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The inside of a eukaryotic cell is a highly organized microscale factory that shuttles components that are created or obtained in one place for use or further modification in another. Diffusion cannot accomplish the feat of translocating an object in the cytoplasm to a particular location that is a micron or more away in a timely fashion, so cells rely instead on processive motor proteins. Microtubule motor proteins are enzymes that harness the chemical energy from ATP hydrolysis to produce force and carry vesicles, membrane-bound organelles, and other cargos along paths in the cell's microtubule filament network to their destinations in the cytoplasm. These proteins recognize the polarity of the microtubule, and different classes of motors walk in different directions with respect to this polarity, giving the cell control over the direction in which a cargo is carried. It has been observed experimentally that many cargos are carried by more than one motor simultaneously, and that these multiple-motor systems can consist both of motors of the same type and of varying numbers of motors of different types. Multiple-motor systems present the possibilities of both enhanced transport performance and of tunable behavior, where the number, type, and arrangement of motors on a group of cargos can be modulated by the cell like an analog-style control to induce those cargos to arrive at a particular distribution of locations in the cytoplasm. In order to resolve the mechanisms by which these things might occur, the combination of experimental and theoretical studies in this thesis focus on the relationship between the basic biophysical properties of the constituent motors in small multiple-motor systems and the degree and nature of the cooperation observed, from the standpoint of several relevant metrics. The results highlight the importance of both the mechanochemistry of the motors and the geometry of the system itself, and offer substantial new insights into why different classes of motors cooperate to different extents, with broad implications.

Thesis (Ph. D.)--University of Washington, 2003. / Vita. Includes bibliographical references (leaves 98-102).

Molecular motors are responsible for all long range transport and organization of organelles within cells. However, little is known about the interaction of multiple similar and dissimilar motors. In this thesis I describe experiments to probe the coordination of the motors kinesin and dynein which move towards the opposite ends of microtubules. Cargos they haul show bidirectional movement at short scales yet there is net transport in one direction or the other. Two distinct models for the bidirectional transport exist: regulation and a tug-of-war. In order to differentiate between them, kinesin-specific antibodies are injected into Drosophila embryos and the effect on transport of lipid droplets is quantified and compared to unperturbed motion. The function-blocking antibodies resulted in an increased run length of dynein-mediated transport and a decrease in that of kinesin. Furthermore, reduced velocities in both directions and a trend towards shorter pauses were observed. Comparison of these results to predictions the models provide for this scenario supports a tug-of-war model rather than regulation. / text

The cell relies on molecular motor proteins for long range transport of vesicles and organelles to maintain the organization required within the cell as it changes over time. Cargos move bidirectionally along microtubules due to the presence of multiple copies of opposite polarity motors. Individual motor properties have been teased out in vitro, but understanding how multiple motors cooperate in vivo has thus far been limited by many obstacles. The goal of this work is to study how multiple similar and dissimilar motors operate together in vivo. Since the function of motors is to generate force to haul cargos, I designed a novel optical trapping system capable of precisely measuring the forces exerted by molecular motors in their native environment, a living cell. Using this system, I find evidence that motors do not fight against each other, supporting the regulation model over the tug-of war model for bidirectional transport. I then study motor regulation in axons in the context of Alzheimer’s disease. I find that GSK-3, a kinase found in abnormal amounts in Alzheimer’s brains, is a negative regulator of transport. I show that GSK-3 regulates motor activity rather than cargo binding. Finally, I also use the optical trap to probe the viscosity of cytosol in vivo and investigate its implications on the cooperation of multiple motors. / text

xiv, 171 p. ; ill. (some col.) A print copy of this title is available through the UO Libraries. Search the library catalog for the location and call number. / Biological molecular motors, which use chemical energy from ATP hydrolysis to generate mechanical force, are involved in a variety of important mechanical processes in eukaryotic cells, such as intracellular transport, cell division and muscle contraction. These motors, which produce motion on the nanoscale, operate in the presence of substantial thermal noise. In this dissertation, two approaches are used to model the physics of nanoscale motors: (1) A theoretically established type of Brownian motor called the "flashing ratchet" is studied. This motor transports diffusive particles in a preferred direction. (2) A coarse-grained mechanical model for the biological molecular motor myosin-V is developed, and used to study the role of Brownian diffusion, and the interaction between chemical and mechanical degrees of freedom, in the transport mechanism of this motor. In chapter III, Brownian dynamics simulations and analytical calculations demonstrate that the average velocity of rigid chains of particles in a flashing ratchet reverses direction in response to changing the size of the chain or the temperature of the heat bath. Recent studies have introduced policies for "closed-loop" control of a flashing ratchet, in which the system is controlled based on information about its internal state (such as the positional distribution of particles). In chapter IV, the effect of time delay on the implementation of closed-loop control of a flashing ratchet is investigated. For a large ensemble, a well-chosen delay time improves the ratchet performance (increasing the velocity) by synchronizing into a quasi-stable mode that takes advantage of the semi-deterministic nature of the time development of average quantities for a large ensemble. I n chapter V, a coarse-grained mechanical model is presented for the transport mechanism of myosin-V, which walks along intracellular filaments. The model is well constrained by experimental data on the mechanical properties of myosin V and on the kinetic cycle. An experimentally motivated model for the intramolecular coordination of the motor's steps is proposed and tested. / Adviser: Heiner Linke

Intracellular transport of membrane-bound vesicles and organelles is a process fundamental for many cellular functions including cell morphogenesis and signaling. The transport is mediated by ensembles of motor proteins, such as kinesins, walking on microtubule tracks. When transporting membrane-bound cargo inside a cell, the motors are linked to diffusive lipid bilayers either directly or via adaptor molecules. The fluidity of the lipid bilayers induces loose inter-motor coupling which is likely to impact the collective motor dynamics and may induce cooperativity. Here, we investigate the influence of loose coupling of kinesin motors on its transport characteristics. In the first part of this thesis, we used truncated kinesin-1 motors with a streptavidin-binding-peptide (SBP) tag and performed gliding motility assays on streptavidin-loaded biotinylated supported lipid bilayers (SLBs), so called ‘membrane-anchored’ gliding motility assays. We show that the membrane-anchored motors act cooperatively; the microtubule gliding velocity increases with increasing motor density. This is in contrast to the transport behavior of multiple motors rigidly bound to a substrate. There, the motility is either insensitive to the motor density or shows negative interference at higher motor density, depending on the structure of the motors. The cooperativity in transport driven by membrane-anchored motors can be explained as following: while stepping on a microtubule, membrane-anchored motors slip backwards in the viscous membrane, thus propelling the microtubule in the solution at a velocity, given by the difference of the motor stepping velocity and the slipping velocity. The motor stepping on the microtubule occurs at maximal stepping velocity because the load on the membrane-anchored motors is minute. Thus, the slipping velocity of membrane-anchored motors determines the microtubule gliding velocity. At steady state, the drag force on the microtubule in the solution is equal to the collective drag force on the membrane-anchored motors slipping in the viscous membrane. As a consequence, at low motor density, membrane-anchored motors slip back faster to balance the drag force of the microtubule in the solution. This results in a microtubule gliding velocity significantly lower than the maximal stepping velocity of the individual motors. In contrast, at high motor density, the microtubules are propelled faster with velocities equal to the maximal stepping velocity of individual motors. Because, in this case, the collective drag force on the motors even at very low slipping velocity, is large enough to balance the microtubule drag in the solution. The theoretical model developed based on this explanation is in good agreement with the experimental data of gliding velocities at different motor densities. The model gives information about the distance that the diffusing motors can isotropically reach to bind to a microtubule, which for membrane-anchored kinesin-1 is ~0.3 µm, an order of magnitude higher as compared to rigidly bound motors, owing to the lateral mobility of motors on the membrane. In addition, the model can be used to predict the number of motors involved in transport of a microtubule based on its gliding velocity. In the second part of the thesis, we investigated the effect of loose inter-motor coupling on the transport behavior of KIF16B, a recently discovered kinesin motor with an inherent lipid-binding domain. Recent studies based on cell biological and cell extract experiments, have postulated that cargo binding of KIF16B is required to activate and dimerize the motor, making it a superprocessive motor. Here, we demonstrate that recombinant full-length KIF16B is a dimer even in the absence of cargo or additional proteins. The KIF16B dimers are active and processive, which demonstrates that the motors are not auto-inhibited in our experiments. Thus, in cells and cell extracts Kif16B may be inhibited by additional factors, which are removed upon cargo binding. Single molecule analysis of KIF16B-GFP reveals that the motors are not superprocessive but exhibit a processivity similar to kinesin-1 indicating that additional factors are most likely necessary to achieve superprocessivity. Transport on membrane-anchored KIF16B motors exhibited a similar cooperative behavior as membrane-anchored kinesin-1 where the microtubule gliding velocity increased with increasing motor density. Taken together, our results demonstrate that the loose coupling of motors via lipid bilayers provides flexibility to cytoskeletal transport systems and induces cooperativity in multi-motor transport. Moreover, our ‘membrane-anchored’ gliding motility assays can be used to study the effects of lipid diffusivity (e.g. the presence of lipid micro-domains and rafts), lipid composition, and adaptor proteins on the collective dynamics of different motors.

Neste trabalho apresentamos um modelo teórico que busca descrever aspectos do movimento bidirecional apresentado por objetos intracelulares (vesículas, organelas, vírus etc, aos quais iremos nos referir simplesmente como (\"vesículas\"), observado, sobretudo em experimentos in vivo. Este movimento nao-difusivo e caracterizado por inversões rápidas em sua direção e é capaz de gerar gradientes de concentração do objeto transportado. Os fenômenos de transporte intracelular são sabidamente mediados por proteínas motoras (como as kinesinas e dinenas) cujo movimento unidirecional sobre _lamentos protéicos e bem caracterizado (kinesinas se movem em direção a extremidade mais enquanto as dinenas se movem em direção a extremidade-menos dos microtúbulos) e é normalmente entendido através de modelos estocásticos que descrevem o comportamento de uma partícula browniana na presença de um potencial assimétrico que varia no tempo (ver Astumian [26], Adjari e Prost [22], Magnasco [23]). Mais recentemente, surgiram na literatura trabalhos que tentam descrever o movimento de partículas motoras interagentes, uma vez que se percebeu que efeitos coletivos que surgem nestas situações podem ser relevantes para os fenômenos de transporte sobre microtúbulos. Uma abordagem para a descrição do comportamento destes sistemas de partículas motoras interagentes é aquela baseada nos modelos para os sistemas difusivos dirigidos\". Em particular, a versão contínua dos modelos do tipo totally asymmetric exclusion processes\" (TASEP) e asymmetric exclusion processes\" (ASEP) tem sido utilizada para o estudo do comportamento da densidade de motores sobre os microtúbulos, através da analise de soluções estacionarias da equação de Burgers correspondente (Parmeggiani et al. [33]). Até agora, entretanto, não existem na literatura tentativas de abordar, com estes modelos, o transporte bidirecional de vesículas mediado por estes motores interagentes. A idéia que apresentamos aqui é associar este estranho tipo de movimento ao movimento de ondas de choque presentes nas soluções transientes da equa_c~ao de Burgers para algumas condições iniciais. Deste modo, as vesículas acompanhando (\"surfando\") os choques fariam o papel de suas correspondentes microscópicas partículas de segunda classe\", introduzidas h_a um bom tempo na literatura [36], [37], [38] para o estudo da dinâmica microscópica dos choques que estão presentes também na versão discreta dos modelos TASEP e ASEP. Neste sentido, é natural que as condições iniciais consideradas, que seriam perturbações no estado estacionário das partículas, possam ser causadas, no sistema real, pela própria interação com a vesícula. É o caso, portanto, de se propor que a geometria deste objeto tenha um papel importante na determinação da direcional de seu próprio movimento no meio intracelular. Esta parece ser, por exemplo, uma alternativa interessante para explicar aspectos do movimento de vírus no interior das células. / In this work we present a theoretical model to describe aspects of the bidirectional movement performed by intracellular structures (vesicles, organelles, viruses etc, to which we refer here simply as \"vesicles\"), observed essentially at in vivo experiments. This nondifusive movement is characterized by rapid inversions in direction and is capable of creating concentration gradients of the transported cargo. The phenomenon of intracellular transport is known to be mediated by motor proteins (such as kinesins and dyneins) whose own unidirectional motion along protein laments is well characterized (kinesins moves to the plus-end direction while dyneins moves to the minus-end direction of the microtubules) and is usually modeled by a stochastic dynamics describing the behavior of a Brownian particle in the presence of a time dependent asymmetrical potential held (see Astumian [26], Adjari and Prost [22], Magnasco [23]). More recently, it appeared in the literature works attempting to describe the movement of interacting motor proteins, since it was realized that collective e_ects emerging from this situation may be relevant to the transport phenomena along microtubules. An approach to describe the behavior of such interacting motor particles is based on existing models for \\driven di_usive systems\". In particular, the continuum versions of the totally asymmetric exclusion processes\" (TASEP) or the asymmetric exclusion processes\" (ASEP) have been used to study the behavior of motors density along microtubules by analyzing the steady state solutions to the corresponding Burgers equation (Parmeggiani et al. [33]). Up to now, however, there are no attempts in the literature to approach in this context the questions related to the bidirecionality of vesicles transported by these interacting motors. The idea we present here is to associate this odd movement to the movement of shock waves presented by the transient solutions of Burgers equation for certain initial conditions. Accordingly, the vesicles accompanying (sur_ng) the shocks fronts would play the role of their microscopic analogous \\particles of second class\" introduced long ago in the literature [36], [37], [38] to study the kinetics of the shocks that are also present in the discrete versions of the TASEP and ASEP. In this regard, it is natural to think that the considered initial conditions, namely perturbations to the motor density with respect to a steady state, can be created in the real systems simply by the interaction with the vesicle. It might then be the case also to propose that the geometry of the vesicle plays an important role to direct its own movement within intracellular environment. This seems to be, for example, an attractive alternative for explaining aspects of virus movement inside the cell.

Herpes simplex virus type 1 (HSV-1) is a common human pathogen that establishes life-long latent infection in sensory neurones. This makes it potentially useful as a gene therapy vector to target neuronal cells. HSV-1 enters cells by membrane fusion, the viral envelope and most tegument proteins dissociate, and the capsid is transported to the cell nucleus to establish infection. There is increasing evidence that the retrograde transport of HSV-1 along sensory axons is mediated by cytoplasmic dynein, but the viral and cellular proteins involved are not known. Cytoplasmic dynein is the major molecular motor involved in minus-end-directed cellular transport along microtubules. It is a large complex molecule, with heavy chains providing motility, while intermediate and light chains are involved in specific cargo binding. A library of HSV-1 capsid and tegument structural genes was constructed and tested for interaction with dynein subunits in a yeast two-hybrid system. A strong interaction was demonstrated between the HSV-1 outer capsid protein VP26 (UL35), as well as the tegument protein VP11/12 (UL46), with the homologous 14 kDa dynein light chains rp3 and Tctex1. In vitro pull-down assays confirmed binding of VP26 to rp3, Tctex1 and cytoplasmic dynein complexes. Recombinant HSV-1 capsids +/- VP26 were used in similar pull-down assays. Only VP26+ capsids bound to rp3. Recombinant HSV-1 capsids were microinjected into living cells and incubated at 37�C. After 1 h capsids were observed to co-localise with rp3, Tctex1 and microtubules. After 2 or 4 h VP26+ capsids had moved closer to the cell nucleus, while VP26- capsids remained in a random distribution. Our results suggest that the HSV-1 outer capsid protein VP26 mediates binding of incoming capsids to the retrograde motor cytoplasmic dynein during cellular infection, through interactions with dynein light chains. It is hoped that these findings will help in the development of a synthetic viral vector, which may allow targeted gene therapy in patients with neurological diseases.

In dieser Arbeit werden Knickinstabilitäten von Filamenten in biologischen Systemen untersucht. Das Zytoskelett von Zellen ist aus solchen Filamenten aufgebaut. Sie sind für die mechanische Stabilität der Zelle verantwortlich und spielen eine große Rolle bei intrazellulären Transportprozessen durch molekulare Motoren, die verschiedene Lasten wie beispielsweise Organellen entlang der Filamente des Zytoskeletts transportieren. Filamente sind semiflexible Polymere, deren Biegeenergie ähnlich groß ist wie die thermische Energie, so dass sie auch als elastische Balken auf der Nanoskala gesehen werden können, die signifikante thermische Fluktuationen zeigen. Wie ein makroskopischer elastischer Balken können auch Filamente eine mechanische Knickinstabilität unter Kompression zeigen. Im ersten Teil dieser Arbeit wird untersucht, wie diese Instabilität durch thermische Fluktuationen der Filamente beeinflusst wird. In Zellen können Kompressionskräfte durch molekulare Motoren erzeugt werden. Das geschieht zum Beispiel während der Zellteilung in der mitotischen Spindel. Im zweiten Teil der Arbeit untersuchen wir, wie die stochastische Natur einer von Motoren generierten Kraft die Knickinstabilität von Filamenten beeinflusst. Zunächst stellen wir kurz das Problem von Knickinstabilitäten auf der makroskopischen Skala dar und führen ein Modell für das Knicken von Filamenten oder elastischen Stäben in zwei Raumdimensionen und in Anwesenheit thermischer Fluktuationen ein. Wir präsentieren eine analytische Lösung für Knickinstabilitäten in Anwesenheit thermischer Fluktuationen, die auf einer Renormierungsgruppenrechnung im Rahmen des nichtlinearen Sigma-Models basiert. Wir integrieren die kurzwelligen Fluktuationen aus, um eine effektive Theorie für die langwelligen Moden zu erhalten, die die Knickinstabilität bestimmen. Wir berechnen die Änderung der kritischen Kraft für die Knickinstabilität und zeigen, dass die thermischen Fluktuationen in zwei Raumdimensionen zu einer Zunahme der kritischen Kraft führen. Außerdem zeigen wir, dass thermische Fluktuationen im geknickten Zustand zu einer Zunahme der mittleren projizierten Länge des Filaments in Richtung der wirkenden Kraft führen. Als Funktion der Konturlänge des Filaments besitzt die mittlere projizierte Länge eine Spitze an der Knickinstabilität, die durch thermische Fluktuationen abgerundet wird. Unser Hauptresultat ist die Beobachtung, dass ein geknicktes Filament unter dem Einfluss thermischer Fluktuationen gestreckt wird, d.h. dass seine mittlere projizierte Länge in Richtung der Kompressionskraft auf Grund der thermischen Fluktuationen zunimmt. Unsere analytischen Resultate werden durch Monte-Carlo Simulationen der Knickinstabilität semiflexibler Filamente in zwei Raumdimensionen bestätigt. Wir führen auch Monte-Carlo Simulationen in höheren Raumdimensionen durch und zeigen, dass die Zunahme der projizierten Länge unter dem Einfluss thermischer Fluktuationen weniger ausgeprägt ist und stark von der Wahl der Randbedingungen abhängt. Im zweiten Teil der Arbeit formulieren wir ein Modell für die Knickinstabilität semiflexibler Filamente unter dem Einfluss molekularer Motoren. Wir untersuchen ein System, in dem sich eine Gruppe von Motoren entlang eines fixierten Filaments bewegt, und dabei ein zweites Filament als Last trägt. Das Last-Filament wird gegen eine Wand gedrückt und knickt. Während des Knickvorgangs können die Motoren, die die Kraft auf das Filament generieren, stochastisch von dem Filament ab- und an das Filament anbinden. Wir formulieren ein stochastisches Model für dieses System und berechnen die “mean first passage time“, d.h. die mittlere Zeit für den Übergang von einem Zustand, in dem alle Motoren gebundenen sind zu einem Zustand, in dem alle Motoren abgebunden sind. Dieser Übergang entspricht auch einem Übergang aus dem gebogenen zurück in einen ungebogenen Zustand des Last-Filaments. Unser Resultat zeigt, dass für genügend kurze Mikrotubuli die Bewegung der Motoren von der durch das Last-Filament generierten Kraft beeinflusst wird. Diese Ergebnisse können in zukünftigen Experimenten überprüft werden. / We study buckling instabilities of filaments in biological systems. Filaments in a cell are the building blocks of the cytoskeleton. They are responsible for the mechanical stability of cells and play an important role in intracellular transport by molecular motors, which transport cargo such as organelles along cytoskeletal filaments. Filaments of the cytoskeleton are semiflexible polymers, i.e., their bending energy is comparable to the thermal energy such that they can be viewed as elastic rods on the nanometer scale, which exhibit pronounced thermal fluctuations. Like macroscopic elastic rods, filaments can undergo a mechanical buckling instability under a compressive load. In the first part of the thesis, we study how this buckling instability is affected by the pronounced thermal fluctuations of the filaments. In cells, compressive loads on filaments can be generated by molecular motors. This happens, for example, during cell division in the mitotic spindle. In the second part of the thesis, we investigate how the stochastic nature of such motor-generated forces influences the buckling behavior of filaments. In chapter 2 we review briefly the buckling instability problem of rods on the macroscopic scale and introduce an analytical model for buckling of filaments or elastic rods in two spatial dimensions in the presence of thermal fluctuations. We present an analytical treatment of the buckling instability in the presence of thermal fluctuations based on a renormalization-like procedure in terms of the non-linear sigma model where we integrate out short-wavelength fluctuations in order to obtain an effective theory for the mode of the longest wavelength governing the buckling instability. We calculate the resulting shift of the critical force by fluctuation effects and find that, in two spatial dimensions, thermal fluctuations increase this force. Furthermore, in the buckled state, thermal fluctuations lead to an increase in the mean projected length of the filament in the force direction. As a function of the contour length, the mean projected length exhibits a cusp at the buckling instability, which becomes rounded by thermal fluctuations. Our main result is the observation that a buckled filament is stretched by thermal fluctuations, i.e., its mean projected length in the direction of the applied force increases by thermal fluctuations. Our analytical results are confirmed by Monte Carlo simulations for buckling of semiflexible filaments in two spatial dimensions. We also perform Monte Carlo simulations in higher spatial dimensions and show that the increase in projected length by thermal fluctuations is less pronounced than in two dimensions and strongly depends on the choice of the boundary conditions. In the second part of this work, we present a model for buckling of semiflexible filaments under the action of molecular motors. We investigate a system in which a group of motors moves along a clamped filament carrying a second filament as a cargo. The cargo-filament is pushed against the wall and eventually buckles. The force-generating motors can stochastically unbind and rebind to the filament during the buckling process. We formulate a stochastic model of this system and calculate the mean first passage time for the unbinding of all linking motors which corresponds to the transition back to the unbuckled state of the cargo filament in a mean-field model. Our results show that for sufficiently short microtubules the movement of kinesin-I-motors is affected by the load force generated by the cargo filament. Our predictions could be tested in future experiments.