Model for processive movement of myosin V and myosin VI

Myosin V and myosin VI are two classes of two-headed molecular motors of the myosin superfamily that move processively along helical actin filaments in opposite directions. Here we present a hand-over-hand model for their processive movements. In the model, the moving direction of a dimeric molecular motor is automatically determined by the relative orientation between its two heads at free state and its head‘s binding orientation on track filament.This determines that myosin V moves toward the barbed end and myosin VI moves toward the pointed end of actin.During the moving period in one step, one head remains bound to actin for myosin V whereas two heads are detached for myosin VI: the moving manner is determined by the length of neck domain. This naturally explains the similar dynamic behaviours but opposite moving directions of myosin VI and mutant myosin V (the neck of which is truncated to only one-sixth of the native length). Because of different moving manners, myosin VI and mutant myosin V exhibit significantly broader step-size distribution than native myosin V. However, all the three motors give the same mean step size of -36nm (the pseudo-repeat of actin helix). All these theoretical results are in agreement with previous experimental ones.     

Impact of Slip Cycles on the Operation Modes and Efficiency of Molecular Motors

Kinesin is a motor molecule that moves processively on microtubule tracks and is involved in active intracellular transport processes. For small loads, it is powered by the hydrolysis of one ATP molecule per step. Here we extent our previously introduced network theory in order to study the possibility of two different mechanical stepping transitions and the general behavior of the motor’s efficiency. Our theory shows explicitly how chemical and mechanical slip cycles emerge that weaken the coupling between ATP hydrolysis and mechanical stepping. Near chemomechanical equilibrium, the motor efficiency η may vary between η=1 for tight coupling and η=0 for loose coupling, depending on the relevance of the slip cycles. Far from chemomechanical equilibrium, on the other hand, the motor efficiency is found to decay as 1/Δμ with increasing Δμ irrespective of the presence of slip cycles, where Δμ represents the reaction free enthalpy or chemical potential difference per ATP hydrolysis.     

Experimental studies of the myosin-actin motor

The mechanical processes generated by the molecular motors, myosin and actin, were measured using single molecule imaging, manipulation, and nanometry techniques. It was shown that the mechanical events of myosin are not tightly coupled with the ATP hydrolysis reaction and that myosin molecules move stochastically. These results indicate that the movement of myosin is driven by thermal motion rather than structural changes occurring in the myosin molecules. Thermal Brownian motion must be biased using the energy released from the hydrolysis of ATP. Thus, the molecular motors can harness thermal energy to perform mechanical work efficiently. Received: 20 November 2001 / Accepted: 11 February 2002 / Published online: 22 April 2002     

Mechanochemical model for myosinⅡdimer that can explain the spontaneous oscillatory contraction of muscle

The spontaneous oscillatory contraction(SPOC) of myofibrils is the essential property inherent to the contractile system of muscle. Muscle contraction results from cyclic interactions between actin filament and myosin II which is a dimeric motor protein with two heads. Taking the two heads of myosin II as an indivisible element and considering the effects of cooperative behavior between the two heads on rate constants in the mechanochemical cycle, the present work proposes the tenstate mechanochemical cycle model for myosin II dimer. The simulations of this model show that the proportion of myosin II in different states periodically changes with time, which results in the sustained oscillations of contractive tension, and serves as the primary factor for SPOC. The good fit of this model to experimental results suggests that the cooperative interaction between the two heads of myosin II dimer may be one of the underlying mechanisms for muscle contraction.     

驱动蛋白单向运动机理

驱动蛋白马达在实验和理论上已被进行了广泛的研究. 然而, 其行进运动的微观机理仍未确定. 在本文中我们基于化学、力学和电学耦合提出了一个交臂模型来描述这种行进运动. 在该模型中，驱动蛋白两个头的ATP水解化学反应速率由作用在其颈上的力（包括内部弹性力和外部负荷）来调控. 在低外部负荷情况下, 驱动蛋白的后头的ATP水解化学反应速率远大于前头的速率, 因而两个头在ATP水解化学反应和力学周期循环中是协调的且马达以每步消耗一个ATP的方式的行走. 在大的前向负荷情况下, 两个头的ATP水解化学反应速率变得可比拟, 因而两个头在ATP水解化学反应和力学周期循环中不再很好地协调. 该模型与驱动蛋白的结构研究结果以及ATP水解化学反应路径一致. 利用此模型所估算的驱动力（约5.8 pN）与实验结果（5~7.5 pN）一致. 所估算的每步中的运动时间（约10）也与实验测量值（0~50）符合. 解释了已观察到的每步（8nm）分为两个半步的现象. 所得到的运动速度-负荷曲线与已有的实验结果一致.     

Hydrogen generation from alcohols (α-hydroxy carboxylic acids) and alcohol–ammonia coupling in aqueous media catalysed by water-soluble bipyridine-Cp*Ir (Rh or Os) catalyst: a computational mechanism insight

Density functional theory (DFT) calculations were performed to elucidate the mechanism of the dehydrogenative oxidation of various primary alcohols (or α-hydroxy carboxylic acids) and the dehydrogenative coupling of alcohols with ammonia catalysed by the same water-soluble Cp^*Ir complex bearing a 2-pyridonate-based ligand (A–Ir). Another two new catalysts A–Rh and A–Os are computationally designed for the dehydrogenative oxidation of alcohols. The plausible pathway for alcohol dehydrogenation includes three steps: alcohol oxidation to aldehyde (step I); the generation of dihydrogen in the metal coordination sphere (step II); and the liberation of dihydrogen accompanied with the regeneration of active catalyst A (step III). Among them, the step I follows bifunctional concerted double hydrogen transfer mechanism rather than the β-H elimination. For step II, the energy barriers involving the addition of one or two water molecules are higher than in absence of water. Our results also confirm that A–Ir can be applied in the dehydrogenation of various α-hydroxy carboxylic acids by the similar mechanism. Remarkably, A–Ir is also found to be efficient for the coupling reactions of various primary benzyl alcohols with ammonia to afford amides.     

Influence of V on the Fe site spin and charge densities in BCC-Iron

Using the Mössbauer effect we studied the influence of substituting iron atoms by vanadium atoms on the Fe site hf field and isomer shift for a series of Fe-V alloys containing up to 18 at% V. We found that the two qualities are correlated with each other as well as that the average hf field H? is correlated with the average number of V atoms in the vicinity of the Fe nuclei, N?. Based on the former correlations we were able to determine the hyperfine coupling constants to be equal to: a) 1735 kOe/s-el for itinerant s-like electrons, b) 3240 and 3450 kOe/s-el for the s-electrons localized in the first- and second-neighbour shell, respectively and c) 3090 kOe/s-el, the average value. Using the estimated hf coupling constants and based on the H? ? N? correlation we calculated the disturbance of the spin or charge density per one V atom per unit cell, η, to be equal to 0.048. The present results are being compared with those obtained previously for other substitutes and they are discussed in terms of Friedel's and Stearns' models.     

耦合时间精度对模拟飞行器自由运动特性的影响

将亚迭代技术引入流体动力学和刚体动力学方程的耦合求解,获得细长三角翼极限环运动的规律.探讨耦合时间精度对飞行器非定常运动特性的影响,细长三角冀的大迎角自由滚运动最终形成极限环振荡的周期性自维持运动,不同攻角自由滚振幅阶跃式的变化特点较好地吻合了自由滚试验的规律.对于多系统耦合问题,亚迭代耦合求解(耦合时间精度为二阶)对物理时间步长的依赖性不明显;而存在一阶时间滞后的解耦推进方法的数值结果强烈地依赖于物理时间步长选取,稍大的时间步长将导致非物理的数值结果.     

Bifurcation in neuronal networks with hub structure

We investigate bifurcations in neuronal networks with a hub structure. It is known that hubs play a leading role in characterizing the network dynamical behavior. However, the dynamics of hubs or star-coupled systems is not well understood. Here, we study rather subnetworks with a star-like configuration. This coupled system is an important motif in complex networks. Thus, our study is a basic step for understanding structure formation in large networks. We use the Morris-Lecar neuron with class I and class II excitabilities as a node. Homogeneous (coupling the same class neurons) and heterogeneous (coupling different class neurons) cases are considered for both excitatory and inhibitory coupling. For the homogeneous system class II neurons are suitable for achieving both complete and cluster synchronization in excitatory and inhibitory coupling, respectively. For the heterogeneous system with inhibitory coupling, the class I hub neuron has a wider parameter region of synchronous firings than the class II hub. Moreover, the class I hub neuron with the excitatory synapse gives rise to bifurcations of synchronized states and multi-stability (coexistence of a few different states) is observed.     

Simultaneous Measurement of Individual ATPase and Mechanical Reactions by a Single Myosin Molecule at Work

Based on techniques for single molecule imaging and nanomanipulation by optical tweezers, we have developed a new technique that allows simultaneous measurement of individual ATPase and mechanical reactions from a single myosin molecule during force generation. We show how the ATPase reaction couples to the mechanical reaction directly at the single molecule level. The results show that the myosin head can produce force even after releasing the bound nucleotide, probably ADP, suggesting that the chemical energy driven by ATP hydrolysis can be hysteretically stored in the myosin molecule. This view does not support a widely accepted hypothesis in which the force generation is tightly coupled to ligand dissociation.This paper was originally presented as an invited paper at the seventh Meeting on Near Field Optics, which was held on July 1, 1998 at Nagoya University, Nagoya, organized by the Research Group on Near Field Optics of the Optical Society of Japan, an affiliate of the Japan Society of Applied Physics.     

Monte Carlo Simulation of Kinesin Movement with a Lattice Model

Kinesin is a processive double-headed molecular motor that moves along a microtubule by taking about 8nm steps. It generally hydrolyzes one ATP molecule for taking each forward step. The processive movement of the kinesin molecular motors is numerically simulated with a lattice model. The motors are considered as Brownian particles and the ATPase processes of both heads are taken into account. The Monte Carlo simulation results agree well with recent experimental observations, especially on the relation of velocity versus ATP and ADP concentrations.     

Stochastic force generation by small ensembles of myosin II motors

Forces in the actin cytoskeleton are generated by small groups of nonprocessive myosin II motors for which stochastic effects are highly relevant. Using a cross-bridge model with the assumptions of fast power-stroke kinetics and equal load sharing between equivalent states, we derive a one-step master equation for the activity of a finite-sized ensemble of mechanically coupled myosin II motors. For constant external load, this approach yields analytical results for duty ratio and force-velocity relation as a function of ensemble size. We find that stochastic effects cannot be neglected for ensemble sizes below 15. The one-step master equation can be used also for efficient computer simulations with linear elastic external load and reveals the sequence of buildup of force and ensemble rupture that is characteristic for reconstituted actomyosin contractility.     

A conservative coupling algorithm between a compressible flow and a rigid body using an Embedded Boundary method

This paper deals with a new solid–fluid coupling algorithm between a rigid body and an unsteady compressible fluid flow, using an Embedded Boundary method. The coupling with a rigid body is a first step towards the coupling with a Discrete Element method. The flow is computed using a finite volume approach on a Cartesian grid. The expression of numerical fluxes does not affect the general coupling algorithm and we use a one-step high-order scheme proposed by Daru and Tenaud [V. Daru, C. Tenaud, J. Comput. Phys. (2004)]. The Embedded Boundary method is used to integrate the presence of a solid boundary in the fluid. The coupling algorithm is totally explicit and ensures exact mass conservation and a balance of momentum and energy between the fluid and the solid. It is shown that the scheme preserves uniform movement of both fluid and solid and introduces no numerical boundary roughness. The efficiency of the method is demonstrated on challenging one- and two-dimensional benchmarks.     

Competing exchange interactions in magnetic multilayers

We have studied alloying of the nonmagnetic spacer layer with a magnetic material as a method of tuning the interlayer coupling in magnetic multilayers. We have specifically studied the Fe/V(100) system by alloying the spacer V with various amounts of Fe. For some Fe concentrations in the spacer, it is possible to create a competition between antiferromagnetic Ruderman-Kittel-Kasuya-Yoshida exchange and direct ferromagnetic exchange coupling. The exchange coupling and transport properties for a large span of systems with different spacer concentrations and thicknesses were calculated and measured experimentally and good agreement between observations and theory was observed. A reduction in magnetoresistance of about 50% was observed close to the switchover from antiferromagnetic to ferromagnetic coupling.     

Structural instabilities and transverse effective charges in IV–VI compounds

Transverse effective charges for some IV–VI, III–V and II–VI compounds are investigated on the basis of the interband electron-phonon coupling with the use of the Penn model for electron energy bands. The results show that the large transverse effective charges of IV–VI compounds are related with strong electron-phonon interaction as well as with the softening of TO phonon in IV–VI compounds.     

Ⅱ-Ⅵ化合物中钒中心的光致发光

通过对Td对称群中V++(d8)所有能量矩阵的完全对角化计算,发现B≈0.4B.、C≈5.0B、Dq≈1.7B时的晶场跃迁4T2(drde2)→4T1(dr2de)能较好的拟合ZnS、CdS、CdSe等化合物中V中心在5000cm-1附近的辐射.其整个光激发谱的基本面貌也能在此模型中得到解释;进一步,还用Y.Tanabe和H.Kaminura的不可约张量法考虑了对称性降低到C3,和旋轨耦合S·L的一级修正,结果和实验符合较好.     

薄层色谱跟踪罗沙替丁醋酸酯的合成展开剂的选择

用薄层色谱(TLC)跟踪监测合成罗沙替丁醋酸酯过程中每一步反应,结果显示:1-3步的合成反应监测过程采用的展开剂都是甲醇∶氯仿∶氨水(1∶4:0,5;V/V/V);第4步合成反应监测过程中,当展开剂石油醚∶氯仿:丙酮:乙醇的配比为23.5∶ 12:2∶2.5(V/V/V/V)时,原料中间体及终产物的Rf值可控制在0.2...     

Attenuation of ultrasound in suspensions of bovine muscle myofibrils and myosin

The attenuation of 1.5-7 MHz ultrasound was measured over the pH range 3-7 in 100 mM KCl suspensions of bovine M. semitendinosus myofibrils, precipitated myosin and the residue of myofibrils after partial extraction of myosin. In all fractions attenuation showed a similar dependence on pH over the range 3-7, with a broad, substantial maximum in the region of pH 4.5-pH 5.5 and similar mass attenuation coefficients (per g protein). At pH 7 and 7 MHz these were 3.49 +/- 0.20 cm2 g-1 in the myofibrils, 3.26 +/- 0.31 cm2 g-1 in the myofibrilar residue and 2.83 +/- 0.68 cm2 g-1 in the precipitated myosin. Measurements at 5.3 MHz of precipitated myosin over a wider pH range revealed an attenuation titration curve similar to that previously observed in homogenates of muscle and muscle myofibrils, with substantial peaks at about pH 5 and 11.5, and a shoulder perhaps indicating a small underlying peak at about pH 8-9. Myosin dissolved in 800 mM KCl gave attenuation levels that were typically 50% lower than precipitated myosin e.g. at pH 7 and 7 MHz: 2.83 +/- 0.68 cm2 g-1 in the precipitated form, 1.29 +/- 0.10 cm2 g-1 in solution. These results indicated that: (a) attenuation by myosin filaments contributed substantially to the total attenuation in suspensions of myofibrils and (b) the peak in the myofibrilar attenuation is caused, or substantially contributed to, by a process taking place in the myosin component.     

From antiferromagnetic to ferromagnetic coupling for V adatoms on Co(001) substrates

We discuss the polarization of V atoms on Co(001) substrates within density functional calculations. For sub-monolayer coverage the coupling between V and Co is clearly of antiferromagnetic type whereas it changes to ferromagnetic coupling in the case of a full V monolayer on Co(001). The results obtained in the case of a sub-monolayer coverage are in agreement with recent X-ray magnetic circular dichroism by Huttel et al. [Phys. Rev. B 68, 174405 (2003)]. The transition from antiferromagnetic coupling (in the case of sub-monolayer coverage) to ferromagnetic coupling (for a full monolayer coverage) is discussed in terms of local coordination numbers and V-Co hybridization. Comparison with Cr and Mn coverages on Co(001) complicates the problem: i) submonolayer Cr coverage stabilizes the antiferromagnetic coupling between Cr and Co atoms (like for V on Co(001) whereas a Cr monolayer on Co presents in-plane antiferromagnetic coupling; ii) submonolayer Mn coverage stabilizes now the ferromagnetic coupling between Mn and Co whereas a Mn monolayer on Co(001) presents an in-plane antiferromagnetic coupling. Competition between Co induced magnetism and surface induced magnetism at V sites is discussed.     

Contemplating charge transport by modeling of DNA nucleobases based nano structures

Electrical charge transport through two basic strands Thymine and Adenine of DNA has been analyzed using jellium model approach. The FFT-2D computations have been performed for semi empirical Extended Huckel Theory using Atomistix Tool kit to contemplate the charge transport metrics like current and conductance. We have scrutinized the behavior of the devices in the range of -2 V–2 V for a step size of 0.2 V. A prominent observation is the drop in HLGs of Adenine and Thymine, when working as device as compared to their intrinsic values and this is comparative more visible in case of Adenine. The current in the thymine based device exhibit linear increase with voltage in spite of having low conductance. Further the broader transmission peaks represent the strong coupling of electrodes to the scattering molecule (Thymine). The NDR effect of Adenine based device for higher bias can be utilized in various future electronics applications.