应用主方程方法研究分子马达的定向运动

利用主方程的方法,研究了在一维三态周期跳跃模型下分子马达的定向运动。首先假定马达在任意两个相邻状态之间的跃迁距离（substeps）相等,对于给定的任意初始分布,得出了与时间有关的几率分布的解析表达式,包括到达稳态之前的所有的瞬态过程,由此可获得马达在各个时刻的漂移速率v、扩散系数D以及描述马达随机性质的随机参数r(randomness parameter）。同时不计算了马达到达稳态所需要的特征时间。根据马达的运动特点,我们又把以上结果推广到了不等间隔的情况,并引入了外力分配系数θj^ 和θj^-来表征外力对跃迁率的影响程度,以便于研究马达在拖动负载运动时的动力学行为,使之更符合生物化学的实际。并把计算结果（漂移速率v和随机参数r分别随[ATP]和外力f的变化关系）同实验进行了比较,与实验值符合较好。     

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。     

马达蛋白定向运动及能量转换效率的研究

通过建立非平衡涨落下的随机跃迁的两态模型,并利用非对称的周期势和Fokker-Planck方程及其本征值法计算两态模型的几率流和稳态几率流密。结果表明马达蛋白的定向运动与有效势的整体倾斜斜率有关,定性讨论了系统能量转换效率与负载有关。     

生物体内的纳米机器——分子马达

分子马达是生物体内具有马达功能的一类蛋白质大分子纳米机器,可以执行完成生命体内的一切活动,包括肌肉的收缩、细胞内部物质的运输、遗传物质(DNA)的复制、细胞的分裂等等。按照分子马达的不同种类,介绍了各类线性分子马达(如驱动蛋白、动力蛋白和肌球蛋白)的结构、运动方式、主要功能等生物特征,并介绍了旋转分子马达(如ATP合酶)的生物特征,最后进行总结,展望未来。     

肌球蛋白Ⅵ定向运动的蒙特卡罗模拟

根据myosin Ⅵ分子马达头部核苷的变化建立一个四态循环,然后利用蒙特卡罗方法模拟分子马达的动力学性质,讨论了myosin Ⅵ速度、滞留时间与溶液中ATP浓度、ADP浓度和负载力F的关系。模拟得到：myosin Ⅵ会在轨道微丝上进行梯跳运动并且每次在微丝上的滞留时间并不相同;另外,myosin Ⅵ的速度会随着ATP浓度的增加而增大,随着ADP浓度和负载力的增加而减小;负载力对myosin Ⅵ在胞内执行输运还是连接功能起一定的调节作用。     

纳米机器——分子马达

介绍了细胞内分子马达的能量转化途径,几种纳米分子马达如驱动蛋白、动力蛋白、肌球蛋白和旋转马达的结构和功能,并展望了分子马达对人类的贡献。     

构建“小”的艺术——从分子开关到分子马达

生物体的复杂结构和功能为我们提供了启发和挑战,即如何在分子水平构建纳米结构,并控制它的功能。通过＂自下而上＂的路线,我们着重在以下方面进行了探索：组装对外界刺激具有响应性的纳米体系,其中关键是在分子和超分子水平控制它的动态过程。分子开关是受外界刺激控制的单元,并可作为分子存储和电子元件。本文介绍了一类受光控制的分子开关,由于光控的简单性和高效性,此类光分子开关有望在分子水平的信息存储领域展现重要的应用价值。此外,通过将另一类光分子开关螺吡喃与通道蛋白结合,成功实现了蛋白孔的光控开关,可以被称为＂分子阀门＂,对未来的可控药物释放提供了很好的模型。分子马达是对纳米科学的巨大挑战,并将是未来分子机器的核心组成部分。本文介绍了新型的光驱动分子马达,对外界能量的利用使马达能够进行循环的定向运动,并且对马达分子结构的设计,能够构建出速度更快的第二代光驱动分子马达。然后,通过化学方法能够将该马达固定在纳米颗粒以至宏观界面的表面上,马达仍然能够受光驱动而高效运行。最后,本文展示了分子马达的一些应用,例如,马达的运动能够引起与之结合的高分子体系、液晶,甚至宏观物体的变化。     

细菌鞭毛马达——一种卓越的分子机器

鞭毛马达(flagellar motor)是一种分子旋转马达,它在细菌鞭毛的结构与功能中起着中心作用.鞭毛马达的结构已基本清楚,主要由Mot A、Mot B、Fli G、Fli M和Fli N 5种蛋白组成定子(stator)和转子(rotor),其驱动力来自于跨膜的H⁺或Na⁺流.目前对鞭毛马达的旋转动力学及旋转力矩产生机制已有初步的了解.鞭毛马达可作为研究分子旋转马达的理想模型,对其深入研究将有助于认识生物能量转化利用及细胞运动的机制并具有广泛的生物学意义.     

分子马达生物传感器检测食源性轮状病毒

通过分子马达生物传感器技术建立一种特异、便捷、快速的食源性轮状病毒检测方法.以F0F1-ATPase为核心构建分子马达,以轮状病毒保守片段VP7设计各血清型通用探针,通过生物素-亲和素系统将探针与分子马达连接构建F0F1-ATPase分子马达检测装置.提取病毒RNA并将其与生物传感器结合的同时启动ATP合成,比较其荧光强度的差别,可以对样品中的RNA进行检测.此方法的病毒RNA检测灵敏度为0.005 ng/mL,对轮状病毒检测特异,与甲肝病毒、诺如病毒无交叉反应,在1h内即可完成检测.运用此方法随机检测15份样品,检测结果与RT-PCR一致.结果表明,分子马达生物传感器检测轮状病毒的方法灵敏、特异,可用于食源性轮状病毒的快速检测.     

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.     

分子发动机研究进展

分子发动机是利用化学能/化学势进行机械作功的生物大分子,包括线性分子发动机与旋转式分子发动机两大类.它们参与了胞质运输、DNA复制、基因转录、ATP合成／水解等一系列重要生命活动过程.目前对于各种分子发动机的结构及作用机制的研究取得了一些重要进展.     

The Relationship Between the Rate of Molecular Evolution and the Rate of Genome Rearrangement in Animal Mitochondrial Genomes

Evolution of mitochondrial genes is far from clock-like. The substitution rate varies considerably between species, and there are many species that have a significantly increased rate with respect to their close relatives. There is also considerable variation among species in the rate of gene order rearrangement. Using a set of 55 complete arthropod mitochondrial genomes, we estimate the evolutionary distance from the common ancestor to each species using protein sequences, tRNA sequences, and breakpoint distances (a measure of the degree of genome rearrangement). All these distance measures are correlated. We use relative rate tests to compare pairs of related species in several animal phyla. In the majority of cases, the species with the more highly rearranged genome also has a significantly higher rate of sequence evolution. Species with higher amino acid substitution rates in mitochondria also have more variable amino acid composition in response to mutation pressure. We discuss the possible causes of variation in rates of sequence evolution and gene rearrangement among species and the possible reasons for the observed correlation between the two rates. [Reviewing Editor: Dr. David Pollock]     

香紫苏开花期蒸腾和光合作用日变化特征及其影响因子研究

对开花期香紫苏功能叶片的蒸腾作用、光合作用日变化规律以及二者与环境因子之间的相互作用进行了研究.结果表明:处于花期的香紫苏蒸腾速率和气孔导度的日变化总体趋势是先升高后降低;不同花期净光合速率的日变化之间则存在明显的差别,初花期的净光合速率明显高于盛花期和终花期;湿度和光合有效辐射是影响香紫苏蒸腾作用的最主要因素,而光合有效辐射和CO2浓度变化则对香紫苏的净光合速率影响最大.     

A Tight-binding Molecular Dynamics Study of the Dissociation of Boron Clusters in c-Si

Boron clusters with silicon self-interstitials have been implicated in the phenomenon of transient enhanced diffusion (TED) following ion implantation of boron and subsequent annealing steps. This paper explores possible dissolution mechanisms for boron-interstitial clusters during the simulation of a typical annealing process. Using tight-binding molecular dynamics (TBMD) and employing a Goodwin-Skinner-Pettifor sp-based TB model, we have been able to observe the complete dissolution of a B 4 I 4 cluster into the surrounding crystalline silicon matrix. Many unsuccessful attempts to observe dissolution are also presented, highlighting the effect of cluster stability, temperature and the role of vacancies in cluster dissolution. Though we can make no unambiguous statements on the definitive dissolution mechanism of boron-defect clusters based on one successful dissolution event, we can hint at key events that appear to be important, such as the diffusion of self-interstitials (presciently predicted by Pelaz et al. ), the "stranding" of boron atoms in their wake, and the importance of mobile boron-self-interstitial (B-I) pairs. The intrinsic diffusivity of boron in a c-Si lattice and its retardation of the diffusivity of Si self-interstitials is also discussed.     

Bayesian Coalescent Analysis Reveals a High Rate of Molecular Evolution in GB Virus C

GB virus C/hepatitis G (GBV-C) is an RNA virus of the family Flaviviridae. Despite replicating with an RNA-dependent RNA polymerase, some previous estimates of rates of evolutionary change in GBV-C suggest that it fixes mutations at the anomalously low rate of ∼10⁻⁷ nucleotide substitution per site, per year. However, these estimates were largely based on the assumption that GBV-C and its close relative GBV-A (New World monkey GB viruses) codiverged with their primate hosts over millions of years. Herein, we estimated the substitution rate of GBV-C using the largest set of dated GBV-C isolates compiled to date and a Bayesian coalescent approach that utilizes the year of sampling and so is independent of the assumption of codivergence. This revealed a rate of evolutionary change approximately four orders of magnitude higher than that estimated previously, in the range of 10⁻² to 10⁻³ sub/site/year, and hence in line with those previously determined for RNA viruses in general and the Flaviviridae in particular. In addition, we tested the assumption of host-virus codivergence in GBV-A by performing a reconciliation analysis of host and virus phylogenies. Strikingly, we found no statistical evidence for host-virus codivergence in GBV-A, indicating that substitution rates in the GB viruses should not be estimated from host divergence times.     

The role of the dynein stalk in cytoplasmic and flagellar motility

We have recently identified a microtubule binding domain within the motor protein cytoplasmic dynein. This domain is situated at the end of a slender 10–12 nm projection which corresponds to the stalks previously observed extending from the heads of both axonemal and cytoplasmic dyneins. The stalks also correspond to the B-links observed to connect outer arm axonemal dyneins to the B-microtubules in flagella and constitute the microtubule attachment sites during dynein motility. The stalks contrast strikingly with the polymer attachment domains of the kinesins and myosins which are found on the surface of the motor head. The difference in dynein's structural design raises intriguing questions as to how the stalk functions in force production along microtubules. In this article, we attempt to integrate the myriad of biochemical and EM structural data that has been previously collected regarding dynein with recent molecular findings, in an effort to begin to understand the mechanism of dynein motility. Received: 13 March 1998 / Revised version: 17 April 1998 / Accepted: 17 April 1998     

放线菌的分子分类

在放线菌分类学研究中,最初是根据形态特征、生理生化特征等表观分类学特征进行研究。随着分子生物学的飞速发展,放线菌的分类鉴定亦从传统的表型分类进入到各种基因型分类水平。分子分类在放线菌分类研究中起到越来越重要的作用,目前放线菌的分子分类研究主要包括:G Cmol%测定、DNA杂交、核酸结构分析以及DNA指纹图谱分析等方面。     

应用PCR技术定向引入DNA小片段的策略

描述一种应用PCR技术定向引入DNA小片段和特异酶切位点的方法。为了获得m2/loxp66EGFPloxp71基因片段。根据EGFP基因序列,设计一对特异引物,上、下游引物分别引入m2/loxp66、loxp71序列和Xhol、Mlu1酶切位点。以pEGFPN1质粒为模板,采用PCR扩增以合成DNA双链,插入到克隆载体pMD18T。对重组子测序结果表明,实现了DNA小片段和酶切位点的定向引入。