Millennial musings on molecular motors

In a universe that is dominated by increasing entropy, living organisms are a curious anomaly. The organization that distinguishes living organisms from their inanimate surroundings relies upon their ability to execute vectorial processes, such as directed movements and the assembly of macromolecules and organelle systems. Many of these phenomena are executed by molecular motors that harness chemical potential energy to perform mechanical work and unidirectional motion. This article explores how these remarkable protein machines might have evolved and what roles they could play in biological and medical research in the coming decades.     

Millennial musings on molecular motors

In a universe that is dominated by increasing entropy, living organisms are a curious anomaly. The organization that distinguishes living organisms from their inanimate surroundings relies upon their ability to execute vectorial processes, such as directed movements and the assembly of macromolecules and organelle systems. Many of these phenomena are executed by molecular motors that harness chemical potential energy to perform mechanical work and unidirectional motion. This article explores how these remarkable protein machines might have evolved and what roles they could play in biological and medical research in the coming decades.     

Molecular motors and the Golgi complex: Staying put and moving through

The Golgi apparatus is a highly dynamic organelle through which nascent proteins released from the endoplasmic reticulum (ER) are trafficked. Proteins are post-translationally modified within the Golgi and subsequently packaged into carriers for transport to a variety of cellular destinations. This transit of proteins, as well as the maintenance of Golgi structure and position, is highly dependent upon the actin and microtubule cytoskeletons and their associated molecular motors. Here we review how motors contribute to the correct functioning of the Golgi in higher eukaryotes and discuss the secretory pathway as a model system for studying cooperation between motor proteins.     

Processive cytoskeletal motors studied with single-molecule fluorescence techniques

Processive cytoskeletal motors from the myosin, kinesin, and dynein families walk on actin filaments and microtubules to drive cellular transport and organization in eukaryotic cells. These remarkable molecular machines are able to take hundreds of successive steps at speeds of up to several microns per second, allowing them to effectively move vesicles and organelles throughout the cytoplasm. Here, we focus on single-molecule fluorescence techniques and discuss their wide-ranging applications to the field of cytoskeletal motor research. We cover both traditional fluorescence and sub-diffraction imaging of motors, providing examples of how fluorescence data can be used to measure biophysical parameters of motors such as coordination, stepping mechanism, gating, and processivity. We also outline some remaining challenges in the field and suggest future directions.     

Processivity of single-headed kinesin motors

The processive movement of single-headed kinesins is studied by using a ratchet model of non-Markov process, which is built on the experimental evidence that the strong binding of kinesin to microtubule in rigor state induces a large apparent change in the local microtubule conformation. In the model, the microtubule plays a crucial active role in the kinesin movement, in contrast to the previous belief that the microtubule only acts as a passive track for the kinesin motility. The unidirectional movement of single-headed kinesin is resulted from the asymmetric periodic potential between kinesin and microtubule while its processivity is determined by its binding affinity for microtubule in the weak ADP state. Using the model, various experimental results for monomeric kinesin KIF1A, such as the mean step size, the step-size distribution, the long run length and the mean velocity versus load, can be well explained quantitatively. This local conformational change of the microtubule may also play important roles in the processive movement of conventional two-headed kinesins. An experiment to verify the model is suggested.     

An electromechanical model of myosin molecular motors

There is a long-running debate on the working mechanism of myosin molecular motors, which, by interacting with actin filaments, convert the chemical energy of ATP into a variety of mechanical work. After the development of technologies for observing and manipulating individual working molecules, experimental results negating the widely accepted 'lever-arm hypothesis' have been reported. In this paper, based on the experimental results so far accumulated, an alternative hypothesis is proposed, in which motor molecules are modelled as electromechanical components that interact with each other through electrostatic force. Electrostatic attractive force between myosin and actin is assumed to cause a conformational change in the myosin head during the attachment process. An elastic energy resulting from the conformational change then produces the power stroke. The energy released at the ATP hydrolysis is mainly used to detach the myosin head from actin filaments. The mechanism presented in this paper is compatible with the experimental results contradictory to the previous theories. It also explains the behavior of myosins V and VI, which are engaged in cellular transport and move processively along actin filaments.     

Analysis of cytoskeletal and motility proteins in the sea urchin genome assembly

The sea urchin embryo is a classical model system for studying the role of the cytoskeleton in such events as fertilization, mitosis, cleavage, cell migration and gastrulation. We have conducted an analysis of gene models derived from the Strongylocentrotus purpuratus genome assembly and have gathered strong evidence for the existence of multiple gene families encoding cytoskeletal proteins and their regulators in sea urchin. While many cytoskeletal genes have been cloned from sea urchin with sequences already existing in public databases, genome analysis reveals a significantly higher degree of diversity within certain gene families. Furthermore, genes are described corresponding to homologs of cytoskeletal proteins not previously documented in sea urchins. To illustrate the varying degree of sequence diversity that exists within cytoskeletal gene families, we conducted an analysis of genes encoding actins, specific actin-binding proteins, myosins, tubulins, kinesins, dyneins, specific microtubule-associated proteins, and intermediate filaments. We conducted ontological analysis of select genes to better understand the relatedness of urchin cytoskeletal genes to those of other deuterostomes. We analyzed developmental expression (EST) data to confirm the existence of select gene models and to understand their differential expression during various stages of early development.     

Modelling the Role of Intrinsic Electric Fields in Microtubules as an Additional Control Mechanism of Bi-directional Intracellular Transport

Active transport is essential for cellular function, while impaired transport has been linked to diseases such as neuronal degeneration. Much long distance transport in cells uses opposite polarity molecular motors of the kinesin and dynein families to move cargos along microtubules. It is clear that many types of cargo are moved by both sets of motors, and frequently in a reverse direction. The general question of how the direction of transport is regulated is still open. The mechanism of the cell's differential control of diverse cargos within the same cytoplasmic background is still unclear as is the answer to the question how endosomes and mitochondria move to different locations within the same cell. To answer these questions we postulate the existence of a local signaling mechanism used by the cell to specifically control different cargos. In particular, we propose an additional physical mechanism that works through the use of constant and alternating intrinsic (endogenous) electric fields as a means of controlling the speed and direction of microtubule-based transport. A specific model is proposed and analyzed in this paper. The model involves the rotational degrees of freedom of the C-termini of tubulin, their interactions and the coupling between elastic and dielectric degrees of freedom. Viscosity of the solution is also included and the resultant equation of motion is found as a nonlinear elliptic equation with dissipation. A particular analytical solution of this equation is obtained in the form of a kink whose properties are analyzed. It is concluded that this solution can be modulated by the presence of electric fields and hence may correspond to the observed behavior of motor protein transport along microtubules.     

The Oligomeric Outer Dynein Arm Assembly Factor CCDC103 Is Tightly Integrated within the Ciliary Axoneme and Exhibits Periodic Binding to Microtubules

CCDC103 is an ∼29-kDa protein consisting of a central RPAP3_C domain flanked by N- and C-terminal coiled coils. Defects in CCDC103 lead to primary ciliary dyskinesia caused by the loss of outer dynein arms. This protein is present along the entire length of the ciliary axoneme and does not require other dynein or docking complex components for its integration. Unlike other known dynein assembly factors within the axoneme, CCDC103 is not solubilized by 0.6 m NaCl and requires more chaotropic conditions, such as 0.5 m KI. Alternatively, it can be extracted using 0.3% sarkosyl. CCDC103 forms stable dimers and other oligomers in solution through interactions involving the central domain. The smallest particle observed by dynamic light scattering has a hydrodynamic diameter of ∼25 nm. Furthermore, CCDC103 binds microtubules directly, forming ∼9-nm diameter particles that exhibit a 12-nm spacing on the microtubule lattice, suggesting that there may be two CCDC103 units per outer arm dynein repeat. Although the outer dynein arm docking complex is necessary to form arrays of dyneins along microtubules, it is not sufficient to set up a single array in a precise location on each axonemal doublet. We propose that CCDC103 helps generate a high-affinity site on the doublets for outer arm assembly, either through direct interactions or indirectly, perhaps by modifying the underlying microtubule lattice.     

构象耦合作用下驱动蛋白的定向运动

用电偶极子的转动来描述驱动蛋白的构象变化。把微管的构象简化为若干电偶极子的线性排列。驱动蛋白和微管之间的相互作用可看作偶极子－偶极子的耦合作用。计算结果表明：这种耦合作用能够产生沿微管的定向粒子流,并且粒子平均位移反映了驱动蛋白实验结果的主要特征。     

Hopping and stalling of processive molecular motors

When a two-headed molecular motor such as kinesin is attached to its track by just a single head in the presence of an applied load, thermally activated head detachment followed by rapid re-attachment at another binding site can cause the motor to ‘hop’ backwards. Such hopping, on its own, would produce a linear force-velocity relation. However, for kinesin, we must incorporate hopping into the motor's alternating-head scheme, where we expect it to be most important for the state prior to neck-linker docking. We show that hopping can account for the backward steps, run length and stalling of conventional kinesin. In particular, although hopping does not hydrolyse ATP, we find that the hopping rate obeys the same Michaelis-Menten relation as the ATP hydrolysis rate. Hopping can also account for the reduced processivity observed in kinesins with mutations in their tubulin-binding loop. Indeed, it may provide a general mechanism for the breakdown of perfect processivity in two-headed molecular motors.     

A possible mechanism for determining the directionality of myosin molecular motors

There is a large superfamily of myosins, which play various fundamental roles in cellular motility. In this superfamily, most of myosins, including myosins II and V, move to the barbed end of an actin filament, whereas myosin VI was found to move in the opposite direction to the pointed end. Although myosin VI has structural differences compared with the other myosins, the mechanism for the reversal of the directionality has not been satisfactorily explained by conventional theories for myosin motility, including the widely accepted lever-arm hypothesis. In this paper, a simple mechanism for determining the directionality is proposed. The mechanism assumes that the driving force for the power stroke is caused by elastic energy stored within a myosin molecule at the joint between the head and the neck. The elastic energy originates from the attractive force between myosin and actin, and accumulates during the docking process. The energy of ATP is used to reduce the attractive force between myosin and actin and to facilitate the dissociation of these molecules. Therefore, it is not directly engaged in the power stroke. With this mechanism, the directionality of the myosin motility is simply determined by the direction of the neck with respect to the head in the dissociated configuration. This structural difference is actually observed in myosin VI. The same mechanism also explains the behavior of a backward moving engineered myosin. Computer simulations demonstrated the feasibility of this working mechanism.     

A simulation model of the conventional kinesin based on the Driven-by-Detachment mechanism

Kinesins are molecular motors that unidirectionally move along microtubules using the chemical energy of ATP. Although the core structure of kinesins is similar to that of myosins, the lever-arm hypothesis, which is widely accepted as a plausible mechanism to explain the behaviors of myosins, cannot be directly applied to kinesins. Masuda has proposed a mechanochemical process called the ‘Driven-by-Detachment (DbD)’ mechanism to explain the characteristic behaviors of myosins, including the backward movement of myosin VI and the loose coupling phenomenon of myosin II. The DbD mechanism assumes that the energy of ATP is mainly used to detach a myosin head from an actin filament by temporarily reducing the affinity of the myosin against the actin. After the affinity is recovered, the detached head has potential energy originating from the attractive force between the myosin and the actin. During the docking process, the potential energy is converted into elastic energy within the myosin molecule, and the intramolecular elastic energy is finally used to produce the power strokes. In the present paper, the DbD mechanism was used to explain the hand-over-hand motion of the conventional kinesin. The neck linker of the kinesin is known to determine the directionality of the motility but, in this paper, it was assumed that the neck linker was not directly engaged in the power strokes, which were driven by the attractive force between the kinesin head and the microtubule. Based on this assumption, simple mechanical simulations showed that the model of a kinesin dimer processively moved along a microtubule protofilament, if the affinity of the kinesin against the microtubule is appropriately controlled. Moreover, if an external force was applied to the center of the kinesin dimer, the dimer moved backward along a microtubule, as observed in experimental motility assays.     

Three approaches to assembling nano-bio-machines using molecular motors

Efforts to use protein molecular motors as nanoactuators are making rapid progress. For instance, it is now possible to carry out directional transport of small cargo along microtracks or microchannels using kinesin-microtubule systems, which could be the basis of micro-conveyor belts or molecular shuttles. However, the applicability of protein-based devices is limited by their poor stability in artificial environments. In addition, assembly of complex, intelligent microdevices or systems will likely require bottom-up self-assembly, and we still do not have sufficient knowledge to rationally design self-assembling protein-based microdevices or systems. One approach to solving the problems associated with protein-based systems is to use DNA-based nanodevices, which are amenable to rational design. Indeed, ingenious design has enabled realization of DNA-based nanoactuators and self-assembled micropatterns of various shapes. One also could use cells, organelles, or tissues as preassembled motile units, and several motile devices have already been realized using this approach. In addition to being less prone to the assemaly problems, cell-based microdevices have the advantage that the motile units reproduce themselves, and genetically encoded functional modifications can be replicated effortlessly. These protein-based, DNA-based, and cell-based systems each have distinct advantages and disadvantages, so that hybrid devices combining the best characteristics of all three would seem the most likely to succeed.     

Mechanism of tail-mediated inhibition of kinesin activities studied using synthetic peptides

We used a truncated form of human conventional kinesin (K560) and a set of synthetic tail-derived peptides to investigate the mechanism by which the kinesin tail domain inhibits the protein's ATPase and motor activities. A peptide that spans residues 904-933 (C3) exhibited the strongest inhibitory effect on steady-state motility and ATPase activity. This inhibition reflected diminished binding of the ADP-bound kinesin head to the microtubule. Although peptide C3 bound to both K560 and microtubules, gliding assays using subtilisin-treated microtubules suggested that the binding to the microtubule contributes only little to the inhibition if there is sufficient affinity between the peptide and kinesin. We suggest that tail-mediated inhibition of kinesin activity is mainly the product of allosteric inhibition induced by the intramolecular binding of the kinesin tail domain to the motor domain, but simultaneous binding of the tail to the microtubule also may exert a minor effect.     

Does 2,3-butanedione monoxime inhibit nonmuscle myosin?

Summary. BDM (2,3-butanedione monoxime) has been used extensively to inhibit nonmuscle myosin. However, recent articles raise the question of what BDM actually does, because of experiments in which BDM did not affect the actin-activated ATPase of nonmuscle myosins. We describe results that indicate that BDM indeed inhibits motility due to nonmuscle myosins: in many different cells BDM has the same effects as anti-actin agents and/or as other anti-myosin agents, and BDM slows or stops the sliding between actin filaments and myosin in vitro. We discuss how the two sets of apparently contradictory results might be resolved, and we suggest possible experiments that might clarify the contradictory interpretations. Correspondence and reprints: Biology Department, York University, 4700 Keele Street, Toronto, ON M3J 1P3, Canada.     

高活性F1-ATP酶单分子旋转初步观察

从基因突变的F1 ATP酶 (基因突变质粒 ,α C193S ,γ S10 7C ,β亚基带有 10个组氨酸标记 (His Tag) ,转入到菌株大肠杆菌JM10 3)的菌株中筛选出一高表达菌株 .该菌株表达的F1 ATP酶经纯化后其水解活性明显高于文献值 .从单分子水平上进行观察 ,发现在水解ATP过程中 ,γ亚基上连接的荧光标记蛋白微丝 ,其旋转速度要比文献中同样条件下快约一倍     

Functional dissection of LIS1 and NDEL1 towards understanding the molecular mechanisms of cytoplasmic dynein regulation

LIS1 and NDEL1 are known to be essential for the activity of cytoplasmic dynein in living cells. We previously reported that LIS1 and NDEL1 directly regulated the motility of cytoplasmic dynein in an in vitro motility assay. LIS1 suppressed dynein motility and inhibited the translocation of microtubules (MTs), while NDEL1 dissociated dynein from MTs and restored dynein motility following suppression by LIS1. However, the molecular mechanisms and detailed interactions of dynein, LIS1, and NDEL1 remain unknown. In this study, we dissected the regulatory effects of LIS1 and NDEL1 on dynein motility using full-length or truncated recombinant fragments of LIS1 or NDEL1. The C-terminal fragment of NDEL1 dissociated dynein from MTs, whereas its N-terminal fragment restored dynein motility following suppression by LIS1, demonstrating that the two functions of NDEL1 localize to different parts of the NDEL1 molecule, and that restoration from LIS1 suppression is caused by the binding of NDEL1 to LIS1, rather than to dynein. The truncated monomeric form of LIS1 had little effect on dynein motility, but an artificial dimer of truncated LIS1 suppressed dynein motility, which was restored by the N-terminal fragment of NDEL1. This suggests that LIS1 dimerization is essential for its regulatory function. These results shed light on the molecular interactions between dynein, LIS1, and NDEL1, and the mechanisms of cytoplasmic dynein regulation.