Self-organization versus watchmaker: molecular motors and protein translocation

Generation of directional movement at the molecular scale is a phenomenon crucial for biological organization and dynamics. It is traditionally described in mechanistic terms, in consistency with the conventional machine-like image of the cell. The designated and highly specialized protein machines and molecular motors are presumed to bring about most of cellular motion. A review of experimental data suggests, however, that uncritical adherence to mechanistic interpretations may limit the ability of researchers to comprehend and model biology. Specifically, this article illustrates that the interpretation of molecular motors and protein translocation in terms of stochasticity and self-organization appears to provide a more adequate and fruitful conceptual framework for understanding of biological organization at the molecular scale.     

Dynamics of translation on the ribosome: molecular mechanics of translocation

The translocation step of protein elongation entails a large-scale rearrangement of the tRNA-mRNA-ribosome complex. Recent years have seen major advances in unraveling the mechanism of the process on the molecular level. A number of intermediate states have been defined and, in part, characterized structurally. The article reviews the recent evidence that suggests a dynamic role of the ribosome and its ligands during translocation. The focus is on dynamic aspects of tRNA movement and on the role of elongation factor G and GTP hydrolysis in translocation catalysis. The significance of structural changes of the ribosome induced by elongation factor G as well the role of ribosomal RNA are addressed. A functional model of elongation factor G as a motor protein driven by GTP hydrolysis is discussed.     

Interaction of the molecular motors

A review addresses the up-to-date evidence on the regulation of the organelle transport along microtubules in a very specific aspect of the interaction of the molecular motors of the opposite directions.     

Transport characteristics of molecular motors

Properties of transport of molecular motors are investigated. A simplified model based on the concept of Brownian ratchets is applied. We analyze a stochastic equation of motion by means of numerical methods. The transport is systematically studied with respect to its energetic efficiency and quality expressed by an effective diffusion coefficient. We demonstrate the role of friction and non-equilibrium driving on the transport quantifiers and identify regions of a parameter space where motors are optimally transported.     

Single molecule measurements and molecular motors

Single molecule imaging and manipulation are powerful tools in describing the operations of molecular machines like molecular motors. The single molecule measurements allow a dynamic behaviour of individual biomolecules to be measured. In this paper, we describe how we have developed single molecule measurements to understand the mechanism of molecular motors. The step movement of molecular motors associated with a single cycle of ATP hydrolysis has been identified. The single molecule measurements that have sensitivity to monitor thermal fluctuation have revealed that thermal Brownian motion is involved in the step movement of molecular motors. Several mechanisms have been suggested in different motors to bias random thermal motion to directional movement.     

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.     

Organelle transport and molecular motors in fungi

Polarized growth, secretion of exoenzymes, organelle inheritance, and organelle positioning require vectorial transport along cytoskeletal elements. The discovery of molecular motors and intensive studies on their biological function during the past 3 years confirmed a central role of these mechanoenzymes in morphogenesis and development of yeasts and filamentous fungi. Saccharomyces cerevisiae proved to be an excellent model system, in which the complete set of molecular motors is presumed to be known. Genetic studies combined with cell biological methods revealed unexpected functional relationships between these motors and has greatly improved our understanding of nuclear migration, exocytosis, and endocytosis in yeasts. Tip growth of elongated hyphae, compared to budding, however, does require vectorial transport over long distances. The identification of ubiquitous motors that are not present in yeast indicates that studies on filamentous fungi might be helpful to elucidate the role of motors in long-distance organelle transport within higher eukaryotic cells. Copyright 1998 Academic Press.     

Fluctuations, responses and energetics of molecular motors

A novel equality relating the rate of energy dissipation to a degree of violation of the fluctuation-response relation (FRR) in non-equilibrium Langevin systems is described. The FRR is a relation between the correlation function of the fluctuations and the response function of macroscopic variables. Although it has been established that the FRR holds in equilibrium, physical significance of violation of the FRR in non-equilibrium systems has been under debate. Recently, the authors have found that an extent of the FRR violation is related in a simple equality to the rate of energy dissipation into the environment in non-equilibrium Langevin systems. In this paper, we fully explain the FRR, the FRR violation, and the new equality with regard to a Langevin model termed a Brownian motor model, which is considered as a simple model of a biological molecular motor. Furthermore, applications of our result to experimental studies of molecular motors are discussed, and, as an illustration, we predict the value of a new time constant regarding the motion of a KIF1A, which is a kind of single-headed kinesin.     

Model for kinetics of myosin-V molecular motors

A hand-over-hand model is presented for the processive movement of myosin-V based on previous biochemical experimental results and structural observations of nucleotide-dependent conformational changes of single-headed myosins. The model shows that the ADP-release rate of the trailing head is much higher than that of the leading head, thus giving a 1 : 1 mechanochemical coupling for the processive movement of the motor. It explains well the previous finding that some 36-nm steps consist of two substeps, while other 36-nm steps consist of no substeps. Using the model, the calculated kinetic behaviors of myosin-V such as the main and intermediate dwell time distributions, the load dependence of the average main and intermediate dwell time and the load dependence of occurrence frequency of the intermediate state under various nucleotide conditions show good quantitative agreement with previous experimental results.     

Crowding of molecular motors determines microtubule depolymerization

The 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. Using an individual-based model, we reproduce experimental findings. Moreover, crowding is identified as the key regulatory mechanism of depolymerization dynamics. Our analysis reveals 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 that 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 affects only the end-residence time of depolymerases and not the depolymerization speed.     

Mechanical transduction mechanisms of RecA-like molecular motors

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.     

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.     

Interactions and regulation of molecular motors in Xenopus melanophores

Many cellular components are transported using a combination of the actin- and microtubule-based transport systems. However, how these two systems work together to allow well-regulated transport is not clearly understood. We investigate this question in the Xenopus melanophore model system, where three motors, kinesin II, cytoplasmic dynein, and myosin V, drive aggregation or dispersion of pigment organelles called melanosomes. During dispersion, myosin V functions as a "molecular ratchet" to increase outward transport by selectively terminating dynein-driven minus end runs. We show that there is a continual tug-of-war between the actin and microtubule transport systems, but the microtubule motors kinesin II and dynein are likely coordinated. Finally, we find that the transition from dispersion to aggregation increases dynein-mediated motion, decreases myosin V--mediated motion, and does not change kinesin II--dependent motion. Down-regulation of myosin V contributes to aggregation by impairing its ability to effectively compete with movement along microtubules.     

Fluctuation driven transport and models of molecular motors and pumps

Non-equilibrium fluctuations can drive vectorial transport along an anisotropic structure in an isothermal medium by biasing the effect of thermal noise (k _B T). Mechanisms based on this principle are often called Brownian ratchets and have been invoked as a possible explanation for the operation of biomolecular motors and pumps. We discuss the thermodynamics and kinetics for the operation of microscopic ratchet motors under conditions relevant to biology, showing how energy provided by external fluctuations or a non-equilibrium chemical reaction can cause unidirectional motion or uphill pumping of a substance. Our analysis suggests that molecular pumps such as Na,K-ATPase and molecular motors such as kinesin and myosin may share a common underlying mechanism. Received: 18 February 1998 / Revised version: 5 May 1998 / Accepted: 14 May 1998     

Velocity of polymer translocation through a pore

We theoretically study the translocation time and the mean velocity of a long polymer threading a long nanopore on an external electric field. Theoretical method, which explicitly takes into account the nucleation theory, is presented based on the built polymer expanded model. We overcame the previous theory's defect which did not consider the real length of the pore. The present model implies that the length scale of a pore plays a very important role in the process of polymer translocation. Our calculation results are in agreement with those of previous experiments.