Propagation of a signal coordinating force generation along an actin filament in actomyosin complexes

Longitudinal distortions and transversal fluctuations of an actin filament sliding on Myosin molecules

An actin filament sliding on myosin moleculesdemonstrates both longitudinal distortions and transversal fluctuationswith the linear dimension far exceeding the diameter of an actinmonomer. Local swaying of a single actin filament was identified byreading speckled fluorescent markers attached on the filament. Theaccuracy of reading each speckled marker was about 10.4 nm (r.m.s.).Longitudinal distortions of an actin filament at a low ATP concentrationof 20 μM were as much as 0.5 μm for the average filament lengthof 5.4 μm. The magnitude of transversal fluctuations was as much as60 nm, that was independent of the filament length. Both longitudinaldistortions and transversal fluctuations are suggested to play a pivotalrole for facilitating a smooth sliding movement of an actin filament.

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

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

Slowly modulating fluctuations as mesoscopic distortions occurring on an actin filament

An actin filament sliding on myosin molecules exhibits fluctuating or staggered movements as responding to changes in the ATP concentration. We previously observed that fluctuations in the sliding velocity enhanced in a manner being independent of the magnitude of the velocity. The present study focused upon a single actin filament bound to a glass surface through avidin-biotin bonding to examine those fluctuations inherent to the filament in the presence of heavy meromyosin. The auto-correlation analysis revealed that the relaxation time of fluctuations in the filamental displacement obtains its maximum value at about 100microM of the ATP concentration in the ambient, while the magnitude of the fluctuations gradually increased with an increase of the concentration. Furthermore, the measurement of the fluorescence intensity from the markers fixed on the filament demonstrated an enhancement of the negative correlation between the measured peak intensity and the spatial spreading of its intensity over the range of 0-200microM of the ATP concentration, as indicating both development and mitigation of local distortions occurring within the filament.

Relationship between the flexibility and the motility of actin filaments: effects of pH

Both the sliding velocity of fluorescently labeled actin filament and its persistence length as an index of the bending flexibility of the filament were examined in the motility assay as varying the pH values of the solution for preparing actin filaments. When the pH value was varied from 5.0 to 9.0 in the solution in which actin filaments were formed from the constituent monomers, the motile performance of Mg(2+) bound actin filaments (Mg-F-actin) was apparently suppressed compared to the case of Ca(2+) bound ones (Ca-F-actin). The persistence length for Ca-F-actin gradually increased with the increase of the pH value while the similar length for Mg-F-actin remained rather independent of the value. The largest sliding velocity of the filament, on the other hand, obtained at the persistence length of roughly 6 microm for both cases of Mg-F-actin and Ca-F-actin.

Enhancing the staggered fluctuations of an actin filament sliding on Chara myosin

We examined both longitudinal and transversal fluctuations of displacements of an actin filament sliding upon Chara myosin molecules. Although the magnitude of transversal fluctuations remained rather independent of ATP concentration, the longitudinal ones were found to increase their magnitude as the concentration increased. In addition, the longitudinal fluctuations gradually increased as the sliding velocity of the filament increased.

Transition from contractile to protractile distortions occurring along an actin filament sliding on myosin molecules

An ATP-activated actin filament sliding on myosin molecules exhibited mechanical distortions or fluctuations both longitudinally and transversally along the filament. Although actin filaments exhibited a uniform sliding movement longitudinally as the ATP concentration increased, the longitudinal fluctuations were found to vary their magnitude with the concentration. The magnitude of longitudinal fluctuations reached its maximum at approximately 100 microM of the ATP concentration. The local enhancement of the longitudinal fluctuations as responding to changes in the ATP concentration is associated with a critical phenomenon bridging the two different kinds of mechanical distortions, either contractile or protractile ones, occurring within a sliding actin filament.

Enhancement of the sliding velocity of actin filaments in the presence of ATP analogue: AMP-PNP

The sliding velocity of actin filaments was found to increase in the presence of ATP analogues. At 0.5 mM ATP, the presence of 2.0 mM of AMP-PNP enhanced the filament velocity from 3.2 up to 4.5 microm/s. However, 2 mM ADP decreased the velocity down to 1.1 microm/s. The results suggest that the complex conformations of myosin cross-bridges interacting with an actin filament in the presence of ATP analogues makes the entire filament move faster.

The role of aqueous interfaces in the cell

The cell is rich with biopolymeric surfaces. Yet, the role of these surfaces and attendant surface-water interfaces has received little attention among biologists, most of whom consider water as a neutral carrier. This review aims to begin bridging the gap between biology and interface science-to show that a surface-oriented approach has power to bring fresh insights into an otherwise impenetrably complex maze. In this approach the cell is treated as a polymer gel. If the cell is a gel, then a logical approach to the understanding of cell function is through an understanding of gel function. Great strides have been made recently in understanding the principles of polymer-gel dynamics, and particularly the role of the polymer-water interface. It has become clear that a central mechanism in biology is the phase-transition-a major structural change prompted by a subtle change of environment. Phase-transitions are capable of doing work and such work could be responsible for much of the work of the cell. Here, we pursue this approach. We set up a polymer-gel-based foundation for cell behavior, and explore the extent to which this foundation explains how the cell achieves its everyday tasks.

Dynamical mechanism for the conversion of energy at a molecular scale

We propose a dynamical mechanism of a molecular machine for energy conversion, by considering a simple model describing the dynamics of two components, the head and the chain. After injection of energy to the head region, the energy is stored at one part for some time, and is used step by step, allowing the head to move directionally along the chain, irrespective of the direction of the input, under a fluctuating environment. Our system can adjust the timing with which the head crosses the energy barrier by taking advantage of internal dynamics and the flexibility of components. Some suggestions are given for molecular machines.

Quantum mechanics in first, second and third person descriptions

Although quantum mechanics in third person descriptions is certainly legitimate insofar as one is sure about what each energy quantum is all about, quantum mechanics in first person descriptions comes to the surface once one raises the issue of how each quantum transforms itself as measuring and interacting with the others of the similar nature. Each energy quantum is taken as the robust confinement of interactions, whose first person descriptions address the quantum involved in the process of measuring other quanta internally. In addition, the issue of how the robust confinement of interactions could come into being and develop is a matter of quantum mechanics in second person descriptions. Biological activities including cell motility and muscle contraction address the issue of quantum coherence accessible in quantum mechanics in second person descriptions.

Is the cell a gel--and why does it matter?

That the cell is a gel is broadly acknowledged. Textbooks begin with this assertion-and then proceed with great abandon to derive mechanisms based on free diffusion, as though the gel concept were groundless and cell was an aqueous solution. This disconnect emerges in part because the behavior of gels is not well understood, particularly among most biologists. Recently, great strides have been made in the understanding of gel behavior. It has become clear, for example, that a central mechanism in gel function is the phase-transition-a qualitative structural change prompted by a subtle change of environment, not unlike the transition from ice to water. Phase-transitions are capable of doing work. If the cell is a gel, then a logical approach to understanding cell function is to understand gel function-especially whether some role may be played by the phase-transition. Here we pursue this approach. We first consider the dichotomy of the cell as a gel and the cell as an aqueous solution. We then set up a gel-based foundation for cell behavior, in which the gels' physical chemical features are used to explore how the cell achieves its everyday tasks. If there is a common underlying mechanism of cell function, it appears that the polymer gel phase-transition could well be a candidate.

Fluctuation of local points of F-actin sliding on the surface-fixed H-meromyosin molecules in the presence of ATP

F-actin fragments fluorescently labeled with rhodamine-phalloidin were copolymerized with non-labeled F-actin fragments. F-actin copolymer consisted of several bright (fluorescent) and dark (non-fluorescent) stripes of approximately 1 microm in width. Local motion of individual speckled F-actin was investigated by measuring translocation fluctuation of several tracing points marked on the actin filament. The tracing points included the borders between neighboring bright and dark stripes, as well as the tip and tail of the filament. For speckled F-actin with an average sliding speed of 4.6 microm/s at 23 degrees C, the translocation distance of the tracing points (per 0.1 s) showed significant fluctuation, of the order of +/-0.12 microm/s, approximately 25% of the sliding speed. The fluctuation correlation of the translocation distance between two tracing points decreased as the distance between them increased. Statistical analysis of the correlation length of the translocation distance L(c) showed that L(c) increased with the sliding speed of the actin filament. The sliding speed, however, saturated as the correlation length became close to the persistence length of the bending elasticity of F-actin. On the contrary, the correlation length of change in the translocation direction was essentially equal to the persistence length of F-actin, independent of the sliding speed. These results suggest that elasticity of the actin filament underlies the sliding velocity of F-actin.

Cell motility and thermodynamic fluctuations tailoring quantum mechanics for biology

Cell motility underlying muscle contraction is an instance of thermodynamics tailoring quantum mechanics for biology. Thermodynamics is intrinsically multi-agential in admitting energy consumers in the form of energy-deficient thermodynamic fluctuations. The onset of sliding movement of an actin filament on myosin molecules in the presence of ATP molecules to be hydrolyzed demonstrates that thermodynamic fluctuations transform their nature so as to accommodate themselves to energy transduction subject to the first law of thermodynamics. The transition from transversal to longitudinal fluctuations of an actin filament with the increase of ATP concentration coincides with the change in the nature of energy consumers acting upon thermal energy in the light of the first law, eventually embodying a uniform sliding movement of an actin filament.

The internalist enterprise on constructing cell motility in a bottom-up manner

Quantum coherence in the biological realm is constructed internally in a bottom-up manner. In particular, an actin filament sliding on myosin molecules in the presence of ATP to be hydrolyzed as a functional unit of muscle contraction exhibits magnetization as a marker of quantum coherence. The uniqueness of quantum coherence in biology is found in precipitating synchronous time in interaction from the interacting energy quanta, each of which has carried with itself synchronous time unique to the quantum in isolation. It exhibits a marked contrast to quantum coherence met in low temperature physics, in the latter of which no transformation of the nature of synchronous time is entertained.

Onset of the sliding movement of an actin filament on myosin molecules: from isotropic to anisotropic fluctuations

An actin filament contacting myosin molecules increased the fluctuation intensity of the filamental displacement as the ATP concentration increased. In particular, fluctuations in the filamental displacement in the planar plane in which the sliding movement takes place were isotropic at a low ATP concentration, and became anisotropic as the concentration increased. The build-up of the sliding movement of an actin filament was associated with the transformation from isotropic to anisotropic fluctuations of the filamental displacement.

Contractile and protractile coordination within an actin filament sliding on myosin molecules

An actin filament exhibits distortions longitudinally when it slides upon myosin molecules. We observed that the actin filament demonstrated contractile distortions at low ATP concentrations and protractile distortions at high concentrations. Temporal development of such distortions was identified, by tracing each of several speckled fluorescent markers attached to the actin filament. Close association of the sliding movement to the moving distortions of an actin filament suggests the presence of a unitary mechanism regulating the apparently two different modes of dynamic movement.

Quantum mechanics in the present progressive mode and its significance in biological information processing

Quantum mechanics practiced in the present progressive mode can incorporate into itself the propagation of a signal of a local character. It is possible to view that any movement in the present progressive mode is mutli-agential in the sense of internal interactions due to the absence of an external agency coordinating the global situation simultaneously. The idea of living memory is discussed as carrying the leftover from those actions completed and registered in the present perfect mode and surviving at any present moment. The occurrence of both the signal propagation of a local character and living memory is upheld upon exchange interaction of a quantum mechanical origin. Empirical evidence suggesting the likelihood of such an exchange interaction is found in the neurotransmitter-gated ion channels located on the plasma membrane of the muscle cell in the vicinity of secretory vesicles containing acetylcholine near the nerve terminal. Another case from the empirical evidence is seen in the actomyosin system demonstrating the unidirectional propagation of variations in the acceleration of the displacement of an actin filament sliding on myosin molecules in the presence of ATP molecules.