用玻耳兹曼方程研究基于分子马达的细胞内特质转运

活细胞内存在基于分子马达的微粒主动运动而引起的物质转运。文中利用玻耳北曼方程采用驰豫近似法，求得一级近似下，活细胞内基于分子马达的微粒主动运动的速度分布函数，将理论结果与实验结果比较，符合较好。进而对基于分子马达的物质转动规律作出了统一的数学物理描述。     

用玻耳兹曼方程研究基于分子马达的细胞内物质转运

活细胞内存在基于分子马达的微粒主动运动而引起的物质转运.文中利用玻耳兹曼方程,采用弛豫近似法,求得一级近似下,活细胞内基于分子马达的微粒主动运动的速度分布函数,将理论结果与实验结果比较,符合较好.进而对基于分子马达的物质转运规律作出了统一的数学物理描述.     

驱动蛋白的结构及运动机制研究进展

驱动蛋白是一种重要的细胞内运输"货物"的分子马达,它基于微管运动,其结构、功能和运动机制是人们主要的研究方面。揭示驱动蛋白的工作机制必将会加深人们对分子马达的认识,而且可以使人类从新的角度去认识、研究和利用这一分子机制。     

分子马达模型综述

对国内外分子马达的研究现状进行综述,以作直线运动的肌动蛋白和肌球蛋白为例,对其运动特点做描述,介绍三类分子马达的结构、功能及其性质,重点概述肌球蛋白的理论模型,展望分子马达的发展前景和应用.     

驱动蛋白及其作用研究进展

驱动蛋白是一种非常重要的细胞内运输"货物"的分子马达,它沿着微管运动来行使其功能.介绍了驱动蛋白的结构、运动及物质运输机制、在精子发生过程中的功能以及在抑制癌症过程中的作用,并对驱动蛋白及其作用研究存在的问题进行了探讨,为今后更进一步深入研究和认识驱动蛋白提供有价值的新信息、新思路.     

分子马达定向运动的合作机制

分子马达是当前生物学和物理学的前沿课题,其定向运动的动力学机制一直是科学家关注的焦点之一.生物体内的分子马达一般是很多个一起协同工作.相互作用与合作在分子马达集体行为中起了很大作用.本文概述了分子马达合作运动的现象和机制.为进一步阐述合作的意义,本文详细讨论了分子马达必须依靠合作才能实现定向输运的两种情况.第一种,分子马达通过合作,在过阻尼条件下克服不停闪烁的棘齿势,实现了定向运动.第二种,分子马达通过合作,可以将一个方向上输入的驱动能量转化到垂直方向上做功,并产生定向输运.     

分子马达模型综述

介绍三类马达酶的结构,功能和生命体内分子马达的研究状况,并详细介绍几类典型分子马达的理论模型,同时展望了分子马达的发展前景和应用。     

同向马达蛋白在细胞内的运输（英文）

细胞内物质的主动运输主要通过马达蛋白这一特殊的纳米机器来完成。在运输过程中，马达蛋白之间的协作性显著影响着距离、速度等重要的运输特性。为了理解这一机制，我们结合Gillespie模拟和理论推导，解释了单马达蛋白的力学特性如何影响了多个马达蛋白之间的协作性，进而对运输距离进行调节。我们建立了一个深度学习模型来帮助快速获得马达蛋白的运动参数。我们的结果揭示了同向马达蛋白在细胞内运输的物理本质。     

活细胞内微粒扩散运动研究

利用统计物理方法，研究活细胞内微粒无规则运动引起的扩散过程，得出了扩散系数的表示式．结果表明，活细胞内微粒的扩散系数等于布朗运动引起的扩散系数与活细胞内微粒跳跃运动引起的扩散系数之和     

分子马达运动机制的基本观点及力-化学耦合

从物理学角度讨论了分子马达定向运动机制的基本观点，介绍了用Fokker-Plank方程求解几率流的一般思想，以及分子马达力学和化学过程可能的耦合方式。     

柴油发动机尾气纳米颗粒演变的TEMOM-LES模型

 中国雾霾主要成因是包括柴油发动机在内的污染源排放导致的二次颗粒物, 本文针对柴油发动机尾气排放的颗粒物进行研究, 主要关注极大数目微纳米颗粒的综合效应导致的颗粒参数的变化, 次了解根据不同柴油含硫标准下产生的颗粒物的分布情况。通过把针对尺度谱演变问题的泰勒展开矩方法(TEMOM)和大涡模拟方法(LES)技术进行结合, 研究了排气管附近柴油二次颗粒物的演变过程, 并在相同流动工况条件下, 对加拿大、新加坡、欧盟、美国、俄罗斯、中国和日本不同国家和地区不同柴油含硫标准所导致的二次颗粒物的总颗粒数浓度、总体积浓度和颗粒大小进行了对比研究。结果显示, 颗粒物在近排气管处主要分布在射流剪切层, 颗粒数浓度和颗粒物直径的最大值在距离喷嘴0.6 m 附近产生, 在射流下游, 射流与下游空气混合稀释效应明显, 颗粒数浓度和颗粒直径趋于一稳定值。通过研究时间平均颗粒场的分布发现, 低燃硫量柴油尾气产生的颗粒数浓度比高燃硫量产生的颗粒数浓度低4 个数量级, 产生的颗粒体积浓度最大相差6 个数量级。     

有限粒子数费米系统温度对顺磁性的影响

根据弱磁场中理想费米气体的粒子数N+的几率分布函数G(β,N+),运用理论解析与数值模拟相结合的方法,研究了有限粒子数理想费米系统的泡利顺磁性,给出了粒子数临界值和上界磁场的解析式,分析了温度和粒子数对顺磁性的影响.研究表明,温度趋于费米温度时,极限磁化率与平均磁化率的偏差减小;当温度高于费米温度时,极限磁化率与平均磁...     

Movement of microtubules by single kinesin molecules

Kinesin is a motor protein that uses energy derived from ATP hydrolysis to move organelles along microtubules. Using a new technique for measuring the movement produced in vitro by individual kinesin molecules, it is shown that a single kinesin molecule can move a microtubule for several micrometers. New information about the mechanism of force generation by kinesin is presented.     

Resolution of distinct rotational substeps by submillisecond kinetic analysis of F1-ATPase

The enzyme F1-ATPase has been shown to be a rotary motor in which the central gamma-subunit rotates inside the cylinder made of alpha3beta3 subunits. At low ATP concentrations, the motor rotates in discrete 120 degrees steps, consistent with sequential ATP hydrolysis on the three beta-subunits. The mechanism of stepping is unknown. Here we show by high-speed imaging that the 120 degrees step consists of roughly 90 degrees and 30 degrees substeps, each taking only a fraction of a millisecond. ATP binding drives the 90 degrees substep, and the 30 degrees substep is probably driven by release of a hydrolysis product. The two substeps are separated by two reactions of about 1 ms, which together occupy most of the ATP hydrolysis cycle. This scheme probably applies to rotation at full speed ( approximately 130 revolutions per second at saturating ATP) down to occasional stepping at nanomolar ATP concentrations, and supports the binding-change model for ATP synthesis by reverse rotation of F1-ATPase.     

Highly coupled ATP synthesis by F1-ATPase single molecules

F1-ATPase is the smallest known rotary motor, and it rotates in an anticlockwise direction as it hydrolyses ATP. Single-molecule experiments point towards three catalytic events per turn, in agreement with the molecular structure of the complex. The physiological function of F1 is ATP synthesis. In the ubiquitous F0F1 complex, this energetically uphill reaction is driven by F0, the partner motor of F1, which forces the backward (clockwise) rotation of F1, leading to ATP synthesis. Here, we have devised an experiment combining single-molecule manipulation and microfabrication techniques to measure the yield of this mechanochemical transformation. Single F1 molecules were enclosed in femtolitre-sized hermetic chambers and rotated in a clockwise direction using magnetic tweezers. When the magnetic field was switched off, the F1 molecule underwent anticlockwise rotation at a speed proportional to the amount of synthesized ATP. At 10 Hz, the mechanochemical coupling efficiency was low for the alpha3beta3gamma subcomplex (F1-epsilon)), but reached up to 77% after reconstitution with the epsilon-subunit (F1+epsilon)). We provide here direct evidence that F1 is designed to tightly couple its catalytic reactions with the mechanical rotation. Our results suggest that the epsilon-subunit has an essential function during ATP synthesis.     

Electrically driven directional motion of a four-wheeled molecule on a metal surface

Propelling single molecules in a controlled manner along an unmodified surface remains extremely challenging because it requires molecules that can use light, chemical or electrical energy to modulate their interaction with the surface in a way that generates motion. Nature's motor proteins have mastered the art of converting conformational changes into directed motion, and have inspired the design of artificial systems such as DNA walkers and light- and redox-driven molecular motors. But although controlled movement of single molecules along a surface has been reported, the molecules in these examples act as passive elements that either diffuse along a preferential direction with equal probability for forward and backward movement or are dragged by an STM tip. Here we present a molecule with four functional units--our previously reported rotary motors--that undergo continuous and defined conformational changes upon sequential electronic and vibrational excitation. Scanning tunnelling microscopy confirms that activation of the conformational changes of the rotors through inelastic electron tunnelling propels the molecule unidirectionally across a Cu(111) surface. The system can be adapted to follow either linear or random surface trajectories or to remain stationary, by tuning the chirality of the individual motor units. Our design provides a starting point for the exploration of more sophisticated molecular mechanical systems with directionally controlled motion.     

Four ATP-binding sites in the midregion of the beta heavy chain of dynein.

The 'motor' proteins of eukaryotic cells contain specialized domains that hydrolyse ATP to produce force and movement along a cytoskeletal polymer (actin in the case of the myosin family; microtubules in the case of the kinesin family and dyneins). There are motor-protein superfamilies in which each member has a conserved force-generating domain joined to a different 'tail' which conveys specific attachment properties. The minus-end-directed microtubule motors, the dyneins, may also constitute a superfamily of force-generating proteins with distinct attachment domains. Axonemal outer-arm dynein from sea urchin spermatozoa is a multimeric protein consisting of two heavy chains (alpha and beta) with ATPase activity, three intermediate chains and several light chains. Here I report the sequence of cloned complementary DNA encoding the beta heavy chain of a dynein motor molecule. The predicted amino-acid sequence reveals four ATP-binding consensus sequences in the central domain. The dynein beta heavy chain is thought to associate transiently with a microtubule during ATP hydrolysis, but the ATP-dependent microtubule-binding sequence common to the kinesin superfamily is not found in the dynein beta heavy chain. These unique features distinguish the dynein beta heavy chain from other motor protein superfamilies and may be characteristic of the dynein superfamily.     

Single-molecule analysis of DNA uncoiling by a type II topoisomerase

Type II DNA topoisomerases are ubiquitous ATP-dependent enzymes capable of transporting a DNA through a transient double-strand break in a second DNA segment. This enables them to untangle DNA and relax the interwound supercoils (plectonemes) that arise in twisted DNA. In vivo, they are responsible for untangling replicated chromosomes and their absence at mitosis or meiosis ultimately causes cell death. Here we describe a micromanipulation experiment in which we follow in real time a single Drosophila melanogaster topoisomerase II acting on a linear DNA molecule which is mechanically stretched and supercoiled. By monitoring the DNA's extension in the presence of ATP, we directly observe the relaxation of two supercoils during a single catalytic turnover. By controlling the force pulling on the molecule, we determine the variation of the reaction rate with the applied stress. Finally, in the absence of ATP, we observe the damping of a DNA crossover by a single topoisomerase on at least two different timescales (configurations). These results show that single molecule experiments are a powerful new tool for the study of topoisomerases.     

Translocation step size and mechanism of the RecBC DNA helicase

DNA helicases are ubiquitous enzymes that unwind double-stranded DNA. They are a diverse group of proteins that move in a linear fashion along a one-dimensional polymer lattice--DNA--by using a mechanism that couples nucleoside triphosphate hydrolysis to both translocation and double-stranded DNA unwinding to produce separate strands of DNA. The RecBC enzyme is a processive DNA helicase that functions in homologous recombination in Escherichia coli; it unwinds up to 6,250 base pairs per binding event and hydrolyses slightly more than one ATP molecule per base pair unwound. Here we show, by using a series of gapped oligonucleotide substrates, that this enzyme translocates along only one strand of duplex DNA in the 3'-->5' direction. The translocating enzyme will traverse, or 'step' across, single-stranded DNA gaps in defined steps that are 23 (+/-2) nucleotides in length. This step is much larger than the amount of double-stranded DNA that can be unwound using the free energy derived from hydrolysis of one molecule of ATP, implying that translocation and DNA unwinding are separate events. We propose that the RecBC enzyme both translocates and unwinds by a quantized, two-step, inchworm-like mechanism that may have parallels for translocation by other linear motor proteins.     

Single kinesin molecules studied with a molecular force clamp.

Kinesin is a two-headed, ATP-driven motor protein that moves processively along microtubules in discrete steps of 8 nm, probably by advancing each of its heads alternately in sequence. Molecular details of how the chemical energy stored in ATP is coupled to mechanical displacement remain obscure. To shed light on this question, a force clamp was constructed, based on a feedback-driven optical trap capable of maintaining constant loads on single kinesin motors. The instrument provides unprecedented resolution of molecular motion and permits mechanochemical studies under controlled external loads. Analysis of records of kinesin motion under variable ATP concentrations and loads revealed several new features. First, kinesin stepping appears to be tightly coupled to ATP hydrolysis over a wide range of forces, with a single hydrolysis per 8-nm mechanical advance. Second, the kinesin stall force depends on the ATP concentration. Third, increased loads reduce the maximum velocity as expected, but also raise the apparent Michaelis-Menten constant. The kinesin cycle therefore contains at least one load-dependent transition affecting the rate at which ATP molecules bind and subsequently commit to hydrolysis. It is likely that at least one other load-dependent rate exists, affecting turnover number. Together, these findings will necessitate revisions to our understanding of how kinesin motors function.