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Register a new userA Design of an Autonomous Molecule Loading/Transporting/Unloading System Using DNA Hybridization and Biomolecular Linear Motors
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This paper describes a design of a molecular propagation system in molecular communication. Molecular communication is a new communication paradigm where biological and artificially-created nanomachines communicate over a short distance using molecules. A molecular propagation system in molecular communication directionally transports molecules from a sender to a receiver. In the design described in this paper, protein filaments glide over immobilized motor proteins along preconfigured microlithographic tracks, and the gliding protein filaments carry and transport molecules from a sender to a receiver. In the design, DNA hybridization is used to load and unload the molecules onto and from the carriers at a sender and a receiver. In the design, loading/transporting/unloading processes are autonomous and require no external control.
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Intelligence is often discussed in terms of neural networks in the cerebral cortex, whose evolution has presumably been influenced by Darwinian selection. Here we present molecular evidence that one of the many kinesin motors, Kif14, has evolved to exhibit special features in its amino acid sequence that could have evolved to improve neural networks. The improvement is quantified by comparison of Kif14 sequences for 12 species. The special feature is level sets of hydrophobic extrema in water wave profiles based on several hydropathic scales. The most effective scale is a new one based on fractals, indicative of approach of globular curvatures to self-organized criticality.
Switching of the direction of flagella rotations is the key control mechanism governing the chemotactic activity of E. coli and many other bacteria. Power-law distributions of switching times are most peculiar because their emergence cannot be deduced from simple thermodynamic arguments. Recently it was suggested that by adding finite-time correlations into Gaussian fluctuations regulating the energy height of barrier between the two rotation states, one can generate a power-law switching statistics. By using a simple model of a regulatory pathway, we demonstrate that the required amount of correlated `noise can be produced by finite number fluctuations of reacting protein molecules, a condition common to the intracellular chemistry. The corresponding power-law exponent appears as a tunable characteristic controlled by parameters of the regulatory pathway network such as equilibrium number of molecules, sensitivities, and the characteristic relaxation time.
Single-molecule experiments provide new insights into biological processes hitherto not accessible by measurements performed on bulk systems. We report on a study of the kinetics of a triple-branch DNA molecule with four conformational states by pulling experiments with optical tweezers and theoretical modelling. Three distinct force rips associated with different transitions between the conformational states are observed in the folding and unfolding trajectories. By applying transition rate theory to a free energy model of the molecule, probability distributions for the first rupture forces of the different transitions are calculated. Good agreement of the theoretical predictions with the experimental findings is achieved. Furthermore, due to our specific design of the molecule, we found a useful method to identify permanently frayed molecules by estimating the number of opened basepairs from the measured force jump values.
Membrane tubes are important elements for living cells to organize many functions. Experiments have found that membrane tube can be extracted from giant lipid vesicles by a group of kinesin. How these motors cooperate in extracting the fluid-like membrane tube is still unclear. In this paper, we propose a new cooperation mechanism called two-track-dumbbell model, in which kinesin is regarded as a dumbbell with an end (tail domain) tightly bound onto the fluid-like membrane and the other end (head domain) stepping on or unbinding from the microtubule. Taking account of the elasticity of kinesin molecule and the exclude volume effect of both the head domain and the tail domain of kinesin, which are not considered in previous models, we simulate the growth process of the membrane tube pulled by kinesin motors. Our results indicate that motors along a single microtubule protofilament can generate enough force to extract membrane tubes from vesicles, and the average number of motors pulling the tube is about 8~9. These results are quite different from previous studies (Ref. cite{camp.08}), and further experimental tests are necessary to elucidate the cooperation mechanism.
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 kinesin-8 motors affect the length of dynamic microtubules in cells is less clear. We study the more biologically realistic problem of microtubule dynamic instability modulated by a motor-dependent increase in the filament catastrophe frequency. This leads to a significant decrease in the mean filament length and a narrowing of the filament length distribution. The results improve our understanding of the biophysics of length regulation in cells.
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