Myosin V随机步长分布的动力学分析

Myosin V利用ATP水解所释放的自由能,朝肌动蛋白微丝正端作连续的定向运动,平均步长约为36nm。最近几年,诸多实验数据表明,myosin V步长并不固定为36nm,马达各步长值和相应步长出现概率的柱状图符合高斯分布;且在负载力大于2pN的情况下会出现“中间步长”和“后退步子”的现象。可根据已有实验数据,同时考虑马达在跃迁过程中所受的溶液摩擦阻力、常负载力和高斯随机力对其跃迁距离的影响,提出一种跃迁模型,并以此为基础对上述现象进行理论解释。     

分子马达定向运动的两态模型

采用非对称周期势来描述马达蛋白与具有周期性和极性的微丝轨道之间的相互作用,计算了马达蛋白两态模型的几率流和有效势之间的关系。计算结果表明：马达蛋白的定向运动不仅与有效势的整体倾斜密切相关,还与有效势的势垒高度有关。有效势倾斜等效于一个平均力的作用,而这一平均力的存在体现了两态跃迁细致平衡的破坏。同时将不同ATP浓度下力与速度的关系曲线与实验作了比较,这些曲线与实验定性吻合。     

多分子马达输运机制的动力学研究

对多分子马达输运机制进行模拟,得到了外加负载力和货物运输速度、马达个数和货物运输距离的关系,定性半定量的解释了一些实验现象,为多分子马达研究开辟了一条全新的途径.     

分子马达不等间距四态跃迁模型

用主方程方法研究分子马达一维周期性四态不等间距随机跃迁模型,得出稳态情况下分子马达的漂移速度V、扩散系数D及随机参数r,将三者随ATP的浓度［ATP］及外力F的变化进行了曲线拟合,并同大量实验结果进行了比较,定性半定量地分析了分子马达在拖动负载运动时的动力学行为.     

驱动蛋白结构与运动机制

驱动蛋白是一类能够利用ATP水解释放的化学能驱动其所携带的“货物”分子沿着微管（microtubule,MT）定向运动的分子马达,在细胞器运输、有丝分裂、轴突运输等方面有着重要的生理作用。随着驱动蛋白结合ADP、ATP和未结合核苷酸（APO）三种特征状态的晶体结构的解析,驱动蛋白构象变化的研究得到了进一步发展,而在力产生机制和运动模型方面仍然存在较大争议。本文以kinesin-1家族为例,分析了驱动蛋白三种特征状态结构的特点、状态结构间的构象转变,论述了驱动蛋白的力产生机制和整个迈步过程。并探讨了驱动蛋白的运动模型,同时采用分子动力学模拟比较了驱动蛋白的两种迈步方式,为深入研究驱动蛋白提供了一定的理论计算。最后,基于本课题组对复杂体系的研究,对驱动蛋白体系的控制机制提出了新的假设,并对未来的研究方向进行了展望。     

ATPase旋转催化运动的随机跃迁动力学研究

ATP合酶既可在跨膜质子势的推动下催化合成ATP,也可以利用水解ATP释放的化学能而充当质子泵,把质子从线粒体基质中输送到内膜外侧,其能量转化效率却高得惊人,几乎达到100%。在旋转分子马达ATP合酶结构为基础上,结合随机主方程方法,提出了描述旋转分子马达ATPase合酶四态随机跃迁不等距旋转催化运动的理论模型;得到其角速度、扩散系数与ATP浓度之间的变化关系,并且得出了符合旋转分子马达生物机理的结果,定性半定量地解释了其动力学行为。     

分子伴侣GroE系统能量传递机制的研究

用SwissPDBViewer软件对分子伴侣GroE系统与底物的相互作用进行了模拟 ,结果表明 :GroEL顶端结构域在GroES和靶蛋白结合之后发生了明显的变化 ;GroEL的cis环上有与三磷酸腺苷ATP相结合的位点 ,ATP水解之后形成的ADP与活性中心的残基相结合 ,而这种结合除导致残基Thr30的构型发生了变化之外 ,其它残基的空间位置和构型基本保持不变 ,暗示其它残基在能量传递过程中形成了刚性骨架 ,而与ADP分子磷酸键结合的残基Thr30则是能量传递的力点。     

封面故事

如果把细胞看作城市,微管和微丝看作四通八达的市内公路,那分子马达则是在公路上高速行驶的货车。细胞内的生命物质,如信使RNA、蛋白质、细胞器和囊泡等,均需借助于分子马达和微管、微丝系统,才能在细胞中正确地定位并发挥功能,分子马达也因其重要的功能成为研究的热点。     

家蚕微孢子虫ADP/ATP转运蛋白的原核表达及间接免疫荧光定位分析

【目的】家蚕微孢子虫Nosema bombycis ADP/ATP转运蛋白可能参与搬运宿主细胞的能量。本研究克隆家蚕微孢子虫ADP/ATP转运蛋白基因,并进行原核表达、抗体制备及间接免疫荧光定位,为控制和防治家蚕微粒子病提供理论基础。【方法】通过同源序列比对鉴定家蚕微孢子虫N. bombycis ADP/ATP转运蛋白序列,采用生物合成的方法将编码3段面向膜内侧肽段的核酸序列拼接合成,在其两端引入BglⅡ和SalⅠ酶切位点,克隆至pUC57载体并测序,再亚克隆至含有二氢叶酸还原酶（dihydrofolate reductase,DHFR）标签的表达载体pQE40中,然后利用BamHⅠ和SalⅠ酶切获得含有DHFR标签的重组序列,并连接至pET30a（+）载体中进行诱导表达。通过SDS-PAGE、镍柱亲和层析和免疫印迹法鉴定表达蛋白,利用间接免疫荧光对ADP/ATP转运蛋白的分布进行检测。【结果】家蚕微孢子虫的ADP/ATP转运蛋白编码序列（GenBank登录号为EOB13854.1）全长1 524 bp,编码蛋白含有507个氨基酸残基,预测分子质量为59 kDa,等电点为9.35。具有12个跨膜结构域和TLC结构域,其中TLC结构域含有4个功能保守位点。与蜜蜂微孢子虫的ADP/ATP转运蛋白比较,氨基酸序列一致性达30%。系统进化分析表明微孢子虫ADP/ATP转运蛋白聚为一类,具有共同的起源。成功构建了NbADP/ATP-△TM-DHFR-pET30a原核表达重组质粒,目的基因获得表达,其融合蛋白分子量约为37 kDa,纯化重组蛋白并制备了多克隆抗体。免疫印迹分析表明,成熟微孢子虫中表达ADP/ATP转运蛋白;间接免疫荧光定位结果显示,家蚕微孢子虫孢子ADP/ATP转运蛋白定位于孢子质膜上。【结论】本研究将为阻断微孢子虫能量来源,达到控制和防治家蚕微粒子病提供新的思路。     

余氯对河流水体微生物灭活效应的评价

【目的】研究不同余氯浓度和暴露时间对细菌的去除效果,分析不同余氯条件对细胞ATP的影响。【方法】以河水中微生物群落为试验对象,利用流式细胞术(Flow cytometry,FCM)评估不同余氯浓度和暴露时间的灭活效果,检测不同余氯浓度时细胞内(外)ATP的变化情况。【结果】不同余氯浓度和暴露时间对细菌的去除效果产生不同的结果。在余氯浓度2 mg/L情况下,延长氯暴露时间可以增加细菌的去除效果,在余氯浓度≥2 mg/L条件下,较短氯暴露时间就可以灭活90%细菌。高核苷酸细菌(HNA)和低核苷酸细菌(LNA)表现出不同氯耐受能力,且HNA细菌相比LNA细菌较容易受到氯的损伤。细胞内ATP随余氯浓度增加而减少,在高浓度余氯条件下(≥2 mg/L)细胞外ATP才会增加。【结论】微生物活性随着余氯作用的增加而降低,FCM法和ATP检测法可以用于评估加氯消毒对微生物稳定性的影响。     

A kinetic mechanism for the fast movement of Chara myosin

Endoplasmic streaming of characean cells of Nitella or Chara is known to be in the range 30-100 microm/second. The Chara myosin extracted from the cells and fixed onto a glass surface was found to move muscle actin filaments at a velocity of 60 microm/second. This is ten times faster than that of skeletal muscle myosin (myosin II). In this study, the displacement caused by single Chara myosin molecules was measured using optical trapping nanometry. The step size of Chara myosin was approximately 19nm. This step size is longer than that of skeletal muscle myosin but shorter than that of myosin V. The dwell time of the steps was relatively long, and this most likely resulted from two rate-limiting steps, the dissociation of ADP and the binding of ATP. The rate of ADP release from Chara myosin after the completion of the force-generation step was similar to that of myosin V, but was considerably slower than that of skeletal muscle myosin. The 19nm step size and the dwell time obtained could not explain the fast movement. The fast movement could be explained by the load-dependent release of ADP. As the load imposed on the myosin decreased, the rate of ADP release increased. We propose that the interaction of Chara myosin with an actin filament resulted in a negative load being imposed on other myosin molecules interacting with the same actin filament. This resulted in an accelerated release of ADP and the fast sliding movement.     

Stepping behavior of two-headed kinesin motors

The stepping behavior of the dimeric kinesin is studied by using our model based on previous biochemical, X-ray crystallography and cryo-electron microscopy studies. It is shown that, when a Pi is released from the trailing head, a forward step is made under a backward load smaller than the stall force; while when a Pi is released from the leading head, no stepping is made under a forward load or no load, and a backward step is made under a backward load. The forward stepping time, i.e., the time from the release of Pi in the trailing head to the binding of the ADP head to next binding site, is much smaller than the dwell time even under the backward load near the stall force. Thus the movement velocity of the kinesin dimer can be considered to be only dependent on ATPase rates of the two heads. The duration of the rising phase, i.e., the actual time taken by the ADP head to transit from the trailing to leading positions, is on the time scale of microseconds under any backward load smaller than the stall force. This is consistent with available experimental results.     

Stepping behavior of two-headed kinesin motors

The stepping behavior of the dimeric kinesin is studied by using our model based on previous biochemical, X-ray crystallography and cryo-electron microscopy studies. It is shown that, when a Pi is released from the trailing head, a forward step is made under a backward load smaller than the stall force; while when a Pi is released from the leading head, no stepping is made under a forward load or no load, and a backward step is made under a backward load. The forward stepping time, i.e., the time from the release of Pi in the trailing head to the binding of the ADP head to next binding site, is much smaller than the dwell time even under the backward load near the stall force. Thus the movement velocity of the kinesin dimer can be considered to be only dependent on ATPase rates of the two heads. The duration of the rising phase, i.e., the actual time taken by the ADP head to transit from the trailing to leading positions, is on the time scale of microseconds under any backward load smaller than the stall force. This is consistent with available experimental results.     

Mutation of a conserved glycine in the SH1-SH2 helix affects the load-dependent kinetics of myosin

The ATP hydrolysis rate and shortening velocity of muscle are load-dependent. At the molecular level, myosin generates force and motion by coupling ATP hydrolysis to lever arm rotation. When a laser trap was used to apply load to single heads of expressed smooth muscle myosin (S1), the ADP release kinetics accelerated with an assistive load and slowed with a resistive load; however, ATP binding was mostly unaffected. To investigate how load is communicated within the motor, a glycine located at the putative fulcrum of the lever arm was mutated to valine (G709V). In the absence of load, stopped-flow and laser trap studies showed that the mutation significantly slowed the rates of ADP release and ATP binding, accounting for the ~270-fold decrease in actin sliding velocity. The load dependence of the mutant's ADP release rate was the same as that of wild-type S1 (WT) despite the slower rate. In contrast, load accelerated ATP binding by ~20-fold, irrespective of loading direction. Imparting mechanical energy to the mutant motor partially reversed the slowed ATP binding by overcoming the elevated activation energy barrier. These results imply that conformational changes near the conserved G709 are critical for the transmission of mechanochemical information between myosin's active site and lever arm.     

Structural characterization of the binding of Myosin*ADP*Pi to actin in permeabilized rabbit psoas muscle

When myosin is attached to actin in a muscle cell, various structures in the filaments are formed. The two strongly bound states (A*M*ADP and A*M) and the weakly bound A*M*ATP states are reasonably well understood. The orientation of the strongly bound myosin heads is uniform ("stereospecific" attachment), and the attached heads exhibit little spatial fluctuation. In the prehydrolysis weakly bound A*M*ATP state, the orientations of the attached myosin heads assume a wide range of azimuthal and axial angles, indicating considerable flexibility in the myosin head. The structure of the other weakly bound state, A*M*ADP*P(i), however, is poorly understood. This state is thought to be the critical pre-power-stroke state, poised to make the transition to the strongly binding, force-generating states, and hence it is of particular interest for understanding the mechanism of contraction. However, because of the low affinity between myosin and actin in the A*M*ADP*P(i) state, the structure of this state has eluded determination both in isolated form and in muscle cells. With the knowledge recently gained in the structures of the weakly binding M*ATP, M*ADP*P(i) states and the weakly attached A*M*ATP state in muscle fibers, it is now feasible to delineate the in vivo structure of the attached state of A*M*ADP*P(i). The series of experiments presented in this article were carried out under relaxing conditions at 25 degrees C, where approximately 95% of the myosin heads in the skinned rabbit psoas muscle contain the hydrolysis products. The affinity for actin is enhanced by adding polyethylene glycol (PEG) or by lowering the ionic strength in the bathing solution. Solution kinetics and binding constants were determined in the presence and in the absence of PEG. When the binding between actin and myosin was increased, both the myosin layer lines and the actin layer lines increased in intensity, but the intensity profiles did not change. The configuration (mode) of attachment in the A*M*ADP*P(i) state is thus unique among the intermediate attached states of the cross-bridge ATP hydrolysis cycle. One of the simplest explanations is that both myosin filaments and actin filaments are stabilized (e.g., undergo reduced spatial fluctuations) by the attachment. The alignment of the myosin heads in the thick filaments and the alignment of the actin monomers in the thin filaments are improved as a result. The compact atomic structure of M*ADP*P(i) with strongly coupled domains may contribute to the unique attachment configuration: the "primed" myosin heads may function as "transient struts" when attached to the thin filaments.     

ATP consumption and efficiency of human single muscle fibers with different myosin isoform composition

Chemomechanical transduction was studied in single fibers isolated from human skeletal muscle containing different myosin isoforms. Permeabilized fibers were activated by laser-pulse photolytic release of 1.5 mM ATP from p(3)-1-(2-nitrophenyl)ethylester of ATP. The ATP hydrolysis rate in the muscle fibers was determined with a fluorescently labeled phosphate-binding protein. The effects of varying load and shortening velocity during contraction were investigated. The myosin isoform composition was determined in each fiber by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. At 12 degrees C large variations (three- to fourfold) were found between slow and fast (2A and 2A-2B) fibers in their maximum shortening velocity, peak power output, velocity at which peak power is produced, isometric ATPase activity, and tension cost. Isometric tension was similar in all fiber groups. The ATP consumption rate increased during shortening in proportion to shortening velocity. At 12 degrees C the maximum efficiency was similar (0.21-0.27) for all fiber types and was reached at a higher speed of shortening for the faster fibers. In all fibers, peak efficiency increased to approximately 0.4 when the temperature was raised from 12 degrees C to 20 degrees C. The results were simulated with a kinetic scheme describing the ATPase cycle, in which the rate constant controlling ADP release is sensitive to the load on the muscle. The main difference between slow and fast fibers was reproduced by increasing the rate constant for the hydrolysis step, which was rate limiting at low loads. Simulation of the effect of increasing temperature required an increase in the force per cross-bridge and an acceleration of the rate constants in the reaction pathway.     

Mechanism of nucleotide binding to actomyosin VI: evidence for allosteric head-head communication

We have examined the kinetics of nucleotide binding to actomyosin VI by monitoring the fluorescence of pyrene-labeled actin filaments. ATP binds single-headed myosin VI following a two-step reaction mechanism with formation of a low affinity collision complex (1/K(1)' = 5.6 mm) followed by isomerization (k(+2)' = 176 s-1) to a state with weak actin affinity. The rates and affinity for ADP binding were measured by kinetic competition with ATP. This approach allows a broader range of ADP concentrations to be examined than with fluorescent nucleotide analogs, permitting the identification and characterization of transiently populated intermediates in the pathway. ADP binding to actomyosin VI, as with ATP binding, occurs via a two-step mechanism. The association rate constant for ADP binding is approximately five times greater than for ATP binding because of a higher affinity in the collision complex (1/K(5b)' = 2.2 mm) and faster isomerization rate constant (k(+5a)' = 366 s(-1)). By equilibrium titration, both heads of a myosin VI dimer bind actin strongly in rigor and with bound ADP. In the presence of ATP, conditions that favor processive stepping, myosin VI does not dwell with both heads strongly bound to actin, indicating that the second head inhibits strong binding of the lead head to actin. With both heads bound strongly, ATP binding is accelerated 2.5-fold, and ADP binding is accelerated >10-fold without affecting the rate of ADP release. We conclude that the heads of myosin VI communicate allosterically and accelerate nucleotide binding, but not dissociation, when both are bound strongly to actin.     

Sliding distance per ATP molecule hydrolyzed by myosin heads during isotonic shortening of skinned muscle fibers.

We measured isotonic sliding distance of single skinned fibers from rabbit psoas muscle when known and limited amounts of ATP were made available to the contractile apparatus. The fibers were immersed in paraffin oil at 20 degrees C, and laser pulse photolysis of caged ATP within the fiber initiated the contraction. The amount of ATP released was measured by photolyzing 3H-ATP within fibers, separating the reaction products by high-pressure liquid chromatography, and then counting the effluent peaks by liquid scintillation. The fiber stiffness was monitored to estimate the proportion of thick and thin filament sites interacting during filament sliding. The interaction distance, Di, defined as the sliding distance while a myosin head interacts with actin in the thin filament per ATP molecule hydrolyzed, was estimated from the shortening distance, the number of ATP molecules hydrolyzed by the myosin heads, and the stiffness. Di increased from 11 to 60 nm as the isotonic tension was reduced from 80% to 6% of the isometric tension. Velocity and Di increased with the concentration of ATP available. As isotonic load was increased, the interaction distance decreased linearly with decrease of the shortening velocity and extrapolated to 8 nm at zero velocity. Extrapolation of the relationship between Di and velocity to saturating ATP concentration suggests that Di reaches 100-190 nm at high shortening velocity. The interaction distance corresponds to the sliding distance while cross-bridges are producing positive (working) force plus the distance while they are dragging (producing negative forces). The results indicate that the working and drag distances increase as the velocity increases. Because Di is larger than the size of either the myosin head or the actin monomer, the results suggest that for each ATPase cycle, a myosin head interacts mechanically with several actin monomers either while working or while producing drag.     

Kinetic mechanism of the fastest motor protein, Chara myosin

Chara corallina class XI myosin is by far the fastest molecular motor. To investigate the molecular mechanism of this fast movement, we performed a kinetic analysis of a recombinant motor domain of Chara myosin. We estimated the time spent in the strongly bound state with actin by measuring rate constants of ADP dissociation from actin.motor domain complex and ATP-induced dissociation of the motor domain from actin. The rate constant of ADP dissociation from acto-motor domain was >2800 s(-1), and the rate constant of ATP-induced dissociation of the motor domain from actin at physiological ATP concentration was 2200 s(-1). From these data, the time spent in the strongly bound state with actin was estimated to be <0.82 ms. This value is the shortest among known values for various myosins and yields the duty ratio of <0.3 with a V(max) value of the actin-activated ATPase activity of 390 s(-1). The addition of the long neck domain of myosin Va to the Chara motor domain largely increased the velocity of the motility without increasing the ATP hydrolysis cycle rate, consistent with the swinging lever model. In addition, this study reveals some striking kinetic features of Chara myosin that are suited for the fast movement: a dramatic acceleration of ADP release by actin (1000-fold) and extremely fast ATP binding rate.     

Dwell Time Distributions of the Molecular Motor Myosin V

The dwell times between two successive steps of the two-headed molecular motor myosin V are governed by non-exponential distributions. These distributions have been determined experimentally for various control parameters such as nucleotide concentrations and external load force. First, we use a simplified network representation to determine the dwell time distributions of myosin V, with the associated dynamics described by a Markov process on networks with absorbing boundaries. Our approach provides a direct relation between the motor’s chemical kinetics and its stepping properties. In the absence of an external load, the theoretical distributions quantitatively agree with experimental findings for various nucleotide concentrations. Second, using a more complex branched network, which includes ADP release from the leading head, we are able to elucidate the motor’s gating effect. This effect is caused by an asymmetry in the chemical properties of the leading and the trailing head of the motor molecule. In the case of an external load acting on the motor, the corresponding dwell time distributions reveal details about the motor’s backsteps.