rotary Motors with Visible Light by Intra- And Intermolecular Energy Transfer from Palladium Porphyrin

    NARCIS (Netherlands)

    Cnossen, Arjen; Hou, Lili; Pollard, Michael M.; Wesenhagen, Philana V.; Browne, Wesley R.; Feringa, Ben L.

    2012-01-01

    Driving molecular rotary motors using visible light (530-550 nm) instead of UV light was achieved using palladium tetraphenylporphyrin as a triplet sensitizer. Visible light driven rotation was confirmed by UV/vis absorption, circular dichroism and H-1 NMR spectroscopy and the rotation was confirmed

  15. On the effect of donor and acceptor substituents on the behaviour of light-driven rotary molecular motors

    NARCIS (Netherlands)

    Pollard, Michael M.; Wesenhagen, Philana V.; Pijper, Dirk; Feringa, Ben L.

    2008-01-01

    Light-driven rotary molecular motors based on overcrowded alkenes can be substituted with electron-donating and electron-withdrawing substituents ( R = OMe, Cl and CN) in direct conjugation with the central double bond ( the axis of rotation) without having a significant influence on the rate-limiti

  16. Electric dipole theory and thermodynamics of actomyosin molecular motor in muscle contraction.

    Science.gov (United States)

    Lampinen, Markku J; Noponen, Tuula

    2005-10-21

    Movements in muscles are generated by the myosins which interact with the actin filaments. In this paper we present an electric theory to describe how the chemical energy is first stored in electrostatic form in the myosin system and how it is then released and transformed into work. Due to the longitudinal polarized molecular structure with the negative phosphate group tail, the ATP molecule possesses a large electric dipole moment (p(0)), which makes it an ideal energy source for the electric dipole motor of the actomyosin system. The myosin head contains a large number of strongly restrained water molecules, which makes the ATP-driven electric dipole motor possible. The strongly restrained water molecules can store the chemical energy released by ATP binding and hydrolysis processes in the electric form due to their myosin structure fixed electric dipole moments (p(i)). The decrease in the electric energy is transformed into mechanical work by the rotational movement of the myosin head, which follows from the interaction of the dipoles p(i) with the potential field V(0) of ATP and with the potential field Psi of the actin. The electrical meaning of the hydrolysis reaction is to reduce the dipole moment p(0)-the remaining dipole moment of the adenosine diphosphate (ADP) is appropriately smaller to return the low negative value of the electric energy nearly back to its initial value, enabling the removal of ADP from the myosin head so that the cycling process can be repeated. We derive for the electric energy of the myosin system a general equation, which contains the potential field V(0) with the dipole moment p(0), the dipole moments p(i) and the potential field psi. Using the previously published experimental data for the electric dipole of ATP (p(0) congruent with 230 debye) and for the amount of strongly restrained water molecules (N congruent with 720) in the myosin subfragment (S1), we show that the Gibbs free energy changes of the ATP binding and

  17. Computational Study of the Binding Mechanism of Actin-Depolymerizing Factor 1 with Actin in Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    Juan Du

    Full Text Available Actin is a highly conserved protein. It plays important roles in cellular function and exists either in the monomeric (G-actin or polymeric form (F-actin. Members of the actin-depolymerizing factor (ADF/cofilin protein family bind to both G-actin and F-actin and play vital roles in actin dynamics by manipulating the rates of filament polymerization and depolymerization. It has been reported that the S6D and R98A/K100A mutants of actin-depolymerizing factor 1 (ADF1 in Arabidopsis thaliana decreased the binding affinity of ADF for the actin monomer. To investigate the binding mechanism and dynamic behavior of the ADF1-actin complex, we constructed a homology model of the AtADF1-actin complex based on the crystal structure of AtADF1 and the twinfilin C-terminal ADF-H domain in a complex with a mouse actin monomer. The model was then refined for subsequent molecular dynamics simulations. Increased binding energy of the mutated system was observed using the Molecular Mechanics Generalized Born Surface Area and Poisson-Boltzmann Surface Area (MM-GB/PBSA methods. To determine the residues that make decisive contributions to the ADF1 actin-binding affinity, per-residue decomposition and computational alanine scanning analyses were performed, which provided more detailed information on the binding mechanism. Root-mean-square fluctuation and principal component analyses confirmed that the S6D and R98A/K100A mutants induced an increased conformational flexibility. The comprehensive molecular insight gained from this study is of great importance for understanding the binding mechanism of ADF1 and G-actin.

  18. Base-catalyzed depolymerization of lignin : separation of monomers

    Energy Technology Data Exchange (ETDEWEB)

    Vigneault, A. [Sherbrooke Univ., PQ (Canada). Dept. of Chemical Engineering; Johnson, D.K. [National Renewable Energy Laboratory, Golden, CO (United States); Chornet, E. [Sherbrooke Univ., PQ (Canada). Dept. of Chemical Engineering; National Renewable Energy Laboratory, Golden, CO (United States)

    2007-12-15

    Biofuels produced from residual lignocellulosic biomass range from ethanol to biodiesel. The use of lignin for the production of alternate biofuels and green chemicals has been studied with particular emphasis on the structure of lignin and its oxyaromatic nature. In an effort to fractionate lignocellulosic biomass and valorize specific constitutive fractions, the authors developed a strategy for the separation of 12 added value monomers produced during the hydrolytic base catalyzed depolymerization (BCD) of a Steam Exploded Aspen Lignin. The separation strategy was similar to vanillin purification to obtain pure monomers, but combining more steps after the lignin depolymerization such as acidification, batch liquid-liquid-extraction (LLE), followed by vacuum distillation, liquid chromatography (LC) and crystallization. The purpose was to develop basic data for an industrial size process flow diagram, and to evaluate both the monomer losses during the separation and the energy requirements. Experimentally testing of LLE, vacuum distillation and flash LC in the laboratory showed that batch vacuum distillation produced up to 4 fractions. Process simulation revealed that a series of 4 vacuum distillation columns could produce 5 distinct monomer streams, of which 3 require further chromatography and crystallization operations for purification. 22 refs., 4 tabs., 8 figs.

  19. Physics of transport and traffic phenomena in biology: from molecular motors and cells to organisms

    Science.gov (United States)

    Chowdhury, Debashish; Schadschneider, Andreas; Nishinari, Katsuhiro

    2005-12-01

    Traffic-like collective movements are observed at almost all levels of biological systems. Molecular motor proteins like, for example, kinesin and dynein, which are the vehicles of almost all intra-cellular transport in eukaryotic cells, sometimes encounter traffic jam that manifests as a disease of the organism. Similarly, traffic jam of collagenase MMP-1, which moves on the collagen fibrils of the extracellular matrix of vertebrates, has also been observed in recent experiments. Novel efforts have been made to utilize some uni-cellular organisms as “micro-transporters”. Traffic-like movements of social insects like ants and termites on trails are, perhaps, more familiar in our everyday life. Experimental, theoretical and computational investigations in the last few years have led to a deeper understanding of the generic or common physical principles involved in these phenomena. In this review we critically examine the current status of our understanding, expose the limitations of the existing methods, mention open challenging questions and speculate on the possible future directions of research in this interdisciplinary area where physics meets not only chemistry and biology but also (nano-)technology.

  20. Reactions driving conformational movements (molecular motors) in gels: conformational and structural chemical kinetics.

    Science.gov (United States)

    Otero, Toribio F

    2017-01-18

    In this perspective the empirical kinetics of conducting polymers exchanging anions and solvent during electrochemical reactions to get dense reactive gels is reviewed. The reaction drives conformational movements of the chains (molecular motors), exchange of ions and solvent with the electrolyte and structural (relaxation, swelling, shrinking and compaction) gel changes. Reaction-driven structural changes are identified and quantified from electrochemical responses. The empirical reaction activation energy (Ea), the reaction coefficient (k) and the reaction orders (α and β) change as a function of the conformational energy variation during the reaction. This conformational energy becomes an empirical magnitude. Ea, k, α and β include and provide quantitative conformational and structural information. The chemical kinetics becomes structural chemical kinetics (SCK) for reactions driving conformational movements of the reactants. The electrochemically stimulated conformational relaxation model describes empirical results and some results from the literature for biochemical reactions. In parallel the development of an emerging technological world of soft, wet, multifunctional and biomimetic tools and anthropomorphic robots driven by reactions of the constitutive material, as in biological organs, can be now envisaged being theoretically supported by the kinetic model.

  1. Parallel computation with molecular-motor-propelled agents in nanofabricated networks.

    Science.gov (United States)

    Nicolau, Dan V; Lard, Mercy; Korten, Till; van Delft, Falco C M J M; Persson, Malin; Bengtsson, Elina; Månsson, Alf; Diez, Stefan; Linke, Heiner; Nicolau, Dan V

    2016-03-01

    The combinatorial nature of many important mathematical problems, including nondeterministic-polynomial-time (NP)-complete problems, places a severe limitation on the problem size that can be solved with conventional, sequentially operating electronic computers. There have been significant efforts in conceiving parallel-computation approaches in the past, for example: DNA computation, quantum computation, and microfluidics-based computation. However, these approaches have not proven, so far, to be scalable and practical from a fabrication and operational perspective. Here, we report the foundations of an alternative parallel-computation system in which a given combinatorial problem is encoded into a graphical, modular network that is embedded in a nanofabricated planar device. Exploring the network in a parallel fashion using a large number of independent, molecular-motor-propelled agents then solves the mathematical problem. This approach uses orders of magnitude less energy than conventional computers, thus addressing issues related to power consumption and heat dissipation. We provide a proof-of-concept demonstration of such a device by solving, in a parallel fashion, the small instance {2, 5, 9} of the subset sum problem, which is a benchmark NP-complete problem. Finally, we discuss the technical advances necessary to make our system scalable with presently available technology.

  2. Impact of 80% F-76/20% Hydrotreated Depolymerized Cellulosic Diesel (HDCD-76) on Coalescence

    Science.gov (United States)

    2014-02-25

    Impact of 80% F-76/20% Hydrotreated Depolymerized Cellulosic Diesel (HDCD-76) on Coalescence NF&LCFT REPORT 441/14-008 25 February 2014... Hydrotreated Depolymerized Cellulosic Diesel IAW...than existing petroleum sourced fuels. One such fuel that is undergoing qualification testing is an 80% petroleum F-76 and 20% Hydrotreated

  3. The Depolymerization of Poly(Ethylene Terephthalate) (PET) Using N-Heterocyclic Carbenes from Ionic Liquids

    Science.gov (United States)

    Kamber, Nahrain E.; Tsujii, Yasuhito; Keets, Kate; Waymouth, Robert M.; Pratt, Russell C.; Nyce, Gregory W.; Hedrick, James L.

    2010-01-01

    The depolymerization of the plastic polyethylene terephthalate (PET or PETE) is described in this laboratory procedure. The transesterification reaction used to depolymerize PET employs a highly efficient N-heterocyclic carbene catalyst derived from a commercially available imidazolium ionic liquid. N-heterocyclic carbenes are potent nucleophilic…

  4. Silanization of quartz, silicon and mica surfaces with light-driven molecular motors: construction of surface-bound photo-active nanolayers.

    Science.gov (United States)

    London, Gábor; Carroll, Gregory T; Feringa, Ben L

    2013-06-07

    The attachment of molecular rotary motors containing triethoxysilane functional groups to quartz, silicon and mica surfaces is described. Motors containing silane coupling agents in their structure form stable molecular layers on quartz and silicon surfaces. Motors attached to these surfaces were found to undergo photochemical and thermal isomerization steps similar to those observed in solution. Additionally, successful formation of molecular "carpets" on atomically flat mica extending micrometer-sized length scales is presented. These "carpets" were found to undergo morphological changes upon irradiation with UV-light.

  5. Irradiation depolymerized guar gum as partial replacement of gum Arabic for microencapsulation of mint oil.

    Science.gov (United States)

    Sarkar, Shatabhisa; Gupta, Sumit; Variyar, Prasad S; Sharma, Arun; Singhal, Rekha S

    2012-11-06

    Spray dried microcapsules of mint oil were prepared using gum Arabic alone and its blends with radiation or enzymatically depolymerized guar gum as wall materials. Microcapsules were evaluated for retention of mint oil during 8-week storage during which qualitative changes in encapsulated mint oil was monitored using principal component analysis. The microcapsules with radiation depolymerized guar gum as wall material component could better retain major mint oil compounds such as menthol and isomenthol. The t(1/2) calculated for mint oil in microcapsules of gum Arabic, gum Arabic:radiation depolymerized guar gum (90:10), gum Arabic:enzyme depolymerized guar gum (90:10) was 25.66, 38.50, and 17.11 weeks, respectively. The results suggested a combination of radiation depolymerized guar gum and gum Arabic to show better retention of encapsulated flavour than gum Arabic alone as wall material.

  6. Elasticity of a semiflexible filament with a discontinuous tension due to a cross-link or a molecular motor

    OpenAIRE

    Razbin, Mohammadhosein; Benetatos, Panayotis; Zippelius, Annette

    2016-01-01

    We analyze the stretching elasticity of a wormlike chain with a tension discontinuity resulting from a Hookean spring connecting its backbone to a fixed point. The elasticity of isolated semiflexible filaments has been the subject in a significant body of literature, primarily because of its relevance to the mechanics of biological matter. In real systems, however, these filaments are usually part of supramolecular structures involving cross-linkers or molecular motors which cause tension dis...

  7. Sequential lignin depolymerization by combination of biocatalytic and formic acid/formate treatment steps.

    Science.gov (United States)

    Gasser, Christoph A; Čvančarová, Monika; Ammann, Erik M; Schäffer, Andreas; Shahgaldian, Patrick; Corvini, Philippe F-X

    2017-03-01

    Lignin, a complex three-dimensional amorphous polymer, is considered to be a potential natural renewable resource for the production of low-molecular-weight aromatic compounds. In the present study, a novel sequential lignin treatment method consisting of a biocatalytic oxidation step followed by a formic acid-induced lignin depolymerization step was developed and optimized using response surface methodology. The biocatalytic step employed a laccase mediator system using the redox mediator 1-hydroxybenzotriazole. Laccases were immobilized on superparamagnetic nanoparticles using a sorption-assisted surface conjugation method allowing easy separation and reuse of the biocatalysts after treatment. Under optimized conditions, as much as 45 wt% of lignin could be solubilized either in aqueous solution after the first treatment or in ethyl acetate after the second (chemical) treatment. The solubilized products were found to be mainly low-molecular-weight aromatic monomers and oligomers. The process might be used for the production of low-molecular-weight soluble aromatic products that can be purified and/or upgraded applying further downstream processes.

  8. The nonlinear chemo-mechanic coupled dynamics of the F 1 -ATPase molecular motor.

    Science.gov (United States)

    Xu, Lizhong; Liu, Fang

    2012-03-01

    The ATP synthase consists of two opposing rotary motors, F0 and F1, coupled to each other. When the F1 motor is not coupled to the F0 motor, it can work in the direction hydrolyzing ATP, as a nanomotor called F1-ATPase. It has been reported that the stiffness of the protein varies nonlinearly with increasing load. The nonlinearity has an important effect on the rotating rate of the F1-ATPase. Here, considering the nonlinearity of the γ shaft stiffness for the F1-ATPase, a nonlinear chemo-mechanical coupled dynamic model of F1 motor is proposed. Nonlinear vibration frequencies of the γ shaft and their changes along with the system parameters are investigated. The nonlinear stochastic response of the elastic γ shaft to thermal excitation is analyzed. The results show that the stiffness nonlinearity of the γ shaft causes an increase of the vibration frequency for the F1 motor, which increases the motor's rotation rate. When the concentration of ATP is relatively high and the load torque is small, the effects of the stiffness nonlinearity on the rotating rates of the F1 motor are obvious and should be considered. These results are useful for improving calculation of the rotating rate for the F1 motor and provide insight about the stochastic wave mechanics of F1-ATPase.

  9. Structural Snapshots of Heparin Depolymerization by Heparin Lyase I

    Energy Technology Data Exchange (ETDEWEB)

    Han, Young-Hyun; Garron, Marie-Line; Kim, Hye-Yeon; Kim, Wan-Seok; Zhang, Zhenqing; Ryu, Kyeong-Seok; Shaya, David; Xiao, Zhongping; Cheong, Chaejoon; Kim, Yeong Shik; Linhardt, Robert J.; Jeon, Young Ho; Cygler, Miroslaw; (SNU); (Korea BSI); (McGill); (UST-Korea); (Rensselaer)

    2010-01-12

    Heparin lyase I (heparinase I) specifically depolymerizes heparin, cleaving the glycosidic linkage next to iduronic acid. Here, we show the crystal structures of heparinase I from Bacteroides thetaiotaomicron at various stages of the reaction with heparin oligosaccharides before and just after cleavage and product disaccharide. The heparinase I structure is comprised of a {beta}-jellyroll domain harboring a long and deep substrate binding groove and an unusual thumb-resembling extension. This thumb, decorated with many basic residues, is of particular importance in activity especially on short heparin oligosaccharides. Unexpected structural similarity of the active site to that of heparinase II with an ({alpha}/{alpha}){sub 6} fold is observed. Mutational studies and kinetic analysis of this enzyme provide insights into the catalytic mechanism, the substrate recognition, and processivity.

  10. Visible-Light-Driven Photoisomerization and Increased Rotation Speed of a Molecular Motor Acting as a Ligand in a Ruthenium(II) Complex

    NARCIS (Netherlands)

    Wezenberg, Sander J.; Chen, Kuang-Yen; Feringa, Ben L.

    2015-01-01

    Toward the development of visible-light-driven molecular rotary motors, an overcrowded alkene-based ligand and the corresponding ruthenium(II) complex is presented. In our design, a 4,5-diazafluorenyl coordination motif is directly integrated into the motor function. The photochemical and thermal

  11. Visible-Light-Driven Photoisomerization and Increased Rotation Speed of a Molecular Motor Acting as a Ligand in a Ruthenium(II) Complex

    NARCIS (Netherlands)

    Wezenberg, Sander J; Chen, Kuang-Yen; Feringa, Ben L

    2015-01-01

    Toward the development of visible-light-driven molecular rotary motors, an overcrowded alkene-based ligand and the corresponding ruthenium(II) complex is presented. In our design, a 4,5-diazafluorenyl coordination motif is directly integrated into the motor function. The photochemical and thermal is

  12. Kinetic modeling of molecular motors: pause model and parameter determination from single-molecule experiments

    Science.gov (United States)

    Morin, José A.; Ibarra, Borja; Cao, Francisco J.

    2016-05-01

    Single-molecule manipulation experiments of molecular motors provide essential information about the rate and conformational changes of the steps of the reaction located along the manipulation coordinate. This information is not always sufficient to define a particular kinetic cycle. Recent single-molecule experiments with optical tweezers showed that the DNA unwinding activity of a Phi29 DNA polymerase mutant presents a complex pause behavior, which includes short and long pauses. Here we show that different kinetic models, considering different connections between the active and the pause states, can explain the experimental pause behavior. Both the two independent pause model and the two connected pause model are able to describe the pause behavior of a mutated Phi29 DNA polymerase observed in an optical tweezers single-molecule experiment. For the two independent pause model all parameters are fixed by the observed data, while for the more general two connected pause model there is a range of values of the parameters compatible with the observed data (which can be expressed in terms of two of the rates and their force dependencies). This general model includes models with indirect entry and exit to the long-pause state, and also models with cycling in both directions. Additionally, assuming that detailed balance is verified, which forbids cycling, this reduces the ranges of the values of the parameters (which can then be expressed in terms of one rate and its force dependency). The resulting model interpolates between the independent pause model and the indirect entry and exit to the long-pause state model

  13. Selective cell-surface labeling of the molecular motor protein prestin

    Energy Technology Data Exchange (ETDEWEB)

    McGuire, Ryan M. [Department of Bioengineering, Rice University, Houston, TX 77251 (United States); Silberg, Jonathan J., E-mail: joff@rice.edu [Department of Bioengineering, Rice University, Houston, TX 77251 (United States); Department of Biochemistry and Cell Biology, Rice University, Houston, TX 77251 (United States); Pereira, Fred A. [Department of Bioengineering, Rice University, Houston, TX 77251 (United States); Huffington Center on Aging, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030 (United States); Raphael, Robert M., E-mail: rraphael@rice.edu [Department of Bioengineering, Rice University, Houston, TX 77251 (United States)

    2011-06-24

    Highlights: {yields} Trafficking to the plasma membrane is required for prestin function. {yields} Biotin acceptor peptide (BAP) was fused to prestin through a transmembrane domain. {yields} BAP-prestin can be metabolically labeled with biotin in HEK293 cells. {yields} Biotin-BAP-prestin allows for selective imaging of fully trafficked prestin. {yields} The biotin-BAP-prestin displays voltage-sensitive activity. -- Abstract: Prestin, a multipass transmembrane protein whose N- and C-termini are localized to the cytoplasm, must be trafficked to the plasma membrane to fulfill its cellular function as a molecular motor. One challenge in studying prestin sequence-function relationships within living cells is separating the effects of amino acid substitutions on prestin trafficking, plasma membrane localization and function. To develop an approach for directly assessing prestin levels at the plasma membrane, we have investigated whether fusion of prestin to a single pass transmembrane protein results in a functional fusion protein with a surface-exposed N-terminal tag that can be detected in living cells. We find that fusion of the biotin-acceptor peptide (BAP) and transmembrane domain of the platelet-derived growth factor receptor (PDGFR) to the N-terminus of prestin-GFP yields a membrane protein that can be metabolically-labeled with biotin, trafficked to the plasma membrane, and selectively detected at the plasma membrane using fluorescently-tagged streptavidin. Furthermore, we show that the addition of a surface detectable tag and a single-pass transmembrane domain to prestin does not disrupt its voltage-sensitive activity.

  14. The molecular motor F-ATP synthase is targeted by the tumoricidal protein HAMLET.

    Science.gov (United States)

    Ho, James; Sielaff, Hendrik; Nadeem, Aftab; Svanborg, Catharina; Grüber, Gerhard

    2015-05-22

    HAMLET (human alpha-lactalbumin made lethal to tumor cells) interacts with multiple tumor cell compartments, affecting cell morphology, metabolism, proteasome function, chromatin structure and viability. This study investigated if these diverse effects of HAMLET might be caused, in part, by a direct effect on the ATP synthase and a resulting reduction in cellular ATP levels. A dose-dependent reduction in cellular ATP levels was detected in A549 lung carcinoma cells, and by confocal microscopy, co-localization of HAMLET with the nucleotide-binding subunits α (non-catalytic) and β (catalytic) of the energy converting F1F0 ATP synthase was detected. As shown by fluorescence correlation spectroscopy, HAMLET binds to the F1 domain of the F1F0 ATP synthase with a dissociation constant (KD) of 20.5μM. Increasing concentrations of the tumoricidal protein HAMLET added to the enzymatically active α3β3γ complex of the F-ATP synthase lowered its ATPase activity, demonstrating that HAMLET binding to the F-ATP synthase effects the catalysis of this molecular motor. Single-molecule analysis was applied to study HAMLET-α3β3γ complex interaction. Whereas the α3β3γ complex of the F-ATP synthase rotated in a counterclockwise direction with a mean rotational rate of 3.8±0.7s(-1), no rotation could be observed in the presence of bound HAMLET. Our findings suggest that direct effects of HAMLET on the F-ATP synthase may inhibit ATP-dependent cellular processes. Copyright © 2015 Elsevier Ltd. All rights reserved.

  15. Filament depolymerization can explain chromosome pulling during bacterial mitosis.

    Science.gov (United States)

    Banigan, Edward J; Gelbart, Michael A; Gitai, Zemer; Wingreen, Ned S; Liu, Andrea J

    2011-09-01

    Chromosome segregation is fundamental to all cells, but the force-generating mechanisms underlying chromosome translocation in bacteria remain mysterious. Caulobacter crescentus utilizes a depolymerization-driven process in which a ParA protein structure elongates from the new cell pole, binds to a ParB-decorated chromosome, and then retracts via disassembly, pulling the chromosome across the cell. This poses the question of how a depolymerizing structure can robustly pull the chromosome that disassembles it. We perform Brownian dynamics simulations with a simple, physically consistent model of the ParABS system. The simulations suggest that the mechanism of translocation is "self-diffusiophoretic": by disassembling ParA, ParB generates a ParA concentration gradient so that the ParA concentration is higher in front of the chromosome than behind it. Since the chromosome is attracted to ParA via ParB, it moves up the ParA gradient and across the cell. We find that translocation is most robust when ParB binds side-on to ParA filaments. In this case, robust translocation occurs over a wide parameter range and is controlled by a single dimensionless quantity: the product of the rate of ParA disassembly and a characteristic relaxation time of the chromosome. This time scale measures the time it takes for the chromosome to recover its average shape after it is has been pulled. Our results suggest explanations for observed phenomena such as segregation failure, filament-length-dependent translocation velocity, and chromosomal compaction.

  16. Filament depolymerization can explain chromosome pulling during bacterial mitosis.

    Directory of Open Access Journals (Sweden)

    Edward J Banigan

    2011-09-01

    Full Text Available Chromosome segregation is fundamental to all cells, but the force-generating mechanisms underlying chromosome translocation in bacteria remain mysterious. Caulobacter crescentus utilizes a depolymerization-driven process in which a ParA protein structure elongates from the new cell pole, binds to a ParB-decorated chromosome, and then retracts via disassembly, pulling the chromosome across the cell. This poses the question of how a depolymerizing structure can robustly pull the chromosome that disassembles it. We perform Brownian dynamics simulations with a simple, physically consistent model of the ParABS system. The simulations suggest that the mechanism of translocation is "self-diffusiophoretic": by disassembling ParA, ParB generates a ParA concentration gradient so that the ParA concentration is higher in front of the chromosome than behind it. Since the chromosome is attracted to ParA via ParB, it moves up the ParA gradient and across the cell. We find that translocation is most robust when ParB binds side-on to ParA filaments. In this case, robust translocation occurs over a wide parameter range and is controlled by a single dimensionless quantity: the product of the rate of ParA disassembly and a characteristic relaxation time of the chromosome. This time scale measures the time it takes for the chromosome to recover its average shape after it is has been pulled. Our results suggest explanations for observed phenomena such as segregation failure, filament-length-dependent translocation velocity, and chromosomal compaction.

  17. Formation of cellulose-carbene complex via depolymerization in ILs: Dependence of IL types on kinetics, conformation and dispersity.

    Science.gov (United States)

    Ahn, Yongjun; Song, Younghan; Kim, Hyungsup; Kwak, Seung-Yeop

    2017-03-01

    This study focused on the influence of anion type on the depolymerization and its effect on the molecular state, dynamics and dispersity of cellulose. GPC and the van Gurp-Palmen plot showed that molar mass was more significantly decreased by 1-butyl-3-methylimidazolium chloride ([C4C1Im][Cl]) comparing to 1-butyl-3-methylimidazolium acetate ([C4C1Im][OAc]). Acid-catalyzed hydrolysis of cellulose in IL was proved using base titration which was monitored by conductivity and pH value. On the contrary to the depolymerization case, [C4C1Im][OAc] solution needed more base to be neutralized than [C4C1Im][Cl] solution. The generated carbene was combined with reducing ends of cellulose, which was facilitated in low molar mass consisting of a large number of reducing ends. The formation of cellulose-carbene substitution caused steric hindrance of cellulose chain, thus resulting in increased segmental friction with high molecular density. The cellulose particle combined with carbene can be dispersed stably in aqueous media.

  18. Symmetric linear potential and imperfect Brownian ratchet in molecular motor function

    Institute of Scientific and Technical Information of China (English)

    Li Fang-Zhen; Hu Kuang-Hu; Su Wan-Fang; Chen Yi-Chen

    2005-01-01

    Biomolecular motors are tiny engines that transport materials at the microscopic level within biological cells. In recent years, Elston and Peskin et al have investigated the effect of the elastic properties of the tether that connects the motor to its cargo at the speed of the motor. In this paper we extend their work and present a tether in the form of symmetric linear potential. Our results show that when the driving mechanism is an imperfect Brownian ratchet, the average speed decreases as the stiffness of the tether increases in the limit of large motor diffusion coefficient, which is similar to the results of Elston and Peskin. However, a threshold for the stiffness of the tether connecting the motor to its cargo is found in our model. Only when the tether is stiffer than the threshold can the motor and its cargo function co-operatively, otherwise, the motor and its cargo depart from each other. This result is more realistic than that of the spring model of Elston and Peskin.

  19. Probing single processive molecular motors with high-speed optical tweezers and fluorescence microscopy

    Science.gov (United States)

    Gardini, L.; Pavone, F. S.; Capitanio, M.

    2017-02-01

    Here we present development of optical techniques for the study of single processive myosin motors based on the combination of high-speed optical tweezers force spectroscopy and single molecule fluorescence imaging. Ultrafast force-clamp spectroscopy1 is applied to study the dependence of single chemo-mechanical steps of processive myosin motors on the applied load. On the other hand, single molecule localization through FIONA (Fluorescence Imaging with One Nanometer Accuracy)2, 3 is applied to in vitro motility assay to measure parameters such as the runlength, velocity and step size of single myosin V motors, labeled with Quantum Dots, under unloaded conditions.

  20. Mechanical operation and intersubunit coordination of ring-shaped molecular motors: insights from single-molecule studies.

    Science.gov (United States)

    Liu, Shixin; Chistol, Gheorghe; Bustamante, Carlos

    2014-05-06

    Ring NTPases represent a large and diverse group of proteins that couple their nucleotide hydrolysis activity to a mechanical task involving force generation and some type of transport process in the cell. Because of their shape, these enzymes often operate as gates that separate distinct cellular compartments to control and regulate the passage of chemical species across them. In this manner, ions and small molecules are moved across membranes, biopolymer substrates are segregated between cells or moved into confined spaces, double-stranded nucleic acids are separated into single strands to provide access to the genetic information, and polypeptides are unfolded and processed for recycling. Here we review the recent advances in the characterization of these motors using single-molecule manipulation and detection approaches. We describe the various mechanisms by which ring motors convert chemical energy to mechanical force or torque and coordinate the activities of individual subunits that constitute the ring. We also examine how single-molecule studies have contributed to a better understanding of the structural elements involved in motor-substrate interaction, mechanochemical coupling, and intersubunit coordination. Finally, we discuss how these molecular motors tailor their operation-often through regulation by other cofactors-to suit their unique biological functions.

  1. Computational design of faster rotating second-generation light-driven molecular motors by control of steric effects.

    Science.gov (United States)

    Oruganti, Baswanth; Fang, Changfeng; Durbeej, Bo

    2015-09-07

    We report a systematic computational investigation of the possibility to accelerate the rate-limiting thermal isomerizations of the rotary cycles of synthetic light-driven overcrowded alkene-based molecular motors through modulation of steric interactions. Choosing as a reference system a second-generation motor known to accomplish rotary motion in the MHz regime and using density functional theory methods, we propose a three-step mechanism for the thermal isomerizations of this motor and show that variation of the steric bulkiness of the substituent at the stereocenter can reduce the (already small) free-energy barrier of the rate-determining step by a further 15-17 kJ mol(-1). This finding holds promise for future motors of this kind to reach beyond the MHz regime. Furthermore, we demonstrate and explain why one particular step is kinetically favored by decreasing and another step is kinetically favored by increasing the steric bulkiness of this substituent, and identify a possible back reaction capable of impeding the rotary rate.

  2. Towards a molecular understanding of the apicomplexan actin motor: on a road to novel targets for malaria remedies?

    Energy Technology Data Exchange (ETDEWEB)

    Kumpula, Esa-Pekka [University of Oulu, PO Box 3000, 90014 Oulu (Finland); Helmholtz Centre for Infection Research, Notkestrasse 85, 22607 Hamburg (Germany); German Electron Synchrotron, Notkestrasse 85, 22607 Hamburg (Germany); Kursula, Inari, E-mail: inari.kursula@helmholtz-hzi.de [University of Oulu, PO Box 3000, 90014 Oulu (Finland); Helmholtz Centre for Infection Research, Notkestrasse 85, 22607 Hamburg (Germany); German Electron Synchrotron, Notkestrasse 85, 22607 Hamburg (Germany); University of Bergen, Jonas Lies vei 91, 5009 Bergen (Norway)

    2015-04-16

    In this review, current structural understanding of the apicomplexan glideosome and actin regulation is described. Apicomplexan parasites are the causative agents of notorious human and animal diseases that give rise to considerable human suffering and economic losses worldwide. The most prominent parasites of this phylum are the malaria-causing Plasmodium species, which are widespread in tropical and subtropical regions, and Toxoplasma gondii, which infects one third of the world’s population. These parasites share a common form of gliding motility which relies on an actin–myosin motor. The components of this motor and the actin-regulatory proteins in Apicomplexa have unique features compared with all other eukaryotes. This, together with the crucial roles of these proteins, makes them attractive targets for structure-based drug design. In recent years, several structures of glideosome components, in particular of actins and actin regulators from apicomplexan parasites, have been determined, which will hopefully soon allow the creation of a complete molecular picture of the parasite actin–myosin motor and its regulatory machinery. Here, current knowledge of the function of this motor is reviewed from a structural perspective.

  3. Um modelo de exclusão assimétrico para o transporte de partículas mediado por motores moleculares

    OpenAIRE

    Elisa Thomé Sena

    2008-01-01

    Motores moleculares são proteínas capazes de transportar objetos tais como vesículas, organelas e macromoléculas ao longo do citoesqueleto. Tratam-se de dispositivos bastante interessantes do ponto de vista físico, pois produzem trabalho em um ambiente extremamente ruidoso. Recentemente, diversos experimentos realizados in vivo têm revelado que objetos transportados por motores moleculares ao longo dos microtúbulos apresentam movimento bidirecional. Embora o movimento unidirecional dos motore...

  4. Improved postharvest quality in patagonian squash ( Cucurbita moschata) coated with radiation depolymerized chitosan

    Science.gov (United States)

    Pugliese, Maria Alicia; Goitia, Maria Teresa; Yossen, Mariana; Cifone, Norma; Agulló, Enrique; Andreucetti, Noemi

    2011-12-01

    Different molecular weight chitosans were evaluated on the decay of coated Anquito squashes ( Cucurbita moschata) as well as the maintenance of the fruit quality along five storage months. The original chitosan (Mw=391 kDa, 83% DD), was depolymerized by gamma radiation. Apart from chain scission, other chemical changes were not detected by FTIR or UV-vis analyses. The molecular weight characterization of chitosans was done by size exclusion chromatography with dual light scattering and concentration detection (SEC-MALLS-RI). The coating effectiveness was evaluated on the following parameters: fungal decay incidence, weight loss, firmness, total reducing sugar, soluble solid, flesh color, carotene content, pH and titratable acidity. No sign of fungal decay was observed in squashes coated with 122 and 56 kDa chitosans, which were also the most effective treatments in reducing the weight loss. The chitosan with Mw=122 kDa was also the best treatment considering firmness, internal aspect, sugar and carotene content. Then, radiation degraded chitosan was better in C. moschata preservation than the original chitosan.

  5. Non-enzymatic depolymerization of cotton cellulose by fungal mimicking metabolites

    DEFF Research Database (Denmark)

    Hastrup, Anne Christine Steenkjær; Howell, Caitlin; Jensen, Bo

    2011-01-01

    peroxide, iron, and oxalic acid. The former two are involved in the Fenton reaction in which they react to form hydroxyl radicals, which cause an accelerated depolymerization in cotton cellulose. We found the same reaction to be caused by both iron Fe3+ and Fe2+. A 10 mM oxalic acid solution showed...... significant depolymerization effect on cotton cellulose. An oxalic acid/sodium oxalate buffered pH gradient had an inhibitory effect on the reduction of cellulose polymers at increased pH values. The organic iron chelator, EDTA, was found to promote depolymerization of cellulose in combination with Fenton......’s reagents, but inhibited the effect of oxalic acid in the absence of iron and hydrogen peroxide. Manganese was tested to see if metals other than iron could generate a significant impact on the degree of polymerization (DP) in cotton cellulose. Depolymerizing properties comparable to iron were seen...

  6. Depolymerization of Poly(bisphenol A carbonate) in Subcritical and Supercritical Toluene

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    The depolymerization of poly(bisphenol A carbonate)(PC) in subcritical and supercritical toluene was studied. The experimental parameters, which influence the depolymerization reaction such as temperature (570-633 K), pressure (4.0-7.0 MPa), reaction time (5-60 min), and toluene to PC weight ratio (3.0-11.0), were investigated, and the reaction products were determined by GC, GC/MS and FT-IR spectrometer. It was found that the main product of the depolymerization reaction was bisphenol A(BPA). BPA accounted for over 55.7% of the depolymerization products at reaction temperature 613 K, pressure 5.0-6.0 MPa, reaction time 15 min and toluene/PC weight ratio of around 7.0.

  7. Thermal depolymerization of plastics - PDU testing. Task 15. Topical report

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1996-01-01

    The process development unit (PDU) test program is part of an ongoing effort at the Energy & Environmental Research Center (EERC) to expand the base of knowledge for the thermal depolymerization of plastics process. This phase of the development effort, initiated after successful completion of a bench-scale program, has concentrated on maximizing liquid yield. The purposes of the PDU program were (1) to demonstrate the process on a commercially scalable unit, (2) to produce quantities of product that could be used to initiate discussions with potential end users, and (3) to gather engineering and yield data. Experimentation consisted of eleven test points on the PDU and seven on the continuous fluid-bed reactor (CFBR) bench-scale unit. Initial PDU tests (PO35-PO39) were carried out using a base blend, which consists of 60% high-density polyethylene (HDPE), 20% polypropylene (PP), and 20% polystyrene (PS) virgin resin pellets. Test PO39 used base blend with 5% polyvinyl chloride (PVC). The base blend decomposed to produce a flowable liquid, with liquid yields ranging from 33% to 45%. The next series of tests, PO40-PO44, used a postconsumer plastics feed. This material did not decompose as readily as the base blend and formed a very waxy, heavy liquid, with {open_quotes}liquid{close_quotes} yields ranging from 18% to 63% (low liquid yields are the result of using excess air in the natural gas burner in some tests in an attempt to increase gas residence time).

  8. On the possibility to accelerate the thermal isomerizations of overcrowded alkene-based rotary molecular motors with electron-donating or electron-withdrawing substituents.

    Science.gov (United States)

    Oruganti, Baswanth; Durbeej, Bo

    2016-09-01

    We employ computational methods to investigate the possibility of using electron-donating or electron-withdrawing substituents to reduce the free-energy barriers of the thermal isomerizations that limit the rotational frequencies achievable by synthetic overcrowded alkene-based molecular motors. Choosing as reference systems one of the fastest motors known to date and two variants thereof, we consider six new motors obtained by introducing electron-donating methoxy and dimethylamino or electron-withdrawing nitro and cyano substituents in conjugation with the central olefinic bond connecting the two (stator and rotator) motor halves. Performing density functional theory calculations, we then show that electron-donating (but not electron-withdrawing) groups at the stator are able to reduce the already small barriers of the reference motors by up to 18 kJ mol(-1). This result outlines a possible strategy for improving the rotational frequencies of motors of this kind. Furthermore, exploring the origin of the catalytic effect, it is found that electron-donating groups exert a favorable steric influence on the thermal isomerizations, which is not manifested by electron-withdrawing groups. This finding suggests a new mechanism for controlling the critical steric interactions of these motors. Graphical Abstract The introduction of electron-donating groups in one of the fastest rotary molecular motors known to date is found to reduce the free-energy barriers of the thermal steps that limit the rotational frequencies by up to 18 kJ mol(-1).

  9. Simultaneous quantification of depolymerization and mineralization rates by a novel 15N tracing model

    Science.gov (United States)

    Andresen, Louise C.; Björsne, Anna-Karin; Bodé, Samuel; Klemedtsson, Leif; Boeckx, Pascal; Rütting, Tobias

    2016-09-01

    The depolymerization of soil organic matter, such as proteins and (oligo-)peptides, into monomers (e.g. amino acids) is currently considered to be the rate-limiting step for nitrogen (N) availability in terrestrial ecosystems. The mineralization of free amino acids (FAAs), liberated by the depolymerization of peptides, is an important fraction of the total mineralization of organic N. Hence, the accurate assessment of peptide depolymerization and FAA mineralization rates is important in order to gain a better process-based understanding of the soil N cycle. In this paper, we present an extended numerical 15N tracing model Ntrace, which incorporates the FAA pool and related N processes in order to provide a more robust and simultaneous quantification of depolymerization and gross mineralization rates of FAAs and soil organic N. We discuss analytical and numerical approaches for two forest soils, suggest improvements of the experimental work for future studies, and conclude that (i) when about half of all depolymerized peptide N is directly mineralized, FAA mineralization can be as important a rate-limiting step for total gross N mineralization as peptide depolymerization rate; (ii) gross FAA mineralization and FAA immobilization rates can be used to develop FAA use efficiency (NUEFAA), which can reveal microbial N or carbon (C) limitation.

  10. Amination of biorefinery technical lignins using Mannich reaction synergy with subcritical ethanol depolymerization.

    Science.gov (United States)

    Wang, Bing; Chen, Tian-Ying; Wang, Han-Min; Li, Han-Yin; Liu, Chuan-Fu; Wen, Jia-Long

    2017-09-06

    The alcoholic depolymerization and Mannich reaction were conducted to improve the chemical activity of biorefinery technical lignins and introduce amino groups into lignins, respectively. To understand the chemical structural transformations and examine the reaction mechanism, GPC and solution-state NMR techniques were performed. Element analysis was also used to quantify the amount of amine groups. The NMR characterization the depolymerized lignins indicated of the depolymerization, demethoxylation, and bond cleavage of linkages occurred during the depolymerization process. Results showed that the depolymerization temperature instead of the addition of capping reagents was the main factor for improving the reactivity of lignin under the given conditions. The Mannich reaction was very selective, primarily occurred at H3,5 and G5 positions, and the H units present a higher chemical reactivity. It is believed that the understanding of the fundamental chemistry of lignin during depolymerization and Mannich reaction process will contribute to the extension of high value-added applications of biorefinery lignin. Copyright © 2017. Published by Elsevier B.V.

  11. Molecular classification of amyotrophic lateral sclerosis by unsupervised clustering of gene expression in motor cortex

    NARCIS (Netherlands)

    Aronica, E.; Baas, F.; Iyer, A.; ten Asbroek, A.L.M.A.; Morello, G.; Cavallaro, S.

    2015-01-01

    Amyotrophic lateral sclerosis (ALS) is a rapidly progressive and ultimately fatal neurodegenerative disease, caused by the loss of motor neurons in the brain and spinal cord. Although 10% of ALS cases are familial (FALS), the majority are sporadic (SALS) and probably associated to a multifactorial e

  12. Vanadyl ions binding to GroEL (HSP60) and inducing its depolymerization

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Several vanadium compounds have been known for the hypoglycemic and anticancer effects. However, the mechanisms of the pharmacological and toxicological effects were not clear. In this work, we investigated the potential targets of vanadium in mitochondria. Vanadyl ions were found to bind to mitochondria from rat liver with a stoichiometry of 244±58 nmol/mg protein and an apparent dissocia- tion constant (Kd) of (2.0±0.8)×10-16 mol/L. Using size exclusion chromatography, a vanadium-binding protein was isolated and identified to be the 60-kDa heat shock protein (HSP60) by mass spectrometry analysis and immunoassays. Additionally, binding of vanadyl ions was found to result in depolymerization of homo-oligomeric HSP60 (GroEL). HSP60 is an indispensable molecular chaperone and involved in many kinds of pathogenesis of inflammatory and autoimmune diseases, e.g. type 1 diabetes. Our results suggested that HSP60 could be a novel important target involved in the biological and/or toxicological effects of vanadium compounds.

  13. Characteristics of deacetylation and depolymerization of β-chitin from jumbo squid (Dosidicus gigas) pens.

    Science.gov (United States)

    Jung, Jooyeoun; Zhao, Yanyun

    2011-09-27

    This study evaluated the deacetylation characteristics of β-chitin from jumbo squid (Dosidicus gigas) pens by using strongly alkaline solutions of NaOH or KOH. Taguchi design was employed to investigate the effect of reagent concentration, temperature, time, and treatment step on molecular mass (MM) and degree of deacetylation (DDA) of the chitosan obtained. The optimal treatment conditions for achieving high MM and DDA of chitosan were identified as: 40% NaOH at 90°C for 6h with three separate steps (2h+2h+2h) or 50% NaOH at 90°C for 6h with one step, or 50% KOH at 90°C for 4h with three steps (1h+1h+2h) or 6h with one step. The most important factor affecting DDA and MM was temperature and time, respectively. The chitosan obtained was then further depolymerized by cellulase or lysozyme with cellulase giving a higher degradation ratio, lower relative viscosity, and a larger amount of reducing-end formations than that of lysozyme due to its higher susceptibility. This study demonstrated that jumbo squid pens are a good source of materials to produce β-chitosan with high DDA and a wide range of MM for various potential applications.

  14. Low-Energy Catalytic Electrolysis for Simultaneous Hydrogen Evolution and Lignin Depolymerization.

    Science.gov (United States)

    Du, Xu; Liu, Wei; Zhang, Zhe; Mulyadi, Arie; Brittain, Alex; Gong, Jian; Deng, Yulin

    2017-03-09

    Here, a new proton-exchange-membrane electrolysis is presented, in which lignin was used as the hydrogen source at the anode for hydrogen production. Either polyoxometalate (POM) or FeCl3 was used as the catalyst and charge-transfer agent at the anode. Over 90 % Faraday efficiency was achieved. In a thermal-insulation reactor, the heat energy could be maintained at a very low level for continuous operation. Compared to the best alkaline-water electrolysis reported in literature, the electrical-energy consumption could be 40 % lower with lignin electrolysis. At the anode, the Kraft lignin (KL) was oxidized to aromatic chemicals by POM or FeCl3 , and reduced POM or Fe ions were regenerated during the electrolysis. Structure analysis of the residual KL indicated a reduction of the amount of hydroxyl groups and the cleavage of ether bonds. The results suggest that POM- or FeCl3 -mediated electrolysis can significantly reduce the electrolysis energy consumption in hydrogen production and, simultaneously, depolymerize lignin to low-molecular-weight value-added aromatic chemicals. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Quasi-steady State Reduction of Molecular Motor-Based Models of Directed Intermittent Search

    KAUST Repository

    Newby, Jay M.

    2010-02-19

    We present a quasi-steady state reduction of a linear reaction-hyperbolic master equation describing the directed intermittent search for a hidden target by a motor-driven particle moving on a one-dimensional filament track. The particle is injected at one end of the track and randomly switches between stationary search phases and mobile nonsearch phases that are biased in the anterograde direction. There is a finite possibility that the particle fails to find the target due to an absorbing boundary at the other end of the track. Such a scenario is exemplified by the motor-driven transport of vesicular cargo to synaptic targets located on the axon or dendrites of a neuron. The reduced model is described by a scalar Fokker-Planck (FP) equation, which has an additional inhomogeneous decay term that takes into account absorption by the target. The FP equation is used to compute the probability of finding the hidden target (hitting probability) and the corresponding conditional mean first passage time (MFPT) in terms of the effective drift velocity V, diffusivity D, and target absorption rate λ of the random search. The quasi-steady state reduction determines V, D, and λ in terms of the various biophysical parameters of the underlying motor transport model. We first apply our analysis to a simple 3-state model and show that our quasi-steady state reduction yields results that are in excellent agreement with Monte Carlo simulations of the full system under physiologically reasonable conditions. We then consider a more complex multiple motor model of bidirectional transport, in which opposing motors compete in a "tug-of-war", and use this to explore how ATP concentration might regulate the delivery of cargo to synaptic targets. © 2010 Society for Mathematical Biology.

  16. Torque, chemistry and efficiency in molecular motors: a study of the rotary-chemical coupling in F1-ATPase.

    Science.gov (United States)

    Mukherjee, Shayantani; Bora, Ram Prasad; Warshel, Arieh

    2015-11-01

    Detailed understanding of the action of biological molecular machines must overcome the challenge of gaining a clear knowledge of the corresponding free-energy landscape. An example for this is the elucidation of the nature of converting chemical energy to torque and work in the rotary molecular motor of F1-ATPase. A major part of the challenge involves understanding the rotary-chemical coupling from a non-phenomenological structure/energy description. Here we focused on using a coarse-grained model of F1-ATPase to generate a structure-based free-energy landscape of the rotary-chemical process of the whole system. In particular, we concentrated on exploring the possible impact of the position of the catalytic dwell on the efficiency and torque generation of the molecular machine. It was found that the experimentally observed torque can be reproduced with landscapes that have different positions for the catalytic dwell on the rotary-chemical surface. Thus, although the catalysis is undeniably required for torque generation, the experimentally observed position of the catalytic dwell at 80° might not have a clear advantage for the force generation by F1-ATPase. This further implies that the rotary-chemical couplings in these biological motors are quite robust and their efficiencies do not depend explicitly on the position of the catalytic dwells. Rather, the specific positioning of the dwells with respect to the rotational angle is a characteristic arising due to the structural construct of the molecular machine and might not bear any clear connection to the thermodynamic efficiency for the system.

  17. Mixed molecular motor traffic on nucleic acid tracks: models of transcriptional interference and regulation of gene expression

    CERN Document Server

    Bameta, Tripti; Ghanti, Dipanwita; Ghosh, Soumendu

    2015-01-01

    RNA polymerase (RNAP) is molecular machine that polymerizes a RNA molecule, a linear heteropolymer, using a single stranded DNA (ssDNA) as the corresponding template; the sequence of monomers of the RNA is dictated by that of monomers on the ssDNA template. While polymerizing a RNA, the RNAP walks step-by-step on the ssDNA template in a specific direction. Thus, a RNAP can be regarded also as a molecular motor and the sites of start and stop of its walk on the DNA mark the two ends of the genetic message that it transcribes into RNA. Interference of transcription of two overlapping genes is believed to regulate the levels of their expression, i.e., the overall rate of the corresponding RNA synthesis, through suppressive effect of one on the other. Here we model this process as a mixed traffic of two groups of RNAP motors that are characterized by two distinct pairs of start and stop sites. Each group polymerizes identical copies of a RNA while the RNAs polymerized by the two groups are different. These models...

  18. Molecular Motors as the Smallest Motors in the World%世界上最小的马达——分子马达

    Institute of Scientific and Technical Information of China (English)

    陈勇; 周宁; 杜海莲; 冯亚兵; 赵玉芬

    2001-01-01

    @@世界上最小的马达在哪里?就在我们每个人的身体里,它被称为"分子马达"(molecular motor).分子马达是生物体内的一类蛋白质,就像传统的马达一样,它们"燃烧"燃料,做出特定的运动,完成特定的功能.它们是生物体内的"化学能与机械能之间的转换器".某些分子马达也有定子、转子,只不过它们的尺寸都非常小,以纳米为单位,所以被称为世界上最小的马达."生命在于运动",这对于分子马达来说最确切不过了.每个生物体内都有成千上万的分子马达,光合作用需要分子马达,细胞的分裂需要分子马达,肌肉运动也是分子马达在起作用生物体内分子马达无处不在.   

  19. Tug-of-war of molecular motors: the effects of uneven load sharing

    CERN Document Server

    Bouzat, Sebastian; 10.1088/1478-3975/8/6/066010

    2011-01-01

    We analyze theoretically the problem of cargo transport along microtubules by motors of two species with opposite polarities. We consider two different one-dimensional models previously developed in the literature. On the one hand, a quite widespread model which assumes equal force sharing, here referred to as mean field model (MFM). On the other hand, a stochastic model (SM) which considers individual motor-cargo links. We find that in generic situations the MFM predicts larger cargo mean velocity, smaller mean run time and less frequent reversions than the SM. These phenomena are found to be consequences of the load sharing assumptions and can be interpreted in terms the probabilities of the different motility states. We also explore the influence of the viscosity in both models and the role of the stiffness of the motor-cargo links within the SM. Our results show that the mean cargo velocity is independent of the stiffness while the mean run time decreases with such a parameter. We explore the case of symm...

  20. 基于冲击力模型的分子马达动力学分析%Molecular Motor Dynamics in Impact Force Model

    Institute of Scientific and Technical Information of China (English)

    李晨璞; 韩英荣; 展永; 胡金江; 谢革英; 张礼刚; 范虹

    2013-01-01

    With transport characteristics and experiment about molecular motor,an impact force model is established,which conforms Langevin equation.Kinetics of molecular motor transport is analyzed.Molecular motors could take stable stepping motion and effective transport in right impact force combined with noise intensity.Direction of motion of molecular motor is adjusted by direction of impulse force.Though average speed is not zero at different noise intensity,efficient transport of molecular motor ensemble indicates that the system is selective on noise intensity.Average speed of molecular motor ensemble decreases with increasing of load force,the motion even changes its direction as load force is great enough.%从分子马达输运特点和实验现象出发,建立满足朗之万方程的冲击力模型,分析分子马达定向输运的动力学行为.研究发现:在合适的冲击力和噪声强度的共同作用下,分子马达可以稳定的梯跳跃迁运动和有效的输运;分子马达在轨运动的方向由冲击力的方向决定;另外,虽然在不同的噪声强度时平均速度都不为零,但是整个分子马达系综的高效输运对噪声强度有一定的选择性;系综的平均速度随着负载力的增大而减小,甚至会产生反方向的运动.

  1. 分子马达的输运方式研究进展%Research Progress on Transport Ways of the Molecular Motors

    Institute of Scientific and Technical Information of China (English)

    吴魏霞

    2012-01-01

    分子马达(molecularmotor)是生物体细胞内一类具有马达功能的蛋白质大分子,几乎执行了生物体的所有生命活动,其中物质的输运是分子马达的一项重要功能。以往人们一直认为分子马达都是沿着单一轨道单独来输运物质,但随着实验的发展,研究发现分子马达的输运方式多种多样,并且输运过程与多种疾病有关。就分子马达的输运方式最新进展进行综述,阐述分子马达在体内可能的输运方式及与输运过程相关的疾病,最后总结并展望未来。%Molecular motors are protein that perform all tasks vital to the life. Intracellular transport is a very important task. In the past years, people insisted that individual molecular motor transported 'cargo' along single track. But in recent years, various transport ways of molecular motors have been observed from experiments. In addition, research results show that many diseases associate with transport of molecular motors. The new process about transport ways of molecular motors is summarized, including the possible transport behavior patterns of molecular motors and the related diseases. A summary is given and possible future directions are discussed.

  2. Ensemble velocity of non-processive molecular motors with multiple chemical states

    CERN Document Server

    Vilfan, Andrej

    2014-01-01

    We study the ensemble velocity of non-processive motor proteins, described with multiple chemical states. In particular, we discuss the velocity as a function of ATP concentration. Even a simple model which neglects the strain-dependence of transition rates, reverse transition rates and nonlinearities in the elasticity can show interesting functional dependencies, which deviate significantly from the frequently assumed Michaelis-Menten form. We discuss how the oder of events in the duty cycle can be inferred from the measured dependence. The model also predicts the possibility of velocity reversal at a certain ATP concentration if the duty cycle contains several conformational changes of opposite directionalities.

  3. Engineering of a novel Ca²⁺-regulated kinesin molecular motor using a calmodulin dimer linker.

    Science.gov (United States)

    Shishido, Hideki; Maruta, Shinsaku

    2012-06-29

    The kinesin-microtubule system holds great promise as a molecular shuttle device within biochips. However, one current barrier is that such shuttles do not have "on-off" control of their movement. Here we report the development of a novel molecular motor powered by an accelerator and brake system, using a kinesin monomer and a calmodulin (CaM) dimer. The kinesin monomer, K355, was fused with a CaM target peptide (M13 peptide) at the C-terminal part of the neck region (K355-M13). We also prepared CaM dimers using CaM mutants (Q3C), (R86C), or (A147C) and crosslinkers that react with cysteine residues. Following induction of K355-M13 dimerization with CaM dimers, we measured K355-M13 motility and found that it can be reversibly regulated in a Ca(2+)-dependent manner. We also found that velocities of K355-M13 varied depending on the type and crosslink position of the CaM dimer used; crosslink length also had a moderate effect on motility. These results suggest Ca(2+)-dependent dimerization of K355-M13 could be used as a novel molecular shuttle, equipped with an accelerator and brake system, for biochip applications.

  4. Molecular genetics and mechanisms of disease in distal hereditary motor neuropathies: insights directing future genetic studies.

    Science.gov (United States)

    Drew, A P; Blair, I P; Nicholson, G A

    2011-11-01

    The distal hereditary motor neuropathies (dHMNs) are a clinically and genetically heterogeneous group of disorders that primarily affect motor neurons, without significant sensory involvement. New dHMN genes continue to be identified. There are now 11 causative genes described for dHMN, and an additional five genetic loci with unidentified genes. This genetic heterogeneity has further delineated the classification of dHMN, which was previously classified according to mode of inheritance, age at onset, and additional complicating features. Some overlap between phenotypically distinct forms of dHMN is also apparent. The mutated genes identified to-date in dHMN include HSPB1, HSPB8, HSPB3, DCTN1, GARS, PLEKHG5, BSCL2, SETX, IGHMBP2, ATP7A and TRPV4. The pathogenesis of mutations remains to be fully elucidated, however common pathogenic mechanisms are emerging. These include disruption of axonal transport, RNA processing defects, protein aggregation and inclusion body formation, disrupted calcium channel activity, and loss of neuroprotective signalling. Some of these dHMN genes are also mutated in Charcot-Marie-Tooth (CMT) disease and spinal muscular atrophy (SMA). This review examines the growing number of identified dHMN genes, discusses recent insights into the functions of these genes and possible pathogenic mechanisms, and looks at the increasing overlap between dHMN and the other neuropathies CMT2 and SMA.

  5. Mixed molecular motor traffic on nucleic acid tracks: models of transcriptional interference and regulation of gene expression

    CERN Document Server

    Ghosh, Soumendu; Ghanti, Dipanwita; Chowdhury, Debashish

    2015-01-01

    While polymerizing a RNA molecule, a RNA polymerase (RNAP) walks step-by-step on the corresponding single-stranded DNA (ssDNA) template in a specific direction. Thus, a RNAP can be regarded as a molecular motor for which the ssDNA template serves as the track. The sites of start and stop of its walk on the DNA mark the two ends of the genetic message that it transcribes into RNA. Interference of transcription of two overlapping genes can strongly influence the levels of their expression, i.e., the overall rate of the synthesis of the corresponding full-length RNA molecules, through suppressive effect of one on the other. Here we model this process as a mixed traffic of two groups of RNAP motors that are characterized by two distinct pairs of on- and off-ramps. Each group polymerizes identical copies of a RNA while the RNAs polymerized by the two groups are different. These models, which may also be viewed as two interfering totally asymmetric simple exclusion processes, account for all modes of transcriptiona...

  6. Elasticity of a semiflexible filament with a discontinuous tension due to a cross-link or a molecular motor

    CERN Document Server

    Razbin, Mohammadhosein; Zippelius, Annette

    2016-01-01

    We analyze the stretching elasticity of a wormlike chain with a tension discontinuity resulting from a Hookean spring connecting its backbone to a fixed point. The elasticity of isolated semiflexible filaments has been the subject in a significant body of literature, primarily because of its relevance to the mechanics of biological matter. In real systems, however, these filaments are usually part of supramolecular structures involving cross-linkers or molecular motors which cause tension discontinuities. Our model is intended as a minimal structural element incorporating such a discontinuity. We obtain analytical results in the weakly bending limit of the filament, concerning its force-extension relation and the response of the two parts in which the filament is divided by the spring. For a small tension discontinuity, the linear response of the filament extension to this discontinuity strongly depends on the external tension. For large external tension $f$, the spring force contributes a subdominant correct...

  7. Hereditary motor and sensory neuropathies: Understanding molecular pathogenesis could lead to future treatment strategies.

    Science.gov (United States)

    Jerath, Nivedita U; Shy, Michael E

    2015-04-01

    Inherited peripheral neuropathies, like many other degenerative disorders, have been challenging to treat. At this point, there is little specific therapy for the inherited neuropathies other than genetic counseling as well as symptomatic treatment and rehabilitation. In the past, ascorbic acid, progesterone antagonists, and subcutaneous neurotrophin-3 (NT3) injections have demonstrated improvement in animal models of CMT 1A, the most common inherited neuropathy, but have failed to translate any effect in humans. Given the difficulty in treatment, it is important to understand the molecular pathogenesis of hereditary neuropathies in order to strategize potential future therapies. The hereditary neuropathies are in an era of molecular insight and over the past 20 years, more than 78 subtypes of Charcot Marie Tooth disease (CMT) have been identified and extensively studied to understand the biological pathways in greater detail. Next generation molecular sequencing has also improved the diagnosis as well as the understanding of CMT. A greater understanding of the molecular pathways will help pave the way to future therapeutics of CMT. This article is part of a Special Issue entitled: Neuromuscular Diseases: Pathology and Molecular Pathogenesis.

  8. Global gene expression analysis of rodent motor neurons following spinal cord injury associates molecular mechanisms with development of post-injury spasticity

    DEFF Research Database (Denmark)

    Wienecke, Jacob; Westerdahl, Ann-Charlotte; Hultborn, Hans;

    2010-01-01

    of endogenous plateau potentials in motor neurons and the development of spasticity after spinalization. To unravel the molecular mechanisms underlying the increased excitability of motor neurons and the return of plateau potentials below a spinal cord injury we investigated changes in gene expression......Spinal cord injury leads to severe problems involving impaired motor, sensory and autonomic functions. After spinal injury there is an initial phase of hypo-reflexia followed by hyper-reflexia, often referred to as spasticity. Previous studies have suggested a relationship between the reappearance...... in this cell population. We adopted a rat tail-spasticity model with a caudal spinal transection that causes a progressive development of spasticity from its onset after two to three weeks until two months post injury. Gene expression changes of fluorescently identified tail motor neurons were studied 21...

  9. Michaelis-Menten at 100 and allosterism at 50: driving molecular motors in a hailstorm with noisy ATPase engines and allosteric transmission.

    Science.gov (United States)

    Chowdhury, Debashish

    2014-01-01

    Cytoskeletal motor proteins move on filamentous tracks by converting input chemical energy that they derive by catalyzing the hydrolysis of ATP. The ATPase site is the analogue of an engine and hydrolysis of ATP is the analogue of burning of chemical fuel. Moreover, the functional role of a segment of the motor is analogous to that of the transmission system of an automobile, which consists of a shaft, gear, clutch, etc. The operation of the engine is intrinsically 'noisy' and the motor faces a molecular 'hailstorm' in the aqueous medium. In this commemorative review, we celebrate the centenary of Michaelis and Menten's landmark paper of 1913 and the golden jubilee of Monod and colleagues classic paper of 1963 by highlighting their relevance with respect to explaining the operational mechanisms of the engine and the transmission system, respectively, of cytoskeletal motors. © 2013 FEBS.

  10. Effect of enzymatic depolymerization on physicochemical and rheological properties of guar gum.

    Science.gov (United States)

    Mudgil, Deepak; Barak, Sheweta; Khatkar, B S

    2012-09-01

    Depolymerization of guar gum using enzymatic hydrolysis was performed to obtain depolymerized guar gum having functional application as soluble dietary fiber. Enzymatic hydrolysis of guar gum significantly affected the physicochemical and rheological characteristics of guar gum. The depolymerized guar gum showed a significant increase in crystallinity index from 3.86% to 13.2% and flow behavior index from 0.31 to 1.7 as compared to native guar gum. Remarkable decrease in intrinsic viscosity and consistency index was also observed from 9 to 0.28 and 4.04 to 0.07, respectively. Results revealed that enzymatic hydrolysis of guar gum resulted in a polysaccharide with low degree of polymerization, viscosity and consistency which could make it useful for incorporation in food products as dietary fiber without affecting the rheology, consistency and texture of the products.

  11. The contribution of glutenin macropolymer depolymerization to the deterioration of frozen steamed bread dough quality.

    Science.gov (United States)

    Wang, Pei; Lee, Tung-Ching; Xu, Xueming; Jin, Zhengyu

    2016-11-15

    Depolymerization of glutenin macropolymers (GMP) widely exists in the frozen dough with little effort in elucidating its effects on steamed bread quality. To clarify this, GMP was fractionated from wheat flour and reconstituted to yeast and chemical leavened dough (YLD/CLD). Results showed that with supplementary GMP fraction, depolymerization degree was alleviated in frozen dough. The bread quality loss from freezing was partially counteracted along with better preserved GMP content. Both of dough elasticity and gas retention capability were enhanced in GMP-enriched frozen dough. Gassing power in frozen YLD decreased while remained constant in CLD. Addition of GMP did not affect the gassing power, which allowed interpreting the improved bread qualities from the enhanced dough elasticity and gas retention capability. Based on the improved facts of frozen steamed bread dough quality with additional GMP fractions, this study revealed the pivotal role of GMP depolymerization on the frozen steamed bread dough quality. Copyright © 2016 Elsevier Ltd. All rights reserved.

  12. Monte Carlo analysis of neck linker extension in kinesin molecular motors.

    Directory of Open Access Journals (Sweden)

    Matthew L Kutys

    2010-11-01

    Full Text Available Kinesin stepping is thought to involve both concerted conformational changes and diffusive movement, but the relative roles played by these two processes are not clear. The neck linker docking model is widely accepted in the field, but the remainder of the step--diffusion of the tethered head to the next binding site--is often assumed to occur rapidly with little mechanical resistance. Here, we investigate the effect of tethering by the neck linker on the diffusive movement of the kinesin head, and focus on the predicted behavior of motors with naturally or artificially extended neck linker domains. The kinesin chemomechanical cycle was modeled using a discrete-state Markov chain to describe chemical transitions. Brownian dynamics were used to model the tethered diffusion of the free head, incorporating resistive forces from the neck linker and a position-dependent microtubule binding rate. The Brownian dynamics and chemomechanical cycle were coupled to model processive runs consisting of many 8 nm steps. Three mechanical models of the neck linker were investigated: Constant Stiffness (a simple spring, Increasing Stiffness (analogous to a Worm-Like Chain, and Reflecting (negligible stiffness up to a limiting contour length. Motor velocities and run lengths from simulated paths were compared to experimental results from Kinesin-1 and a mutant containing an extended neck linker domain. When tethered by an increasingly stiff spring, the head is predicted to spend an unrealistically short amount of time within the binding zone, and extending the neck is predicted to increase both the velocity and processivity, contrary to experiments. These results suggest that the Worm-Like Chain is not an adequate model for the flexible neck linker domain. The model can be reconciled with experimental data if the neck linker is either much more compliant or much stiffer than generally assumed, or if weak kinesin-microtubule interactions stabilize the diffusing

  13. Cooperation, competition, and coalitions in enzyme-producing microbes: Social evolution and nutrient depolymerization rates

    Directory of Open Access Journals (Sweden)

    Henry Joseph Folse

    2012-09-01

    Full Text Available Extracellular enzymes represent a public good for microbial communities, as they break down complex molecules into simple molecules that microbes can take up. These communities are vulnerable to cheating by microbes that do not produce enzymes, but benefit from those produced by others. However, extracellular enzymes are ubiquitous and play an important role in the depolymerization of nutrients. We developed a multi-genotype, multi-nutrient model of a community of exoenzyme-producing microbes, in order to investigate the relationship between diversity, social interactions, and nutrient depolymerization. We focused on coalitions between complementary types of microbes and their implications for spatial pattern formation and nutrient depolymerization. The model included polymers containing carbon, nitrogen, or phosphorus, and eight genotypes of bacteria, which produced different subsets of the three enzymes responsible for hydrolyzing these polymers. We allowed social dynamics to emerge from a mechanistic model of enzyme production, action, and diffusion. We found that diversity was maximized at high rates of either diffusion or enzyme production (but not both. Conditions favoring cheating also favored the emergence of coalitions. We characterized the spatial patterns formed by different interactions, showing that same-type cooperation leads to aggregation, but between-type cooperation leads to an interwoven, filamentous pattern. Contrary to expectations based on niche complementarity, we found that nutrient depolymerization declined with increasing diversity due to a negative competitive effect of coalitions on generalist producers, leading to less overall enzyme production. This decline in depolymerization was stronger for non-limiting nutrients in the system. This study shows that social interactions among microbes foraging for complementary resources can influence microbial diversity, microbial spatial distributions, and rates of nutrient

  14. Cooperation, competition, and coalitions in enzyme-producing microbes: social evolution and nutrient depolymerization rates.

    Science.gov (United States)

    Folse, Henry J; Allison, Steven D

    2012-01-01

    Extracellular enzymes represent a public good for microbial communities, as they break down complex molecules into simple molecules that microbes can take up. These communities are vulnerable to cheating by microbes that do not produce enzymes, but benefit from those produced by others. However, extracellular enzymes are ubiquitous and play an important role in the depolymerization of nutrients. We developed a multi-genotype, multi-nutrient model of a community of exoenzyme-producing microbes, in order to investigate the relationship between diversity, social interactions, and nutrient depolymerization. We focused on coalitions between complementary types of microbes and their implications for spatial pattern formation and nutrient depolymerization. The model included polymers containing carbon, nitrogen, or phosphorus, and eight genotypes of bacteria, which produced different subsets of the three enzymes responsible for hydrolyzing these polymers. We allowed social dynamics to emerge from a mechanistic model of enzyme production, action, and diffusion. We found that diversity was maximized at high rates of either diffusion or enzyme production (but not both). Conditions favoring cheating also favored the emergence of coalitions. We characterized the spatial patterns formed by different interactions, showing that same-type cooperation leads to aggregation, but between-type cooperation leads to an interwoven, filamentous pattern. Contrary to expectations based on niche complementarity, we found that nutrient depolymerization declined with increasing diversity due to a negative competitive effect of coalitions on generalist producers, leading to less overall enzyme production. This decline in depolymerization was stronger for non-limiting nutrients in the system. This study shows that social interactions among microbes foraging for complementary resources can influence microbial diversity, microbial spatial distributions, and rates of nutrient depolymerization.

  15. Alternating Sulfone Copolymers Depolymerize in Response to Both Chemical and Mechanical Stimuli.

    Science.gov (United States)

    Kumar, Kaushlendra; Goodwin, Andrew P

    2015-09-15

    This work describes the depolymerization of poly(vinyl acetate-alt-sulfur dioxide) (PVAS) as initiated by chemical and mechanical stimuli. In recent years, macromolecules that are able to depolymerize in response to specific stimuli have been highly sought because of their ability to amplify signal for sensing and drug delivery. Examples include self-immolative polymers from alkoxyphenol derivatives and polyaldehydes. We show here that alternating copolymers of sulfur dioxide and vinyl acetate are able to undergo similar depolymerization into their monomer components in response to various chemical and mechanical stimuli. Certain vinyl monomers such as vinyl acetate are able to polymerize with sulfur dioxide in a perfectly alternating manner, and the resulting copolymer possesses a low ceiling temperature. We show that this polymer is able to break down into its monomer components when subjected to UV/acetone, various Reactive Oxygen Species (ROS), and ultrasonication. In the case of UV, the acetone reacted via a Norrish reaction to produce free radicals that caused clean monomer production. For ROS, the polymer showed reactivity to both oxidizing and radical-containing ROS. Through kinetic studies, these polymers were shown to proceed via a two-part, first-order kinetic model with a fast initiation phase and a slow depolymerization phase. Finally, the polymers were subjected to probe ultrasonication, and depolymerization occurred as well. Most tellingly, the polymer again showed a fast initiation step and continued to depolymerize even after ultrasonication stopped. This class of polymers shows potential for drug delivery in response to both endogenous chemical and externally-applied mechanical cues.

  16. Metabolic disposition in rats of regular and enzymatically depolymerized sodium carboxymethylcellulose.

    Science.gov (United States)

    Bär, A; Van Ommen, B; Timonen, M

    1995-11-01

    Partially enzyme-hydrolysed sodium carboxymethylcellulose (CMC-ENZ), which holds promise as a new, functional food ingredient, is obtained from sodium carboxymethylcellulose (CMC) by enzymatic hydrolysis with a cellulase preparation from Trichoderma longibrachiatum. In the safety evaluation of CMC-ENZ, a comparative disposition study on 14C-labelled CMC and CMC-ENZ was conducted in conventionally kept rats. The 14C label was in the two C atoms of the carboxymethyl group. Two groups of four male and four female rats each were fed diets with 5% unlabelled CMC or CMC-ENZ for a 2-wk adaptation period. A single oral dose of 14C-CMC or 14C-CMC-ENZ solution was then given by gavage (500 mg/kg body weight). Respiratory CO2, urine and faeces were collected at regular intervals, and after 120 hr organs, tissues and the carcass were sampled as well. For both experimental groups, total mean recovery of 14C was 98%, about 95% of the label being excreted with the faeces, 2% or less in the urine, 1% or less with CO2 and a small fraction being retained in the body (CMC, 0.58%; CMC-ENZ, 0.75%). Tissue retention of 14C was highest in the liver of rats of both experimental groups. Only about 49 and 65% of the faecal 14C was extracted with water in the 14C-CMC and 14C-CMC-ENZ dosed rats, respectively. Gel permeation chromatography (GPC) of the dosing solutions and the faecal extracts revealed that CMC is depolymerized during intestinal passage whereas CMC-ENZ is excreted nearly unchanged. Consequently, the molecular weight distribution of the 14C-CMC and 14C-CMC-ENZ faecal excretion products was similar. It is concluded that there is no toxicologically relevant difference between the disposition of CMC and CMC-ENZ.

  17. Specific microtubule-depolymerizing agents augment efficacy of dendritic cell-based cancer vaccines

    Directory of Open Access Journals (Sweden)

    Chang Wei-Ting

    2011-06-01

    Full Text Available Abstract Background Damage-associated molecular patterns (DAMPs are associated with immunogenic cell death and have the ability to enhance maturation and antigen presentation of dendritic cells (DCs. Specific microtubule-depolymerizing agents (MDAs such as colchicine have been shown to confer anti-cancer activity and also trigger activation of DCs. Methods In this study, we evaluated the ability of three MDAs (colchicine and two 2-phenyl-4-quinolone analogues to induce immunogenic cell death in test tumor cells, activate DCs, and augment T-cell proliferation activity. These MDAs were further evaluated for use as an adjuvant in a tumor cell lysate-pulsed DC vaccine. Results The three test phytochemicals considerably increased the expression of DAMPs including HSP70, HSP90 and HMGB1, but had no effect on expression of calreticulin (CRT. DC vaccines pulsed with MDA-treated tumor cell lysates had a significant effect on tumor growth, showed cytotoxic T-lymphocyte activity against tumors, and increased the survival rate of test mice. In vivo antibody depletion experiments suggested that CD8+ and NK cells, but not CD4+ cells, were the main effector cells responsible for the observed anti-tumor activity. In addition, culture of DCs with GM-CSF and IL-4 during the pulsing and stimulation period significantly increased the production of IL-12 and decreased production of IL-10. MDAs also induced phenotypic maturation of DCs and augmented CD4+ and CD8+ T-cell proliferation when co-cultured with DCs. Conclusions Specific MDAs including the clinical drug, colchicine, can induce immunogenic cell death in tumor cells, and DCs pulsed with MDA-treated tumor cell lysates (TCLs can generate potent anti-tumor immunity in mice. This approach may warrant future clinical evaluation as a cancer vaccine.

  18. Subchronic oral toxicity study with regular and enzymatically depolymerized sodium carboxymethylcellulose in rats.

    Science.gov (United States)

    Bär, A; Til, H P; Timonen, M

    1995-11-01

    Enzymatically depolymerized sodium carboxymethylcellulose (CMC-ENZ) is a new functional food ingredient which has a lower molecular weight and viscosity than regular sodium carboxymethylcellulose (CMC). Both compounds are known not to be absorbed to a significant extent, and the human safety of CMC as a thickening agent and stabilizer in food is well established. In the present study, the subchronic oral toxicity of CMC-ENZ was examined and compared with that of CMC in Wistar rats. Seven groups of 20 rats/sex were fed diets with 0 (controls), 2.5, 5 and 10% CMC and 2.5, 5 and 10% CMC-ENZ for a 3-month period. There was only one death that was unrelated to the treatment. Water intake, urine production and urinary sodium excretion increased with increasing doses of CMC and CMC-ENZ due to their sodium content of about 7-8%. The treatment-related occurrence of diarrhoea and caecal enlargement in the mid- and high-dose groups, a slight increase of plasma alkaline phosphatase, and increased urinary calcium and citrate excretions were considered to be generic effects that typically are observed in rodent studies with low digestible carbohydrates. The increased occurrence of nephrocalcinosis and hyperplasia of the urothelial epithelium in some of the treated groups was interpreted as an indirect consequence of a more alkaline urine coupled with an increased calcium excretion. As the frequency and severity of all these changes did not differ between corresponding CMC and CMC-ENZ dose groups, it is concluded that the two products have a similar toxicological profile.

  19. The microtubule-depolymerizing agent ansamitocin P3 programs dendritic cells toward enhanced anti-tumor immunity.

    Science.gov (United States)

    Martin, Kea; Müller, Philipp; Schreiner, Jens; Prince, Spasenija Savic; Lardinois, Didier; Heinzelmann-Schwarz, Viola A; Thommen, Daniela S; Zippelius, Alfred

    2014-09-01

    In addition to direct tumor cell cytotoxicity, chemotherapy can mediate tumor reduction through immune modulation of the tumor microenvironment to promote anti-tumor immunity. Mature dendritic cells (DCs) play key roles in priming robust immune responses in tumor-bearing hosts. Here, we screened a panel of 21 anticancer agents with defined molecular targets for their ability to induce direct maturation of DCs. We identified ansamitocin P3, a microtubule-depolymerizing agent, as a potent inducer of phenotypic and functional maturation of DCs. Exposure of both murine spleen-derived and human monocyte-derived DCs to ansamitocin P3 triggered up-regulation of maturation markers and production of pro-inflammatory cytokines, resulting in an enhanced T cell stimulatory capacity. Local administration of ansamitocin P3 induced maturation of skin Langerhans cells in vivo and promoted antigen uptake and extensive homing of tumor-resident DCs to tumor-draining lymph nodes. When used as an adjuvant in a specific vaccination approach, ansamitocin P3 dramatically increased activation of antigen-specific T cells. Finally, we demonstrate that ansamitocin P3, due to its immunomodulatory properties, acts in synergy with antibody-mediated blockade of the T cell inhibitory receptors PD-1 and CTLA-4. The combination treatment was most effective and induced durable growth inhibition of established tumors. Mechanistically, we observed a reduced regulatory T cell frequency and improved T cell effector function at the tumor site. Taken together, our study unravels an immune-based anti-tumor mechanism exploited by microtubule-depolymerizing agents, including ansamitocin P3, and paves the way for future clinical trials combining this class of agents with immunotherapy.

  20. Motor effect in electron transport through a molecular junction with torsional vibrations

    OpenAIRE

    Pshenichnyuk, Ivan A.; Čížek, Martin

    2010-01-01

    We propose a model for a molecular junction with internal anharmonic torsional vibrations interacting with an electric current. The Wangsness-Bloch-Redfield master equation approach is used to determine the stationary reduced density matrix of the molecule. The dependence of the current, excitation energy and angular momentum of the junction on the applied voltage is studied. Negative differential conductance is observed in the current-voltage characteristics. It is shown that a model with vi...

  1. Collective cargo hauling by a bundle of parallel microtubules: bi-directional motion caused by load-dependent polymerization and depolymerization

    Science.gov (United States)

    Ghanti, Dipanwita; Chowdhury, Debashish

    2015-01-01

    A microtubule (MT) is a hollow tube of approximately 25 nm diameter. The two ends of the tube are dissimilar and are designated as ‘plus’ and ‘minus’ ends. Motivated by the collective push and pull exerted by a bundle of MTs during chromosome segregation in a living cell, we have developed here a much simplified theoretical model of a bundle of parallel dynamic MTs. The plus-end of all the MTs in the bundle is permanently attached to a movable ‘wall’ by a device whose detailed structure is not treated explicitly in our model. The only requirement is that the device allows polymerization and depolymerization of each MT at the plus-end. In spite of the absence of external force and direct lateral interactions between the MTs, the group of polymerizing MTs attached to the wall create a load force against the group of depolymerizing MTs and vice versa; the load against a group is shared equally by the members of that group. Such indirect interactions among the MTs give rise to the rich variety of possible states of collective dynamics that we have identified by computer simulations of the model in different parameter regimes. The bi-directional motion of the cargo, caused by the load-dependence of the polymerization kinetics, is a ‘proof-of-principle’ that the bi-directional motion of chromosomes before cell division does not necessarily need active participation of motor proteins.

  2. Engineering of a novel Ca{sup 2+}-regulated kinesin molecular motor using a calmodulin dimer linker

    Energy Technology Data Exchange (ETDEWEB)

    Shishido, Hideki [Department of Bioinformatics, Faculty of Engineering, Soka University, Hachioji, Tokyo 192-8577 (Japan); Maruta, Shinsaku, E-mail: maruta@soka.ac.jp [Department of Bioinformatics, Faculty of Engineering, Soka University, Hachioji, Tokyo 192-8577 (Japan)

    2012-06-29

    Highlights: Black-Right-Pointing-Pointer Engineered kinesin-M13 and calmodulin involving single cysteine were prepared. Black-Right-Pointing-Pointer CaM mutant was cross-linked to dimer by bifunctional thiol reactive reagent. Black-Right-Pointing-Pointer Kinesin-M13 was dimerized via CaM dimer in the presence of calcium. Black-Right-Pointing-Pointer Function of the engineered kinesin was regulated by a Ca{sup 2+}-calmodulin dimer linker. -- Abstract: The kinesin-microtubule system holds great promise as a molecular shuttle device within biochips. However, one current barrier is that such shuttles do not have 'on-off' control of their movement. Here we report the development of a novel molecular motor powered by an accelerator and brake system, using a kinesin monomer and a calmodulin (CaM) dimer. The kinesin monomer, K355, was fused with a CaM target peptide (M13 peptide) at the C-terminal part of the neck region (K355-M13). We also prepared CaM dimers using CaM mutants (Q3C), (R86C), or (A147C) and crosslinkers that react with cysteine residues. Following induction of K355-M13 dimerization with CaM dimers, we measured K355-M13 motility and found that it can be reversibly regulated in a Ca{sup 2+}-dependent manner. We also found that velocities of K355-M13 varied depending on the type and crosslink position of the CaM dimer used; crosslink length also had a moderate effect on motility. These results suggest Ca{sup 2+}-dependent dimerization of K355-M13 could be used as a novel molecular shuttle, equipped with an accelerator and brake system, for biochip applications.

  3. Molecular mapping of movement-associated areas in the avian brain: a motor theory for vocal learning origin.

    Science.gov (United States)

    Feenders, Gesa; Liedvogel, Miriam; Rivas, Miriam; Zapka, Manuela; Horita, Haruhito; Hara, Erina; Wada, Kazuhiro; Mouritsen, Henrik; Jarvis, Erich D

    2008-03-12

    Vocal learning is a critical behavioral substrate for spoken human language. It is a rare trait found in three distantly related groups of birds-songbirds, hummingbirds, and parrots. These avian groups have remarkably similar systems of cerebral vocal nuclei for the control of learned vocalizations that are not found in their more closely related vocal non-learning relatives. These findings led to the hypothesis that brain pathways for vocal learning in different groups evolved independently from a common ancestor but under pre-existing constraints. Here, we suggest one constraint, a pre-existing system for movement control. Using behavioral molecular mapping, we discovered that in songbirds, parrots, and hummingbirds, all cerebral vocal learning nuclei are adjacent to discrete brain areas active during limb and body movements. Similar to the relationships between vocal nuclei activation and singing, activation in the adjacent areas correlated with the amount of movement performed and was independent of auditory and visual input. These same movement-associated brain areas were also present in female songbirds that do not learn vocalizations and have atrophied cerebral vocal nuclei, and in ring doves that are vocal non-learners and do not have cerebral vocal nuclei. A compilation of previous neural tracing experiments in songbirds suggests that the movement-associated areas are connected in a network that is in parallel with the adjacent vocal learning system. This study is the first global mapping that we are aware for movement-associated areas of the avian cerebrum and it indicates that brain systems that control vocal learning in distantly related birds are directly adjacent to brain systems involved in movement control. Based upon these findings, we propose a motor theory for the origin of vocal learning, this being that the brain areas specialized for vocal learning in vocal learners evolved as a specialization of a pre-existing motor pathway that controls

  4. Molecular mapping of movement-associated areas in the avian brain: a motor theory for vocal learning origin.

    Directory of Open Access Journals (Sweden)

    Gesa Feenders

    Full Text Available Vocal learning is a critical behavioral substrate for spoken human language. It is a rare trait found in three distantly related groups of birds-songbirds, hummingbirds, and parrots. These avian groups have remarkably similar systems of cerebral vocal nuclei for the control of learned vocalizations that are not found in their more closely related vocal non-learning relatives. These findings led to the hypothesis that brain pathways for vocal learning in different groups evolved independently from a common ancestor but under pre-existing constraints. Here, we suggest one constraint, a pre-existing system for movement control. Using behavioral molecular mapping, we discovered that in songbirds, parrots, and hummingbirds, all cerebral vocal learning nuclei are adjacent to discrete brain areas active during limb and body movements. Similar to the relationships between vocal nuclei activation and singing, activation in the adjacent areas correlated with the amount of movement performed and was independent of auditory and visual input. These same movement-associated brain areas were also present in female songbirds that do not learn vocalizations and have atrophied cerebral vocal nuclei, and in ring doves that are vocal non-learners and do not have cerebral vocal nuclei. A compilation of previous neural tracing experiments in songbirds suggests that the movement-associated areas are connected in a network that is in parallel with the adjacent vocal learning system. This study is the first global mapping that we are aware for movement-associated areas of the avian cerebrum and it indicates that brain systems that control vocal learning in distantly related birds are directly adjacent to brain systems involved in movement control. Based upon these findings, we propose a motor theory for the origin of vocal learning, this being that the brain areas specialized for vocal learning in vocal learners evolved as a specialization of a pre-existing motor

  5. Physics in cell biology: on the physics of biopolymers and molecular motors.

    Science.gov (United States)

    Frey, Erwin

    2002-03-12

    "What is Life?" is the title of a book by Erwin Schrödinger, first published in 1944. This book is a bold attempt to try to understand some of the wonders of life in terms of physics, in particular statistical mechanics. Since the publication of this visionary book, we have seen a revolution in molecular biology complemented by the development of new physical tools like single-molecule spectroscopy. The goal of this article is to highlight some examples where physics can contribute to questions in cell biology. One might hope that through interdisciplinary research one can get closer to answering Schrödinger's fundamental question.

  6. fMRI as a molecular imaging procedure for the functional reorganization of motor systems in chronic stroke

    OpenAIRE

    Lazaridou, Asimina; ASTRAKAS, LOUKAS; Mintzopoulos, Dionyssios; KHANCHICEH, AZADEH; Singhal, Aneesh; Moskowitz, Michael; Rosen, Bruce; Tzika, Aria

    2013-01-01

    Previous brain imaging studies suggest that stroke alters functional connectivity in motor execution networks. Moreover, current understanding of brain plasticity has led to new approaches in stroke rehabilitation. Recent studies showed a significant role of effective coupling of neuronal activity in the SMA (supplementary motor area) and M1 (primary motor cortex) network for motor outcome in patients after stroke. After a subcortical stroke, functional magnetic resonance imaging (fMRI) durin...

  7. Molecular determinants of survival motor neuron (SMN protein cleavage by the calcium-activated protease, calpain.

    Directory of Open Access Journals (Sweden)

    Jennifer L Fuentes

    Full Text Available Spinal muscular atrophy (SMA is a leading genetic cause of childhood mortality, caused by reduced levels of survival motor neuron (SMN protein. SMN functions as part of a large complex in the biogenesis of small nuclear ribonucleoproteins (snRNPs. It is not clear if defects in snRNP biogenesis cause SMA or if loss of some tissue-specific function causes disease. We recently demonstrated that the SMN complex localizes to the Z-discs of skeletal and cardiac muscle sarcomeres, and that SMN is a proteolytic target of calpain. Calpains are implicated in muscle and neurodegenerative disorders, although their relationship to SMA is unclear. Using mass spectrometry, we identified two adjacent calpain cleavage sites in SMN, S192 and F193. Deletion of small motifs in the region surrounding these sites inhibited cleavage. Patient-derived SMA mutations within SMN reduced calpain cleavage. SMN(D44V, reported to impair Gemin2 binding and amino-terminal SMN association, drastically inhibited cleavage, suggesting a role for these interactions in regulating calpain cleavage. Deletion of A188, a residue mutated in SMA type I (A188S, abrogated calpain cleavage, highlighting the importance of this region. Conversely, SMA mutations that interfere with self-oligomerization of SMN, Y272C and SMNΔ7, had no effect on cleavage. Removal of the recently-identified SMN degron (Δ268-294 resulted in increased calpain sensitivity, suggesting that the C-terminus of SMN is important in dictating availability of the cleavage site. Investigation into the spatial determinants of SMN cleavage revealed that endogenous calpains can cleave cytosolic, but not nuclear, SMN. Collectively, the results provide insight into a novel aspect of the post-translation regulation of SMN.

  8. Molecular hydrogen alleviates motor deficits and muscle degeneration in mdx mice.

    Science.gov (United States)

    Hasegawa, Satoru; Ito, Mikako; Fukami, Mayu; Hashimoto, Miki; Hirayama, Masaaki; Ohno, Kinji

    2017-01-01

    Duchenne muscular dystrophy (DMD) is a devastating muscle disease caused by a mutation in DMD encoding dystrophin. Oxidative stress accounts for dystrophic muscle pathologies in DMD. We examined the effects of molecular hydrogen in mdx mice, a model animal for DMD. The pregnant mother started to take supersaturated hydrogen water (>5 ppm) ad libitum from E15.5 up to weaning of the offspring. The mdx mice took supersaturated hydrogen water from weaning until age 10 or 24 weeks when they were sacrificed. Hydrogen water prevented abnormal body mass gain that is commonly observed in mdx mice. Hydrogen improved the spontaneous running distance that was estimated by a counter-equipped running-wheel, and extended the duration on the rota-rod. Plasma creatine kinase activities were decreased by hydrogen at ages 10 and 24 weeks. Hydrogen also decreased the number of central nuclei of muscle fibers at ages 10 and 24 weeks, and immunostaining for nitrotyrosine in gastrocnemius muscle at age 24 weeks. Additionally, hydrogen tended to increase protein expressions of antioxidant glutathione peroxidase 1, as well as anti-apoptotic Bcl-2, in skeletal muscle at age 10 weeks. Although molecular mechanisms of the diverse effects of hydrogen remain to be elucidated, hydrogen potentially improves muscular dystrophy in DMD patients.

  9. Depolymerization of organosolv lignin using doped porous metal oxides in supercritical methanol

    NARCIS (Netherlands)

    Warner, Genoa; Hansen, Thomas S; Riisager, Anders; Beach, Evan S; Barta, Katalin; Anastas, Paul T

    An isolated, solvent-extracted lignin from candlenut (Aleurites moluccana) biomass was subjected to catalytic depolymerization in the presence of supercritical methanol, using a range of porous metal oxides derived from hydrotalcite-like precursors. The most effective catalysts in terms of lignin

  10. High-speed depolymerization at actin filament ends jointly catalysed by Twinfilin and Srv2/CAP.

    Science.gov (United States)

    Johnston, Adam B; Collins, Agnieszka; Goode, Bruce L

    2015-11-01

    Purified actin filaments depolymerize slowly, and cytosolic conditions strongly favour actin assembly over disassembly, which has left our understanding of how actin filaments are rapidly turned over in vivo incomplete. One mechanism for driving filament disassembly is severing by factors such as Cofilin. However, even after severing, pointed-end depolymerization remains slow and unable to fully account for observed rates of actin filament turnover in vivo. Here we describe a mechanism by which Twinfilin and Cyclase-associated protein work in concert to accelerate depolymerization of actin filaments by 3-fold and 17-fold at their barbed and pointed ends, respectively. This mechanism occurs even under assembly conditions, allowing reconstitution and direct visualization of individual filaments undergoing tunable, accelerated treadmilling. Further, we use specific mutations to demonstrate that this activity is critical for Twinfilin function in vivo. These findings fill a major gap in our knowledge of cellular disassembly mechanisms, and suggest that depolymerization and severing may be deployed separately or together to control the dynamics and architecture of distinct actin networks.

  11. High Speed Depolymerization at Actin Filament Ends Jointly Catalyzed by Twinfilin and Srv2/CAP

    Science.gov (United States)

    Johnston, Adam B.; Collins, Agnieszka; Goode, Bruce L.

    2015-01-01

    Purified actin filaments depolymerize slowly, and cytosolic conditions strongly favor actin assembly over disassembly, which has left our understanding of how actin filaments are rapidly turned over in vivo incomplete 1,2. One mechanism for driving filament disassembly is severing by factors such as Cofilin. However, even after severing, pointed end depolymerization remains slow and unable to fully account for observed rates of actin filament turnover in vivo. Here we describe a mechanism by which Twinfilin and Cyclase-associated protein work in concert to accelerate depolymerization of actin filaments by 3-fold and 17-fold at their barbed and pointed ends, respectively. This mechanism occurs even under assembly conditions, allowing reconstitution and direct visualization of individual filaments undergoing tunable, accelerated treadmilling. Further, we use specific mutations to demonstrate that this activity is critical for Twinfilin function in vivo. These findings fill a major gap in our knowledge of mechanisms, and suggest that depolymerization and severing may be deployed separately or together to control the dynamics and architecture of distinct actin networks. PMID:26458246

  12. Depolymerization of organosolv lignin using doped porous metal oxides in supercritical methanol

    NARCIS (Netherlands)

    Warner, Genoa; Hansen, Thomas S; Riisager, Anders; Beach, Evan S; Barta, Katalin; Anastas, Paul T

    2014-01-01

    An isolated, solvent-extracted lignin from candlenut (Aleurites moluccana) biomass was subjected to catalytic depolymerization in the presence of supercritical methanol, using a range of porous metal oxides derived from hydrotalcite-like precursors. The most effective catalysts in terms of lignin co

  13. Depolymerization of organosolv lignin to aromatic compounds over Cu-doped porous metal oxides

    NARCIS (Netherlands)

    Barta, Katalin; Warner, Genoa R.; Beach, Evan S.; Anastas, Paul T.

    2014-01-01

    Isolated, solvent-extracted lignin from candlenut (Aleurites moluccana) biomass was subjected to catalytic depolymerization in methanol with an added pressure of H-2, using a porous metal oxide catalyst (PMO) derived from a Cu-doped hydrotalcite-like precursor. The Cu-PMO was effective in converting

  14. Depolymerization of organosolv lignin to aromatic compounds over Cu-doped porous metal oxides

    NARCIS (Netherlands)

    Barta, Katalin; Warner, Genoa R.; Beach, Evan S.; Anastas, Paul T.

    2014-01-01

    Isolated, solvent-extracted lignin from candlenut (Aleurites moluccana) biomass was subjected to catalytic depolymerization in methanol with an added pressure of H-2, using a porous metal oxide catalyst (PMO) derived from a Cu-doped hydrotalcite-like precursor. The Cu-PMO was effective in converting

  15. Lewis acid-catalyzed depolymerization of soda lignin in supercritical ethanol/water mixtures

    NARCIS (Netherlands)

    Güvenatam, Burcu; Heeres, Erik H.J.; Pidko, Evgeny A.; Hensen, Emiel J M

    2016-01-01

    The depolymerization of lignin model compounds and soda lignin by super Lewis acidic metal triflates has been investigated in a mixture of ethanol and water at 400 °C. The strong Lewis acids convert representative model compounds for the structure-forming linkages in lignin, namely α-O-4, 5-O-4

  16. Lewis-acid catalyzed depolymerization of Protobind lignin in supercritical water and ethanol

    NARCIS (Netherlands)

    Guvenatam, Burcu; Heeres, Erik H.J.; Pidko, Evgeny A.; Hensen, Ernie J. M.

    2016-01-01

    The use of metal acetates, metal chlorides and metal triflates as Lewis acid catalysts for the depolymerization of soda lignin under supercritical conditions was investigated. The reactions were carried out at 400 degrees C in water and ethanol. Lignin conversion in supercritical water led to format

  17. Depolymerization of organosolv lignin using doped porous metal oxides in supercritical methanol

    NARCIS (Netherlands)

    Warner, Genoa; Hansen, Thomas S; Riisager, Anders; Beach, Evan S; Barta, Katalin; Anastas, Paul T

    2014-01-01

    An isolated, solvent-extracted lignin from candlenut (Aleurites moluccana) biomass was subjected to catalytic depolymerization in the presence of supercritical methanol, using a range of porous metal oxides derived from hydrotalcite-like precursors. The most effective catalysts in terms of lignin co

  18. Lewis-acid catalyzed depolymerization of Protobind lignin in supercritical water and ethanol

    NARCIS (Netherlands)

    Guvenatam, Burcu; Heeres, Erik H.J.; Pidko, Evgeny A.; Hensen, Ernie J. M.

    2016-01-01

    The use of metal acetates, metal chlorides and metal triflates as Lewis acid catalysts for the depolymerization of soda lignin under supercritical conditions was investigated. The reactions were carried out at 400 degrees C in water and ethanol. Lignin conversion in supercritical water led to

  19. Methyl de-esterification as a major factor regulating the extent of pectin depolymerization during fruit ripening: a comparison of the action of avocado (Persea americana) and tomato (Lycopersicon esculentum) polygalacturonases.

    Science.gov (United States)

    Wakabayashi, Kazuyuki; Hoson, Takayuki; Huber, Donald J

    2003-06-01

    Pectinmethylesterase (PME, EC 3.2.1.11) and polygalacturonase (PG, EC 3.2.1.15) are known to operate in tandem to degrade methylesterified polyuronides. In this study, PGs purified from tomato and avocado fruit were compared in terms of their capacity to hydrolyze water-soluble polyuronides from avocado before and following enzymic or chemical de-esterification. When assayed using polygalacturonic acid or polyuronides from avocado fruit, the activity of PG from tomato fruit was 3-4 times higher than that from avocado fruit. High molecular mass, low methylesterified (33%) water-soluble polyuronides (WSP) from pre-ripe avocado fruit (day 0) were partially depolymerized upon incubation with purified avocado and tomato PGs. In contrast, middle molecular mass, highly methylesterified (74%) WSP from day 2 fruit were largely resistant to the action of both PGs. PME or weak alkali treatment of highly methylesterified WSP decreased the methylesterification values to 11 and 4.5%, respectively. Treatment of de-esterified WSP with either avocado or tomato PGs caused extensive molecular mass downshifts, paralleling those observed during avocado fruit ripening. Although PME and PG are found in many fruits, the pattern of depolymerization of native polyuronides indicates that the degree of cooperativity between these enzymes in vivo differs dramatically among fruits. The contribution of PME to patterns of polyuronide depolymerization observed during ripening compared with physically compromised fruit tissues is discussed.

  20. From molecular chaperones to membrane motors: through the lens of a mass spectrometrist

    Science.gov (United States)

    2017-01-01

    Twenty-five years ago, we obtained our first mass spectra of molecular chaperones in complex with protein ligands and entered a new field of gas-phase structural biology. It is perhaps now time to pause and reflect, and to ask how many of our initial structure predictions and models derived from mass spectrometry (MS) datasets were correct. With recent advances in structure determination, many of the most challenging complexes that we studied over the years have become tractable by other structural biology approaches enabling such comparisons to be made. Moreover, in the light of powerful new electron microscopy methods, what role is there now for MS? In considering these questions, I will give my personal view on progress and problems as well as my predictions for future directions. PMID:28202679

  1. Taking a molecular motor for a spin: helicase mechanism studied by spin labeling and PELDOR

    Science.gov (United States)

    Constantinescu-Aruxandei, Diana; Petrovic-Stojanovska, Biljana; Schiemann, Olav; Naismith, James H.; White, Malcolm F.

    2016-01-01

    The complex molecular motions central to the functions of helicases have long attracted attention. Protein crystallography has provided transformative insights into these dynamic conformational changes, however important questions about the true nature of helicase configurations during the catalytic cycle remain. Using pulsed EPR (PELDOR or DEER) to measure interdomain distances in solution, we have examined two representative helicases: PcrA from superfamily 1 and XPD from superfamily 2. The data show that PcrA is a dynamic structure with domain movements that correlate with particular functional states, confirming and extending the information gleaned from crystal structures and other techniques. XPD in contrast is shown to be a rigid protein with almost no conformational changes resulting from nucleotide or DNA binding, which is well described by static crystal structures. Our results highlight the complimentary nature of PELDOR to crystallography and the power of its precision in understanding the conformational changes relevant to helicase function. PMID:26657627

  2. Electromagnetic probes of molecular motors in the electron transport chains of mitochondria and chloroplasts

    Science.gov (United States)

    Miller, J. H., Jr.; Nawarathna, D.; Vajrala, V.; Gardner, J.; Widger, W. R.

    2005-12-01

    We report on measurements of harmonics generated by whole cells, mitochondria, and chloroplasts in response to applied sinusoidal electric fields. The frequency- and amplitude-dependence of the induced harmonics exhibit features that correlate with physiological processes. Budding yeast (S. cerevisiae) cells produce numerous harmonics, the amplitudes of which depend strongly on frequency. When the second or third harmonic amplitude is plotted vs. applied frequency, we observe two peaks, around 3 kHz and 12 kHz, which are suppressed by respiratory inhibitors. We observe similar peaks when measuring the harmonic response of B. indicas, a relative of the mitochondrial ancestor. In uncoupled mitochondria, in which most of the electron transport chain is active but the ATP-synthase molecular turbine is inactive, only one (lower frequency) of the two peaks is present. Finally, we find that harmonics generated by chloroplasts depend dramatically on incident light, and vanish in the absence of light.

  3. M(o)TOR of aging: MTOR as a universal molecular hypothalamus.

    Science.gov (United States)

    Blagosklonny, Mikhail V

    2013-07-01

    A recent ground-breaking publication described hypothalamus-driven programmatic aging. As a Russian proverb goes "everything new is well-forgotten old". In 1958, Dilman proposed that aging and its related diseases are programmed by the hypothalamus. This theory, supported by beautiful experiments, remained unnoticed just to be re-discovered recently. Yet, it does not explain all manifestations of aging. And would organism age without hypothalamus? Do sensing pathways such as MTOR (mechanistic Target of Rapamycin) and IKK-beta play a role of a "molecular hypothalamus" in every cell? Are hypothalamus-driven alterations simply a part of quasi-programmed aging manifested by hyperfunction and secondary signal-resistance? Here are some answers.

  4. 分子马达定向运动的合作机制%Cooperative Mechanism in Directed Motion of Molecular Motors

    Institute of Scientific and Technical Information of China (English)

    陈宏斌; 郑志刚

    2012-01-01

    Molecular motors are the frontier topic in biology and physics, and the dynamic mechanism of directed transport attracts much attention. In most cases,molecular motors operate in groups. The interaction and cooperation among motors play an important role in the collective behaviors of molecular motors. The behaviors and mechanism of collective transport of molecular motors are sketched out. Furthermore, two cases are detailedly discussed in which the cooperation among motors is needed for the implementation of directed transport. In the first case, the cooperation impels directed motion under overdamping condition. In the second case, through cooperation molecular motors can gain energy from driving in one direction and do work in the vertical direction,and then cause transversal drift.%分子马达是当前生物学和物理学的前沿课题,其定向运动的动力学机制一直是科学家关注的焦点之一.生物体内的分子马达一般是很多个一起协同工作.相互作用与合作在分子马达集体行为中起了很大作用.本文概述了分子马达合作运动的现象和机制.为进一步阐述合作的意义,本文详细讨论了分子马达必须依靠合作才能实现定向输运的两种情况.第一种,分子马达通过合作,在过阻尼条件下克服不停闪烁的棘齿势,实现了定向运动.第二种,分子马达通过合作,可以将一个方向上输入的驱动能量转化到垂直方向上做功,并产生定向输运.

  5. Elasticity of a semiflexible filament with a discontinuous tension due to a cross-link or a molecular motor

    Science.gov (United States)

    Razbin, Mohammadhosein; Benetatos, Panayotis; Zippelius, Annette

    2016-05-01

    We analyze the stretching elasticity of a wormlike chain with a tension discontinuity resulting from a Hookean spring connecting its backbone to a fixed point. The elasticity of isolated semiflexible filaments has been the subject in a significant body of literature, primarily because of its relevance to the mechanics of biological matter. In real systems, however, these filaments are usually part of supramolecular structures involving cross-linkers or molecular motors, which cause tension discontinuities. Our model is intended as a minimal structural element incorporating such a discontinuity. We obtain analytical results in the weakly bending limit of the filament, concerning its force-extension relation and the response of the two parts in which the filament is divided by the spring. For a small tension discontinuity, the linear response of the filament extension to this discontinuity strongly depends on the external tension. For large external tension f , the spring force contributes a subdominant correction ˜1 /f3 /2 to the well-known ˜1 /√{f } -dependence of the end-to-end extension.

  6. Direct observation of bis(dicarbollyl)nickel conformers in solution by fluorescence spectroscopy: an approach to redox-controlled metallacarborane molecular motors.

    Science.gov (United States)

    Safronov, Alexander V; Shlyakhtina, Natalia I; Everett, Thomas A; VanGordon, Monika R; Sevryugina, Yulia V; Jalisatgi, Satish S; Hawthorne, M Frederick

    2014-10-06

    As a continuation of work on metallacarborane-based molecular motors, the structures of substituted bis(dicarbollyl)nickel complexes in Ni(III) and Ni(IV) oxidation states were investigated in solution by fluorescence spectroscopy. Symmetrically positioned cage-linked pyrene molecules served as fluorescent probes to enable the observation of mixed meso-trans/dl-gauche (pyrene monomer fluorescence) and dl-cis/dl-gauche (intramolecular pyrene excimer fluorescence with residual monomer fluorescence) cage conformations of the nickelacarboranes in the Ni(III) and Ni(IV) oxidation states, respectively. The absence of energetically disfavored conformers in solution--dl-cis in the case of nickel(III) complexes and meso-trans in the case of nickel(IV)--was demonstrated based on spectroscopic data and conformer energy calculations in solution. The conformational persistence observed in solution indicates that bis(dicarbollyl)nickel complexes may provide attractive templates for building electrically driven and/or photodriven molecular motors.

  7. Growth-promotion of plants with depolymerized alginates by irradiation

    Science.gov (United States)

    Hien, Nguyen Quoc; Nagasawa, Naotsugu; Tham, Le Xuan; Yoshii, Fumio; Dang, Vo Huy; Mitomo, Hiroshi; Makuuchi, Keizo; Kume, Tamikazu

    2000-07-01

    Alginate has been degraded by gamma-ray irradiation from a Co-60 source in liquid state (aqueous solution) and in solid state (powder form). The irradiated alginate with a molecular weight less than 10 4 shows a strong effect on the growth-promotion of rice and peanut. Low concentration of degraded alginate from 4% solution irradiated at 100 kGy is effective for the growth-promotion of plants and the suitable concentrations are ca 50 ppm for rice and ca 100 ppm for peanut.

  8. fMRI as a molecular imaging procedure for the functional reorganization of motor systems in chronic stroke

    Science.gov (United States)

    LAZARIDOU, ASIMINA; ASTRAKAS, LOUKAS; MINTZOPOULOS, DIONYSSIOS; KHANCHICEH, AZADEH; SINGHAL, ANEESH; MOSKOWITZ, MICHAEL; ROSEN, BRUCE; TZIKA, ARIA

    2013-01-01

    Previous brain imaging studies suggest that stroke alters functional connectivity in motor execution networks. Moreover, current understanding of brain plasticity has led to new approaches in stroke rehabilitation. Recent studies showed a significant role of effective coupling of neuronal activity in the SMA (supplementary motor area) and M1 (primary motor cortex) network for motor outcome in patients after stroke. After a subcortical stroke, functional magnetic resonance imaging (fMRI) during movement reveals cortical reorganization that is associated with the recovery of function. The aim of the present study was to explore connectivity alterations within the motor-related areas combining motor fMRI with a novel MR-compatible hand-induced robotic device (MR_CHIROD) training. Patients completed training at home and underwent serial MR evaluation at baseline and after 8 weeks of training. Training at home consisted of squeezing a gel exercise ball with the paretic hand at ~75% of maximum strength for 1 h/day, 3 days/week. The fMRI analysis revealed alterations in M1, SMA, PMC (premotor cortex) and Cer (cerebellum) in both stroke patients and healthy controls after the training. Findings of the present study suggest that enhancement of SMA activity could benefit M1 dysfunction in stroke survivors. These results also indicate that connectivity alterations between motor areas might assist the counterbalance of a functionally abnormal M1 in chronic stroke survivors and possibly other patients with motor dysfunction. PMID:23900349

  9. Rapid room temperature solubilization and depolymerization of polymeric lignin at high loadings

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Jian; Dutta, Tanmoy; Parthasarathi, Ramakrishnan; Kim, Kwang Ho; Tolic, Nikola; Chu, Rosalie K.; Isern, Nancy G.; Cort, John R.; Simmons, Blake A.; Singh, Seema

    2016-10-03

    The relatively poor solubility of lignin in most pretreatment solvents remains one of the biggest challegnes in lignin valorization to improve overall biorefinery economics. In this work, rapid room temperature solubilization of lignin at high solid loadings (>30 wt%) can be easily achieved in a single step using ethylene glycol (EG). The solubilized lignin can be rapidly and quantitively recovered with the addtion of ethanol. The computational and nuclear magnetic resonance (NMR) spectroscopic studies confirm that strong hydrogen bond interactions between EG and the free hydroxyl groups present in lignin contribute to the lignin dissolution. In addition, hydrogen peroxide mediated depolymerization of dissolved lignin at low temperature (80 oC) was tested and the effect of EG molecules on depolymerization of ligin was also theoritically studied. The findings of this work provide mechanistic insights of hydrogen bond interactions in high lignin solubilization and valorization.

  10. Tandem Catalytic Depolymerization of Lignin by Water-Tolerant Lewis Acids and Rhodium Complexes.

    Science.gov (United States)

    Jastrzebski, Robin; Constant, Sandra; Lancefield, Christopher S; Westwood, Nicholas J; Weckhuysen, Bert M; Bruijnincx, Pieter C A

    2016-08-23

    Lignin is an attractive renewable feedstock for aromatic bulk and fine chemicals production, provided that suitable depolymerization procedures are developed. Here, we describe a tandem catalysis strategy for ether linkage cleavage within lignin, involving ether hydrolysis by water-tolerant Lewis acids followed by aldehyde decarbonylation by a Rh complex. In situ decarbonylation of the reactive aldehydes limits loss of monomers by recondensation, a major issue in acid-catalyzed lignin depolymerization. Rate of hydrolysis and decarbonylation were matched using lignin model compounds, allowing the method to be successfully applied to softwood, hardwood, and herbaceous dioxasolv lignins, as well as poplar sawdust, to give the anticipated decarbonylation products and, rather surprisingly, 4-(1-propenyl)phenols. Promisingly, product selectivity can be tuned by variation of the Lewis-acid strength and lignin source. © 2016 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

  11. Selective and recyclable depolymerization of cellulose to levulinic acid catalyzed by acidic ionic liquid.

    Science.gov (United States)

    Ren, Huifang; Girisuta, Buana; Zhou, Yonggui; Liu, Li

    2015-03-01

    Cellulose depolymerization to levulinic acid (LA) was catalyzed by acidic ionic liquids (ILs) selectively and recyclably under hydrothermal conditions. The effects of reaction temperature, time, water amount and cellulose intake were investigated. Dilution effect becomes more pronounced at lower cellulose intake, dramatically improving the yield of LA to 86.1%. A kinetic model has been developed based on experimental data, whereby a good fit was obtained and kinetic parameters were derived. The relationships between IL structure, polymeric structure and depolymerization efficiency were established, shedding light on the in-depth catalytic mechanism of IL, inclusive of acidity and hydrogen bonding ability. The LA product can be readily separated through extraction by methyl isobutyl ketone (MIBK) and IL can be reused over five cycles without loss of activity. This environmentally friendly methodology can be applied to selective production of LA from versatile biomass feedstocks, including cellulose and derivatives, glucose, fructose and HMF.

  12. Biomimetic Fenton-catalyzed lignin depolymerization to high-value aromatics and dicarboxylic acids.

    Science.gov (United States)

    Zeng, Jijiao; Yoo, Chang Geun; Wang, Fei; Pan, Xuejun; Vermerris, Wilfred; Tong, Zhaohui

    2015-03-01

    By mimicking natural lignin degradation systems, the Fenton catalyst (Fe(3+), H2O2) can effectively facilitate lignin depolymerization in supercritical ethanol (7 MPa, 250 °C) to give organic oils that consist of mono- and oligomeric aromatics, phenols, dicarboxylic acids, and their derivatives in yields up to (66.0±8.5) %. The thermal properties, functional groups, and surface chemistry of lignin before and after Fenton treatment were examined by thermogravimetric analysis, pyrolysis-gas chromatography-mass spectrometry, (31)P NMR spectroscopy, and X-ray photoelectron spectroscopy. The results suggest that the Fenton catalyst facilitates lignin depolymerization through cleavage of β-ether bonds between lignin residues. The formation of a lignin-iron chelating complex effectively depresses lignin recondensation; thus minimizing charcoal formation and enhancing the yield of liquid products.

  13. Impact of the fouling mechanism on enzymatic depolymerization of xylan in different configurations of membrane reactors

    DEFF Research Database (Denmark)

    Mohd Sueb, Mohd Shafiq Bin; Luo, Jianquan; Meyer, Anne S.

    2017-01-01

    ) and the simultaneous reaction-filtration with both enzymes, respectively. This study thus confirmed that the reactor configuration has a crucial impact on the performance of both the reaction and the separation process of xylose during enzymatic xylan degradation, and that the type of fouling mechanism varies......In order to maximize enzymatic xylan depolymerization while simultaneously purifying the resulting monosaccharide (xylose), different ultrafiltration (UF) membrane reactor configurations were evaluated. Initial results showed that the two hydrolytic enzymes required for complete depolymerization...... of xylan, endo-1,4-β-xylanase and β-xylosidase, promoted different types of fouling, which had a direct impact on the extent of xylan hydrolysis achieved during reaction. Endo-1,4-β-xylanase generated DP 1-6 xylo-oligomers. These products contributed to partial pore blocking of the 1 kDa polysulfone...

  14. A comparative study on the activity of fungal lytic polysaccharide monooxygenases for the depolymerization of cellulose in soybean spent flakes

    DEFF Research Database (Denmark)

    Pierce, Brian; Wittrup Agger, Jane; Zhang, Zhenghong

    2017-01-01

    Lytic polysaccharide monooxygenases (LPMOs) are copper-dependent enzymes capable of the oxidative breakdown of polysaccharides. They are of industrial interest due to their ability to enhance the enzymatic depolymerization of recalcitrant substrates by glycoside hydrolases. In this paper, twenty-...

  15. Power Stroke Angular Velocity Profiles of Archaeal A-ATP Synthase Versus Thermophilic and Mesophilic F-ATP Synthase Molecular Motors.

    Science.gov (United States)

    Sielaff, Hendrik; Martin, James; Singh, Dhirendra; Biuković, Goran; Grüber, Gerhard; Frasch, Wayne D

    2016-12-02

    The angular velocities of ATPase-dependent power strokes as a function of the rotational position for the A-type molecular motor A3B3DF, from the Methanosarcina mazei Gö1 A-ATP synthase, and the thermophilic motor α3β3γ, from Geobacillus stearothermophilus (formerly known as Bacillus PS3) F-ATP synthase, are resolved at 5 μs resolution for the first time. Unexpectedly, the angular velocity profile of the A-type was closely similar in the angular positions of accelerations and decelerations to the profiles of the evolutionarily distant F-type motors of thermophilic and mesophilic origins, and they differ only in the magnitude of their velocities. M. mazei A3B3DF power strokes occurred in 120° steps at saturating ATP concentrations like the F-type motors. However, because ATP-binding dwells did not interrupt the 120° steps at limiting ATP, ATP binding to A3B3DF must occur during the catalytic dwell. Elevated concentrations of ADP did not increase dwells occurring 40° after the catalytic dwell. In F-type motors, elevated ADP induces dwells 40° after the catalytic dwell and slows the overall velocity. The similarities in these power stroke profiles are consistent with a common rotational mechanism for A-type and F-type rotary motors, in which the angular velocity is limited by the rotary position at which ATP binding occurs and by the drag imposed on the axle as it rotates within the ring of stator subunits.

  16. Depolymerization of coal by oxidation and alkylation; Sanka bunkai to alkyl ka ni yoru sekitan kaijugo

    Energy Technology Data Exchange (ETDEWEB)

    Tomita, H.; Isoda, T.; Kusakabe, K.; Morooka, S. [Kyushu University, Fukuoka (Japan). Faculty of Engineering; Hayashi, J. [Hokkaido University, Sapporo (Japan). Center for Advanced Research of Energy Technology

    1996-10-28

    Change in depolymerization degree and coal structure was studied for depolymerization treatment of coal in various alcohol containing aqueous hydrogen peroxide. In experiment, the mixture of Yallourn coal, alcohol and aqueous hydrogen peroxide was agitated in nitrogen atmosphere of normal pressure at 70{degree}C for 12 hours. As the experimental result, the methanol solubility of only 5% of raw coal increased up to 35.2% by hydrogen peroxide treatment, while the yield of insoluble matters also decreased from 94% to 62%. Most of the gas produced during treatment was composed of inorganic gases such as CO and CO2, and its carbon loss was extremely decreased by adding alcohol. From the analytical result of carbon loss in hydrogen peroxide treatment, it was clarified that alkylation advances with introduction of alkyl group derived from alcohol into coal by hydrogen peroxide treatment under a coexistence of alcohol, and depolymerization reaction of coal itself is thus promoted by alcohol. 4 refs., 7 figs., 1 tab.

  17. Peroxynitrite induces F-actin depolymerization and blockade of myosin ATPase stimulation.

    Science.gov (United States)

    Tiago, Teresa; Ramos, Susana; Aureliano, Manuel; Gutiérrez-Merino, Carlos

    2006-03-31

    Treatment of F-actin with the peroxynitrite-releasing agent 3-morpholinosydnonimine (SIN-1) produced a dose-dependent F-actin depolymerization. This is due to released peroxynitrite because it is not produced by 'decomposed SIN-1', and it is prevented by superoxide dismutase concentrations efficiently preventing peroxynitrite formation. F-actin depolymerization has been found to be very sensitive to peroxynitrite, as exposure to fluxes as low as 50-100nM peroxynitrite leads to nearly 50% depolymerization in about 1h. G-actin polymerization is also impaired by peroxynitrite although with nearly 2-fold lower sensitivity. Exposure of F-actin to submicromolar fluxes of peroxynitrite produced cysteine oxidation and also a blockade of the ability of actin to stimulate myosin ATPase activity. Our results suggest that an imbalance of the F-actin/G-actin equilibrium can account for the observed structural and functional impairment of myofibrils under the peroxynitrite-mediated oxidative stress reported for some pathophysiological conditions.

  18. Fermentation Process of Cocoa Based on Optimum Condition of Pulp PectinDepolymerization by Endogenous Pectolityc Enzymes

    Directory of Open Access Journals (Sweden)

    G.P. Ganda-Putra

    2010-08-01

    Full Text Available Pulp degradation during cocoa fermentation can be carried out by depolymerization process of pulp pectin using endogenous pectolytic enzymes at optimum condition. The objectives of this research were to study the effect of fermentation process based on optimum condition in terms of temperature and pH of pulp pectin depolymerization using endogenous pectolytic enzymes polygalakturonase (PG and pectin metyl esterase (PME and fermentation period in cocoa processing on quality characteristics of cocoa beans produced and to study the role of those fermentation process in reducing fermentation time to produce cocoa beans with standard quality. This research used split plot design, with treatments of process condition of cocoa fermentation as main plot and fermentation period as split plot. Treatment of process condition of cocoa fermentation consisted of optimum condition for pulp pectin depolymerization by PGs (temperature 47.5OC; initial pulp pH 4.6; optimum condition of depolymerization on sequence depolymerization by PGs (temperature 48.5OC; initial pulp pH 8.0 during 1 day; last temperature 47.5OC; initial pulp pH 4.6 during 6 days, and natural fermentation process a control. While treatment of fermentation period consisted of 0, 1, 2, 3, 4, 5, 6 and 7 days. Evaluation of fermentation period was carried out based on pursuant to criteria of unfermented beans content and fermentation index. The results showed that process condition and fermentation time of cocoa affected quality characteristic of cocoa beans produced. Period of cocoa fermentation process based on optimum condition for pulp pectin depolymerization using endogenous pectolytic enzymes was 2 days shorter compared to natural fermentation. Cocoa beans quality of grade I and II were obtained from fermentation time of 4 and 2 days, respectively, using fermentation process based on optimum condition of pulp pectin depolymerization using endogenous pectolytic enzymes, whereas 6 and 4 days

  19. Influence of litter chemistry and stoichiometry on glucan depolymerization during decomposition of beech (Fagus sylvatica L.) litter.

    Science.gov (United States)

    Leitner, Sonja; Wanek, Wolfgang; Wild, Birgit; Haemmerle, Ieda; Kohl, Lukas; Keiblinger, Katharina M; Zechmeister-Boltenstern, Sophie; Richter, Andreas

    2012-07-01

    Glucans like cellulose and starch are a major source of carbon for decomposer food webs, especially during early- and intermediate-stages of decomposition. Litter quality has previously been suggested to notably influence decomposition processes as it determines the decomposability of organic material and the nutrient availability to the decomposer community. To study the impact of chemical and elemental composition of resources on glucan decomposition, a laboratory experiment was carried out using beech (Fagus sylvatica, L.) litter from four different locations in Austria, differing in composition (concentration of starch, cellulose and acid unhydrolyzable residue or AUR fraction) and elemental stoichiometry (C:N:P ratio). Leaf litter was incubated in mesocosms for six months in the laboratory under controlled conditions. To investigate the process of glucan decomposition and its controls, we developed an isotope pool dilution (IPD) assay using (13)C-glucose to label the pool of free glucose in the litter, and subsequently measured the dilution of label over time. This enabled us to calculate gross rates of glucose production through glucan depolymerization, and glucose consumption by the microbial community. In addition, potential activities of extracellular cellulases and ligninases (peroxidases and phenoloxidases) were measured to identify effects of resource chemistry and stoichiometry on microbial enzyme production. Gross rates of glucan depolymerization and glucose consumption were highly correlated, indicating that both processes are co-regulated and intrinsically linked by the microbial demand for C and energy and thereby to resource allocation to enzymes that depolymerize glucans. At early stages of decomposition, glucan depolymerization rates were correlated with starch content, indicating that starch was the primary source for glucose. With progressing litter decomposition, the correlation with starch diminished and glucan depolymerization rates were

  20. Random walks of cytoskeletal motors in open and closed compartments

    NARCIS (Netherlands)

    Lipowsky, R.; Klumpp, S.

    2001-01-01

    Random walks of molecular motors, which bind to and unbind from cytoskeletal filaments, are studied theoretically. The bound and unbound motors undergo directed and nondirected motion, respectively. Motors in open compartments exhibit anomalous drift velocities. Motors in closed compartments generat

  1. Pigment granule translocation in red ovarian chromatophores from the palaemonid shrimp Macrobrachium olfersi (Weigmann, 1836): functional roles for the cytoskeleton and its molecular motors.

    Science.gov (United States)

    Milograna, Sarah Ribeiro; Ribeiro, Márcia Regina; Baqui, Munira Muhammad Abdel; McNamara, John Campbell

    2014-12-01

    The binding of red pigment concentrating hormone (RPCH) to membrane receptors in crustacean chromatophores triggers Ca²⁺/cGMP signaling cascades that activate cytoskeletal motors, driving pigment granule translocation. We investigate the distributions of microfilaments and microtubules and their associated molecular motors, myosin and dynein, by confocal and transmission electron microscopy, evaluating a functional role for the cytoskeleton in pigment translocation using inhibitors of polymer turnover and motor activity in vitro. Microtubules occupy the chromatophore cell extensions whether the pigment granules are aggregated or dispersed. The inhibition of microtubule turnover by taxol induces pigment aggregation and inhibits re-dispersion. Phalloidin-FITC actin labeling, together with tannic acid fixation and ultrastructural analysis, reveals that microfilaments form networks associated with the pigment granules. Actin polymerization induced by jasplaquinolide strongly inhibits RPCH-induced aggregation, causes spontaneous pigment dispersion, and inhibits pigment re-dispersion. Inhibition of actin polymerization by latrunculin-A completely impedes pigment aggregation and re-dispersion. Confocal immunocytochemistry shows that non-muscle myosin II (NMMII) co-localizes mainly with pigment granules while blebbistatin inhibition of NMMII strongly reduces the RPCH response, also inducing spontaneous pigment dispersion. Myosin II and dynein also co-localize with the pigment granules. Inhibition of dynein ATPase by erythro-9-(2-hydroxy-3-nonyl) adenine induces aggregation, inhibits RPCH-triggered aggregation, and inhibits re-dispersion. Granule aggregation and dispersion depend mainly on microfilament integrity although microtubules may be involved. Both cytoskeletal polymers are functional only when subunit turnover is active. Myosin and dynein may be the molecular motors that drive pigment aggregation. These mechanisms of granule translocation in crustacean

  2. 分数阶双头分子马达的欠扩散输运现象%Subdiffusive transport of fractional two-headed molecular motor

    Institute of Scientific and Technical Information of China (English)

    林丽烽; 周兴旺; 马洪

    2013-01-01

    Focusing on the directed transport phenomena of the two-headed molecular motor, we adopt power function as the damping kernel function of general Langevin equation due to the power-law memory characteristics of cytosol in biological cells and present the model of fractional coupling Brownian motor in overdamped condition in this paper. We also discuss the influences of fractional order and coupling factor on the transport speed. From the simulation results there are found the directed transport phenomena and the inverse transport which is not seen in the conventional Brownian motor, in the overdamped fractional coupling Brownian motor. When the noise density is fixed, the generalized stochastic resonance appears when transport speed varies with the fractional order and coupling factor. In particular, the results reveal that the magnitude and direction of the directional flow are controlled by coupling the noise with the interaction force between the two heads, which is the movement characteristic of the two-headed molecular motor in the memory ratchet, rather than of the single-headed motor.%研究具有幂律记忆性的细胞液中双头分子马达的定向输运现象,选取幂函数作为广义Langevin方程的阻尼核函数,建立了分数阶过阻尼耦合Brown马达模型,讨论了阶数及耦合系数对双头分子马达定向输运速度的影响。仿真结果表明,分数阶过阻尼双头分子马达也会产生定向输运现象,并且在某些阶数下会产生整数阶情形所不具有的反向定向流。当噪声强度固定时,输运速度随着阶数以及耦合系数的变化均会出现广义随机共振现象。特别地,研究发现双头分子马达在记忆闪烁棘轮势中具有某些单头分子马达所不具备的运动特性,定向流的大小和方向由噪声与双头间作用力相互耦合控制。

  3. Enzymatic depolymerization of gum Tragacanth: Bifidogenic potential of low molecular weight oligosaccharides

    DEFF Research Database (Denmark)

    Ahmadi Gavlighi, Hassan; Michalak, Malwina; Meyer, Anne S.

    2013-01-01

    Gum tragacanth derived from the plant “goat’s horn” (Astragalus sp.) has a long history of use as a stabilizing, viscosity-enhancing agent in food emulsions. The gum contains pectinaceous arabinogalactans and fucose-substituted xylogalacturonans. In this work, gum tragacanth from Astragalus...... that these three fractions also varied with respect to composition and structural elements: HAG1 and HAG2 were enriched in arabinose, galactose, and galacturonic acid, but low in fucose and xylose; whereas HAG3 was high in (terminal) xylose, fucose and 1,4-bonded galacturonic acid, but low in arabinose...

  4. Bacterial Flagellar Motor: A Splendid Molecular Motor%细菌鞭毛马达--一种卓越的分子机器

    Institute of Scientific and Technical Information of China (English)

    邓国宏; 徐启旺; 刘俊康; 丛严广

    2000-01-01

    鞭毛马达(flagellar motor)是一种分子旋转马达,它在细菌鞭毛的结构与功能中起着中心作用.鞭毛马达的结构已基本清楚,主要由Mot A、Mot B、Fli G、Fli M和Fli N 5种蛋白组成定子(stator)和转子(rotor),其驱动力来自于跨膜的H+或Na+流.目前对鞭毛马达的旋转动力学及旋转力矩产生机制已有初步的了解.鞭毛马达可作为研究分子旋转马达的理想模型,对其深入研究将有助于认识生物能量转化利用及细胞运动的机制并具有广泛的生物学意义.

  5. A reconsideration of the link between the energetics of water and of ATP hydrolysis energy in the power strokes of molecular motors in protein structures.

    Science.gov (United States)

    Widdas, Wilfred F

    2008-09-01

    Mechanical energy from oxygen metabolism by mammalian tissues has been studied since 1837. The production of heat by mechanical work was studied by Fick in about 1860. Prior to Fick's work, energetics were revised by Joule's experiments which founded the First Law of Thermodynamics. Fenn in 1923/24 found that frog muscle contractions generated extra heat proportional to the amount of work done in shortening the muscle. This was fully consistent with the Joule, Helmholtz concept used for the First Law of Thermodynamics. The link between the energetics of water and ATP hydrolysis in molecular motors is recommended for reconsideration.

  6. Depolymerization of organosolv lignin using doped porous metal oxides in supercritical methanol

    DEFF Research Database (Denmark)

    Warner, Genoa; Hansen, Thomas Søndergaard; Riisager, Anders

    2014-01-01

    conversion to methanol-soluble products, without char formation, were based on copper in combination with other dopants based on relatively earth-abundant metals. Nearly complete conversion of lignin to bio-oil composed of monomers and low-mass oligomers with high aromatic content was obtained in 6. h at 310......An isolated, solvent-extracted lignin from candlenut (Aleurites moluccana) biomass was subjected to catalytic depolymerization in the presence of supercritical methanol, using a range of porous metal oxides derived from hydrotalcite-like precursors. The most effective catalysts in terms of lignin...

  7. LIGNIN, STRUCTURE AND APPLICATIONS: DEPOLYMERIZATION METHODS FOR OBTAINING AROMATIC DERIVATIVES OF INDUSTRIAL INTEREST

    Directory of Open Access Journals (Sweden)

    Marvin Chávez-Sifontes

    2013-12-01

    Full Text Available In this article significant data related to the structural characteristics of lignin, the extraction and isolation processes from biomass, and also the characteristics of different types of commercial lignins are presented. The review focuses on the different depolymerization processes (hydrolysis, hydrogenolysis, hydrodeoxygenation, pyrolysis, among others up to now developed and investigated analyzing the different aromatic derivatives obtained in each case, as well as the interesting reactions some of them may undergo. Application possibilities for lignin and its derivatives in new industrial processes integrated into the bio-refinery of the future are finally assessed

  8. 基于三磷酸腺苷调节的分子马达单向能量跃迁模型%The single-direction energy transition model of molecular motor based on the control of adenosine triphosphate

    Institute of Scientific and Technical Information of China (English)

    李晨璞; 韩英荣; 展永; 谢革英; 胡金江; 张礼刚; 贾利云

    2013-01-01

    分子马达的梯跳运动和在过阻尼溶液中动力学原理尚未揭示清楚,从分子马达输运特点和实验现象出发,构建满足朗之万方程的单向能量跃迁模型,并通过Monte Carlo方法分析了分子马达的随机动力学行为。结果表明,在合适的跃迁能量作用下,分子马达可以利用噪声进行稳定的梯跳运动和有效的输运,但负载力会减弱分子马达系统的输运能力;轨道周期势虽影响分子马达速度的大小但不会改变其运动方向,分子马达运动方向由跃迁能量决定;另外,虽然在不同的噪声强度时平均速度不为零,但是分子马达系统的高效输运对噪声有一定选择性。%The dynamic principle of molecular motor transport in overdamped solution remains unclear. Starting from the transport charac-teristics and phenomenon of the molecular motor system, the single-direction energy transition model is established, which conforms to the Langevin equation, and the stochastic dynamics of molecular motors is analyzed by Monte Carlo simulations. Results show that with the right transition energy, molecular motors could take a stable stepping motion and effective transport by means of the environment noise, and the load force can weaken material transportation of the molecular motor system. The potential field between a molecular motor and its orbit can affect the magnitude of the velocity of motor, but cannot change the direction of the velocity, the direction of motion of the molecular motor therefore is adjusted by the transition energy of the motor. In addition, although the average velocity is not zero for different noise intensities, the efficient transport of a molecular motor system indicates that the system is selective for the noise intensity.

  9. Functional interactions of VirB11 traffic ATPases with VirB4 and VirD4 molecular motors in type IV secretion systems.

    Science.gov (United States)

    Ripoll-Rozada, Jorge; Zunzunegui, Sandra; de la Cruz, Fernando; Arechaga, Ignacio; Cabezón, Elena

    2013-09-01

    Pilus biogenesis and substrate transport by type IV secretion systems require energy, which is provided by three molecular motors localized at the base of the secretion channel. One of these motors, VirB11, belongs to the superfamily of traffic ATPases, which includes members of the type II secretion system and the type IV pilus and archaeal flagellar assembly apparatus. Here, we report the functional interactions between TrwD, the VirB11 homolog of the conjugative plasmid R388, and TrwK and TrwB, the motors involved in pilus biogenesis and DNA transport, respectively. Although these interactions remained standing upon replacement of the traffic ATPase by a homolog from a phylogenetically related conjugative system, namely, TraG of plasmid pKM101, this homolog could not replace the TrwD function for DNA transfer. This result suggests that VirB11 works as a switch between pilus biogenesis and DNA transport and reinforces a mechanistic model in which VirB11 proteins act as traffic ATPases by regulating both events in type IV secretion systems.

  10. Different pathways of molecular pathophysiology underlie cognitive and motor tauopathy phenotypes in transgenic models for Alzheimer's disease and frontotemporal lobar degeneration.

    Science.gov (United States)

    Melis, V; Zabke, C; Stamer, K; Magbagbeolu, M; Schwab, K; Marschall, P; Veh, R W; Bachmann, S; Deiana, S; Moreau, P-H; Davidson, K; Harrington, K A; Rickard, J E; Horsley, D; Garman, R; Mazurkiewicz, M; Niewiadomska, G; Wischik, C M; Harrington, C R; Riedel, G; Theuring, F

    2015-06-01

    A poorly understood feature of the tauopathies is their very different clinical presentations. The frontotemporal lobar degeneration (FTLD) spectrum is dominated by motor and emotional/psychiatric abnormalities, whereas cognitive and memory deficits are prominent in the early stages of Alzheimer's disease (AD). We report two novel mouse models overexpressing different human tau protein constructs. One is a full-length tau carrying a double mutation [P301S/G335D; line 66 (L66)] and the second is a truncated 3-repeat tau fragment which constitutes the bulk of the PHF core in AD corresponding to residues 296-390 fused with a signal sequence targeting it to the endoplasmic reticulum membrane (line 1; L1). L66 has abundant tau pathology widely distributed throughout the brain, with particularly high counts of affected neurons in hippocampus and entorhinal cortex. The pathology is neuroanatomically static and declines with age. Behaviourally, the model is devoid of a higher cognitive phenotype but presents with sensorimotor impairments and motor learning phenotypes. L1 displays a much weaker histopathological phenotype, but shows evidence of neuroanatomical spread and amplification with age that resembles the Braak staging of AD. Behaviourally, the model has minimal motor deficits but shows severe cognitive impairments affecting particularly the rodent equivalent of episodic memory which progresses with advancing age. In both models, tau aggregation can be dissociated from abnormal phosphorylation. The two models make possible the demonstration of two distinct but nevertheless convergent pathways of tau molecular pathogenesis. L1 appears to be useful for modelling the cognitive impairment of AD, whereas L66 appears to be more useful for modelling the motor features of the FTLD spectrum. Differences in clinical presentation of AD-like and FTLD syndromes are therefore likely to be inherent to the respective underlying tauopathy, and are not dependent on presence or absence

  11. The Ndc80 complex uses a tripartite attachment point to couple microtubule depolymerization to chromosome movement.

    Science.gov (United States)

    Tooley, John G; Miller, Stephanie A; Stukenberg, P Todd

    2011-04-15

    In kinetochores, the Ndc80 complex couples the energy in a depolymerizing microtubule to perform the work of moving chromosomes. The complex directly binds microtubules using an unstructured, positively charged N-terminal tail located on Hec1/Ndc80. Hec1/Ndc80 also contains a calponin homology domain (CHD) that increases its affinity for microtubules in vitro, yet whether it is required in cells and how the tail and CHD work together are critical unanswered questions. Human kinetochores containing Hec1/Ndc80 with point mutations in the CHD fail to align chromosomes or form productive microtubule attachments. Kinetochore architecture and spindle checkpoint protein recruitment are unaffected in these mutants, and the loss of CHD function cannot be rescued by removing Aurora B sites from the tail. The interaction between the Hec1/Ndc80 CHD and a microtubule is facilitated by positively charged amino acids on two separate regions of the CHD, and both are required for kinetochores to make stable attachments to microtubules. Chromosome congression in cells also requires positive charge on the Hec1 tail to facilitate microtubule contact. In vitro binding data suggest that charge on the tail regulates attachment by directly increasing microtubule affinity as well as driving cooperative binding of the CHD. These data argue that in vertebrates there is a tripartite attachment point facilitating the interaction between Hec1/Ndc80 and microtubules. We discuss how such a complex microtubule-binding interface may facilitate the coupling of depolymerization to chromosome movement.

  12. The Bistable Behaviour of Pseudomonas putida KT2440 during PHA Depolymerization under Carbon Limitation

    Directory of Open Access Journals (Sweden)

    Stephanie Karmann

    2017-06-01

    Full Text Available Poly(hydroxyalkanoates (PHAs are bacterial polyesters offering a biodegradable alternative to petrochemical plastics. The intracellular formation and degradation of PHAs is a dynamic process that strongly depends on the availability of carbon and other nutrients. Carbon excess and nitrogen limitation are considered to favor PHA accumulation, whereas carbon limitation triggers PHA depolymerization when all other essential nutrients are present in excess. We studied the population dynamics of Pseudomonas putida KT2440 at the single cell level during different physiological conditions, favoring first PHA polymerization during growth on octanoic acid, and then PHA depolymerization during carbon limitation. PHAs accumulate intracellularly in granules, and were proposed to separate preferentially together with nucleic acids, leading to two daughter cells containing approximately equal amounts of PHA. However, we could show that such P. putida KT2440 cells show bistable behavior when exposed to carbon limitation, and separate into two subpopulations: one with high and one with low PHA. This suggests an asymmetric PHA distribution during cell division under carbon limitation, which has a significant influence on our understanding of PHA mobilization.

  13. Kinetics and Thermodynamic Studies of Depolymerization of Nylon Waste by Hydrolysis Reaction

    Directory of Open Access Journals (Sweden)

    D. B. Patil

    2014-01-01

    Full Text Available Depolymerization reaction of nylon waste was carried out by hydrolysis reaction. Yield of depolymerization products was up to 72.20% for a two-hour reaction time. The products obtained were characterized by melting point and FTIR spectra. The values obtained for dibenzoyl derivative of hexamethylenediamine (DBHMD agreed with those of the pure substance. Chemical kinetics of this reaction shows that it is a first-order reaction with respect to hexamethylenediamine (HMD concentration with velocity constant 7.32×10-3 min−1. The energy of activation and Arrhenius constant obtained by Arrhenius plot were 87.22 KJg−1 and 0.129, respectively. The other thermodynamic parameters such as enthalpy of activation (ΔH‡ and entropy of activation (ΔS‡ and free energy of activation were 5975.85 J and −270.86 J·K−1·mol−1 and 101.59 KJ·mol−1, respectively.

  14. Snapshots of lignin oxidation and depolymerization in archaeological wood: an EGA-MS study.

    Science.gov (United States)

    Tamburini, Diego; Łucejko, Jeannette Jacqueline; Ribechini, Erika; Colombini, Maria Perla

    2015-10-01

    Evolved gas analysis-mass spectrometry (EGA-MS) was used for the first time to study archaeological wood, in order to investigate its chemical degradation. The archaeological wood was from an oak pile from a stilt house found in the Neolithic 'La Marmotta' village (Lake Bracciano, Rome, Italy). The sampling was performed from the external to the internal part of the pile, following the annual growth rings in groups of five. In addition, sound oak wood and isolated wood components (holocellulose and cellulose) were also analyzed, and the results were used to highlight differences because of degradation. Our study demonstrated that EGA-MS provides information on the thermo-chemistry of archaeological wood along with in-depth compositional data thanks to the use of MS. Our investigations not only highlighted wood degradation in terms of differences between carbohydrates and lignin content, but also showed that lignin oxidation and depolymerization took place in the archaeological wood. Mass spectral data revealed differences among the archaeological samples from the internal to the external part of the pile. An increase in the formation of wood pyrolysis products bearing a carbonyl group at the benzylic position and a decrease in the amount of lignin dimers were observed. These were related to oxidation and depolymerization reactions, respectively.

  15. Depolymerization of the waste polymers in municipal solid waste streams using induction-coupled plasma technology

    Science.gov (United States)

    Guddeti, Ravikishan Reddy

    2000-10-01

    A significant, valuable percentage of today's municipal solid waste stream consists of polymeric materials, for which almost no economic recycling technology currently exists. This polymeric waste is incinerated, landfilled or recycled via downgraded usage. Thermal plasma treatment is a potentially viable means of recycling these materials by converting them back into monomers or into other useful compounds. The technical, laboratory scale, feasibility of using an induction-coupled RF plasma [ICP] heated reactor for this purpose has been demonstrated in the present study. Polyethylene [PE], polypropylene [PP] and polyethylene terephthalate [PET], the model polymers chosen for the study, were injected axially through the center of an ICP torch. 68% of PE, 78% of PP and 75% of PET were converted into gaseous products. Ethylene and propylene were the primary gaseous products of decomposition of the former two polymers and acetylene was the primary product of the depolymerization of PET. The amount of propylene obtained in PE depolymerization was significantly higher than anticipated and was believed to be due to beta-scission reactions occurring at the high plasma temperatures. Statistical design of experiments was used to determine the influence of individual variables. Analysis of results showed that plasma plate power, central gas flow rate, probe gas flow rate, powder feed rate and the interaction between the quench gas flow rate and power input were the key process parameters affecting the yield of monomer in the product gas stream. Depolymerization of a PE + PP mixture yielded concentrations of propylene and ethylene close to those predicted from weighting the concentrations of products from the individual polymers. 75.5 wt.% of the mixture was converted into monomers. TEM analysis of the carbon residues collected from different locations of the reactor indicated the formation of some novel carbon structures, including carbon nanotubes. The presence of these

  16. Actin-Depolymerizing Factor2-Mediated Actin Dynamics Are Essential for Root-Knot Nematode Infection of Arabidopsis

    NARCIS (Netherlands)

    Clement, M.; Ketelaar, T.; Rodiuc, N.; Banora, M.Y.; Smertenko, A.; Engler, G.; Abad, P.; Hussey, P.J.; Almeida Engler, De J.

    2009-01-01

    Reorganization of the actin and microtubule networks is known to occur in targeted vascular parenchymal root cells upon infection with the nematode Meloidogyne incognita. Here, we show that actin-depolymerizing factor (ADF) is upregulated in the giant feeding cells of Arabidopsis thaliana that devel

  17. Actin-Depolymerizing Factor2-Mediated Actin Dynamics Are Essential for Root-Knot Nematode Infection of Arabidopsis

    NARCIS (Netherlands)

    Clement, M.; Ketelaar, T.; Rodiuc, N.; Banora, M.Y.; Smertenko, A.; Engler, G.; Abad, P.; Hussey, P.J.; Almeida Engler, De J.

    2009-01-01

    Reorganization of the actin and microtubule networks is known to occur in targeted vascular parenchymal root cells upon infection with the nematode Meloidogyne incognita. Here, we show that actin-depolymerizing factor (ADF) is upregulated in the giant feeding cells of Arabidopsis thaliana that

  18. A Reconsideration of the Link between the Energetics of Water and of ATP Hydrolysis Energy in the Power Strokes of Molecular Motors in Protein Structures

    Directory of Open Access Journals (Sweden)

    Wilfred F. Widdas

    2008-09-01

    Full Text Available Mechanical energy from oxygen metabolism by mammalian tissues has been studied since 1837. The production of heat by mechanical work was studied by Fick in about 1860. Prior to Fick’s work, energetics were revised by Joule’s experiments which founded the First Law of Thermodynamics. Fenn in 1923/24 found that frog muscle contractions generated extra heat proportional to the amount of work done in shortening the muscle. This was fully consistent with the Joule, Helmholtz concept used for the First Law of Thermodynamics. The link between the energetics of water and ATP hydrolysis in molecular motors is recommended for reconsideration.

  19. Depolymerization of organosolv lignin using doped porous metal oxides in supercritical methanol.

    Science.gov (United States)

    Warner, Genoa; Hansen, Thomas S; Riisager, Anders; Beach, Evan S; Barta, Katalin; Anastas, Paul T

    2014-06-01

    An isolated, solvent-extracted lignin from candlenut (Aleurites moluccana) biomass was subjected to catalytic depolymerization in the presence of supercritical methanol, using a range of porous metal oxides derived from hydrotalcite-like precursors. The most effective catalysts in terms of lignin conversion to methanol-soluble products, without char formation, were based on copper in combination with other dopants based on relatively earth-abundant metals. Nearly complete conversion of lignin to bio-oil composed of monomers and low-mass oligomers with high aromatic content was obtained in 6h at 310°C using a catalyst based on a Cu- and La-doped hydrotalcite-like precursor. Product mixtures were characterized by NMR spectroscopy, gel permeation chromatography, and GC-MS.

  20. Lignin depolymerization/repolymerization and its critical role for delignification of aspen wood by steam explosion.

    Science.gov (United States)

    Li, Jiebing; Henriksson, Gunnar; Gellerstedt, Göran

    2007-11-01

    Steam explosion is an important process for the fractionation of biomass components. In order to understand the behaviour of lignin under the conditions encountered in the steam explosion process, as well as in other types of steam treatment, aspen wood and isolated lignin from aspen were subjected to steam treatment under various conditions. The lignin portion was analyzed using NMR and size exclusion chromatography as major analytical techniques. Thereby, the competition between lignin depolymerization and repolymerization was revealed and the conditions required for these two types of reaction identified. Addition of a reactive phenol, 2-naphthol, was shown to inhibit the repolymerization reaction strongly, resulting in a highly improved delignification by subsequent solvent extraction and an extracted lignin of uniform structure.

  1. Monte Carlo Simulation of Linear Polymer Thermal Depolymerization under Isothermal and Dynamic Modes

    Directory of Open Access Journals (Sweden)

    Elena V. Bystritskaya

    2011-01-01

    Full Text Available Kinetics of linear polymer thermal depolymerization under isothermal and dynamic TGA modes was simulated by the Monte Carlo method. The simulation was carried out on model arrays having the same initial degree of polymerization =100 and different width (polydispersity index, PDI=/=1∼3 at three constant temperatures and five heating rates. Kinetics of the process in both modes is described by the Avrami equation, the exponent in which decreasing as the distribution width increases. Treatment of the model kinetic curves of degradation using the nonlinear regression method by the Avrami equation, under both isothermal and dynamic modes, gives correct activation energy and pre-exponential factor values independently of the initial PDI. Data obtained in the dynamic mode were also treated by two isoconversion methods, widely applied to kinetic analysis of TGA curves (Flynn-Wall-Ozawa method and Kissinger-Akahira-Sunose (KAS method.

  2. Temperature effects on protein depolymerization and amino acid immobilization rates in soils.

    Science.gov (United States)

    Noll, Lisa; Hu, Yuntao; Zhang, Shasha; Zheng, Qing; Wanek, Wolfgang

    2017-04-01

    Increasing N deposition, land use change, elevated atmospheric CO2 concentrations and global warming have altered soil nitrogen (N) cycling during the last decades. Those changes affected ecosystem services, such as C and N sequestration in soils, which calls for a better understanding of soil N transformation processes. The cleavage of macromolecular organic N by extracellular enzymes maintains an ongoing flow of new bioavailable organic N into biotic systems and is considered to be the bottle neck of terrestrial N cycling in litter and soils. Recent studies showed that protein depolymerization is susceptible to changes in C and N availabilities. Based on general biological observations the temperature sensitivity of soil organic N processes is expected to depend on whether they are rather enzyme limited (i.e. Q10=2) or diffusion limited (i.e. Q10= 1.0 - 1.3). However, temperature sensitivities of protein depolymerization and amino acid immobilization are still unknown. We therefore here report short-term temperature effects on organic N transformation rates in soils differing in physicochemical parameters but not in climate. Soil samples were collected from two geologically distinct sites close to the LFZ Raumberg-Gumpenstein, Styria, Austria, each from three different management types (arable land, grassland, forest). Four replicates of mineral soil were taken from every site and management type. The area provides a unique opportunity to study geological and management controls in soils without confounding effects of climate and elevation. The soils differ in several soil chemical parameters, such as soil pH, base saturation, soil C: N ratio and SOM content as well as in soil physical parameters, such as soil texture, bulk density and water holding capacity. Soils were pre-incubated at 5, 15 and 25˚ C for one day. Protein depolymerization rates and amino acid immobilization rates were assessed by an isotope pool dilution assay with 15N labeled amino acids at

  3. Mechanistic Investigation of Acid-Catalyzed Cleavage of Aryl-Ether Linkages: Implications for Lignin Depolymerization

    Energy Technology Data Exchange (ETDEWEB)

    Sturgeon, M. R.; Kim, S.; Chmely, S. C.; Foust, T. D.; Beckham, G. T.

    2013-01-01

    Carbon-oxygen bonds are the primary inter-monomer linkages lignin polymers in plant cell walls, and as such, catalyst development to cleave these linkages is of paramount importance to deconstruct biomass to its constituent monomers for the production of renewable fuels and chemicals. For many decades, acid catalysis has been used to depolymerize lignin. Lignin is a primary component of plant cell walls, which is connected primarily by aryl-ether linkages, and the mechanism of its deconstruction by acid is not well understood, likely due to its heterogeneous and complex nature compared to cellulose. For effective biomass conversion strategies, utilization of lignin is of significant relevance and as such understanding the mechanisms of catalytic lignin deconstruction to constituent monomers and oligomers is of keen interest. Here, we present a comprehensive experimental and theoretical study of the acid catalysis of a range of dimeric species exhibiting the b-O-4 linkage, the most common inter-monomer linkage in lignin. We demonstrate that the presence of a phenolic species dramatically increases the rate of cleavage in acid at 150 degrees C. Quantum mechanical calculations on dimers with the para-hydroxyl group demonstrate that this acid-catalyzed pathway differs from the nonphenolic dimmers. Importantly, this result implies that depolymerization of native lignin in the plant cell wall will proceed via an unzipping mechanism wherein b-O-4 linkages will be cleaved from the ends of the branched, polymer chains inwards toward the center of the polymer. To test this hypothesis further, we synthesized a homopolymer of b-O-4 with a phenolic hydroxyl group, and demonstrate that it is cleaved in acid from the end containing the phenolic hydroxyl group. This result suggests that genetic modifications to lignin biosynthesis pathways in plants that will enable lower severity processes to fractionate lignin for upgrading and for easier access to the carbohydrate fraction of

  4. Tuning Multiple Motor Travel Via Single Motor Velocity

    Science.gov (United States)

    Xu, Jing; Shu, Zhanyong; King, Stephen J.; Gross, Steven P.

    2012-01-01

    Microtubule-based molecular motors often work in small groups to transport cargos in cells. A key question in understanding transport (and its regulation in vivo) is to identify the sensitivity of multiple-motor-based motion to various single molecule properties. Whereas both single-motor travel distance and microtubule binding rate have been demonstrated to contribute to cargo travel, the role of single-motor velocity is yet to be explored. Here, we recast a previous theoretical study, and make explicit a potential contribution of velocity to cargo travel. We test this possibility experimentally, and demonstrate a strong negative correlation between single-motor velocity and cargo travel for transport driven by two motors. Our study thus discovers a previously unappreciated role of single-motor velocity in regulating multiple-motor transport. PMID:22672518

  5. Characterization of oxidized tannins: comparison of depolymerization methods, asymmetric flow field-flow fractionation and small-angle X-ray scattering.

    Science.gov (United States)

    Vernhet, Aude; Dubascoux, Stéphane; Cabane, Bernard; Fulcrand, Hélène; Dubreucq, Eric; Poncet-Legrand, Céline

    2011-09-01

    Condensed tannins are a major class of plant polyphenols. They play an important part in the colour and taste of foods and beverages. Due to their chemical reactivity, tannins are not stable once extracted from plants. A number of chemical reactions can take place, leading to structural changes of the native structures to give so-called derived tannins and pigments. This paper compares results obtained on native and oxidized tannins with different techniques: depolymerization followed by high-performance liquid chromatography analysis, small-angle X-ray scattering (SAXS) and asymmetric flow field-flow fractionation (AF4). Upon oxidation, new macromolecules were formed. Thioglycolysis experiments showed no evidence of molecular weight increase, but thioglycolysis yields drastically decreased. When oxidation was performed at high concentration (e.g., 10 g L(-1)), the weight average degree of polymerization determined from SAXS increased, whereas it remained stable when oxidation was done at low concentration (0.1 g L(-1)), indicating that the reaction was intramolecular, yet the conformations were different. Differences in terms of solubility were observed; ethanol being a better solvent than water. We also separated soluble and non-water-soluble species of a much oxidized fraction. Thioglycolysis showed no big differences between the two fractions, whereas SAXS and AF4 showed that insoluble macromolecules have a weight average molecular weight ten times higher than the soluble ones.

  6. Chemistry: No turning back for motorized molecules

    Science.gov (United States)

    Clayden, Jonathan

    2016-06-01

    Two molecular motors have been developed that use chemical energy to drive rotational motion in a single direction. The findings bring the prospect of devices powered by such motors a tantalizing step closer. See Letter p.235

  7. Molecular, physiological, and motor performance defects in DMSXL mice carrying >1,000 CTG repeats from the human DM1 locus.

    Directory of Open Access Journals (Sweden)

    Aline Huguet

    Full Text Available Myotonic dystrophy type 1 (DM1 is caused by an unstable CTG repeat expansion in the 3'UTR of the DM protein kinase (DMPK gene. DMPK transcripts carrying CUG expansions form nuclear foci and affect splicing regulation of various RNA transcripts. Furthermore, bidirectional transcription over the DMPK gene and non-conventional RNA translation of repeated transcripts have been described in DM1. It is clear now that this disease may involve multiple pathogenic pathways including changes in gene expression, RNA stability and splicing regulation, protein translation, and micro-RNA metabolism. We previously generated transgenic mice with 45-kb of the DM1 locus and >300 CTG repeats (DM300 mice. After successive breeding and a high level of CTG repeat instability, we obtained transgenic mice carrying >1,000 CTG (DMSXL mice. Here we described for the first time the expression pattern of the DMPK sense transcripts in DMSXL and human tissues. Interestingly, we also demonstrate that DMPK antisense transcripts are expressed in various DMSXL and human tissues, and that both sense and antisense transcripts accumulate in independent nuclear foci that do not co-localize together. Molecular features of DM1-associated RNA toxicity in DMSXL mice (such as foci accumulation and mild missplicing, were associated with high mortality, growth retardation, and muscle defects (abnormal histopathology, reduced muscle strength, and lower motor performances. We have found that lower levels of IGFBP-3 may contribute to DMSXL growth retardation, while increased proteasome activity may affect muscle function. These data demonstrate that the human DM1 locus carrying very large expansions induced a variety of molecular and physiological defects in transgenic mice, reflecting DM1 to a certain extent. As a result, DMSXL mice provide an animal tool to decipher various aspects of the disease mechanisms. In addition, these mice can be used to test the preclinical impact of systemic

  8. Molecular, physiological, and motor performance defects in DMSXL mice carrying >1,000 CTG repeats from the human DM1 locus.

    Science.gov (United States)

    Huguet, Aline; Medja, Fadia; Nicole, Annie; Vignaud, Alban; Guiraud-Dogan, Céline; Ferry, Arnaud; Decostre, Valérie; Hogrel, Jean-Yves; Metzger, Friedrich; Hoeflich, Andreas; Baraibar, Martin; Gomes-Pereira, Mário; Puymirat, Jack; Bassez, Guillaume; Furling, Denis; Munnich, Arnold; Gourdon, Geneviève

    2012-01-01

    Myotonic dystrophy type 1 (DM1) is caused by an unstable CTG repeat expansion in the 3'UTR of the DM protein kinase (DMPK) gene. DMPK transcripts carrying CUG expansions form nuclear foci and affect splicing regulation of various RNA transcripts. Furthermore, bidirectional transcription over the DMPK gene and non-conventional RNA translation of repeated transcripts have been described in DM1. It is clear now that this disease may involve multiple pathogenic pathways including changes in gene expression, RNA stability and splicing regulation, protein translation, and micro-RNA metabolism. We previously generated transgenic mice with 45-kb of the DM1 locus and >300 CTG repeats (DM300 mice). After successive breeding and a high level of CTG repeat instability, we obtained transgenic mice carrying >1,000 CTG (DMSXL mice). Here we described for the first time the expression pattern of the DMPK sense transcripts in DMSXL and human tissues. Interestingly, we also demonstrate that DMPK antisense transcripts are expressed in various DMSXL and human tissues, and that both sense and antisense transcripts accumulate in independent nuclear foci that do not co-localize together. Molecular features of DM1-associated RNA toxicity in DMSXL mice (such as foci accumulation and mild missplicing), were associated with high mortality, growth retardation, and muscle defects (abnormal histopathology, reduced muscle strength, and lower motor performances). We have found that lower levels of IGFBP-3 may contribute to DMSXL growth retardation, while increased proteasome activity may affect muscle function. These data demonstrate that the human DM1 locus carrying very large expansions induced a variety of molecular and physiological defects in transgenic mice, reflecting DM1 to a certain extent. As a result, DMSXL mice provide an animal tool to decipher various aspects of the disease mechanisms. In addition, these mice can be used to test the preclinical impact of systemic therapeutic

  9. [Influence of microtubule depolymerization of myocardial cells on mitochondria distribution and energy metabolism in adult rats].

    Science.gov (United States)

    Dang, Yong-ming; Fang, Ya-dong; Hu, Jiong-yu; Zhang, Jia-ping; Song, Hua-pei; Zhang, Yi-ming; Zhang, Qiong; Huang, Yue-sheng

    2010-02-01

    To investigate the influence of microtubule depolymerization of myocardial cells on distribution and activity of mitochondria, and energy metabolism of cells in adult rats. Myocardial cells of SD adult rats and SD suckling rats were isolated and cultured. They were divided into adult and suckling rats control groups (AC and SC, normally cultured without any stimulating factor), adult and suckling rats microtubule depolymerization agent groups (AMDA and SMDA, cultured with 8 micromol/L colchicine containing nutrient solution for 30 minutes) according to the random number table. (1) The expression of polymerized beta tubulin in myocardial cells of adult and suckling rats was detected with Western blot. (2) Myocardial cells of rats in AC and AMDA groups were collected. The expression of cytochrome c was detected with Western blot. Distribution of voltage-dependent anion channels (VDAC) and polymerized beta tubulin in myocardial cells were observed with immunofluorescent staining. Mitochondrial inner membrane potential was determined with immunocytochemical method. Activity of myocardial cells was detected with MTT method. Contents of ATP, adenosine diphosphate (ADP), and adenosine monophosphate (AMP) and energy charge of cells were determined with high performance liquid chromatography. (1) The expression of polymerized beta tubulin:in AMDA group it was 0.52 + or - 0.07, which was obviously lower than that (1.25 + or - 0.12) in AC group (F = 31.002, P = 0.000); in SMDA group it was 0.76 + or - 0.12, which was significantly lower than that (1.11 + or - 0.24) in SC group (F = 31.002, P = 0.000), but was obviously higher than that in AMDA group (F = 31.002, P = 0.009). (2) The expression of cytochrome c in AC group was 0.26 + or - 0.03, which was obviously lower than that (1.55 + or - 0.13) in AMDA group (t = -24.056, P = 0.000). (3) Immunofluorescent staining result: in AC group, microtubules of myocardial cells were in linear tubiform, distributed in parallel with

  10. The Autophagy Receptor TAX1BP1 and the Molecular Motor Myosin VI Are Required for Clearance of Salmonella Typhimurium by Autophagy.

    Directory of Open Access Journals (Sweden)

    David A Tumbarello

    2015-10-01

    Full Text Available Autophagy plays a key role during Salmonella infection, by eliminating these pathogens following escape into the cytosol. In this process, selective autophagy receptors, including the myosin VI adaptor proteins optineurin and NDP52, have been shown to recognize cytosolic pathogens. Here, we demonstrate that myosin VI and TAX1BP1 are recruited to ubiquitylated Salmonella and play a key role in xenophagy. The absence of TAX1BP1 causes an accumulation of ubiquitin-positive Salmonella, whereas loss of myosin VI leads to an increase in ubiquitylated and LC3-positive bacteria. Our structural studies demonstrate that the ubiquitin-binding site of TAX1BP1 overlaps with the myosin VI binding site and point mutations in the TAX1BP1 zinc finger domains that affect ubiquitin binding also ablate binding to myosin VI. This mutually exclusive binding and the association of TAX1BP1 with LC3 on the outer limiting membrane of autophagosomes may suggest a molecular mechanism for recruitment of this motor to autophagosomes. The predominant role of TAX1BP1, a paralogue of NDP52, in xenophagy is supported by our evolutionary analysis, which demonstrates that functionally intact NDP52 is missing in Xenopus and mice, whereas TAX1BP1 is expressed in all vertebrates analysed. In summary, this work highlights the importance of TAX1BP1 as a novel autophagy receptor in myosin VI-mediated xenophagy. Our study identifies essential new machinery for the autophagy-dependent clearance of Salmonella typhimurium and suggests modulation of myosin VI motor activity as a potential therapeutic target in cellular immunity.

  11. Peracetic Acid Depolymerization of Biorefinery Lignin for Production of Selective Monomeric Phenolic Compounds.

    Science.gov (United States)

    Ma, Ruoshui; Guo, Mond; Lin, Kuan-Ting; Hebert, Vincent R; Zhang, Jinwen; Wolcott, Michael P; Quintero, Melissa; Ramasamy, Karthikeyan K; Chen, Xiaowen; Zhang, Xiao

    2016-07-25

    Lignin is the largest source of renewable material with an aromatic skeleton. However, due to the recalcitrant and heterogeneous nature of the lignin polymer, it has been a challenge to effectively depolymerize lignin and produce high-value chemicals with high selectivity. In this study, a highly efficient lignin-to-monomeric phenolic compounds (MPC) conversion method based on peracetic acid (PAA) treatment was reported. PAA treatment of two biorefinery lignin samples, diluted acid pretreated corn stover lignin (DACSL) and steam exploded spruce lignin (SESPL), led to complete solubilization and production of selective hydroxylated monomeric phenolic compounds (MPC-H) and monomeric phenolic acid compounds (MPC-A) including 4-hydroxy-2-methoxyphenol, p-hydroxybenzoic acid, vanillic acid, syringic acid, and 3,4-dihydroxybenzoic acid. The maximized MPC yields obtained were 18 and 22 % based on the initial weight of the lignin in SESPL and DACSL, respectively. However, we found that the addition of niobium pentoxide catalyst to PAA treatment of lignin can significantly improve the MPC yields up to 47 %. The key reaction steps and main mechanisms involved in this new lignin-to-MPC valorization pathway were investigated and elucidated.

  12. Glycosaminoglycan-depolymerizing enzymes produced by anaerobic bacteria isolated from the human mouth.

    Science.gov (United States)

    Tipler, L S; Embery, G

    1985-01-01

    A number of obligately anaerobic bacteria, some implicated in periodontal disease, were screened for their ability to produce enzymes capable of degrading hyaluronic acid and chondroitin-4-sulphate. Two screening methods were used following anaerobic incubation at 37 degrees C for 7 days. One involved incorporating the respective substrates and bovine-serum albumin into agar plates and, after incubation, flooding the plates with 2 M acetic acid. Clear zones were produced around colonies which produced enzymes capable of depolymerizing the substrates. The second was a sensitive spectrophotometric procedure based on the ability of certain bacteria to produce eliminase enzymes, which degrade the substrates to unsaturated products having a characteristic u.v. absorption at 232 nm. Strains of Bacteroides gingivalis and Bacteroides melaninogenicus degraded both substrates whereas Bacteroides asaccharolyticus degraded neither substrate by either method. Some bacteria gave negative results with the plate method whereas the more sensitive spectrophotometric assay proved positive. The number of anaerobic bacteria capable of degrading hyaluronic acid and chondroitin-4-sulphate in vitro may therefore have been underestimated in previous studies.

  13. Peracetic Acid Depolymerization of Biorefinery Lignin for Production of Selective Monomeric Phenolic Compounds

    Energy Technology Data Exchange (ETDEWEB)

    Ma, Ruoshui [Voiland School of Chemical Engineering and Bioengineering, Bioproducts, Science & Engineering Laboratory, Washington State University, 2710 Crimson Way Richland WA 99354 USA; Guo, Mond [Voiland School of Chemical Engineering and Bioengineering, Bioproducts, Science & Engineering Laboratory, Washington State University, 2710 Crimson Way Richland WA 99354 USA; Lin, Kuan-ting [Voiland School of Chemical Engineering and Bioengineering, Bioproducts, Science & Engineering Laboratory, Washington State University, 2710 Crimson Way Richland WA 99354 USA; Hebert, Vincent R. [Food and Environmental Laboratory, Washington State, University-TriCities, 2710 Crimson Way Richland WA 99354 USA; Zhang, Jinwen [Wood Materials and Engineering Laboratory, Washington State University, Pullman WA 99164 USA; Wolcott, Michael P. [Wood Materials and Engineering Laboratory, Washington State University, Pullman WA 99164 USA; Quintero, Melissa [Voiland School of Chemical Engineering and Bioengineering, Bioproducts, Science & Engineering Laboratory, Washington State University, 2710 Crimson Way Richland WA 99354 USA; Ramasamy, Karthikeyan K. [Chemical and Biological Process Development Group, Pacific Northwest National Laboratory, Richland WA 99354 USA; Chen, Xiaowen [National Bioenergy Center, National Renewable Energy Lab, 1617 Cole Blvd Golden CO 80127 USA; Zhang, Xiao [Voiland School of Chemical Engineering and Bioengineering, Bioproducts, Science & Engineering Laboratory, Washington State University, 2710 Crimson Way Richland WA 99354 USA

    2016-07-04

    Lignin is the largest source of renewable material with an aromatic skeleton. However, due to the recalcitrant and heterogeneous nature of the lignin polymer as well as its complex side chain structures, it has been a challenge to effectively depolymerize lignin and produce high value chemicals with high selectivity. In this study, a highly efficient lignin-to-monomeric phenolic compounds (MPC) conversion method based on peracetic acid (PAA) treatment was reported. PAA treatment of two biorefinery lignin samples, diluted acid pretreated corn stover lignin (DACSL) and steam exploded spruce lignin (SESPL), led to complete solubilization and production of selective hydroxylated monomeric phenolic compounds (MPC-H) and monomeric phenolic acid compounds (MPC-A) inclduing 4-hydroxy-2-methoxyphenol, p-hydroxybenzoic acid, vanillic acid, syringic acid, and 3,4-dihydroxybenzoic acid. The maximized MPCs yields obtained were 18% and 22% based on the initial weight of the lignin in SESPL and DACSL respectively. However, we found that the addition of niobium pentoxide catalyst to PAA treatment of lignin can significantly improve the MPC yields up to 47%. The key reaction steps and main mechanisms involved in this new lignin-to-MPC valorization pathway were investigated and elucidated.

  14. Peracetic Acid Depolymerization of Biorefinery Lignin for Production of Selective Monomeric Phenolic Compounds

    Energy Technology Data Exchange (ETDEWEB)

    Ma, Ruoshui [Voiland School of Chemical Engineering and Bioengineering, Bioproducts, Science & Engineering Laboratory, Washington State University, 2710 Crimson Way Richland WA 99354 USA; Guo, Mond [Voiland School of Chemical Engineering and Bioengineering, Bioproducts, Science & Engineering Laboratory, Washington State University, 2710 Crimson Way Richland WA 99354 USA; Lin, Kuan-ting [Voiland School of Chemical Engineering and Bioengineering, Bioproducts, Science & Engineering Laboratory, Washington State University, 2710 Crimson Way Richland WA 99354 USA; Hebert, Vincent R. [Food and Environmental Laboratory, Washington State, University-TriCities, 2710 Crimson Way Richland WA 99354 USA; Zhang, Jinwen [Wood Materials and Engineering Laboratory, Washington State University, Pullman WA 99164 USA; Wolcott, Michael P. [Wood Materials and Engineering Laboratory, Washington State University, Pullman WA 99164 USA; Quintero, Melissa [Voiland School of Chemical Engineering and Bioengineering, Bioproducts, Science & Engineering Laboratory, Washington State University, 2710 Crimson Way Richland WA 99354 USA; Ramasamy, Karthikeyan K. [Chemical and Biological Process Development Group, Pacific Northwest National Laboratory, Richland WA 99354 USA; Chen, Xiaowen [National Bioenergy Center, National Renewable Energy Lab, 1617 Cole Blvd Golden CO 80127 USA; Zhang, Xiao [Voiland School of Chemical Engineering and Bioengineering, Bioproducts, Science & Engineering Laboratory, Washington State University, 2710 Crimson Way Richland WA 99354 USA

    2016-07-04

    Lignin is the largest source of renewable material with an aromatic skeleton. However, due to the recalcitrant and heterogeneous nature of the lignin polymer, it has been a challenge to effectively depolymerize lignin and produce high-value chemicals with high selectivity. In this study, a highly efficient lignin-to-monomeric phenolic compounds (MPC) conversion method based on peracetic acid (PAA) treatment was reported. PAA treatment of two biorefinery lignin samples, diluted acid pretreated corn stover lignin (DACSL) and steam exploded spruce lignin (SESPL), led to complete solubilization and production of selective hydroxylated monomeric phenolic compounds (MPC-H) and monomeric phenolic acid compounds (MPC-A) including 4-hydroxy-2-methoxyphenol, p-hydroxybenzoic acid, vanillic acid, syringic acid, and 3,4-dihydroxybenzoic acid. The maximized MPC yields obtained were 18 and 22 % based on the initial weight of the lignin in SESPL and DACSL, respectively. However, we found that the addition of niobium pentoxide catalyst to PAA treatment of lignin can significantly improve the MPC yields up to 47 %. The key reaction steps and main mechanisms involved in this new lignin-to-MPC valorization pathway were investigated and elucidated.

  15. 聚乳酸解聚方法研究进展%Research Progress in Depolymerization of Polylactic Acid

    Institute of Scientific and Technical Information of China (English)

    张晓静; 杨学群; 刘仕伟; 刘福胜; 于世涛

    2012-01-01

    The research progresses in depolymerization of polylactic acid at home and abroad in recent years are reviewed. The depolymerization processes include pyrolysis, acidic hydrolysis, basic hydrolysis, neutral hydrolysis, high-temperature high-pressure hydrolysis, enzyme catalysis, methanol alcoholysis, n-butylalcohol alcoholysis, and so on. The feasibility of polylactic acid chemical depolymerization in ionic liquor environment is discussed and prospected.%综述了近年来国内外关于聚乳酸的热解聚法和酸性水解法、碱性水解法、中性水解法、高温高压水解法、酶催化法、甲醇醇解法、正丁醇醇解法等化学解聚法的研究进展,并对聚乳酸在离子液体环境中进行化学解聚的可行性进行了探讨和展望.

  16. New insights into the function of a versatile class of membrane molecular motors from studies of Myxococcus xanthus surface (gliding motility

    Directory of Open Access Journals (Sweden)

    Tâm Mignot

    2017-03-01

    Full Text Available Cell motility is a central function of living cells, as it empowers colonization of new environmental niches, cooperation, and development of multicellular organisms. This process is achieved by complex yet precise energy-consuming machineries in both eukaryotes and bacteria. Bacteria move on surfaces using extracellular appendages such as flagella and pili but also by a less-understood process called gliding motility. During this process, rod-shaped bacteria move smoothly along their long axis without any visible morphological changes besides occasional bending. For this reason, the molecular mechanism of gliding motility and its origin have long remained a complete mystery. An important breakthrough in the understanding of gliding motility came from single cell and genetic studies in the delta-proteobacterium Myxococcus xanthus. These early studies revealed, for the first time, the existence of bacterial Focal Adhesion complexes (FA. FAs are formed at the bacterial pole and rapidly move towards the opposite cell pole. Their attachment to the underlying surface is linked to cell propulsion, in a process similar to the rearward translocation of actomyosin complexes in Apicomplexans. The protein machinery that forms at FAs was shown to contain up to seventeen proteins predicted to localize in all layers of the bacterial cell envelope, the cytosolic face, the inner membrane (IM, the periplasmic space and the outer membrane (OM. Among these proteins, a proton-gated channel at the inner membrane was identified as the molecular motor. Thus, thrust generation requires the transduction of traction forces generated at the inner membrane through the cell envelope beyond the rigid barrier of the bacterial peptidoglycan.

  17. Actin-interacting Protein 1 Promotes Disassembly of Actin-depolymerizing Factor/Cofilin-bound Actin Filaments in a pH-dependent Manner.

    Science.gov (United States)

    Nomura, Kazumi; Hayakawa, Kimihide; Tatsumi, Hitoshi; Ono, Shoichiro

    2016-03-04

    Actin-interacting protein 1 (AIP1) is a conserved WD repeat protein that promotes disassembly of actin filaments when actin-depolymerizing factor (ADF)/cofilin is present. Although AIP1 is known to be essential for a number of cellular events involving dynamic rearrangement of the actin cytoskeleton, the regulatory mechanism of the function of AIP1 is unknown. In this study, we report that two AIP1 isoforms from the nematode Caenorhabditis elegans, known as UNC-78 and AIPL-1, are pH-sensitive in enhancement of actin filament disassembly. Both AIP1 isoforms only weakly enhance disassembly of ADF/cofilin-bound actin filaments at an acidic pH but show stronger disassembly activity at neutral and basic pH values. However, a severing-defective mutant of UNC-78 shows pH-insensitive binding to ADF/cofilin-decorated actin filaments, suggesting that the process of filament severing or disassembly, but not filament binding, is pH-dependent. His-60 of AIP1 is located near the predicted binding surface for the ADF/cofilin-actin complex, and an H60K mutation of AIP1 partially impairs its pH sensitivity, suggesting that His-60 is involved in the pH sensor for AIP1. These biochemical results suggest that pH-dependent changes in AIP1 activity might be a novel regulatory mechanism of actin filament dynamics. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  18. Human spinal motor control

    DEFF Research Database (Denmark)

    Nielsen, Jens Bo

    2016-01-01

    interneurons and exert a direct (willful) muscle control with the aid of a context-dependent integration of somatosensory and visual information at cortical level. However, spinal networks also play an important role. Sensory feedback through spinal circuitries is integrated with central motor commands...... the central motor command by opening or closing sensory feedback pathways. In the future, human studies of spinal motor control, in close collaboration with animal studies on the molecular biology of the spinal cord, will continue to document the neural basis for human behavior. Expected final online...... and contributes importantly to the muscle activity underlying voluntary movements. Regulation of spinal interneurons is used to switch between motor states such as locomotion (reciprocal innervation) and stance (coactivation pattern). Cortical regulation of presynaptic inhibition of sensory afferents may focus...

  19. Motor Neurons

    DEFF Research Database (Denmark)

    Hounsgaard, Jorn

    2017-01-01

    Motor neurons translate synaptic input from widely distributed premotor networks into patterns of action potentials that orchestrate motor unit force and motor behavior. Intercalated between the CNS and muscles, motor neurons add to and adjust the final motor command. The identity and functional...... properties of this facility in the path from synaptic sites to the motor axon is reviewed with emphasis on voltage sensitive ion channels and regulatory metabotropic transmitter pathways. The catalog of the intrinsic response properties, their underlying mechanisms, and regulation obtained from motoneurons...... in in vitro preparations is far from complete. Nevertheless, a foundation has been provided for pursuing functional significance of intrinsic response properties in motoneurons in vivo during motor behavior at levels from molecules to systems....

  20. Ansamitocin P3 depolymerizes microtubules and induces apoptosis by binding to tubulin at the vinblastine site.

    Directory of Open Access Journals (Sweden)

    Jubina B Venghateri

    Full Text Available Maytansinoid conjugates are currently under different phases of clinical trials and have been showing promising activity for various types of cancers. In this study, we have elucidated the mechanism of action of ansamitocin P3, a structural analogue of maytansine for its anticancer activity. Ansamitocin P3 potently inhibited the proliferation of MCF-7, HeLa, EMT-6/AR1 and MDA-MB-231 cells in culture with a half-maximal inhibitory concentration of 20±3, 50±0.5, 140±17, and 150±1.1 pM, respectively. Ansamitocin P3 strongly depolymerized both interphase and mitotic microtubules and perturbed chromosome segregation at its proliferation inhibitory concentration range. Treatment of ansamitocin P3 activated spindle checkpoint surveillance proteins, Mad2 and BubR1 and blocked the cells in mitotic phase of the cell cycle. Subsequently, cells underwent apoptosis via p53 mediated apoptotic pathway. Further, ansamitocin P3 was found to bind to purified tubulin in vitro with a dissociation constant (Kd of 1.3±0.7 µM. The binding of ansamitocin P3 induced conformational changes in tubulin. A docking analysis suggested that ansamitocin P3 may bind partially to vinblastine binding site on tubulin in two different positions. The analysis indicated that the binding of ansamitocin P3 to tubulin is stabilized by hydrogen bonds. In addition, weak interactions such as halogen-oxygen interactions may also contribute to the binding of ansamitocin P3 to tubulin. The study provided a significant insight in understanding the antiproliferative mechanism of action of ansamitocin P3.

  1. Ansamitocin P3 depolymerizes microtubules and induces apoptosis by binding to tubulin at the vinblastine site.

    Science.gov (United States)

    Venghateri, Jubina B; Gupta, Tilak Kumar; Verma, Paul J; Kunwar, Ambarish; Panda, Dulal

    2013-01-01

    Maytansinoid conjugates are currently under different phases of clinical trials and have been showing promising activity for various types of cancers. In this study, we have elucidated the mechanism of action of ansamitocin P3, a structural analogue of maytansine for its anticancer activity. Ansamitocin P3 potently inhibited the proliferation of MCF-7, HeLa, EMT-6/AR1 and MDA-MB-231 cells in culture with a half-maximal inhibitory concentration of 20±3, 50±0.5, 140±17, and 150±1.1 pM, respectively. Ansamitocin P3 strongly depolymerized both interphase and mitotic microtubules and perturbed chromosome segregation at its proliferation inhibitory concentration range. Treatment of ansamitocin P3 activated spindle checkpoint surveillance proteins, Mad2 and BubR1 and blocked the cells in mitotic phase of the cell cycle. Subsequently, cells underwent apoptosis via p53 mediated apoptotic pathway. Further, ansamitocin P3 was found to bind to purified tubulin in vitro with a dissociation constant (Kd) of 1.3±0.7 µM. The binding of ansamitocin P3 induced conformational changes in tubulin. A docking analysis suggested that ansamitocin P3 may bind partially to vinblastine binding site on tubulin in two different positions. The analysis indicated that the binding of ansamitocin P3 to tubulin is stabilized by hydrogen bonds. In addition, weak interactions such as halogen-oxygen interactions may also contribute to the binding of ansamitocin P3 to tubulin. The study provided a significant insight in understanding the antiproliferative mechanism of action of ansamitocin P3.

  2. Biochemical and Structural Insights into Enzymatic Depolymerization of Polylactic Acid and Other Polyesters by Microbial Carboxylesterases.

    Science.gov (United States)

    Hajighasemi, Mahbod; Nocek, Boguslaw P; Tchigvintsev, Anatoli; Brown, Greg; Flick, Robert; Xu, Xiaohui; Cui, Hong; Hai, Tran; Joachimiak, Andrzej; Golyshin, Peter N; Savchenko, Alexei; Edwards, Elizabeth A; Yakunin, Alexander F

    2016-06-13

    Polylactic acid (PLA) is a biodegradable polyester derived from renewable resources, which is a leading candidate for the replacement of traditional petroleum-based polymers. Since the global production of PLA is quickly growing, there is an urgent need for the development of efficient recycling technologies, which will produce lactic acid instead of CO2 as the final product. After screening 90 purified microbial α/β-hydrolases, we identified hydrolytic activity against emulsified PLA in two uncharacterized proteins, ABO2449 from Alcanivorax borkumensis and RPA1511 from Rhodopseudomonas palustris. Both enzymes were also active against emulsified polycaprolactone and other polyesters as well as against soluble α-naphthyl and p-nitrophenyl monoesters. In addition, both ABO2449 and RPA1511 catalyzed complete or extensive hydrolysis of solid PLA with the production of lactic acid monomers, dimers, and larger oligomers as products. The crystal structure of RPA1511 was determined at 2.2 Å resolution and revealed a classical α/β-hydrolase fold with a wide-open active site containing a molecule of polyethylene glycol bound near the catalytic triad Ser114-His270-Asp242. Site-directed mutagenesis of both proteins demonstrated that the catalytic triad residues are important for the hydrolysis of both monoester and polyester substrates. We also identified several residues in RPA1511 (Gln172, Leu212, Met215, Trp218, and Leu220) and ABO2449 (Phe38 and Leu152), which were not essential for activity against soluble monoesters but were found to be critical for the hydrolysis of PLA. Our results indicate that microbial carboxyl esterases can efficiently hydrolyze various polyesters making them attractive biocatalysts for plastics depolymerization and recycling.

  3. Movimento browniano e motores brownianos

    OpenAIRE

    Rezende, Guilherme Rocha de

    2012-01-01

    Neste trabalho utilizamos o formalismo da equação de Langevin generalizada, desenvolvido inicialmente por Robert Zwanzig e Hazime Mori, para estudarmos o comportamento de um tipo de motor browniano o motor liga-desliga aplicado no estudo de um separador de partículas e em um tipo de motor molecular: a cinesina. Neste estudo escolhemos quatro funções memórias diferentes e analisamos a influência destas memórias na velocidade e eficiência do motor browniano. ____________________________________...

  4. Self-Assembly Supramolecular Systems toward Molecular Machines and Motors%具有分子机器、分子开关功能的自组装超分子体系

    Institute of Scientific and Technical Information of China (English)

    陈慧兰

    2001-01-01

    Self-assembly, self-organization and self-replication, that are central to nature' s forms and functions, are now becoming feasible to construct large and intricate, yet highly ordered functioning molecular and supramolecular entities. This paper introduced the recently new progress for a kind of special rotaxane and catenane supramoculars having functions of molecular shuttle or molecular switch, as well as the chemical and biological systems toward molecular machines and motors.%本文介绍了具有分子梭或分子开关性质的新型轮烷和索烃超分子以及具有分子机器功能的其它类型化学和生物分子的国际研究最新动态。

  5. Molecular Motor MYO1C, Acetyltransferase KAT6B and Osteogenetic Transcription Factor RUNX2 Expression in Human Masseter Muscle Contributes to Development of Malocclusion

    Science.gov (United States)

    Desh, Heather; Gray, S Lauren; Horton, Michael J; Raoul, Gwenael; Rowlerson, Anthea M; Ferri, Joel; Vieira, Alexandre R; Sciote, James J

    2014-01-01

    Objective Type I myosins are molecular motors necessary for glucose transport in the cytoplasm and initiation of transcription in the nucleus. Two of these, MYO1H and MYO1C, are paralogs which may be important in the development of malocclusion. The objective of this study was to investigate their gene expression in the masseter muscle of malocclusion subjects. Two functionally related proteins known to contribute to malocclusion were also investigated: KAT6B (a chromatin remodeling epigenetic enzyme which is activated by MYO1C) and RUNX2 (a transcription factor regulating osteogenesis which is activated by KAT6B). Design Masseter muscle samples and malocclusion classifications were obtained from orthognathic surgery subjects. Muscle was sectioned and immunostained to determine fiber type properties. RNA was isolated from the remaining sample to determine expression levels for the four genes by TaqMan® RT-PCR. Fiber type properties, gene expression quantities and malocclusion classification were compared. Results There were very significant associations (P<0.0000001) between MYO1C and KAT6B expressions. There were also significant associations (P<0.005) between RUNX2 expression and masseter muscle type II fiber properties. Very few significant associations were identified between MYO1C and masseter muscle fiber type properties. Conclusions The relationship between MYO1C and KAT6B suggests that the two are interacting in chromatin remodeling for gene expression. This is the nuclear myosin1 (NM1) function of MYO1C. A surprising finding is the relationship between RUNX2 and type II masseter muscle fibers, since RUNX2 expression in mature muscle was previously unknown. Further investigations are necessary to elucidate the role of RUNX2 in adult masseter muscle. PMID:24698832

  6. Crystallographic and molecular dynamics analysis of loop motions unmasking the peptidoglycan-binding site in stator protein MotB of flagellar motor.

    Directory of Open Access Journals (Sweden)

    Cyril F Reboul

    Full Text Available BACKGROUND: The C-terminal domain of MotB (MotB-C shows high sequence similarity to outer membrane protein A and related peptidoglycan (PG-binding proteins. It is believed to anchor the power-generating MotA/MotB stator unit of the bacterial flagellar motor to the peptidoglycan layer of the cell wall. We previously reported the first crystal structure of this domain and made a puzzling observation that all conserved residues that are thought to be essential for PG recognition are buried and inaccessible in the crystal structure. In this study, we tested a hypothesis that peptidoglycan binding is preceded by, or accompanied by, some structural reorganization that exposes the key conserved residues. METHODOLOGY/PRINCIPAL FINDINGS: We determined the structure of a new crystalline form (Form B of Helicobacter pylori MotB-C. Comparisons with the existing Form A revealed conformational variations in the petal-like loops around the carbohydrate binding site near one end of the β-sheet. These variations are thought to reflect natural flexibility at this site required for insertion into the peptidoglycan mesh. In order to understand the nature of this flexibility we have performed molecular dynamics simulations of the MotB-C dimer. The results are consistent with the crystallographic data and provide evidence that the three loops move in a concerted fashion, exposing conserved MotB residues that have previously been implicated in binding of the peptide moiety of peptidoglycan. CONCLUSION/SIGNIFICANCE: Our structural analysis provides a new insight into the mechanism by which MotB inserts into the peptidoglycan mesh, thus anchoring the power-generating complex to the cell wall.

  7. Motor syndromes.

    Science.gov (United States)

    Corea, Francesco; Micheli, Sara

    2012-01-01

    Motor disturbances alone or associated with other focal deficits are the most common symptoms suggesting a neurovascular event. An appropriate clinical assessment of these signs and symptoms may help physicians to better diagnose and to both better treat and predict outcome. In this paper the main clinical features of motor deficit are described together with other motor-related events such as ataxia and movement disturbances.

  8. 木质素在异丙醇中的降解研究%Depolymerization of Lignin in Isopropanol Solvent

    Institute of Scientific and Technical Information of China (English)

    田晓东; 叶跃元; 刘运权

    2015-01-01

    采用正交试验法对有机溶剂木质素在异丙醇中的降解进行了研究,得出木质素在异丙醇中降解的较优水平为:催化剂Ru/C用量0.20 g、温度280℃、压力2.5 MPa、时间8 h。在该条件下,降解产物中生物油的产率最高可达74.13%,生物油中酚类和醇、酮以及烃类的GC含量总和接近60%。木质素原料和生物油的元素分析说明解聚过程中发生了脱氧;傅里叶红外光谱分析表明木质素的解聚过程中有酚羟基、烷基等新的结构基团产生。%The depolymerization of lignin in isopropanol was studied by orthogonal array test. It was found that the excellent levels of the lignin depolymerization in isopropanol were as follows: Ru/C catalyst amount 0. 20 g, temperature 280 ℃, pressure 2. 5 MPa, reaction time 8 h. Under these conditions, the yield of bio-oil could reach 74. 13%, and a combined GC content of phenolics, cyclic alcohols, cyclic ketones, and hydrocarbons achieved 60%. The elemental analyses of lignin feedstock and bio-oil products indicated that deoxygenation was carried out during the depolymerization. The fourier infrared spectrum ( FT-IR) further indicated that new functional groups such as phenolic hydroxyl and alkyl were formed.

  9. 木质素催化解聚的研究进展%Progress in catalytic depolymerization of lignin

    Institute of Scientific and Technical Information of China (English)

    舒日洋; 徐莹; 张琦; 马隆龙; 王铁军

    2016-01-01

    木质素是一种芳环结构来源丰富且价格低廉的可再生资源。从木质素出发催化解聚制备单酚类高附加值精细化学品和芳香烃烷烃等高品位生物燃料,可以部分替代以化石燃料为原料的生产过程,是生物质资源全组分高效综合利用的重要组成部分。在木质素催化解聚方法中,催化氢解可以直接将木质素转化为低氧含量的液体燃料,在生物燃料利用方面展现出巨大的潜力。本文详细总结了木质素的催化解聚方法,从催化剂类型、溶剂种类、反应机理及催化剂循环使用性等方面介绍了国内外的主要研究进展,着重阐述了木质素催化氢解方法。最后总结了当前木质素催化解聚过程中存在的难题,并对未来的技术发展提出了建议和展望。%Lignin is a cheap and renewable resource with rich aromatic units. It can be efficiently transformed into highly value-added fine chemicals such as phenolic monomers and other high-grade biofuels such as arenes and alkanes through catalytic depolymerization methods, which has long been regarded as an important constituent part of biomass resources comprehensive utilization approaches. This process is able to replace the chemicals production from the fossil fuel partly. Among the lignin depolymerization methods, the catalytic hydrogenolysis process can directly convert lignin into liquid fuel with low oxygen contents, and these biofuels show a great potential in the replacement of traditional energy sources. This paper focuses on the catalytic lignin depolymerization methods. The recent progress at home and abroad is reviewed based on the catalysts, solvents, catalysis mechanism and catalyst recyclability. Wherein, the catalytic hydrogenolysis method is emphatically introduced in detail. Furthermore, the current technique challenges during the lignin catalytic depolymerization process are summarized. Many future technologic explorations and

  10. Base-Catalyzed Depolymerization of Lignin with Heterogeneous Catalysts: Cooperative Research and Development Final Report, CRADA Number CRD-13-513

    Energy Technology Data Exchange (ETDEWEB)

    Beckham, Gregg T. [National Renewable Energy Lab. (NREL), Golden, CO (United States)

    2015-08-04

    We will synthesize and screen solid catalysts for the depolymerization of lignin to monomeric and oligomeric oxygenated species, which could be fractionated and integrated into refinery intermediate streams for selective upgrading, or catalytically upgraded to fuels and chemicals. This work will primarily focus on the synthesis and application of layered double hydroxides (LDHs) as recyclable, heterogeneous catalysts for depolymerization of lignin model compounds and softwood lignin. LDHs have been shown in our group to offer good supports and catalysts to promote base-catalyzed depolymerization of lignin model compounds and in preliminary experiments for the depolymerization of lignin from an Organosolv process. We will also include additional catalyst supports such as silica, alumina, and carbon as identified in ongoing and past efforts at NREL. This work will consist of two tasks. Overall, this work will be synergistic with ongoing efforts at NREL, funded by the DOE Biomass Program, on the development of catalysts for lignin depolymerization in the context of biochemical and thermochemical conversion of corn stover and other biomass feedstocks to advanced fuels and chemicals.

  11. "New" Compounds from Old Plastics: Recycling PET Plastics via Depolymerization. An Activity for the Undergraduate Organic Lab

    Science.gov (United States)

    Kaufman, Don; Wright, Geoff; Kroemer, Ryan; Engel, Josh

    1999-11-01

    This paper describes work done to develop a meaningful undergraduate organic lab activity that illustrates chemistry of the real world while utilizing reactions typically included in the organic lecture and lab. We show how a common plastic can be converted into several compounds using ester hydrolysis and SN2 reactions. Contributing to the critical shortage of landfill space faced by many communities is the large quantity of plastic refuse. Thus, there is a real need to recycle plastic products. One way to recycle plastics such as polyethyleneterephthalate (PET), the polyester from which numerous consumer products such as 2-liter soda bottles are made, is to depolymerize them and then to use the resulting monomers to produce new products. PET is industrially depolymerized via an acid-catalyzed transesterification reaction conducted under conditions of high temperature and pressure that are not feasible in the undergraduate lab. Despite literature reports that PET is remarkably resistant to hydrolysis, we found that PET can be readily hydrolyzed by refluxing with potassium hydroxide or potassium tert-butoxide in amyl alcohol to give terephthalic acid in high yield. It is then possible to readily synthesize terephthalate diesters via SN2 reactions of ammonium terephthalate salts with alkyl halides. Fischer esterification can also be used to prepare the diesters, but yields are significantly lower.

  12. Efficient preparation of catechin thio conjugates by one step extraction/depolymerization of pine (Pinus pinaster) bark procyanidins.

    Science.gov (United States)

    Selga, Ariadna; Torres, Josep Lluís

    2005-10-05

    The skin penetrating antioxidant cysteamine derivative of (-)-epicatechin as well as other thio conjugates were efficiently obtained with high yields from pine (Pinus pinaster) bark by simultaneous one pot extraction and depolymerization using water and cysteamine hydrochloride. The influence of the concentration of bark, acid, and cysteamine, as well as the reaction time on the total conversion, was studied. The total conversion into the epicatechin and catechin conjugates was as high as 47 g/kg pine bark with 1666 g cysteamine/kg bark and 28 g/kg with 166 g cysteamine/kg bark. A fast cleanup step by absorption/desorption on XAD-16 greatly facilitated further purification of the active major component. At a pilot scale, 4beta-(2-aminoethylthio)epicatechin (1) (conversion 263 g, purity 35% by reversed phase high-performance liquid chromatography/weight) was obtained from 17 kg of pine bark after simultaneous extraction/depolymerization followed by cleanup with the polymeric resin in approximately 10 h. The results show that pine (P. pinaster) bark is a suitable source of flavanols for the preparation of active thio derivatives. Conditions are given for the fast and efficient preparation of the conjugates.

  13. Motor homopolar

    OpenAIRE

    Agustín Martín Muñoz

    2007-01-01

    Mostramos la construcción de un modelo de motor homopolar, uno de los más antiguos tipos de motores eléctricos. Se caracterizan porque el campo magnético del imán mantiene siempre la misma polaridad (de ahí su nombre, del griego homos, igual), de modo que, cuando una corriente eléctrica atraviesa el campo magnético, aparece una fuerza que hace girar los elementos no fijados mecánicamente. En el sencillísimo motor homopolar colgado (Schlichting y Ucke 2004), el imán puede girar ...

  14. Ultrasonic Motors

    Science.gov (United States)

    2003-06-01

    and T. Higuchi, "Cylindrical Micro Ultrasonic Motor Utilizing Bulk Lead Zirconate Titanate (PZT)," Japanese Journal of Applied Physics Part 1-Regular Papers Short Notes & Review Papers, vol. 38, pp. 3347-3350, 1999.

  15. An elastic-diffusion model for myosin VI molecular motor in a periodic potential field%肌球蛋白VI分子马达周期势场下的弹性扩散模型

    Institute of Scientific and Technical Information of China (English)

    李晨璞; 韩英荣; 展永; 胡金江; 张礼刚; 曲蛟

    2013-01-01

    Because of the special structure and intracellular functions of myosin VI molecular motor, its dynamic principle has become a research focus. Starting from its structure and experimental phenomenon, the elastic-diffusion model of myosin VI in a periodic potential field is established, and the stochastic dynamics of the molecular motors, which conform to the Langevin equation, is analyzed by Monte Carlo simulations. By means of the environmental noise, myosin VI molecular motors could take stable stepping motion and effective transport according to its elastic potential energy and periodic potential of track, and a load can weaken the transportation power of the molecular motor system. For a given elastic coefficient, the longer the elastic chain of myosin VI, the lower the average velocity of it. By selecting a reasonable size of elasticity coefficient, the average velocity can be the maximum for a given elastic chain. In addition, the load can increase exponentially the mean dwelling time of myosin VI at the connection site.%肌球蛋白VI分子马达因其特殊的结构及胞内功能,其动力学原理成为研究的热点。从肌球蛋白VI自身结构和实验现象出发,建立其弹性扩散模型,并通过Monte Carlo方法分析了肌球蛋白VI满足朗之万方程的随机动力学行为。结果表明,在环境噪声作用下,具有弹性势能和轨道周期势能的肌球蛋白VI可以进行梯跳运动和有效的输运,但负载力会减弱分子马达系统的输运能力;当弹性系数一定时,弹性链越长平均速度越小,当弹性链长度一定时,合理选择弹性系数平均速度可达到最大值;另外,负载力的存在使肌球蛋白VI在接触位点的平均驻留时间呈指数增加。

  16. [Chitosan depolymerization by enzymes from hepatopancreas of the crab Paralithodes camtschaticus].

    Science.gov (United States)

    Novikov, V Iu; Mukhin, V A

    2003-01-01

    An enzyme preparation was isolated from the Paralithodes camtschaticus hepatopancreas that exhibited chitinase and chitosanase activities. Treatment of chitin and chitosan with this preparation decreased their viscosity-average molecular weights by 96 and 41%, respectively. The chromatographic profiles of the products of chitin and chitosan hydrolysis suggested that the crab hepatopancreas in rich in endochitinases. Enzymatic digestion of chitosan increased its solubility and moderately reduced the extent of its acetylation. A mathematical approach was proposed for calculating the molecular weights of chitosan fractions from weight-average molecular weights determined viscometrically.

  17. Catalytic Depolymerization and Upgrading of Lignin for Vanillin Production: Cooperative Research and Development Final Report, CRADA Number CRD-14-545

    Energy Technology Data Exchange (ETDEWEB)

    Beckham, Gregg [National Renewable Energy Lab. (NREL), Golden, CO (United States)

    2017-03-31

    Examine catalytic conversion of lignin using multifunctional catalysts that are able to depolymerize and oxidize lignin to a vanillin-rich stream. Examine separation processes for isolation of vanillin from product mixtures. Conduct preliminary experiments to determine if deconstructed lignin streams can be metabolized by Pseudomonas putida.

  18. Motor Planning.

    Science.gov (United States)

    Wong, Aaron L; Haith, Adrian M; Krakauer, John W

    2015-08-01

    Motor planning colloquially refers to any process related to the preparation of a movement that occurs during the reaction time prior to movement onset. However, this broad definition encompasses processes that are not strictly motor-related, such as decision-making about the identity of task-relevant stimuli in the environment. Furthermore, the assumption that all motor-planning processes require processing time, and can therefore be studied behaviorally by measuring changes in the reaction time, needs to be reexamined. In this review, we take a critical look at the processes leading from perception to action and suggest a definition of motor planning that encompasses only those processes necessary for a movement to be executed-that is, processes that are strictly movement related. These processes resolve the ambiguity inherent in an abstract goal by defining a specific movement to achieve it. We propose that the majority of processes that meet this definition can be completed nearly instantaneously, which means that motor planning itself in fact consumes only a small fraction of the reaction time. © The Author(s) 2014.

  19. On the Cyclo-Depolymerization of Alkyl Aromatic Polyesters and the in Situ Polymerization of the Cyclic Oligomers Produced

    Science.gov (United States)

    Alessi, M.; Stagnaro, P.; Conzatti, L.; Scafati, S. Tagliatatela; Hodge, P.

    2008-08-01

    Macrocyclic oligomers (MCOs) of some commercial alkyl aromatic polyesters (PET, PTT, PBT) were prepared by cyclo-depolymerization (CDP) of the polymers in refluxing 1, 2-dichlorobenzene with di-n-butyltin oxide as a transesterification catalyst. The mixtures of MCOs and residual polymer obtained at varying polymer/solvent ratios were separated and characterized by thorough GPC and DSC analyses. The higher the initial polymer concentration the lower was the yield of MCOs, and vice versa. Rheological measurements carried out on polymer/MCO mixtures showed a decrease in the melt viscosity with increasing amount of MCOs. Moreover, the MCOs present in these systems easily underwent entropically-driven ring-opening polymerizations (ED-ROPs) to reform the parent polyesters.

  20. Mathematical analysis of physicochemical phenomena in the catalyst during hydrogenating depolymerization of coal extract benzene insoluble fraction

    Institute of Scientific and Technical Information of China (English)

    Jerzy Szczygieł; Marek Stolarski

    2015-01-01

    Efficiency and selectivity of hydrogenating depolymerization of the coal extract benzene-insoluble part over the heterogeneous Co–Mo/Al2O3 catalyst were assessed using a mathematical model. The analytical equations of the mathematical model were generated based on material balance incorporating the physico-chemical phenomena (reaction and diffusion) both in the autoclave and the catalyst grain. The equations offer the possibility for predicting changes of the reactants in the autoclave during the process and for determining the distribution of reactant concentrations in the grain as a function of its radius. The analytical equations of the model serve as the basis of the algorithm for assessing the influence of restrictive diffusion on the effectiveness and selectivity of the catalyst, and also for defining the optimal radi of the catalyst's pores to enable free transport of reactants in the grain interior.

  1. A molecular analysis of L-arabinan degradation in Aspergillus niger and Aspergillus nidulans.

    NARCIS (Netherlands)

    Flipphi, M.J.A.

    1995-01-01

    This thesis describes a molecular study of the genetics ofL-arabinan degradation in Aspergillus niger and Aspergillus nidulans. These saprophytic hyphal fungi produce an extracellular hydrolytic enzyme system to depolymerize the plant cell wall polysaccharideL<

  2. Intensified depolymerization of aqueous polyacrylamide solution using combined processes based on hydrodynamic cavitation, ozone, ultraviolet light and hydrogen peroxide.

    Science.gov (United States)

    Prajapat, Amrutlal L; Gogate, Parag R

    2016-07-01

    The present work deals with intensification of depolymerization of polyacrylamide (PAM) solution using hydrodynamic cavitation (HC) reactors based on a combination with hydrogen peroxide (H2O2), ozone (O3) and ultraviolet (UV) irradiation. Effect of inlet pressure in hydrodynamic cavitation reactor and power dissipation in the case of UV irradiation on the extent of viscosity reduction has been investigated. The combined approaches such as HC+UV, HC+O3, HC+H2O2, UV+H2O2 and UV+O3 have been subsequently investigated and found to be more efficient as compared to individual approaches. For the approach based on HC+UV+H2O2, the extent of viscosity reduction under the optimized conditions of HC (3 bar inlet pressure)+UV (8 W power)+H2O2 (0.2% loading) was 97.27% in 180 min whereas individual operations of HC (3 bar inlet pressure) and UV (8 W power) resulted in about 35.38% and 40.83% intrinsic viscosity reduction in 180 min respectively. In the case of HC (3 bar inlet pressure)+UV (8 W power)+ozone (400 mg/h flow rate) approach, the extent of viscosity reduction was 89.06% whereas individual processes of only ozone (400 mg/h flow rate), ozone (400 mg/h flow rate)+HC (3 bar inlet pressure) and ozone (400 mg/h flow rate)+UV (8 W power) resulted in lower extent of viscosity reduction as 50.34%, 60.65% and 75.31% respectively. The chemical structure of the treated PAM by all approaches was also characterized using FTIR (Fourier transform infrared) spectra and it was established that no significant chemical structure changes were obtained during the treatment. Overall, it can be said that the combination of HC+UV+H2O2 is an efficient approach for the depolymerization of PAM solution.

  3. Intensification of depolymerization of polyacrylic acid solution using different approaches based on ultrasound and solar irradiation with intensification studies.

    Science.gov (United States)

    Prajapat, Amrutlal L; Gogate, Parag R

    2016-09-01

    Depolymerization of polyacrylic acid (PAA) as sodium salt has been investigated using ultrasonic and solar irradiations with process intensification studies based on combination with hydrogen peroxide (H2O2) and ozone (O3). Effect of solar intensity, ozone flow and ultrasonic power dissipation on the extent of viscosity reduction has been investigated for individual treatment approaches. The combined approaches such as US+solar, solar+O3, solar+H2O2, US+H2O2 and US+O3 have been subsequently investigated under optimum conditions and established to be more efficient as compared to individual approaches. Approach based on US (60W)+solar+H2O2 (0.01%) resulted in the maximum extent of viscosity reduction as 98.97% in 35min whereas operation of solar+H2O2 (0.01%), US (60W), H2O2 (0.3%) and solar irradiation resulted in about 98.08%, 90.13%, 8.91% and 90.77% intrinsic viscosity reduction in 60min respectively. Approach of US (60W)+solar+ozone (400mg/h flow rate) resulted in extent of viscosity reduction as 99.47% in 35min whereas only ozone (400mg/h flow rate), ozone (400mg/h flow rate)+US (60W) and ozone (400mg/h flow rate)+solar resulted in 69.04%, 98.97% and 98.51% reduction in 60min, 55min and 55min respectively. The chemical identity of the treated polymer using combined approaches was also characterized using FTIR (Fourier transform infrared) spectra and it was established that no significant structural changes were obtained during the treatment. Overall, it can be said that the combination technique based on US and solar irradiations in the presence of hydrogen peroxide is the best approach for the depolymerization of PAA solution.

  4. Role of nitric oxide in actin depolymerization and programmed cell death induced by fusicoccin in sycamore (Acer pseudoplatanus) cultured cells.

    Science.gov (United States)

    Malerba, Massimo; Contran, Nicla; Tonelli, Mariagrazia; Crosti, Paolo; Cerana, Raffaella

    2008-06-01

    Programmed cell death (PCD) plays a vital role in plant development and is involved in defence mechanisms against biotic and abiotic stresses. Different forms of PCD have been described in plants on the basis of the cell organelle first involved. In sycamore (Acer pseudoplatanus L.) cultured cells, the phytotoxin fusicoccin (FC) induces cell death. However, only a fraction of the dead cells shows the typical hallmarks of animal apoptosis, including cell shrinkage, chromatin condensation, DNA fragmentation and release of cytochrome c from the mitochondrion. In this work, we show that the scavenging of nitric oxide (NO), produced in the presence of FC, by 2-(4-carboxyphenyl)-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide (cPTIO) and rutin inhibits cell death without affecting DNA fragmentation and cytochrome c release. In addition, we show that FC induces a massive depolymerization of actin filaments that is prevented by the NO scavengers. Finally, the addition of actin-depolymerizing drugs induces PCD in control cells and overcomes the inhibiting effect of cPTIO on FC-induced cell death. Vice versa, the addition of actin-stabilizing drugs to FC-treated cells partially inhibits the phytotoxin-induced PCD. These results suggest that besides an apoptotic-like form of PCD involving the release of cytochrome c, FC induces at least another form of cell death, likely mediated by NO and independent of cytochrome c release, and they make it tempting to speculate that changes in actin cytoskeleton are involved in this form of PCD.

  5. Role of sodium ions in the vitrification process: glass matrix modification, slag structure depolymerization, and influence of metal immobilization.

    Science.gov (United States)

    Kuo, Yi-Ming

    2014-07-01

    This study investigates the role of Na ions, a common flux, in the vitrification process. Artificial glass systems composed of Al2O3, CaO, and SiO2 with various Na concentrations were melted at 1450 degrees C. The specimens were cooled by air cooling and water quenching and the metal mobility was evaluated using a sequential extraction procedure. The X-ray diffraction analysis and scanning electron microscopy observations showed that Na ions governed the air-cooled slag's structure. Na ions initially depolymerized CaSiO3-linked chains into CaSiO3 chains, and further cut them into shorter and nonuniform ones, making the slag structure amorphous. With even more Na ions, CaSiO3 chains were divided into single SiO4 tetrahedrons and formed Na-related crystals (Na2Ca3Si2O8 and NaAlSiO4). The phase distributions of Al, Cr, Cu Mn, and Ni showed that Na has a positive effect on the immobilization of heavy metals at suitable concentrations, but a negative effect when in excess amounts. Implications: Vitrification has been widely used to treat hazardous materials. The Na-bearing additives were often used as a flux to improve the melting process. This study described the role of Na played in the vitrification process. The Na ions acted as glass modifier and depolymerize the chain structure of slag. With adequate addition amount of Na ions, the immobilization of heavy metals was improved. The results provided much information about the crystalline phase variation, metal mobility, and surface characteristics while Na serves as a flux.

  6. Selective chemical oxidation and depolymerization of switchgrass [corrected] (Panicum virgatum L.) xylan with [corrected] oligosaccharide product analysis by mass spectrometry.

    Science.gov (United States)

    Bowman, Michael J; Dien, Bruce S; O'Bryan, Patricia J; Sarath, Gautam; Cotta, Michael A

    2011-04-15

    Xylan is a barrier to enzymatic hydrolysis of plant cell walls. It is well accepted that the xylan layer needs to be removed to efficiently hydrolyze cellulose; consequently, pretreatment conditions are (in part) optimized for maximal xylan depolymerization or displacement. Xylan consists of a long chain of β-1,4-linked xylose units substituted with arabinose (typically α-1,3-linked in grasses) and glucuronic acid (α-1,2-linked). Xylan has been proposed to have a structural function in plants and therefore may play a role in determining biomass reactivity to pretreatment. It has been proposed that substitutions along xylan chains are not random and, based upon studies of pericarp xylan, are organized in domains that have specific structural functions. Analysis of intact xylan is problematic because of its chain length (> degree of polymerization (d.p.) 100) and heterogeneous side groups. Traditionally, enzymatic end-point products have been characterized due to the limited products generated. Analysis of resultant arabino-xylo-oligosaccharides by mass spectrometry is complicated by the isobaric pentose sugars that primarily compose xylan. In this report, the variation in pentose ring structures was exploited for selective oxidation of the arabinofuranose primary alcohols followed by acid depolymerization to provide oligosaccharides with modified arabinose branches intact. Switchgrass samples were analyzed by hydrophilic interaction chromatography (HILIC)-liquid chromatography (LC)-mass spectrometry/mass spectrometry (MSMS) and off-line nanospray MS to demonstrate the utility of this chemistry for determination of primary hydroxyl groups on oligosaccharide structures, with potential applications for determining the sequence of arabino-xylo-oligosaccharides present in plant cell wall material.

  7. Depolymerization of cortical actin inhibits UT-A1 urea transporter endocytosis but promotes forskolin-stimulated membrane trafficking.

    Science.gov (United States)

    Xu, Gang; Su, Hua; Carter, Conner B; Fröhlich, Otto; Chen, Guangping

    2012-04-01

    The cytoskeleton participates in many aspects of transporter protein regulation. In this study, by using yeast two-hybrid screening, we identified the cytoskeletal protein actin as a binding partner with the UT-A1 urea transporter. This suggests that actin plays a role in regulating UT-A1 activity. Actin specifically binds to the carboxyl terminus of UT-A1. A serial mutation study shows that actin binding to UT-A1's carboxyl terminus was abolished when serine 918 was mutated to alanine. In polarized UT-A1-MDCK cells, cortical filamentous (F) actin colocalizes with UT-A1 at the apical membrane and the subapical cytoplasm. In the cell surface, both actin and UT-A1 are distributed in the lipid raft microdomains. Disruption of the F-actin cytoskeleton by latrunculin B resulted in UT-A1 accumulation in the cell membrane as measured by biotinylation. This effect was mainly due to inhibition of UT-A1 endocytosis in both clathrin and caveolin-mediated endocytic pathways. In contrast, actin depolymerization facilitated forskolin-stimulated UT-A1 trafficking to the cell surface. Functionally, depolymerization of actin by latrunculin B significantly increased UT-A1 urea transport activity in an oocyte expression system. Our study shows that cortical F-actin not only serves as a structural protein, but directly interacts with UT-A1 and plays an important role in controlling UT-A1 cell surface expression by affecting both endocytosis and trafficking, therefore regulating UT-A1 bioactivity.

  8. A polymerization–depolymerization model for generation of contractile force during bacterial cell division

    Indian Academy of Sciences (India)

    Biplab Ghosh; Anirban Sain

    2008-08-01

    During the last phase of cell division in bacteria, a polymeric ring forms at the division site. The ring, made of intracellular proteins, anchors to the cell wall and starts to contract. That initiates a dividing septum to close in, like the shutter of a camera, eventually guillotining the cell into two daughters. All through, the ring remains at the leading edge of the septum and seems to power its closure. It is not understood why does the ring contract. We propose a theoretical model to explain this. It is worth mentioning that a similar contraction phenomenon occurs for the actin ring in eukaryotes, but there it is due to motor proteins, which however, are absent in bacteria.

  9. Restructuring the crystalline cellulose hydrogen bond network enhances its depolymerization rate

    Science.gov (United States)

    Shishir P.S. Chundawat; Giovanni Bellesia; Nirmal Uppugundla; Leonardo da Costa Sousa; Dahai Gao; Albert M. Cheh; Umesh P. Agarwal; Christopher M. Bianchetti; George N. Phillips; Paul Langan; Venkatesh Balan; S. Gnanakaran; Bruce E. Dale

    2011-01-01

    Conversion of lignocellulose to biofuels is partly inefficient due to the deleterious impact of cellulose crystallinity on enzymatic saccharification. We demonstrate how the synergistic activity of cellulases was enhanced by altering the hydrogen bond network within crystalline cellulose fibrils. We provide a molecular-scale explanation of these phenomena through...

  10. THE MOTOR

    DEFF Research Database (Denmark)

    Gammelgaard Nielsen, Anders

    2011-01-01

    MOTOR is the first assignment that students at Unit 1a of the School of Architecture are introduced to. The purpose of the assignment is to shake up the students and their preconceptions of what architec- ture is. This is done by introducing them to a working method that al- lows them to develop...

  11. THE MOTOR

    DEFF Research Database (Denmark)

    Gammelgaard Nielsen, Anders

    2011-01-01

    MOTOR is the first assignment that students at Unit 1a of the School of Architecture are introduced to. The purpose of the assignment is to shake up the students and their preconceptions of what architec- ture is. This is done by introducing them to a working method that al- lows them to develop...

  12. Locomotion of chemically powered autonomous nanowire motors

    Science.gov (United States)

    Wang, Lin; Li, Longqiu; Li, Tianlong; Zhang, Guangyu; Sun, Qian

    2015-08-01

    Physical insights on the hydrodynamics and locomotion of self-propelled nanowire motor under nonequilibrium steady state are investigated using finite element method in accordance with hybrid molecular dynamics/multiparticle collision dynamics and rigid body dynamics. Nanowire motor is discretized into finite segments, and forces of solvent molecule acting on the motor are assumed to be the sum of forces acting on all segments of the motor. We show that the locomotion of nanowire motor is mainly determined by the imbalance forces acting on the catalytic and noncatalytic segments. The average velocity along the axis increases significantly as a function of time prior to reaching equilibrium. The length of nanowire motor shows negligible effect on the velocity of the motor. Preliminary experimental results are provided to validate the current model.

  13. Molecular Weight Distributions of Cotton Cellulose Treated with a Polycarboxylic Acid at Different pH

    Institute of Scientific and Technical Information of China (English)

    MAO Zhi-ping; Charles Q. Yang

    2004-01-01

    In last paper, the average molecular weight of a control cotton fabric and cotton fabrics treated with the polycarboxylic acid at different pH were measured. The result doesn't support the hypothesis that the pH of the finishing bath can affect the depolymerization of the finished cotton fabric. In order to understand more about it, the molecular weight distributions of the control and finished cotton fabrics were measured and the reason was fund. From the ratio and the molecular weight of the low molecular part one can see that the pH of the finishing bath can affect the depolymerization of the finished cotton fabrics. The phenomenon that the average molecular weights of the cotton fabric crosslinked with BTCA at different pH are almost same is attributed to that the crosslinks are not broken completely when treated with 0.5M NaOH solution at 50℃ for 144h.

  14. Self-Immolative Chemiluminescence Polymers: Innate Assimilation of Chemiexcitation in a Domino-like Depolymerization.

    Science.gov (United States)

    Gnaim, Samer; Shabat, Doron

    2017-07-26

    Self-immolative polymers are distinctive materials able to disassemble in a domino-like mechanism from head-to-tail upon a triggering event induced by an external stimulus. We have developed an effective molecular method to intrinsically assimilate a chemiluminescence turn-ON mechanism with a domino-like fragmentation mechanism. A unique molecular unit was synthesized, which could combine the abilities of executing the duel function of quinone-methide elimination and chemiexcitation. Incorporation of this unit as a monomer, results with the first class of stimuli-responsive self-immolative polymers with amplified chemiluminescence output. Responsive groups for various analytes were introduced as a head-trigger during the polymer synthesis. The polymers were demonstrated as chemiluminescence probes for detection of different chemical analytes. The obtained polymers were able to amplify the intensity and the duration of the light emission signal by factors correlated to their length. We anticipate that the chemiluminescence self-immolative polymers described here will find use for various research topics such as signal amplification, light-emitting new materials, and molecular probes with long-lasting light emission and imaging capabilities.

  15. The Infection of Cucumber (Cucumis sativus L.) Roots by Meloidogyne incognita Alters the Expression of Actin-Depolymerizing Factor (ADF) Genes, Particularly in Association with Giant Cell Formation

    Science.gov (United States)

    Liu, Bin; Liu, Xingwang; Liu, Ying; Xue, Shudan; Cai, Yanling; Yang, Sen; Dong, Mingming; Zhang, Yaqi; Liu, Huiling; Zhao, Binyu; Qi, Changhong; Zhu, Ning; Ren, Huazhong

    2016-01-01

    Cucumber (Cucumis sativus L.) is threatened by substantial yield losses due to the south root-knot nematode (Meloidogyne incognita). However, understanding of the molecular mechanisms underlying the process of nematode infection is still limited. In this study, we found that M. incognita infection affected the structure of cells in cucumber roots and treatment of the cytoskeleton inhibitor (cytochalasin D) reduced root-knot nematode (RKN) parasitism. It is known that Actin-Depolymerizing Factor (ADF) affects cell structure, as well as the organization of the cytoskeleton. To address the hypothesis that nematode-induced abnormal cell structures and cytoskeletal rearrangements might be mediated by the ADF genes, we identified and characterized eight cucumber ADF (CsADF) genes. Phylogenetic analysis showed that the cucumber ADF gene family is grouped into four ancient subclasses. Expression analysis revealed that CsADF1, CsADF2-1, CsADF2-2, CsADF2-3 (Subclass I), and CsADF6 (Subclass III) have higher transcript levels than CsADF7-1, CsADF7-2 (Subclass II genes), and CsADF5 (Subclass IV) in roots. Members of subclass I genes (CsADF1, CsADF2-1, CsADF2-2, and CsADF2-3), with the exception of CsADF2-1, exhibited a induction of expression in roots 14 days after their inoculation (DAI) with nematodes. However, the expression of subclass II genes (CsADF7-1 and CsADF7-2) showed no significant change after inoculation. The transcript levels of CsADF6 (Subclass III) showed a specific induction at 21 DAI, while CsADF5 (Subclass IV) was weakly expressed in roots, but was strongly up-regulated as early as 7 DAI. In addition, treatment of roots with cytochalasin D caused an approximately 2-fold down-regulation of the CsADF genes in the treated plants. These results suggest that CsADF gene mediated actin dynamics are associated with structural changes in roots as a consequence of M. incognita infection. PMID:27695469

  16. The Infection of Cucumber (Cucumis sativus L. Roots by Meloidogyne incognita Alters the Expression of Actin-Depolymerizing Factor (ADF Genes, Particularly in Association with Giant Cell Formation

    Directory of Open Access Journals (Sweden)

    Bin Liu

    2016-09-01

    Full Text Available Cucumber (Cucumis sativus L. is threatened by substantial yield losses due to the south root-knot nematode (Meloidogyne incognita. However, understanding of the molecular mechanisms underlying the process of nematode infection is still limited. In this study, we found that M. incognita infection affected the structure of cells in cucumber roots and treatment of the cytoskeleton inhibitor (cytochalasin D reduced root-knot nematode (RKN parasitism. It is known that Actin-Depolymerizing Factor (ADF affects cell structure, as well as the organization of the cytoskeleton. To address the hypothesis that nematode-induced abnormal cell structures and cytoskeletal rearrangements might be mediated by the ADF genes, we identified and characterized eight cucumber ADF (CsADF genes. Phylogenetic analysis showed that the cucumber ADF gene family is grouped into four ancient subclasses. Expression analysis revealed that CsADF1, CsADF2-1, CsADF2-2, CsADF2-3 (Subclass I and CsADF6 (Subclass III have higher transcript levels than CsADF7-1, CsADF7-2 (Subclass II genes and CsADF5 (Subclass IV in roots. Members of subclass I genes (CsADF1, CsADF2-1, CsADF2-2 and CsADF2-3, with the exception of CsADF2-1, exhibited a induction of expression in roots 14 days after their inoculation (DAI with nematodes. However, the expression of subclass II genes (CsADF7-1 and CsADF7-2 showed no significant change after inoculation. The transcript levels of CsADF6 (Subclass III showed a specific induction at 21 DAI, while CsADF5 (Subclass IV was weakly expressed in roots, but was strongly up-regulated as early as 7 DAI. In addition, treatment of roots with cytochalasin D caused an approximately two-fold down-regulation of the CsADF genes in the treated plants. These results suggest that CsADF gene mediated actin dynamics are associated with structural changes in roots as a consequence of M. incognita infection.

  17. RETRACTED: In vivo and in vitro antithrombus activities of depolymerized holothurian polysaccharides.

    Science.gov (United States)

    Yang, Jie; Mou, Jiaojiao; Ding, Dejun; Wang, Xuedong

    2017-01-01

    This article has been retracted: please see Elsevier Policy on Article Withdrawal (https://www.elsevier.com/about/our-business/policies/article-withdrawal). This article has been retracted at the request of authors. The authors have recently found a serious mistake in Table 1 of the article, where the molecular ratio of different monosaccharides is inconsistent with their previously published work. This error flaws the paper and so the authors wish it to be retracted to avoid misunderstanding and misinterpretation of their research work. The authors apologise for any concern or confusion that might have resulted in publishing this article. Copyright © 2016 Elsevier B.V. All rights reserved.

  18. Functional and molecular plasticity of gamma and alpha-1 GABAA receptor subunits in the dorsal motor nucleus of the vagus after experimentally-induced diabetes.

    Science.gov (United States)

    Boychuk, Carie R; Smith, Katalin Cs; Smith, Bret N

    2017-08-23

    Chronic experimentally-induced hyperglycemia augments subunit specific gamma-aminobutyric acid A (GABAA) receptor-mediated inhibition of parasympathetic preganglionic motor neurons in the dorsal motor nucleus of the vagus (DMV). However, the contribution of α1 or γ GABAA receptor subunits, which are ubiquitously expressed on central nervous system neurons, to this elevation in inhibitory tone have not been determined. This study investigated the effect of chronic hyperglycemia/hypoinsulinemia on α1- and γ-subunit specific GABAA receptor-mediated inhibition using electrophysiological recordings in vitro and quantitative (q)RT-PCR. DMV neurons from streptozotocin-treated mice demonstrated enhancement of both phasic and tonic inhibitory currents in response to application of the α1-subunit selective GABAA receptor positive allosteric modulator, zolpidem. Responses to low concentrations of the GABAA receptor antagonist, gabazine suggested an additional increased contribution of γ-subunit-containing receptors to tonic currents in DMV neurons. Consistent with the functional elevation in α1- and γ-subunit-dependent activity, transcription of both the α1- and γ2-subunits was increased in the dorsal vagal complex of streptozotocin-treated mice. Overall these findings suggest an increased sensitivity to both zolpidem and gabazine after several days of hyperglycemia/hypoinsulinemia, which could contribute to altered parasympathetic output from DMV neurons in diabetes. Copyright © 2017, Journal of Neurophysiology.

  19. The Molecular Motor KIF1A Transports the TrkA Neurotrophin Receptor and Is Essential for Sensory Neuron Survival and Function.

    Science.gov (United States)

    Tanaka, Yosuke; Niwa, Shinsuke; Dong, Ming; Farkhondeh, Atena; Wang, Li; Zhou, Ruyun; Hirokawa, Nobutaka

    2016-06-15

    KIF1A is a major axonal transport motor protein, but its functional significance remains elusive. Here we show that KIF1A-haploinsufficient mice developed sensory neuropathy. We found progressive loss of TrkA(+) sensory neurons in Kif1a(+/-) dorsal root ganglia (DRGs). Moreover, axonal transport of TrkA was significantly disrupted in Kif1a(+/-) neurons. Live imaging and immunoprecipitation assays revealed that KIF1A bound to TrkA-containing vesicles through the adaptor GTP-Rab3, suggesting that TrkA is a cargo of the KIF1A motor. Physiological measurements revealed a weaker capsaicin response in Kif1a(+/-) DRG neurons. Moreover, these neurons were hyposensitive to nerve growth factor, which could explain the reduced neuronal survival and the functional deficiency of the pain receptor TRPV1. Because phosphatidylinositol 3-kinase (PI3K) signaling significantly rescued these phenotypes and also increased Kif1a mRNA, we propose that KIF1A is essential for the survival and function of sensory neurons because of the TrkA transport and its synergistic support of the NGF/TrkA/PI3K signaling pathway.

  20. Effects of laccase on lignin depolymerization and enzymatic hydrolysis of ensiled corn stover.

    Science.gov (United States)

    Chen, Qin; Marshall, Megan N; Geib, Scott M; Tien, Ming; Richard, Tom L

    2012-08-01

    The aim of this study was to explore the synergies of laccase, a ligninolytic enzyme, with cellulose and hemicellulase amendments on ensiled corn stover. Molecular signals of lignin decomposition were observed by tetramethylammonium hydroxide thermochemolysis and gas chromatography-mass spectroscopy (TMAH-GC-MS) analysis. The significant findings suggest that ensilage might provide a platform for biological pretreatment. By partially hydrolyzing cellulose and hemicellulose into soluble sugars, ensilage facilitates laccase penetration into the lignocellulose complex to enhance lignin degradation. Downstream cellulose hydrolysis was improved 7% with increasing laccase loading rate. These results demonstrate the potential of enzymes, either directly amended or expressed by microbes during ensilage, to maximize utilization of corn stover for cellulosic biofuels and other downstream fermentations. Copyright © 2012. Published by Elsevier Ltd.

  1. Thermal depolymerization mechanisms of poly(3-hydroxybutyrate-co-3-hydroxyvalerate

    Directory of Open Access Journals (Sweden)

    Hengxue Xiang

    2016-02-01

    Full Text Available Thermal degradation processes and decomposition mechanisms of poly(3-hydroxybutyrate-co-3-hydroxyvalerate (PHBV were investigated by using thermal gravity analysis(TGA, Gel permeation chromatography (GPC, elemental analyzer, pyrolysis-gas chromatography-mass spectrometry (PyGC-MS and 1H nuclear magnetic resonance (1H NMR. The degradation activation energy was calculated via the dependence of residual mass on isothermal temperature. 1H NMR and PyGC-MS were used to investigate the chemical structure and component proportion of volatile gases and degradation residues which were produced by thermal decomposition, and to infer the process of macromolecular chain scission. Besides, the influence of the factors, such as outfield atmosphere, residual metal ions, on the degradation behaviors of PHBV was also studied. Finally, the PHBV thermal decomposition mechanisms were speculated on the basis of the degradation behaviors of molecular and chemical structure.

  2. Thermal depolymerization mechanisms of poly (3-hydroxybutyrate-co-3-hydroxyvalerate)

    Institute of Scientific and Technical Information of China (English)

    Hengxue Xiang; Xiaoshuang Wen; Xiaohui Miu; Yan Li; Zhe Zhou; Meifang Zhu

    2016-01-01

    Thermal degradation processes and decomposition mechanisms of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) were investigated by using thermal gravity analysis(TGA), Gel permeation chromatography (GPC), elemental analyzer, pyrolysis-gas chromatography-mass spectrometry (PyGC-MS) and 1H nuclear magnetic resonance (1H NMR). The degradation activation energy was calculated via the dependence of residual mass on isothermal temperature. 1H NMR and PyGC-MS were used to investigate the chemical structure and component proportion of volatile gases and degradation residues which were produced by thermal decomposition, and to infer the process of macromolecular chain scission. Besides, the influence of the factors, such as outfield atmosphere, residual metal ions, on the degradation behaviors of PHBV was also studied. Finally, the PHBV thermal decomposition mechanisms were speculated on the basis of the degradation behaviors of molecular and chemical structure.

  3. Microwave irradiated synthesis and characterization of 1, 4-phenylene bis-oxazoline form bis-(2-hydroxyethyl) terephthalamide obtained by depolymerization of poly (ethylene terephthalate) (PET) bottle wastes

    OpenAIRE

    Yogesh S. Parab; Rikhil V. Shah; Sanjeev R. Shukla

    2012-01-01

    The aminolytic depolymerization of PET bottle waste with ethanolamine by conventional heating and microwave irradiation heating method was attempted with heterogeneous, recyclable acid catalysts such as beta zeolite (SiO2/ AlO2= 15 Na- form) and montmorillonite KSF. The pure product bis-(2-hydroxyethyl) terephthalamide (BHETA) of aminolysis was obtained in good yield (85- 88%). The BHETA, thus obtained, was subjected to cyclization reaction by heating with polyphosphoric acid as well as by ch...

  4. A comparative study on the activity of fungal lytic polysaccharide monooxygenases for the depolymerization of cellulose in soybean spent flakes.

    Science.gov (United States)

    Pierce, Brian C; Agger, Jane Wittrup; Zhang, Zhenghong; Wichmann, Jesper; Meyer, Anne S

    2017-09-08

    Lytic polysaccharide monooxygenases (LPMOs) are copper-dependent enzymes capable of the oxidative breakdown of polysaccharides. They are of industrial interest due to their ability to enhance the enzymatic depolymerization of recalcitrant substrates by glycoside hydrolases. In this paper, twenty-four lytic polysaccharide monooxygenases (LPMOs) expressed in Trichoderma reesei were evaluated for their ability to oxidize the complex polysaccharides in soybean spent flakes, an abundant and industrially relevant substrate. TrCel61A, a soy-polysaccharide-active AA9 LPMO from T. reesei, was used as a benchmark in this evaluation. In total, seven LPMOs demonstrated activity on pretreated soy spent flakes, with the products from enzymatic treatments evaluated using mass spectrometry and high performance anion exchange chromatography. The hydrolytic boosting effect of the top-performing enzymes was evaluated in combination with endoglucanase and beta-glucosidase. Two enzymes (TrCel61A and Aspte6) showed the ability to release more than 36% of the pretreated soy spent flake glucose - a greater than 75% increase over the same treatment without LPMO addition. Copyright © 2017 Elsevier Ltd. All rights reserved.

  5. A Fast and Robust UHPLC-MRM-MS Method to Characterize and Quantify Grape Skin Tannins after Chemical Depolymerization

    Directory of Open Access Journals (Sweden)

    Lucie Pinasseau

    2016-10-01

    Full Text Available A rapid, sensitive, and selective analysis method using ultra high performance liquid chromatography coupled with triple-quadrupole mass spectrometry (UHPLC-QqQ-MS has been developed for the characterization and quantification of grape skin flavan-3-ols after acid-catalysed depolymerization in the presence of phloroglucinol (phloroglucinolysis. The compound detection being based on specific MS transitions in Multiple Reaction Monitoring (MRM mode, this fast gradient robust method allows analysis of constitutive units of grape skin proanthocyanidins, including some present in trace amounts, in a single injection, with a throughput of 6 samples per hour. This method was applied to a set of 214 grape skin samples from 107 different red and white grape cultivars grown under two conditions in the vineyard, irrigated or non-irrigated. The results of triplicate analyses confirmed the robustness of the method, which was thus proven to be suitable for high-throughput and large-scale metabolomics studies. Moreover, these preliminary results suggest that analysis of tannin composition is relevant to investigate the genetic bases of grape response to drought.

  6. Leukaemic cells from chronic lymphocytic leukaemia patients undergo apoptosis following microtubule depolymerization and Lyn inhibition by nocodazole.

    Science.gov (United States)

    Frezzato, Federica; Trimarco, Valentina; Martini, Veronica; Gattazzo, Cristina; Ave, Elisa; Visentin, Andrea; Cabrelle, Anna; Olivieri, Valeria; Zambello, Renato; Facco, Monica; Zonta, Francesca; Cristiani, Andrea; Brunati, Anna Maria; Moro, Stefano; Semenzato, Gianpietro; Trentin, Livio

    2014-06-01

    Functional abnormalities of chronic lymphocytic leukaemia (CLL) cells may be related to the microtubular network of cell cytoskeleton; specifically tubulin involvement in cells after B-cell receptor engagement. As microtubule inhibitors could represent a therapeutic strategy for CLL, this study investigated the capability of nocodazole, a synthetic depolymerizing agent, to kill CLL leukaemic cells. We demonstrated that nocodazole was highly specific for the in vitro induction of apoptosis in leukaemic cells from 90 CLL patients, without affecting the viability of T-cells and/or mesenchymal stromal cells (MSCs) recovered from the same patients. Nocodazole was observed to overcome the pro-survival signals provided by MSCs. Competing with ATP for the nucleotide-binding site, nocodazole has been observed to turn off the high basal tyrosine phosphorylation of leukaemic cells mediated by the Src-kinase Lyn. Considering that most anti-microtubule drugs have limited clinical use because of their strong toxic effects, the high selectivity of nocodazole for leukaemic cells in CLL and its capability to bypass microenvironmental pro-survival stimuli, suggests the use of this inhibitor for designing new therapeutic strategies in CLL treatment.

  7. Microtubule depolymerization normalizes in vivo myocardial contractile function in dogs with pressure-overload left ventricular hypertrophy

    Science.gov (United States)

    Koide, M.; Hamawaki, M.; Narishige, T.; Sato, H.; Nemoto, S.; DeFreyte, G.; Zile, M. R.; Cooper G, I. V.; Carabello, B. A.

    2000-01-01

    BACKGROUND: Because initially compensatory myocardial hypertrophy in response to pressure overloading may eventually decompensate to myocardial failure, mechanisms responsible for this transition have long been sought. One such mechanism established in vitro is densification of the cellular microtubule network, which imposes a viscous load that inhibits cardiocyte contraction. METHODS AND RESULTS: In the present study, we extended this in vitro finding to the in vivo level and tested the hypothesis that this cytoskeletal abnormality is important in the in vivo contractile dysfunction that occurs in experimental aortic stenosis in the adult dog. In 8 dogs in which gradual stenosis of the ascending aorta had caused severe left ventricular (LV) pressure overloading (gradient, 152+/-16 mm Hg) with contractile dysfunction, LV function was measured at baseline and 1 hour after the intravenous administration of colchicine. Cardiocytes obtained by biopsy before and after in vivo colchicine administration were examined in tandem. Microtubule depolymerization restored LV contractile function both in vivo and in vitro. CONCLUSIONS: These and additional corroborative data show that increased cardiocyte microtubule network density is an important mechanism for the ventricular contractile dysfunction that develops in large mammals with adult-onset pressure-overload-induced cardiac hypertrophy.

  8. Regenerated Cellulose Capsules for Controlled Drug Delivery, Part 2: Modulating Membrane Permeability by Incorporation of Depolymerized Cellulose and Altering Membrane Thickness.

    Science.gov (United States)

    Bhatt, Bhavik; Kumar, Vijay

    2015-12-01

    For application of regenerated cellulose (RC) membranes in capsule dosage forms, the methods to modify drug release from these membranes are described. Membranes were fabricated by blending native and depolymerized celluloses dissolved in dimethyl sulfoxide and paraformaldehyde solvent system, prior to casting on molds, precipitation in water, and thermal annealing. The effect of laminating layers of RC to fabricate membranes with increasing thickness was also investigated. Solute diffusion studies using ionic and hydrophobic solutes, as well as large protein molecules, were conducted in side-by-side diffusion cells. Microscopic as well as physiological evaluation of these membranes indicated that pore size, porosity, and water uptake decreased as the fraction of depolymerized cellulose increased in the membranes. Permeability analysis of small ionic and hydrophobic solutes indicated that the solute transport across the hydrated membrane occurs through diffusion in the water-filled pores that are formed in situ. The apparent path for solute diffusion increases as the fraction of depolymerized cellulose increases. Permeability analysis of large protein molecules indicated that the pore sizes and distribution in these membranes is heterogeneous. Increasing the membrane thickness by lamination of RC does not influence porosity but causes formation of dead-end pores because of blocking by subsequent laminate layers.

  9. Molecular hydrogen (H2) emissions and their isotopic signatures (H/D) from a motor vehicle : implications on atmospheric H2

    NARCIS (Netherlands)

    Vollmer, M.K.; Walter, S.; Bond, S.W.; Soltic, P.; Röckmann, T.

    2010-01-01

    Molecular hydrogen (H2), its isotopic signature (deuterium/hydrogen, δD), carbon monoxide (CO) and other compounds were studied in the exhaust of a passenger car engine fuelled with gasoline or methane and run under variable air-fuel ratios and operating modes. H2 and CO concentrations were largely

  10. Molecular hydrogen (H2) emissions and their isotopic signatures (H/D) from a motor vehicle : implications on atmospheric H2

    NARCIS (Netherlands)

    Vollmer, M.K.; Walter, S.; Bond, S.W.; Soltic, P.; Röckmann, T.

    2010-01-01

    Molecular hydrogen (H2), its isotopic signature (deuterium/hydrogen, δD), carbon monoxide (CO) and other compounds were studied in the exhaust of a passenger car engine fuelled with gasoline or methane and run under variable air-fuel ratios and operating modes. H2 and CO concentrations were largely

  11. Engineering molecular machines

    Science.gov (United States)

    Erman, Burak

    2016-04-01

    Biological molecular motors use chemical energy, mostly in the form of ATP hydrolysis, and convert it to mechanical energy. Correlated thermal fluctuations are essential for the function of a molecular machine and it is the hydrolysis of ATP that modifies the correlated fluctuations of the system. Correlations are consequences of the molecular architecture of the protein. The idea that synthetic molecular machines may be constructed by designing the proper molecular architecture is challenging. In their paper, Sarkar et al (2016 New J. Phys. 18 043006) propose a synthetic molecular motor based on the coarse grained elastic network model of proteins and show by numerical simulations that motor function is realized, ranging from deterministic to thermal, depending on temperature. This work opens up a new range of possibilities of molecular architecture based engine design.

  12. Motor neurons and the sense of place.

    Science.gov (United States)

    Jessell, Thomas M; Sürmeli, Gülşen; Kelly, John S

    2011-11-03

    Seventy years ago George Romanes began to document the anatomical organization of the spinal motor system, uncovering a multilayered topographic plan that links the clustering and settling position of motor neurons to the spatial arrangement and biomechanical features of limb muscles. To this day, these findings have provided a structural foundation for analysis of the neural control of movement and serve as a guide for studies to explore mechanisms that direct the wiring of spinal motor circuits. In this brief essay we outline the core of Romanes's findings and place them in the context of recent studies that begin to provide insight into molecular programs that assign motor pool position and to resolve how motor neuron position shapes circuit assembly. Romanes's findings reveal how and why neuronal positioning contributes to sensory-motor connectivity and may have relevance to circuit organization in other regions of the central nervous system. Copyright © 2011 Elsevier Inc. All rights reserved.

  13. Polygamain, a new microtubule depolymerizing agent that occupies a unique pharmacophore in the colchicine site.

    Science.gov (United States)

    Hartley, R M; Peng, J; Fest, G A; Dakshanamurthy, S; Frantz, D E; Brown, M L; Mooberry, S L

    2012-03-01

    Bioassay-guided fractionation was used to isolate the lignan polygamain as the microtubule-active constituent in the crude extract of the Mountain torchwood, Amyris madrensis. Similar to the effects of the crude plant extract, polygamain caused dose-dependent loss of cellular microtubules and the formation of aberrant mitotic spindles that led to G(2)/M arrest. Polygamain has potent antiproliferative activities against a wide range of cancer cell lines, with an average IC(50) of 52.7 nM. Clonogenic studies indicate that polygamain effectively inhibits PC-3 colony formation and has excellent cellular persistence after washout. In addition, polygamain is able to circumvent two clinically relevant mechanisms of drug resistance, the expression of P-glycoprotein and the βIII isotype of tubulin. Studies with purified tubulin show that polygamain inhibits the rate and extent of purified tubulin assembly and displaces colchicine, indicating a direct interaction of polygamain within the colchicine binding site on tubulin. Polygamain has structural similarities to podophyllotoxin, and molecular modeling simulations were conducted to identify the potential orientations of these compounds within the colchicine binding site. These studies suggest that the benzodioxole group of polygamain occupies space similar to the trimethoxyphenyl group of podophyllotoxin but with distinct interactions within the hydrophobic pocket. Our results identify polygamain as a new microtubule destabilizer that seems to occupy a unique pharmacophore within the colchicine site of tubulin. This new pharmacophore will be used to design new colchicine site compounds that might provide advantages over the current agents.

  14. Expression of NR2B in cerebellar granule cells specifically facilitates effect of motor training on motor learning.

    Science.gov (United States)

    Jiao, Jianwei; Nakajima, Akira; Janssen, William G M; Bindokas, Vytautas P; Xiong, Xiaoli; Morrison, John H; Brorson, James R; Tang, Ya-Ping

    2008-02-27

    It is believed that gene/environment interaction (GEI) plays a pivotal role in the development of motor skills, which are acquired via practicing or motor training. However, the underlying molecular/neuronal mechanisms are still unclear. Here, we reported that the expression of NR2B, a subunit of NMDA receptors, in cerebellar granule cells specifically enhanced the effect of voluntary motor training on motor learning in the mouse. Moreover, this effect was characterized as motor learning-specific and developmental stage-dependent, because neither emotional/spatial memory was affected nor was the enhanced motor learning observed when the motor training was conducted starting at the age of 3 months old in these transgenic mice. These results indicate that changes in the expression of gene(s) that are involved in regulating synaptic plasticity in cerebellar granule cells may constitute a molecular basis for the cerebellum to be involved in the GEI by facilitating motor skill learning.

  15. Expression of NR2B in cerebellar granule cells specifically facilitates effect of motor training on motor learning.

    Directory of Open Access Journals (Sweden)

    Jianwei Jiao

    Full Text Available It is believed that gene/environment interaction (GEI plays a pivotal role in the development of motor skills, which are acquired via practicing or motor training. However, the underlying molecular/neuronal mechanisms are still unclear. Here, we reported that the expression of NR2B, a subunit of NMDA receptors, in cerebellar granule cells specifically enhanced the effect of voluntary motor training on motor learning in the mouse. Moreover, this effect was characterized as motor learning-specific and developmental stage-dependent, because neither emotional/spatial memory was affected nor was the enhanced motor learning observed when the motor training was conducted starting at the age of 3 months old in these transgenic mice. These results indicate that changes in the expression of gene(s that are involved in regulating synaptic plasticity in cerebellar granule cells may constitute a molecular basis for the cerebellum to be involved in the GEI by facilitating motor skill learning.

  16. 基于分子马达生物传感器技术的副溶血性弧菌分子分型方法的初步研究%A preliminary study on molecular typing method for Vibrio parahaemolyticus based on molecular motor biosensor

    Institute of Scientific and Technical Information of China (English)

    张捷; 李兆杰; 王煜; 张惠媛; 陆琳; 王静; 刘岩; 顾德周; 汪琦

    2013-01-01

    [Objective] To establish a simple and rapid molecular typing method tor Vibrio parahaemolyticus carrying and non-carrying virulence genes based on molecular motor.[Methods] Four probes specific to virulence genes tdh and trh,species-specific genes tlh and toxR of V.parahaemolyticus were synthesized,and four molecular motor biosensors were constructed by connecting probes to F0F1-ATPase molecular motors through biotin-streptavidin system,respectively.Ten strains of V.parahaemolyticus were classified by the biosensors,and the results were compared with PCR-Electrophoresis-Gel imaging results.Further more,the detection sensitivities and specificities of the molecular motor biosensors were studied.[Results] There were ten strains carrying tdh and none carrying trh,while all ten strains carry tlh and toxR,which was consisitent with the results of PCR-Electrophoresis-Gel imaging.The detection limits of molecular motor biosensors for tlh,toxR,tdh and trh were estimated to be 1 pg/reaction system,and the detection limits of PCR-Electrophoresis-Gel imaging for tlh,toxR,tdh and trh were estimated to be 10 pg/reaction system.The molecular motor biosensors could recognize tlh,toxR,tdh and trh of V.parahaemolyticus specifically.[Conclusion] A molecular typing method was constructed based on molecular motor biosensors and was used to diagnose the pathogenicity of V.parahaemolyticus rapidly and specifically.The detection limits was 10 times higher than those of PCR-Electrophoresis-Gel imaging.The method is easy,rapid,time-saving and labor-saving,especially suitable for the basic laboratories of CDC and port quarantine departments to perform suiveillance and epidemiological traceability of cholera.%[目的]建立基于分子马达技术的简便快速的分子分型方法,对携带和非携带毒力基因的副溶血性弧菌进行快速分类.[方法]以F0F1-ATPase为核心构建分子马达,以副溶血性弧菌毒力基因tdh、trh和种特异性

  17. Gross motor control

    Science.gov (United States)

    Gross motor control is the ability to make large, general movements (such as waving an arm or lifting a leg). ... Gross motor control is a milestone in the development of an infant. Infants develop gross motor control before they develop ...

  18. Nuclear Function of Subclass I Actin-Depolymerizing Factor Contributes to Susceptibility in Arabidopsis to an Adapted Powdery Mildew Fungus.

    Science.gov (United States)

    Inada, Noriko; Higaki, Takumi; Hasezawa, Seiichiro

    2016-03-01

    Actin-depolymerizing factors (ADFs) are conserved proteins that function in regulating the structure and dynamics of actin microfilaments in eukaryotes. In this study, we present evidence that Arabidopsis (Arabidopsis thaliana) subclass I ADFs, particularly ADF4, functions as a susceptibility factor for an adapted powdery mildew fungus. The null mutant of ADF4 significantly increased resistance against the adapted powdery mildew fungus Golovinomyces orontii. The degree of resistance was further enhanced in transgenic plants in which the expression of all subclass I ADFs (i.e. ADF1-ADF4) was suppressed. Microscopic observations revealed that the enhanced resistance of adf4 and ADF1-4 knockdown plants (ADF1-4Ri) was associated with the accumulation of hydrogen peroxide and cell death specific to G. orontii-infected cells. The increased resistance and accumulation of hydrogen peroxide in ADF1-4Ri were suppressed by the introduction of mutations in the salicylic acid- and jasmonic acid-signaling pathways but not by a mutation in the ethylene-signaling pathway. Quantification by microscopic images detected an increase in the level of actin microfilament bundling in ADF1-4Ri but not in adf4 at early G. orontii infection time points. Interestingly, complementation analysis revealed that nuclear localization of ADF4 was crucial for susceptibility to G. orontii. Based on its G. orontii-infected-cell-specific phenotype, we suggest that subclass I ADFs are susceptibility factors that function in a direct interaction between the host plant and the powdery mildew fungus.

  19. Impact of the structural differences between α- and β-chitosan on their depolymerizing reaction and antibacterial activity.

    Science.gov (United States)

    Jung, Jooyeoun; Zhao, Yanyun

    2013-09-18

    The polymeric structure characteristics of β-chitosan from jumbo squid (Dosidicus gigas) pens and α-chitosan from shrimp shells during depolymerization by cellulase hydrolysis at different degrees of deacetylation (DDA) (60, 75, and 90%) were investigated by using Fourier transform infrared spectroscopy and X-ray diffraction. Antibacterial activity of β-chitosan against Escherichia coli and Listeria innocua was compared with that of α-chitosan at similar Mw and degrees of deacetylation (DDA) by studying inhibition ratio and minimal inhibition concentration (MIC) and was coordinated with the structural characteristics of the two forms of chitosan. β-Chitosan was more reactive to cellulase hydrolysis than α-chitosan due to its relatively lower crystallinity (CI) and loose crystal property, and the 75% DDA chitosan was more susceptible to cellulase than the 90% DDA ones with the 75% DDA of β-chitosan mostly reactive. Both forms of chitosan showed more inhibition against E. coli than against L. innocua, and no difference against L. innocua between the two forms of chitosan was observed. However, the two forms of chitosan exhibited different levels of antibacterial activity against E. coli, in which 75% DDA/31 kDa β-chitosan demonstrated significantly higher inhibition (lower MIC) than that of 75% DDA/31 kDa α-chitosan, whereas 90% DDA/74-76 kDa α-chitosan had a higher inhibition ratio than that of 90% DDA/74-76 kDa of β-chitosan. This result may be explained by the impact of the different structural properties between α- and β-chitosan on chitosan conformations in the solution. This study provided new information about the biological activities of β-chitosan, a bioactive compound with unique functionalities and great potential for food and other applications.

  20. Motor control for a brushless DC motor

    Science.gov (United States)

    Peterson, William J. (Inventor); Faulkner, Dennis T. (Inventor)

    1985-01-01

    This invention relates to a motor control system for a brushless DC motor having an inverter responsively coupled to the motor control system and in power transmitting relationship to the motor. The motor control system includes a motor rotor speed detecting unit that provides a pulsed waveform signal proportional to rotor speed. This pulsed waveform signal is delivered to the inverter to thereby cause an inverter fundamental current waveform output to the motor to be switched at a rate proportional to said rotor speed. In addition, the fundamental current waveform is also pulse width modulated at a rate proportional to the rotor speed. A fundamental current waveform phase advance circuit is controllingly coupled to the inverter. The phase advance circuit is coupled to receive the pulsed waveform signal from the motor rotor speed detecting unit and phase advance the pulsed waveform signal as a predetermined function of motor speed to thereby cause the fundamental current waveform to be advanced and thereby compensate for fundamental current waveform lag due to motor winding reactance which allows the motor to operate at higher speeds than the motor is rated while providing optimal torque and therefore increased efficiency.

  1. High efficiency motors; Motores de alta eficiencia

    Energy Technology Data Exchange (ETDEWEB)

    Uranga Favela, Ivan Jaime [Energia Controlada de Mexico, S. A. de C. V., Mexico, D. F. (Mexico)

    1992-12-31

    This paper is a technical-financial study of the high efficiency and super-premium motors. As it is widely known, more than 60% of the electrical energy generated in the country is used for the operation of motors, in industry as well as in commerce. Therefore the importance that the motors have in the efficient energy use. [Espanol] El presente trabajo es un estudio tecnico-financiero de los motores de alta eficiencia y los motores super premium. Como es ampliamente conocido, mas del 60% de la energia electrica generada en el pais, es utilizada para accionar motores, dentro de la industria y el comercio. De alli la importancia que los motores tienen en el uso eficiente de la energia.

  2. Plant villin, lily P-135-ABP, possesses G-actin binding activity and accelerates the polymerization and depolymerization of actin in a Ca2+-sensitive manner.

    Science.gov (United States)

    Yokota, Etsuo; Tominaga, Motoki; Mabuchi, Issei; Tsuji, Yasunori; Staiger, Christopher J; Oiwa, Kazuhiro; Shimmen, Teruo

    2005-10-01

    From germinating pollen of lily, two types of villins, P-115-ABP and P-135-ABP, have been identified biochemically. Ca(2+)-CaM-dependent actin-filament binding and bundling activities have been demonstrated for both villins previously. Here, we examined the effects of lily villins on the polymerization and depolymerization of actin. P-115-ABP and P-135-ABP present in a crude protein extract prepared from germinating pollen bound to a DNase I affinity column in a Ca(2+)-dependent manner. Purified P-135-ABP reduced the lag period that precedes actin filament polymerization from monomers in the presence of either Ca(2+) or Ca(2+)-CaM. These results indicated that P-135-ABP can form a complex with G-actin in the presence of Ca(2+) and this complex acts as a nucleus for polymerization of actin filaments. However, the nucleation activity of P-135-ABP is probably not relevant in vivo because the assembly of G-actin saturated with profilin, a situation that mimics conditions found in pollen, was not accelerated in the presence of P-135-ABP. P-135-ABP also enhanced the depolymerization of actin filaments during dilution-mediated disassembly. Growth from filament barbed ends in the presence of Ca(2+)-CaM was also prevented, consistent with filament capping activity. These results suggested that lily villin is involved not only in the arrangement of actin filaments into bundles in the basal and shank region of the pollen tube, but also in regulating and modulating actin dynamics through its capping and depolymerization (or fragmentation) activities in the apical region of the pollen tube, where there is a relatively high concentration of Ca(2+).

  3. Effect of stereogenic centers on the self-sorting, depolymerization, and atropisomerization kinetics of porphyrin-based aggregates.

    Science.gov (United States)

    Helmich, Floris; Smulders, Maarten M J; Lee, Cameron C; Schenning, Albertus P H J; Meijer, E W

    2011-08-10

    We present our results on the mixing of different porphyrin molecules in supramolecular assemblies. Herein, chiral amplification experiments reveal the subtle role of the structural (mis)match between these monomers. We show that according to the "sergeant-and-soldiers" principle, a chiral porphyrin "sergeant" efficiently mixes with achiral "soldiers" in the same helical aggregate and strongly biases its handedness. However, when we mix two porphyrin enantiomers in a majority-rules experiment, no chiral amplification is observed at all, which is due to their narcissistic self-sorting into conglomerate-like aggregates. The mixing between two enantiomers in the same stack only occurs in a diluted-majority-rules experiment, in which enantiomeric mixtures of sergeants are diluted with achiral soldiers. The different outcomes of these chiral amplification phenomena are verified by modeling studies that reveal high mismatch penalties, which are ascribed to the high stereocenter loading of 12 methyl groups onto the monomers. Mixed-metal chiral amplification experiments between copper- and zinc-porphyrins show the same distinction in their mixing behavior, which is further supported by fluorescence measurements. The selective removal of chiral Zn-porphyrins from these mixed-metal systems is performed with the Lewis base quinuclidine that depolymerizes the Zn-porphyrins upon axial ligation. This extraction process proceeds at different time scales, depending on the mixed state: slow extraction kinetics for the mixed sergeant-and-soldiers and diluted-majority-rules systems and an instant extraction for the phase-separated majority-rules system. By simultaneously monitoring the supramolecular chirality during extraction, a chiral memory effect is observed for both mixed systems that show slow extraction kinetics. For the sergeant-and-soldiers system, the remaining supramolecular backbone contains achiral monomers only, which give rise to a long lasting chiral memory with slow

  4. Noise-induced cochlear F-actin depolymerization is mediated via ROCK2/p-ERM signaling.

    Science.gov (United States)

    Han, Yu; Wang, Xianren; Chen, Jun; Sha, Su-Hua

    2015-06-01

    Our previous work has suggested that traumatic noise activates Rho-GTPase pathways in cochlear outer hair cells (OHCs), resulting in cell death and noise-induced hearing loss (NIHL). In this study, we investigated Rho effectors, Rho-associated kinases (ROCKs), and the targets of ROCKs, the ezrin-radixin-moesin (ERM) proteins, in the regulation of the cochlear actin cytoskeleton using adult CBA/J mice under conditions of noise-induced temporary threshold shift (TTS) and permanent threshold shift (PTS) hearing loss, which result in changes to the F/G-actin ratio. The levels of cochlear ROCK2 and p-ERM decreased 1 h after either TTS- or PTS-noise exposure. In contrast, ROCK2 and p-ERM in OHCs decreased only after PTS-, not after TTS-noise exposure. Treatment with lysophosphatidic acid, an activator of the Rho pathway, resulted in significant reversal of the F/G-actin ratio changes caused by noise exposure and attenuated OHC death and NIHL. Conversely, the down-regulation of ROCK2 by pretreatment with ROCK2 siRNA reduced the expression of ROCK2 and p-ERM in OHCs, exacerbated TTS to PTS, and worsened OHC loss. Additionally, pretreatment with siRNA against radixin, an ERM protein, aggravated TTS to PTS. Our results indicate that a ROCK2-mediated ERM-phosphorylation signaling cascade modulates noise-induced hair cell loss and NIHL by targeting the cytoskeleton. We propose the following cascade following noise trauma leading to alteration of the F-actin arrangement in the outer hair cell cytoskeleton: Noise exposure reduces the levels of GTP-RhoA and subsequently diminishes levels of RhoA effector ROCK2 (Rho-associated kinase 2). Phosphorylation of ezrin-radixin-moesin (ERM) by ROCK2 normally allows ERM to cross-link actin filaments with the plasma membrane. Noise-decreased levels of ROCK results in reduction of phosphorylation of ERM that leads to depolymerization of actin filaments. Lysophosphatidic acid (LPA), an agonist of RhoA, binds to the G-protein-coupled receptor

  5. Motor Priming in Neurorehabilitation

    OpenAIRE

    Stoykov, Mary Ellen; Madhavan, Sangeetha

    2015-01-01

    Priming is a type of implicit learning wherein a stimulus prompts a change in behavior. Priming has been long studied in the field of psychology. More recently, rehabilitation researchers have studied motor priming as a possible way to facilitate motor learning. For example, priming of the motor cortex is associated with changes in neuroplasticity that are associated with improvements in motor performance. Of the numerous motor priming paradigms under investigation, only a few ...

  6. Motor Priming in Neurorehabilitation

    OpenAIRE

    Stoykov, Mary Ellen; Madhavan, Sangeetha

    2015-01-01

    Priming is a type of implicit learning wherein a stimulus prompts a change in behavior. Priming has been long studied in the field of psychology. More recently, rehabilitation researchers have studied motor priming as a possible way to facilitate motor learning. For example, priming of the motor cortex is associated with changes in neuroplasticity that are associated with improvements in motor performance. Of the numerous motor priming paradigms under investigation, only a few ...

  7. Motor neuropathies and lower motor neuron syndromes.

    Science.gov (United States)

    Verschueren, A

    2017-05-01

    Motor or motor-predominant neuropathies may arise from disease processes affecting the motor axon and/or its surrounding myelin. Lower motor neuron syndrome (LMNS) arises from a disease process affecting the spinal motor neuron itself. The term LMNS is more generally used, rather than motor neuronopathy, although both entities are clinically similar. Common features are muscle weakness (distal or proximal) with atrophy and hyporeflexia, but no sensory involvement. They can be acquired or hereditary. Immune-mediated neuropathies (multifocal motor neuropathy, motor-predominant chronic inflammatory demyelinating polyneuropathy) are important to identify, as effective treatments are available. Other acquired neuropathies, such as infectious, paraneoplastic and radiation-induced neuropathies are also well known. Focal LMNS is an amyotrophic lateral sclerosis (ALS)-mimicking syndrome especially affecting young adults. The main hereditary LMNSs in adulthood are Kennedy's disease, late-onset spinal muscular atrophy and distal hereditary motor neuropathies. Motor neuropathies and LMNS are all clinical entities that should be better known, despite being rare diseases. They can sometimes be difficult to differentially diagnose from other diseases, particularly from the more frequent ALS in its pure LMN form. Nevertheless, correct identification of these syndromes is important because their treatment and prognoses are definitely different. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  8. Molecular hydrogen (H2 emissions and their isotopic signatures (H/D from a motor vehicle: implications on atmospheric H2

    Directory of Open Access Journals (Sweden)

    T. Röckmann

    2010-06-01

    Full Text Available Molecular hydrogen (H2, its isotopic signature (deuterium/hydrogen, δD, carbon monoxide (CO, and other compounds were studied in the exhaust of a passenger car engine fuelled with gasoline or methane and run under variable air-fuel ratios and operating modes. H2 and CO concentrations were largely reduced downstream of the three-way catalytic converter (TWC compared to levels upstream, and showed a strong dependence on the air-fuel ratio (expressed as lambda, λ. The isotopic composition of H2 ranged from δD = −140‰ to δD = −195‰ upstream of the TWC but these values decreased to −270‰ to −370‰ after passing through the TWC. Post-TWC δD values for the fuel-rich range showed a strong dependence on TWC temperature with more negative δD for lower temperatures. These effects are attributed to a rapid temperature-dependent H-D isotope equilibration between H2 and water (H2O. In addition, post TWC δD in H2 showed a strong dependence on the fraction of removed H2, suggesting isotopic enrichment during catalytic removal of H2 with enrichment factors (ε ranging from −39.8‰ to −15.5‰ depending on the operating mode. Our results imply that there may be considerable variability in real-world δD emissions from vehicle exhaust, which may mainly depend on TWC technology and exhaust temperature regime. This variability is suggestive of a δD from traffic that varies over time, by season, and by geographical location. An earlier-derived integrated pure (end-member δD from anthropogenic activities of −270‰ (Rahn et al., 2002 can be explained as a mixture of mainly vehicle emissions from cold starts and fully functional TWCs, but enhanced δD values by >50‰ are likely for regions where TWC technology is not fully implemented. Our results also suggest that a full hydrogen isotope analysis on fuel and exhaust gas may greatly aid at understanding process-level reactions in the exhaust gas, in particular in the TWC.

  9. Molecular hydrogen (H2 emissions and their isotopic signatures (H/D from a motor vehicle: implications on atmospheric H2

    Directory of Open Access Journals (Sweden)

    T. Röckmann

    2010-02-01

    Full Text Available Molecular hydrogen (H2, its isotopic signature (deuterium/hydrogen, δD, carbon monoxide (CO and other compounds were studied in the exhaust of a passenger car engine fuelled with gasoline or methane and run under variable air-fuel ratios and operating modes. H2 and CO concentrations were largely reduced downstream of the three-way catalytic converter (TWC compared to levels upstream, and showed a strong dependence on the air-fuel ratio (expressed as lambda, λ. The isotopic composition of H2 ranged from δD=–140‰ to δD=–195‰ upstream of the TWC but these values decreased to –270‰ to –370‰ after passing through the TWC. Post-TWC δD values for the fuel-rich range showed a strong dependence on TWC temperature with more negative δD for lower temperatures. These effects are attributed to a rapid temperature-dependent H-D isotope equilibration between H2 and water (H2O. In addition, post TWC δD in H2 showed a strong dependence on the fraction of removed H2, suggesting isotopic enrichment during catalytic removal of H2 with enrichment factors (ε ranging from –39.8‰ to –15.5‰ depending on the operating mode. Our results imply that there may be considerable variability in real-world δD emissions from vehicle exhaust, which may mainly depend on TWC technology and exhaust temperature regime. This variability is suggestive of a δD from traffic that varies over time, by season, and by geographical location. An earlier-derived integrated pure (end-member δD from anthropogenic activities of –270‰ (Rahn et al., 2002 can be explained as a mixture of mainly vehicle emissions from cold starts and fully functional TWCs, but enhanced δD values by >50‰ are likely for regions where TWC technology is not fully implemented. Our results also suggest that a full hydrogen isotope analysis on fuel and exhaust gas may greatly aid at understanding process-level reactions in the exhaust gas, in particular in the TWC.

  10. Crosstalk between non-processive myosin motors mediated by the actin filament elasticity

    OpenAIRE

    2011-01-01

    Many biological processes involve the action of molecular motors that interact with the cell cytoskeleton. Some processes, such as the transport of cargoes is achieved mainly by the action of individual motors. Other, such as cell motility and division, require the cooperative work of many motors. Collective motor dynamics can be quite complex and unexpected. One beautiful example is the bidirectional ("back and forth") motion of filaments which is induced when the motors within a group exert...

  11. Depolymerization of coal by O2 oxidation followed by acid hydrolysis; Sanso sanka-kasui bunkai ni yoru sekitan no teionkai jugo

    Energy Technology Data Exchange (ETDEWEB)

    Aizawa, S.; Hayashi, J.; Kumagai, H.; Chiba, T. [Hokkaido University, Sapporo (Japan). Center for Advanced Research of Energy Technology; Morooka, S. [Kyushu University, Fukuoka (Japan). Faculty of Engineering

    1996-10-28

    With an objective to elucidate characteristics of oxygen addition to coal, and characteristics of solvent extraction by means of depolymerization, experiments were performed on oxygen oxidation and acid hydrolysis of brown coals. Coals used for the experiments are Morwell (MW), Yallourn (YL) , South Banko (SB) and Wyoming (WY) coals. Test samples were suspended in weak alkaline aqueous solution, and then oxygen was blown into them with pressure kept at atmospheric pressure. After a lapse of a predetermined time, the samples were cooled, and made as acidic as pH 1.3 in hydrochloric acid, followed by acid hydrolysis. Oxygen consumption increased with the reaction time, and with the MW coal, one mol oxygen reacted to 11 mols of coal. Spectral analysis on the YL and WY coal experiments revealed that aliphatic carbon combined with aromatic carbon or ether group has turned to peroxide, whose C-C or C-O bond was broken down as a result of acid hydrolysis of the peroxide, producing oxygen containing compounds. As a result of the depolymerization, the rate of extraction by using DMF, DMSO and methanol/THF mixed solvent increased to 90% or higher. Proportion of bond and cutting-off affects largely collapse of the cross-link structure. The carbon conversion to volatiles was at most 4%. 1 ref., 10 figs.

  12. Electric motor handbook

    CERN Document Server

    Chalmers, B J

    2013-01-01

    Electric Motor Handbook aims to give practical knowledge in a wide range of capacities such as plant design, equipment specification, commissioning, operation and maintenance. The book covers topics such as the modeling of steady-state motor performance; polyphase induction, synchronous, and a.c. commutator motors; ambient conditions, enclosures, cooling and loss dissipation; and electrical supply systems and motor drives. Also covered are topics such as variable-speed drives and motor control; materials and motor components; insulation types, systems, and techniques; and the installation, sit

  13. Molecular Stirrers in Action

    NARCIS (Netherlands)

    Chen, Jiawen; Kistemaker, Jos C. M.; Robertus, Jort; Feringa, Ben L.

    2014-01-01

    A series of first-generation light-driven molecular motors with rigid substituents of varying length was synthesized to act as "molecular stirrers". Their rotary motion was studied by H-1 NMR and UV-vis absorption spectroscopy in a variety of solvents with different polarity and viscosity. Quantitat

  14. Introduction to ultrasonic motors

    Energy Technology Data Exchange (ETDEWEB)

    Sashida, Toshiiku; Kenjo, Takashi.

    1993-01-01

    The ultrasonic motor, invented in 1980, utilizes the piezoelectric effect in the ultrasonic frequency range to provide the motive force. (In conventional electric motors the motive force is electromagnetic.) The result is a motor with unusually good low-speed high-torque and power-to-weight characteristics. It has already found applications in camera autofocus mechanisms, medical equipment subject to high magnetic fields, and motorized car accessories. Its applications will increase as designers become more familiar with its unique characteristics. This book is the result of a collaboration between the inventor and an expert in conventional electric motors: the result is an introduction to the general theory presented in a way that links it to conventional motor theory. It will be invaluable both to motor designers and to those who design with and use electric motors as an introduction to this important new invention.

  15. Chronic motor tic disorder

    Science.gov (United States)

    Chronic vocal tic disorder; Tic - chronic motor tic disorder ... Chronic motor tic disorder is more common than Tourette syndrome . Chronic tics may be forms of Tourette syndrome. Tics usually start ...

  16. Can molecular cell biology explain chromosome motions?

    Directory of Open Access Journals (Sweden)

    Gagliardi L

    2011-05-01

    Full Text Available Abstract Background Mitotic chromosome motions have recently been correlated with electrostatic forces, but a lingering "molecular cell biology" paradigm persists, proposing binding and release proteins or molecular geometries for force generation. Results Pole-facing kinetochore plates manifest positive charges and interact with negatively charged microtubule ends providing the motive force for poleward chromosome motions by classical electrostatics. This conceptual scheme explains dynamic tracking/coupling of kinetochores to microtubules and the simultaneous depolymerization of kinetochore microtubules as poleward force is generated. Conclusion We question here why cells would prefer complex molecular mechanisms to move chromosomes when direct electrostatic interactions between known bound charge distributions can accomplish the same task much more simply.

  17. Molecular aggregation of humic substances

    Science.gov (United States)

    Wershaw, R. L.

    1999-01-01

    Humic substances (HS) form molecular aggregates in solution and on mineral surfaces. Elucidation of the mechanism of formation of these aggregates is important for an understanding of the interactions of HS in soils arid natural waters. The HS are formed mainly by enzymatic depolymerization and oxidation of plant biopolymers. These reactions transform the aromatic and lipid plant components into amphiphilic molecules, that is, molecules that consist of separate hydrophobic (nonpolar) and hydrophilic (polar) parts. The nonpolar parts of the molecules are composed of relatively unaltered segments of plant polymers and the polar parts of carboxylic acid groups. These amphiphiles form membrane-like aggregates on mineral surfaces and micelle-like aggregates in solution. The exterior surfaces of these aggregates are hydrophilic, and the interiors constitute separate hydrophobic liquid-like phases.

  18. Piezoelectric Motors, an Overview

    OpenAIRE

    Karl Spanner; Burhanettin Koc

    2016-01-01

    Piezoelectric motors are used in many industrial and commercial applications. Various piezoelectric motors are available in the market. All of the piezoelectric motors use the inverse piezoelectric effect, where microscopically small oscillatory motions are converted into continuous or stepping rotary or linear motions. Methods of obtaining long moving distance have various drive and functional principles that make these motors categorized into three groups: resonance-drive (piezoelectric ult...

  19. Sliding of microtubules by a team of dynein motors: Understanding the effect of spatial distribution of motor tails and mutual exclusion of motor heads on microtubules

    Science.gov (United States)

    Singh, Hanumant Pratap; Takshak, Anjneya; Mall, Utkarsh; Kunwar, Ambarish

    2016-06-01

    Molecular motors are natural nanomachines that use the free energy released from ATP hydrolysis to generate mechanical forces. Cytoplasmic dynein motors often work collectively as a team to drive important processes such as axonal growth, proplatelet formation and mitosis, as forces generated by single motors are insufficient. A large team of dynein motors is used to slide cytoskeletal microtubules with respect to one another during the process of proplatelet formation and axonal growth. These motors attach to a cargo microtubule via their tail domains, undergo the process of detachment and reattachment of their head domains on another track microtubule, while sliding the cargo microtubule along the track. Traditional continuum/mean-field approaches used in the past are not ideal for studying the sliding mechanism of microtubules, as they ignore spatial and temporal fluctuations due to different possible distributions of motor tails on cargo filament, as well as binding/unbinding of motors from their track. Therefore, these models cannot be used to address important questions such as how the distribution of motor tails on microtubules, or how the mutual exclusion of motor heads on microtubule tracks affects the sliding velocity of cargo microtubule. To answer these, here we use a computational stochastic model where we model each dynein motor explicitly. In our model, we use both random as well as uniform distributions of dynein motors on cargo microtubule, as well as mutual exclusion of motors on microtubule tracks. We find that sliding velocities are least affected by the distribution of motor tails on microtubules, whereas they are greatly affected by mutual exclusion of motor heads on microtubule tracks. We also find that sliding velocity depends on the length of cargo microtubule if mutual exclusion among motor heads is considered.

  20. Electric Motor Thermal Management

    Energy Technology Data Exchange (ETDEWEB)

    Bennion, Kevin S [National Renewable Energy Laboratory (NREL), Golden, CO (United States)

    2017-09-01

    Thermal management enables more efficient and cost-effective motors. This Annual Merit Review presentation describes the technical accomplishments and progress in electric motor thermal management R&D over the last year. This project supports a broad industry demand for data, analysis methods, and experimental techniques to improve and better understand motor thermal management.

  1. Fine tuning of molecular rotor function in photochemical molecular switches

    NARCIS (Netherlands)

    ter Wiel, Matthijs K. J.; Feringa, Ben L.

    2009-01-01

    Molecular switches are used as scaffolds for the construction of controlled molecular rotors. The internal position of the switching entity in the molecule controls the dynamic behaviour of the rotor moiety in the molecule. Six new molecular motors with o-xylyl rotor moieties were prepared on the ba

  2. A Reconfigurable Stepping Motor

    Science.gov (United States)

    Rogers, Charles; Selvaggi, Richard

    2009-04-01

    Multiphase brushless actuators, commonly known as the stepper motors, are ubiquitous for many precision control applications. Developments in the microelectronics have lead to their use as efficient drive motors for modern electric vehicles. Understanding the physics and the control logic for interfacing these transducers continues to be important for scientists and engineers. An overview of the stepping motor principles and interfacing requirements is presented and a simple working model used to teach the concepts of stepper motors is described and demonstrated. This model was used to design a much larger stepper motor required to precisely rotate a massive optical system in the undergraduate advanced physics laboratory.

  3. Induction motor control design

    CERN Document Server

    Marino, Riccardo; Verrelli, Cristiano M

    2010-01-01

    ""Nonlinear and Adaptive Control Design for Induction Motors"" is a unified exposition of the most important steps and concerns in the design of estimation and control algorithms for induction motors. A single notation and modern nonlinear control terminology is used to make the book accessible to readers who are not experts in electric motors at the same time as giving a more theoretical control viewpoint to those who are. In order to increase readability, the book concentrates on the induction motor, eschewing the much more complex and less-well-understood control of asynchronous motors. The

  4. Solid propellant motor

    Science.gov (United States)

    Shafer, J. I.; Marsh, H. E., Jr. (Inventor)

    1978-01-01

    A case bonded end burning solid propellant rocket motor is described. A propellant with sufficiently low modulus to avoid chamber buckling on cooling from cure and sufficiently high elongation to sustain the stresses induced without cracking is used. The propellant is zone cured within the motor case at high pressures equal to or approaching the pressure at which the motor will operate during combustion. A solid propellant motor with a burning time long enough that its spacecraft would be limited to a maximum acceleration of less than 1 g is provided by one version of the case bonded end burning solid propellant motor of the invention.

  5. Motor/generator

    Science.gov (United States)

    Hickam, Christopher Dale

    2008-05-13

    A motor/generator is provided for connecting between a transmission input shaft and an output shaft of a prime mover. The motor/generator may include a motor/generator housing, a stator mounted to the motor/generator housing, a rotor mounted at least partially within the motor/generator housing and rotatable about a rotor rotation axis, and a transmission-shaft coupler drivingly coupled to the rotor. The transmission-shaft coupler may include a clamp, which may include a base attached to the rotor and a plurality of adjustable jaws.

  6. Motor degradation prediction methods

    Energy Technology Data Exchange (ETDEWEB)

    Arnold, J.R.; Kelly, J.F.; Delzingaro, M.J.

    1996-12-01

    Motor Operated Valve (MOV) squirrel cage AC motor rotors are susceptible to degradation under certain conditions. Premature failure can result due to high humidity/temperature environments, high running load conditions, extended periods at locked rotor conditions (i.e. > 15 seconds) or exceeding the motor`s duty cycle by frequent starts or multiple valve stroking. Exposure to high heat and moisture due to packing leaks, pressure seal ring leakage or other causes can significantly accelerate the degradation. ComEd and Liberty Technologies have worked together to provide and validate a non-intrusive method using motor power diagnostics to evaluate MOV rotor condition and predict failure. These techniques have provided a quick, low radiation dose method to evaluate inaccessible motors, identify degradation and allow scheduled replacement of motors prior to catastrophic failures.

  7. Neuroplasticity & Motor Learning

    DEFF Research Database (Denmark)

    Jensen, Jesper Lundbye

    Practice of a new motor task is usually associated with an improvement in performance. Indeed, if we stop practicing and return the next day to the same task, we find that our performance has been maintained and may even be better than it was at the start of the first day. This improvement...... is a measure of our ability to form and store a motor memory of the task. However, the initial memory of the task is labile and may be subject to interference. During and following motor learning plastic changes occur within the central nervous system. On one hand these changes are driven by motor practice......, on the other hand the changes underlie the formation of motor memory and the retention of improved motor performance. During motor learning changes may occur at many different levels within the central nervous system dependent on the type of task and training. Here, we demonstrate different studies from our...

  8. Piezoelectric Motors, an Overview

    Directory of Open Access Journals (Sweden)

    Karl Spanner

    2016-02-01

    Full Text Available Piezoelectric motors are used in many industrial and commercial applications. Various piezoelectric motors are available in the market. All of the piezoelectric motors use the inverse piezoelectric effect, where microscopically small oscillatory motions are converted into continuous or stepping rotary or linear motions. Methods of obtaining long moving distance have various drive and functional principles that make these motors categorized into three groups: resonance-drive (piezoelectric ultrasonic motors, inertia-drive, and piezo-walk-drive. In this review, a comprehensive summary of piezoelectric motors, with their classification from initial idea to recent progress, is presented. This review also includes some of the industrial and commercial applications of piezoelectric motors that are presently available in the market as actuators.

  9. Depolymerization of post-consumer PET with multifunctional alcohol through melt processing; Despolimerizacao de PET pos-consumo com alcool multifuncional atraves de processamento por fusao

    Energy Technology Data Exchange (ETDEWEB)

    Lessa, Tathiane C.R.F.; Mendes, Luis C.; Dias, Marcos L., E-mail: tathianecr@ima.ufrj.b [Universidade Federal do Rio de Janeiro (IMA/UFRJ), RJ (Brazil). Inst. de Macromoleculas Professora Eloisa Mano. Centro de Tecnologia

    2009-07-01

    The purpose of this study was to prepare oligomers from post-consumer PET with multifunctional alcohol, through melt processing, aiming to develop a new material, able to play a role as filler or property modifier. Maintaining constants the process conditions, content and kind of catalyst, the influence of the solvolysis agent on the PET depolymerization was investigated. The products were evaluated by wide-angle X-ray diffraction (WAXD) and thermogravimetry (TG/DTG). The changes in the WAXD curves and the shift of the maximum degradation temperature suggested that the ester linkages were broken being the ethylene glycol moieties replaced with hydroxyl-terminal groups of the multifunctional alcohol, as result of a transesterification reaction. The chemical structure of the new ester was named 'star-branching polymer'. (author)

  10. Underediting of GluR2 mRNA, a neuronal death inducing molecular change in sporadic ALS, does not occur in motor neurons in ALS1 or SBMA.

    Science.gov (United States)

    Kawahara, Yukio; Sun, Hui; Ito, Kyoko; Hideyama, Takuto; Aoki, Masashi; Sobue, Gen; Tsuji, Shoji; Kwak, Shin

    2006-01-01

    Deficient RNA editing of the AMPA receptor subunit GluR2 at the Q/R site is a primary cause of neuronal death and recently has been reported to be a tightly linked etiological cause of motor neuron death in sporadic amyotrophic lateral sclerosis (ALS). We quantified the RNA editing efficiency of the GluR2 Q/R site in single motor neurons of rats transgenic for mutant human Cu/Zn-superoxide dismutase (SOD1) as well as patients with spinal and bulbar muscular atrophy (SBMA), and found that GluR2 mRNA was completely edited in all the motor neurons examined. It seems likely that the death cascade is different among the dying motor neurons in sporadic ALS, familial ALS with mutant SOD1 and SBMA.

  11. Dynamics and Thermodynamics of Molecular Machines

    DEFF Research Database (Denmark)

    Golubeva, Natalia

    2014-01-01

    Molecular machines, or molecular motors, are small biophysical devices that perform a variety of essential metabolic processes such as DNA replication, protein synthesis and intracellular transport. Typically, these machines operate by converting chemical energy into motion and mechanical work. Due...... to their microscopic size, molecular motors are governed by principles fundamentally different from those describing the operation of man-made motors such as car engines. In this dissertation the dynamic and thermodynamic properties of molecular machines are studied using the tools of nonequilibrium statistical...... of the important trade-off between power output and efficiency. Steric motor-motor interactions are shown to play an important thermodynamic role by enhancing the EMP as compared to the noninteracting case. Remarkably, the enhancement occurs at biologically relevant parameters. Finally, a generic model of motor...

  12. Bidirectionality From Cargo Thermal Fluctuations in Motor-Mediated Transport

    CERN Document Server

    Miles, Christopher E

    2016-01-01

    Molecular motor proteins serve as an essential component of intracellular transport by generating forces to haul cargoes along cytoskeletal filaments. In some circumstances, two species of motors that are directed oppositely (e.g. kinesin, dynein) can be attached to the same cargo. The resulting net motion is known to be bidirectional, but the mechanism of switching remains unclear. In this work, we propose a mean-field mathematical model of the mechanical interactions of two populations of molecular motors with diffusion of the cargo (thermal fluctuations) as the fundamental noise source. By studying a simplified model, the delayed response of motors to rapid fluctuations in the cargo is quantified, allowing for the reduction of the full model to two "characteristic positions" of each of the motor populations. The system is then found to be "metastable", switching between two distinct directional transport states, or bidirectional motion. The time to switch between these states is then investigated using WKB...

  13. Modularity for Motor Control and Motor Learning.

    Science.gov (United States)

    d'Avella, Andrea

    2016-01-01

    How the central nervous system (CNS) overcomes the complexity of multi-joint and multi-muscle control and how it acquires or adapts motor skills are fundamental and open questions in neuroscience. A modular architecture may simplify control by embedding features of both the dynamic behavior of the musculoskeletal system and of the task into a small number of modules and by directly mapping task goals into module combination parameters. Several studies of the electromyographic (EMG) activity recorded from many muscles during the performance of different tasks have shown that motor commands are generated by the combination of a small number of muscle synergies, coordinated recruitment of groups of muscles with specific amplitude balances or activation waveforms, thus supporting a modular organization of motor control. Modularity may also help understanding motor learning. In a modular architecture, acquisition of a new motor skill or adaptation of an existing skill after a perturbation may occur at the level of modules or at the level of module combinations. As learning or adapting an existing skill through recombination of modules is likely faster than learning or adapting a skill by acquiring new modules, compatibility with the modules predicts learning difficulty. A recent study in which human subjects used myoelectric control to move a mass in a virtual environment has tested this prediction. By altering the mapping between recorded muscle activity and simulated force applied on the mass, as in a complex surgical rearrangement of the tendons, it has been possible to show that it is easier to adapt to a perturbation that is compatible with the muscle synergies used to generate hand force than to a similar but incompatible perturbation. This result provides direct support for a modular organization of motor control and motor learning.

  14. ELECTRIC MOTOR CARS.

    Science.gov (United States)

    PASSENGER VEHICLES , ELECTRIC MOTORS), FEASIBILITY STUDIES, BATTERY COMPONENTS, ELECTRIC BATTERIES, FUEL CELLS, ENERGY CONVERSION, NUCLEAR ENERGY, THERMIONIC CONVERTERS , THERMOELECTRICITY, POWER EQUIPMENT, COSTS

  15. Roles of the orexin system in central motor control.

    Science.gov (United States)

    Hu, Bo; Yang, Nian; Qiao, Qi-Cheng; Hu, Zhi-An; Zhang, Jun

    2015-02-01

    The neuropeptides orexin-A and orexin-B are produced by one group of neurons located in the lateral hypothalamic/perifornical area. However, the orexins are widely released in entire brain including various central motor control structures. Especially, the loss of orexins has been demonstrated to associate with several motor deficits. Here, we first summarize the present knowledge that describes the anatomical and morphological connections between the orexin system and various central motor control structures. In the next section, the direct influence of orexins on related central motor control structures is reviewed at molecular, cellular, circuitry, and motor activity levels. After the summarization, the characteristic and functional relevance of the orexin system's direct influence on central motor control function are demonstrated and discussed. We also propose a hypothesis as to how the orexin system orchestrates central motor control in a homeostatic regulation manner. Besides, the importance of the orexin system's phasic modulation on related central motor control structures is highlighted in this regulation manner. Finally, a scheme combining the homeostatic regulation of orexin system on central motor control and its effects on other brain functions is presented to discuss the role of orexin system beyond the pure motor activity level, but at the complex behavioral level.

  16. Modeling Induction Motor Imbalances

    DEFF Research Database (Denmark)

    Armah, Kabenla; Jouffroy, Jerome; Duggen, Lars

    2016-01-01

    This paper gives a study into the development of a generalized model for a three-phase induction motor that offers flexibility of simulating balanced and unbalanced parameter scenarios. By analyzing the interaction of forces within the motor, we achieve our main objective of deriving the system...

  17. To What Extent Can Motor Imagery Replace Motor Execution While Learning a Fine Motor Skill?

    NARCIS (Netherlands)

    Sobierajewicz, Jagna; Szarkiewicz, Sylwia; Prekoracka-Krawczyk, Anna; Jaskowski, Wojciech; van der Lubbe, Robert Henricus Johannes

    2016-01-01

    Motor imagery is generally thought to share common mechanisms with motor execution. In the present study, we examined to what extent learning a fine motor skill by motor imagery may substitute physical practice. Learning effects were assessed by manipulating the proportion of motor execution and

  18. Induction motor control

    Science.gov (United States)

    Hansen, Irving G.

    Electromechanical actuators developed to date have commonly ultilized permanent magnet (PM) synchronous motors. More recently switched reluctance (SR) motors have been advocated due to their robust characteristics. Implications of work which utilized induction motors and advanced control techniques are discussed. When induction motors are operated from an energy source capable of controlling voltages and frequencies independently, drive characteristics are obtained which are superior to either PM or SR motors. By synthesizing the machine frequency from a high-frequency carrier (nominally 20 kHz), high efficiencies, low distortion, and rapid torque response are available. At this time multiple horsepower machine drives were demonstrated, and work is on-going to develop a 20 hp average, 40 hp peak class of aerospace actuators. This effort is based upon high-frequency power distribution and management techniques developed by NASA for Space Station Freedom.

  19. Induction motor control

    Science.gov (United States)

    Hansen, Irving G.

    1990-01-01

    Electromechanical actuators developed to date have commonly ultilized permanent magnet (PM) synchronous motors. More recently switched reluctance (SR) motors have been advocated due to their robust characteristics. Implications of work which utilized induction motors and advanced control techniques are discussed. When induction motors are operated from an energy source capable of controlling voltages and frequencies independently, drive characteristics are obtained which are superior to either PM or SR motors. By synthesizing the machine frequency from a high-frequency carrier (nominally 20 kHz), high efficiencies, low distortion, and rapid torque response are available. At this time multiple horsepower machine drives were demonstrated, and work is on-going to develop a 20 hp average, 40 hp peak class of aerospace actuators. This effort is based upon high-frequency power distribution and management techniques developed by NASA for Space Station Freedom.

  20. MISR Motor Data V003

    Data.gov (United States)

    National Aeronautics and Space Administration — This file contains the output for the Level 1A Motor data (Suggested Usage: MISR SCF processing needs the MISR motor data samples for the analysis of motor anomalies...