一个改进的马尔科夫模型

离子通道是细胞膜里的大分子孔道,是跨越细胞膜里的蛋白质大分子,是神经、肌肉等细胞膜兴奋性的基础.人体细胞均具有完成特殊功能的离子通道,构建离子通道,尤其其门控行为的动力学模型,对于研究离子通道的相关课题具有重要意义.离子通道的开关反映了蛋白质构象变化的动力学过程.本文介绍了细胞膜离子通道的基本内容和几种常用模型,并根据Markov链对离子通道门控行为的一个二态(闭、开)模型的Markov过程进行了改进,得到了包含失活状态的离子通道门控行为的Markov模型.     

离子通道数学模型

介绍了离子通道记录的记忆性及其反映这种记忆的齐次Markov模型和具有随机环境的Markov模型,并且上述模型较好的解决“Omission”问题,讨论了模型反映的离子通道记录的物理及生理机制,认为离子通道记录记忆性反映离子通道记忆性。     

电压门控性离子通道的药理

一、引言离子通道是细胞膜上的特殊蛋白质大分子,在脂质双层膜上构成具有高度选择性的亲水性孔道,容许适当大小和适当电荷的离子通过。细胞膜内、外离子浓度差决定离子扩散的方向。大多数离子通道大部分时间是关闭的,只是在特殊刺激下,打开的机率才大大增加,这种现象称为门控(gating)。通道蛋白的构象     

PC12细胞钾离子通道门控动力学随机建模与参数估计(Ⅰ)

本文以PC12细胞钾离子通门控机理分析为例证,探索离子通道门控动力学马尔科夫模型的建模方法,并详述建模过程,为通过研究者提供启示与借鉴．在此基础上提出PC12细胞钾离子通道门控动力学的三个备择方案,然后试用Ball等人建议的适用于片膜中只含一个通道记录的极大似然算法估计速率参数,根据AIC及SC准则将模型作了比较,选择较适宜的模型刻划PC12细胞钾离子通道门控动力学．     

动物离子通道毒素与药物开发

就离子通道和动物离子通道毒素的来源、种类、特性及其对新药开发的意义进行了综述。各种来源的动物毒素通常分子量较小,富含二硫键,是直接作用于分子靶标（如离子通道、受体及酶）的小分子蛋白质。很多动物毒素对电压门控离子通道具有高度的专一性和有效性,具有独特、简洁的三维空间结构。其对新药的发现、设计以及寻找潜在的治疗靶标具有重要的指导意义。     

荧光膜片钳新技术的应用及进展

荧光膜片钳(patch-clamp fluorometry,PCF)是将离子通道蛋白局部的构象变化和门控紧密结合,实时记录同一膜片上离子通道的荧光和电流信号的创新型生物物理学技术,其特点是将经典的膜片钳和现代光学记录结合起来,实时同步完美呈现离子通道执行其功能时的蛋白质构象信息.与研究结构的X射线和冰冻电镜不同,荧光膜片钳提供离子通道处于真实细胞膜生理环境并执行功能的实时动态结构信息.随着新的光学技术、显微成像技术、图像分析技术等的进步,大大地扩展了荧光膜片钳技术的记录范围、分辨精度及敏感度,使研究者以前所未有的时空分辨率来实时观察和记录离子通道蛋白的结构变化.     

电压门控离子通道功能与结构分子模型

离子通道是细胞膜上特殊跨膜蛋白构成的亲水孔道,越来越多的证据表明其与兴奋性,腺体分泌、机体运动、甚至学习和记忆行为等重要生理现象密切相关,由此该领域成为当今年生命学科广为注目的前沿之一。本将简要介绍离子通道的分类和功能,并侧重阐明通道压控原理有压控通道的跨膜拓扑结构和功能分子模型。     

景观动态的Markov模型研究——以长白山自然保护区为例

在 Markov模型假设的基础上 ,利用长白山自然保护区 1975年 MSS、1985年和 1997年 TM卫星遥感数据 ,在遥感图象处理软件和 GIS软件协助下 ,对遥感影像的计算机监督分类结果 (共分为 13类 )进行处理 ,对 Markov模型的可利用性进行分析与检验 ,得出长白山自然保护区景观变化无后效性 ,符合 Markov模型条件。根据 1985～ 1997年转移概率计算步长 10 a(1985～ 1995年 )的转移概率矩阵 ,从 1975年计算 1985年各景观类型的面积与 1985年各景观类型的实际面积值对比 ,计算得 χ2 >χ20 .0 5(12 ) ;再分别用 1975～ 1985年和 1985～ 1997年的转移矩阵计算 1995年和 2 0 4 7年各景观类型的面积 ,分析得χ2 >χ20 .0 5(12 ) ;对两阶段的转移概率矩阵分析得到 χ2 >χ20 .0 5(14 4 ) ;说明两阶段的 Markov转移过程不具同一性 ,属于两个不同的 Markov过程。不同景观类型转移方式对χ2 值的贡献率可以说明其对景观动态的重要性 ,分析结果表明有重要贡献的类型分别为 :阔叶红松林 5 2 .0 0 % >山杨白桦林 2 4 .6 6 % >云冷杉林 11.4 2 % >落叶松林 2 .4 3% ,说明这 4种景观类型的转移方式对长白山自然保护区的景观动态起重要作用 ,尤其以阔叶松林的作用最大 ;同时对 Markov模型在长白山自然保护区长期景观变化预测的可     

味觉感受细胞离子通道和动作电位的建模与仿真

结合膜片钳测量的味觉感受细胞离子通道实验数据,提出了一个哺乳动物味觉感受细胞动作电位的数学模型.首先,建立了味觉感受细胞的电压门控Na＋通道和外向延迟整流K＋通道的模型,在此基础上建立了味觉感受细胞的单细胞计算模型.其次,仿真研究了味觉感受细胞在电刺激和酸味刺激下产生的动作电位,以及离子通道动力学特性对其的影响.该模型对于研究味觉感受细胞在味觉物质刺激下产生的动作电位及其离子通道的工作机制,以及味觉信息在外周神经的传递和信息编码具有指导意义。     

大电导钾离子通道(BK)结构与功能的研究进展

大电导钙离子激活钾通道(BK)是细胞膜上唯一接受细胞内Ca2+和膜电位双重调控的离子通道.最新发表的关于BK通道电镜结构及其胞质功能域的晶体结构的文章,第一次展示了BK通道各亚基的组装,并证实通道各功能域在通道门控机制中存在紧密的相互作用.近年来,针对BK通道的功能调节及其门控动力学模拟的研究取得较多进展,有助于更好地理解BK通道发挥生理功能的门控机制,并揭示BK通道相关疾病的病理生理学基础.     

Computing transient gating charge movement of voltage-dependent ion channels

The opening of voltage-gated sodium, potassium, and calcium ion channels has a steep relationship with voltage. In response to changes in the transmembrane voltage, structural movements of an ion channel that precede channel opening generate a capacitative gating current. The net gating charge displacement due to membrane depolarization is an index of the voltage sensitivity of the ion channel activation process. Understanding the molecular basis of voltage-dependent gating of ion channels requires the measurement and computation of the gating charge, Q. We derive a simple and accurate semianalytic approach to computing the voltage dependence of transient gating charge movement (Q–V relationship) of discrete Markov state models of ion channels using matrix methods. This approach allows rapid computation of Q–V curves for finite and infinite length step depolarizations and is consistent with experimentally measured transient gating charge. This computational approach was applied to Shaker potassium channel gating, including the impact of inactivating particles on potassium channel gating currents.     

Effects of stochastic channel gating and distribution on the cardiac action potential

Ion channels exhibit stochastic conformational changes determining their gating behavior. In addition, the process of protein turnover leads to a natural variability of the number of membrane and gap junctional channels. Nevertheless, in computational models, these two aspects are scarcely considered and their impacts are largely unknown. We investigated the effects of stochastic current fluctuations and channel distributions on action potential duration (APD), intercellular conduction delays (ICDs) and conduction blocks using a modified ventricular cell model (Rudy et al.) with Markovian formulations of the principal ion currents (to simulate their stochastic open-close gating behavior) and with channel counts drawn from Poisson distributions (to simulate their natural variability). In single cells, APD variability (coefficient of variation: 1.6% at BCL=1000 ms) was essentially caused by stochastic channel gating of I_Ks, persistent I_Na and I_Ca,L. In cell strands, ICD variability induced by stochastic channel gating and Poissonian channel distributions was low under normal conditions. Nonetheless, at low intercellular coupling levels, Poissonian gap junctional channel distribution resulted in a large ICD variability (coefficient of variation >20%), highly heterogeneous conduction patterns and conduction blocks. Therefore, the stochastic behavior of current fluctuations and channel distributions can contribute to the heterogeneity of conduction patterns and to conduction block, as observed previously in experiments in cardiac tissue with altered intercellular coupling.     

Statistical properties of ion channel records. Part II: estimation from the macroscopic current

Macroscopic ion channel current is the summation of the stochastic records of individual channel currents and therefore relates to their statistical properties. As a consequence of this relationship, it may be possible to derive certain statistical properties of single channel records or even generate some estimates of the records themselves from the macroscopic current when the direct measurement of single channel currents is not applicable. We present a procedure for generating the single channel records of an ion channel from its macroscopic current when the stochastic process of channel gating has the following two properties: (I) the open duration is independent of the time of opening event and has a single exponential probability density function (pdf), (II) all the channels have the same probability to open at time t. The application of this procedure is considered for cases where direct measurement of single channel records is difficult or impossible. First, the probability density function (pdf) of opening events, a statistical property of single channel records, is derived from the normalized macroscopic current and mean channel open duration. Second, it is shown that under the conditions (I) and (II), a non-stationary Markov model can represent the stochastic process of channel gating. Third, the non-stationary Markov model is calibrated using the results of the first step. The non-stationary formulation increases the model ability to generate a variety of different single channel records compared to common stationary Markov models. The model is then used to generate single channel records and to obtain other statistical properties of the records. Experimental single channel records of inactivating BK potassium channels are used to evaluate how accurately this procedure reconstructs measured single channel sweeps.     

Gating of a voltage-dependent channel (colicin E1) in planar lipid bilayers: translocation of regions outside the channel-forming domain

Summary C-terminal fragments of colicin E1, ranging in mol wt from 14.5 to 20kD, form channels with voltage dependence and ion selectivity qualitatively similar to those of whole E1, placing an upper limit on the channel-forming domain. Under certain conditions, however, the gating kinetics and ion selectivity of channels formed by these different E1 peptides can be distinguished. The differences in channel behavior appear to be correlated with peptide length. Enzymatic digestion with trypsin of membrane-bound E1 peptides converts channel behavior of longer peptides to that characteristic of channels formed by shorter fragments. Apparently trypsin removes segments of protein N-terminal to the channel-forming region, since gating behavior of the shortest fragment is little affected by the enzyme. The success of this conversion depends on the side of the membrane to which trypsin is added and on the state, open or closed, of the channel. Trypsin modifies only closed channels from thecis side (the side to which protein has been added) and only open channels from thetrans side. These results suggest that regions outside the channel-forming domain affect ion selectivity and gating, and they also provide evidence that large protein segments outside the channel-forming domain are translocated across the membrane with channel gating.     

Exploring voltage-dependent ion channels in silico by hysteretic conductance

Kinetic models of voltage-dependent ion channels are normally inferred from time records of macroscopic current relaxation or microscopic single channel data. A complementary explorative approach is outlined. Hysteretic conductance refers to conductance delays in response to voltage changes, delays at either macroscopic or microscopic levels of observation. It enables complementary assessments of model assumptions and gating schemes of voltage-dependent channels, e.g. independent versus cooperative gating, and multiple gating modes. Under the Hodgkin-Huxley condition of independent gating, and under ideal measurement conditions, hysteretic conductance makes it also possible to estimate voltage-dependent rate functions. The argument is mainly theoretical, based on experimental observations, and illustrated by simulations of Markov kinetic models.     

Insights into the biophysical properties of GABA(A) ion channels: modulation of ion permeation by drugs and protein interactions

The fundamental properties of ion channels assure their selectivity for a particular ion, its rapid permeation through a central pore and that such electrical activity is modulated by factors that control the opening and closing (gating) of the channel. All cell types possess ion channels and their regulated flux of ions across the membrane play critical roles in all steps of life. An ion channel does not act alone to control cell excitability but rather forms part of larger protein complexes. The identification of protein interaction partners of ion channels and their influence on both the fundamental biophysical properties of the channel and its expression in the membrane are revealing the many ways in which electrical activity may be regulated. Highlighted here is the novel use of the patch clamp method to dissect out the influence of protein interactions on the activity of individual GABA(A) receptors. The studies demonstrate that ion conduction is a dynamic property of a channel and that protein interactions in a cytoplasmic domain underlie the channel's ability to alter ion permeation. A structural model describing a reorganisation of the conserved cytoplasmic gondola domain and the influence of drugs on this process are presented.     

Stochastic Ion Channel Gating in Dendritic Neurons: Morphology Dependence and Probabilistic Synaptic Activation of Dendritic Spikes

Neuronal activity is mediated through changes in the probability of stochastic transitions between open and closed states of ion channels. While differences in morphology define neuronal cell types and may underlie neurological disorders, very little is known about influences of stochastic ion channel gating in neurons with complex morphology. We introduce and validate new computational tools that enable efficient generation and simulation of models containing stochastic ion channels distributed across dendritic and axonal membranes. Comparison of five morphologically distinct neuronal cell types reveals that when all simulated neurons contain identical densities of stochastic ion channels, the amplitude of stochastic membrane potential fluctuations differs between cell types and depends on sub-cellular location. For typical neurons, the amplitude of membrane potential fluctuations depends on channel kinetics as well as open probability. Using a detailed model of a hippocampal CA1 pyramidal neuron, we show that when intrinsic ion channels gate stochastically, the probability of initiation of dendritic or somatic spikes by dendritic synaptic input varies continuously between zero and one, whereas when ion channels gate deterministically, the probability is either zero or one. At physiological firing rates, stochastic gating of dendritic ion channels almost completely accounts for probabilistic somatic and dendritic spikes generated by the fully stochastic model. These results suggest that the consequences of stochastic ion channel gating differ globally between neuronal cell-types and locally between neuronal compartments. Whereas dendritic neurons are often assumed to behave deterministically, our simulations suggest that a direct consequence of stochastic gating of intrinsic ion channels is that spike output may instead be a probabilistic function of patterns of synaptic input to dendrites.     

Gating kinetics of potassium channel in rat dorsal root ganglion neurons analyzed with fractal model

The kinetics of ion channels have been widely modeled as a Markov process. In these models it is assumed that the channel protein has a small number of discrete conformational states and kinetic rate constants connecting these states are constant. To study the gating kinetics of voltage-dependent K(+) channel in rat dorsal root ganglion neurons, K(+) channel current were recorded using cell-attached patch-clamp technique. The K(+) channel characteristic of kinetics were found to be statistically self-similar at different time scales as predicted by the fractal model. The fractal dimension D for the closed times and for the open times depend on the pipette potential. For the open and closed times of kinetic setpoint, it was found dependent on the applied pipette potential, which indicated that the ion channel gating kinetics had nonlinear kinetic properties. Thus, the open and closed durations, which had the voltage dependence of the gating of this ion channel, were well described by the fractal model.     

Energetics of gating MscS by membrane tension in azolectin liposomes and giant spheroplasts

Mechanosensitive (MS) ion channels are molecular sensors that detect and transduce signals across prokaryotic and eukaryotic cell membranes arising from external mechanical stimuli or osmotic gradients. They play an integral role in mechanosensory responses including touch, hearing, and proprioception by opening or closing in order to facilitate or prevent the flow of ions and organic osmolytes. In this study we use a linear force model of MS channel gating to determine the gating membrane tension (γ) and the gating area change (ΔA) associated with the energetics of MscS channel gating in giant spheroplasts and azolectin liposomes. Analysis of Boltzmann distribution functions describing the dependence of MscS channel gating on membrane tension indicated that the gating area change (ΔA) was the same for MscS channels recorded in both preparations. The comparison of the membrane tension (γ) gating the channel, however, showed a significant difference between the MscS channel activities in these two preparations.