膜脂依赖的CD3构象改变为TCR复合体功能多态性提供了结构基础

<正>T淋巴细胞通过TCR-CD3复合体与抗原呈递细胞MHC结合,从而特异性识别抗原,启动适应性免疫应答。TCR不仅"开"和"关"两种状态,将随着抗原的不同呈现不同的结构和功能。TCR-CD3复合物有四个亚基,分别为TCRαβ、CD3εδ、CD3εγ、CD3ζζ。其中TCRα、β亚基胞内段太短无法将信号直接传递至胞内,需借助CD3进行传导。已知免疫受体酪氨酸激活基序(ITAM)是TCR免疫信号传递的重要途径,而ITAM存在于所有的CD3链中。相似的,CD3胞内段的碱性残基富集区     

果蝇中整合素αPS3／βν介导吞噬细胞吞噬凋亡细胞和细菌

整合素是由2个跨膜α和β亚基组成的异源二聚体,具有各种细胞功能。整合素βν是果蝇整合素的β亚基,参与吞噬凋亡的细胞和细菌。该研究搜寻了与βν亚基形成复合物并共同作用的α亚基,通过RNAi感染动物模型检测发现,αPS3（而不是其他4个α亚基）是果蝇胚胎有效吞噬凋亡细胞所必需的。αPS3编码scb突变时,包括缺失突变、插入P元件或改变核苷酸序列,都能降低吞噬能力。这种降低作用能被过表达scb逆转。此外,用干扰RNA（RNAi）同时干扰苍蝇中αPS3和βν后,其吞噬能力与干扰任一个亚基相同。αPS3缺失也能降低幼虫血细胞吞噬金黄色葡萄球菌的能力。采用免疫共沉淀分析化学交联处理的果蝇细胞系发现,αPS3与βν具有物理相互作用。结果提示,整合素αPS3／βν是果蝇吞噬细胞吞噬凋亡细胞和细菌的受体。     

β-TC3细胞膜与胰岛素受体结合G蛋白的鉴定

目的:用免疫共沉淀的方法检测β-TC3(小鼠胰岛β细胞瘤细胞)细胞膜中与胰岛素受体结合的G蛋白.方法:提取β-TC3细胞膜蛋白,通过免疫共沉淀及蛋白质印迹的方法,检测G蛋白α及β亚基的表达.结果:抗胰岛素受体抗体沉淀胰岛素受体结合的G蛋白复合物后,分别用抗胰岛素受体抗体、抗G蛋白α亚基抗体及抗G蛋白β亚基抗体,检测到胰岛素受体、G蛋白α亚基及G蛋白β亚基的表达.结论:在β-TC3细胞膜中,胰岛素受体与G蛋白共存,G蛋白α亚基及β亚基与胰岛素受体可能存在直接的相互作用.     

G—蛋白异三聚体（G—protein heterotrimer）的晶体结构

继１９９４年Ｓｉｇｌｅｒ－Ｈａｍｍ和Ｓｐｒａｎｇ－Ｇｉｌｍａｎ实验室报道Ｇｉα１的晶体结构之后,１９９５年１２月和１９９６年１月这两个实验室又相继报道了Ｇ－蛋白异三聚体（ＧαＧＤＰ）βγ和Ｇβγ二聚体的晶体结构,这些研究结果表明Ｇ－蛋白复合物象一台由操纵杆（受体）,开关（Ｇα）和螺旋浆（Ｇβγ）组成的信号转导纳米机器,并揭示了α和β亚基间可能存两种不同的功能界面,β和γ亚基间,α和γ的相互作用,以     

G－蛋白异三聚体（G－proteinheterotrimer）的晶体结构

继１９９４年Ｓｉｇｌｅｒ－ｈａｍｍ和Ｓｐｒａｎｇ－Ｇｉｌｍａｎ实验室报道了Ｇｉα１的晶体结构之后,１９９５年１２月和１９９６年１月这两个实验室又相继报道了Ｇ－蛋白异三聚体（ＧαＧＤＰ）βγ和Ｇβγ二聚体的晶体结构．这些研究结果表明Ｇ－蛋白复合物象一台由操纵杆（受体）、开关（Ｇα）和螺旋桨（Ｇβγ）组成的信号转导纳米机器,并揭示了α和β亚基间可能存在两种不同的功能界面,β和γ亚基间、α和γ的相互作用,以及信号传导过程中,ＧＴＰ诱导开关Ⅱ区重排和亚基解高的机制．βγ亚基能稳定α亚基和ＧＤＰ的紧密结合,使Ｇ－蛋白维持在失活状态．β亚基的ＷＤ４０重复序列形成７叶片的螺旋桨（ｓｅｖｅｎｆｏｌｄｐｒｏｐｅｌｌｅｒ）构造,每个叶片的外侧面显露出许多可变的接触位点．β亚基部分地为伸展的γ亚基包围。关键词     

棉蚜乙酰胆碱受体亚基的选择性剪接和多重转录起始位点分析

乙酰胆碱受体在神经突触传导过程中具有重要作用,也是氯化胆碱类杀虫剂的作用靶标。采用RACE技术,成功地从棉蚜中克隆了3个nAChR亚基,其中2个为α亚型, 1个为β亚型,分别命名为Agα1、Agα2和Agβ1。通过锚定mRNA的5′mG结构, 5′RACE结果表明Agβ1有三个不同的剪接变体,具有不同长度的5′UTR区,表明Agβ1亚基具有多重的转录起始位点。其中,最短的剪接变体Agβ1C在蛋白编码区域也存在选择性剪接,位于D环区域的186 bp碱基缺失。3′RACE实验结果表明,Agα1亚基虽然具有ploy ( A)和加尾信号AATAAA等完整的mRNA基因结构,但缺失了终止子和乙酰胆碱受体α亚基保守的第4个跨膜区,文中对此做了进一步分析。分子进化树的分析表明,昆虫乙酰胆碱受体亚基应当被划分为三个不同的亚类群αⅠ,αⅡandβ。本文的研究揭示了昆虫乙酰胆碱受体亚基复杂的基因结构[动物学报51 (5) : 867 -878 , 2005]。     

芋螺毒素与钙离子通道相互作用的计算机模拟

电压门控N－型钙离子通道是与神经元中释放的神经信号传递有关的跨细胞膜的特殊蛋白质分子,它由好几个蛋白质亚基组成,其中的α1亚基包含了电压敏感器和钙离子的选择性孔道,该亚基的一级结构已经发表,一般认为α1亚基包含4个重复单位（I－Ⅳ）,每个重复单位包括6段跨膜区（S1－S6）,其中跨膜区S4上有很多正电荷,被认为是通道的电压敏感器,S5和S6之间的连接区（P区）被认为是形成通道的门孔的部分,N－型钙离子通道能够被一些w-芋螺毒素特异性在阻断,这些ω－芋螺毒素的三维结构已经由二维核磁共振方法测定,尽管还没有被证实,但一般认为w-芋螺毒素占据了通道的孔道,有实验证明,钙离子第三个重复单位的P区（ⅢP区）是通道的芋螺毒素结合的主要部位,在本中,我们用分子模拟程序建模了ⅢP区的结构,为了通道的阻断机理有一个清楚的了解,我们利用分子对接程序模拟了IIIP区和三种芋螺毒素GVA,MVIIA和S03作用的理论模型,在我们的模型中,GVIA与钙通道的作用方式可能与MVIIA不同,而M VII A和SO3与钙通道的作用方式可能相同,我们还讨论了这些芋螺毒素中的关键残基的作用。     

膜结合型淋巴毒素及其LP—β亚基

淋巴毒素（ＬＴ）存在分泌型及膜结合型两种表达形式。膜型ＬＴ早由分泌型亚单位ＬＴ－α通过跨膜亚单位ＬＴ－β连续接在细胞膜上,构成一个异源三聚体结构。ＬＴ－β亚基为ＴＮＦ配体超家族成员之一,其相应的特异笥受体为ＴＮＦ受体相关蛋白（ＴＮＦＲｒｐ）,称作ＬＴ－β受体。膜型ＬＴ可能具有独特的生物学功能,特别是对正常淋巴结的发育形成可能起着重要作用。     

胰岛素受体结构与功能研究概况

胰岛素受体(IR)是由两个α-亚基和两个β-亚基构成的跨膜糖蛋白。α-亚基位于细胞表面,是胰岛素结合区域。β-亚基的1/3也位于细胞表面,其余2/3则跨膜并插入胞浆中,后者是IR的活力区域,具有受胰岛素调节的酪氨酸蛋白激酶活性,此活性受多位点磷酸化的调节并表现出变构酶行为。不同组织的IR在分子结构,化学性质和生理功能上均有差异,其中脑IR代表了IR的一个结构和功能亚型。IR的生物合成类似于胰岛素的生物合成。     

跨膜蛋白CD3ε与磷脂酰肌醇二磷酸在脂筏域体系中蛋白质-脂质相互作用的粗粒化模拟研究

细胞膜局部区域可形成富含饱和脂质、胆固醇、鞘脂的脂筏域作为其信号转导调控平台。传统实验手段在研究脂筏及其功能时受到系统复杂度高及区域结构瞬时性强等制约。近年来,分子动力学模拟技术为细胞膜的组织原则提供了重要的理论支撑,从简单的单一组分模型到多组分系统转变,最终形成了越来越多的细胞膜仿真模型。其中,粗粒化模拟由于其简化模型,可大副拓展模拟体系的复杂程度与模拟时间,在细胞膜以及蛋白质-脂质相互作用相关研究中得到了广泛应用。本文采用MARTINI粗粒化力场模拟,构建了一种含有阴离子脂质磷脂酰肌醇二磷酸(phosphatidylinositol diphosphate, PIP2)的混合膜体系。模拟结果表明,该体系在适当温度及饱和度条件下,能自发分层形成脂筏域;膜厚度、膜组分分布、膜组分流动性等多种参数均表明,脂筏结构形成且符合其结构特征;少量PIP2添加不影响分层特性且PIP2对脂筏具有显著亲和性。此外,利用该模型以跨膜信号蛋白CD3ε为例研究了脂筏域体系中蛋白质-脂质相互作用。结果表明,PIP2-CD3ε胞内区相互作用可能是脂筏招募CD3ε的驱动力,且该过程可受钙离子调控。本工作体现了粗粒化模拟在仿真膜相关研究中的巨大优势及良好应用前景。     

From Molecular to Process Simulation: Novel Approaches to the Prediction of Phase Equilibria and PVT Behavior Based on Molecular/Quantum Mechanics and Molecular Dynamics Simulations

Abstract

Actually, in modern process simulators, more than 75% of the code implemented is dedicated to physical properties estimation, calculation and predictions. Data banks storing pure component parameters and binary interaction parameters for phase equilibrium calculations are extensively used and continuously implemented in actual process simulators. This gives an idea of the important role physical properties availability plays in process simulation.

In this paper we propose a new way for coupling molecular and process simulation. The basic machinery is to resort to molecular/quantum mechanics and molecular dynamics simulation techniques for generating the parameters of some equations of state that will subsequently be used for the prediction of phase equilibria and PVT behavior of small and polymeric molecules as well. This information, in turn, will be used as input in the process simulator, thus creating a final and well-defined bridge between molecular and process simulations in chemical engineering.     

树干径流单因子模拟实验分析

树干径流是发生在森林生态系统中的重要水文现象之一。已往,有关这方面的观测研究工作并不少见,但主要侧重于野外实际观测。由于影响因素错综复杂,单因子对干流影响的分析得不出比较满意的结果。     

Biochemical simulations: stochastic, approximate stochastic and hybrid approaches

Computer simulations have become an invaluable tool to studythe sometimes counterintuitive temporal dynamics of (bio-)chemicalsystems. In particular, stochastic simulation methods have attractedincreasing interest recently. In contrast to the well-knowndeterministic approach based on ordinary differential equations,they can capture effects that occur due to the underlying discretenessof the systems and random fluctuations in molecular numbers.Numerous stochastic, approximate stochastic and hybrid simulationmethods have been proposed in the literature. In this article,they are systematically reviewed in order to guide the researcherand help her find the appropriate method for a specific problem.      

Computerized scheme for the reaction of hemoglobin with ligands

A scheme for the reaction of hemoglobin with ligands is described, which postulates the functional heterogeneity of the chains, considers all possible combinations of the distribution of the ligand on the four chains of hemoglobin, and does not require simplifying assumptions about the hemoglobin reactivity. Ten tetrameric species are considered, together with 16 reactions between these species, each with an on and an off rate constant. The dissociation of hemoglobin tetramers into dimers is also considered, with four on and four off rate constants for the reactions between dimers, and ten equilibrium constants for the reactions between tetramers and dimers. Moreover, some side reactions, such as the trapping of ligands by a hemoglobin competitor, are included. A FORTRAN program, suitable for microcomputers, is described for handling this scheme, with some examples showing its advantages.     

Molecular Dynamics Simulation of Protein Folding with Supersecondary Structure Constraints

We integrate molecular dynamics simulation methods with a newly developed supersecondary structure prediction method and compute the structure of a protein molecule, crambin. The computed structure is similar to the crystal structure with an rms error of 3.94 Å.     

Monte Carlo Study of Structural and Thermodynamic Properties of Liquid Chloroform Using a Five Site Model

A five site potential model combining Lennard–Jones plus Coulomb potential functions has been developed for chloroform molecule. The partial charges needed for Coulombic interactions were derived using the chelpg procedure implemented in the gaussian 92 program. These calculations were performed at the MP2 level with MC-311G* basis set for Cl and 6-311G** for C and H atoms. The parameters for the Lennard–Jones potentials were optimized to reproduce experimental values for the density and enthalpy of vaporization of the pure liquid at 298 K and 1 atm. The statistical mechanics calculations were performed with the Monte Carlo method in the isothermic and isobaric (NpT) ensemble. Besides the values obtained for density, ρ, and molar enthalpy of vaporization at constant pressure, Δ H_V, for liquid chloroform, results for molar volume, V_m, molar heat capacity, C_p, isobaric thermal expansivity, α_p, and isothermal compressibility, κ_T, for this pure liquid are also in very good agreement with experimental observations. Size effects on the values of thermodynamic properties were investigated. The potential model was also tested by computing the free energy for solvating one chloroform molecule into its own liquid at 298 K using a statistical perturbation approach. The result obtained compares well with the experimental value. Site–site pair correlation functions were calculated and are in good accordance with theoretical results available in the literature. Dipole–dipole correlation functions for the present five site model were also calculated at different carbon–carbon distances. These correlations were compared to those obtained using the four site model reported in the literature. An investigation of the solvent dependence of the relative free energy for cis/trans conversion of a hypothetical solute in TIP4P water and chloroform was accomplished. The results show strong interaction of water and chloroform molecules with the gauche conformer. The value obtained for the free energy barrier for cis/trans rotation in TIP4P water is higher than that for chloroform. This result is in agreement with the continuous theory for solvation as the conformer with higher dipole moment is more favoured by the solvent with higher dieletric constant. The results also show an increase in entropy as the solute goes from the cis to the trans geometry and this result is more appreciable in the aqueous solution. This revised version was published online in June 2006 with corrections to the Cover Date.     

常规模拟定位和CT模拟定位的比较

目的:对比食管癌放射治疗中CT模拟定位和常规模拟定位的优劣。方法:对60例食管中、下段癌患者,同时行CT扫描和常规模拟定位;用三维计划系统制定治疗方案,比较分析这两种定位方法所描述靶区肿瘤的最大直径和等剂量分布情况。结果:两种定位方法肿瘤最大直径对比差别前后、右后、和左后分别为:2.0±0.5、4.3±1.2、1.4±0.35、4.0±1.1、1.5±0.4、3.6±1.2;等剂量曲线分布为60例和31例,差异有统计学意义。结论:CT模拟定位较常规模拟定位能更充分显示肿瘤外侵范围并反映其非对称性生长。     

An approach to generate noncontact ACL-injury prone situations on a computer using kinematic data of non-injury situations and Monte Carlo simulation

ACL-injuries are one of the most common knee injuries in noncontact sports. Kinematic data of injury prone situations provide important information to study the underlying ACL-injury mechanisms. However, these data are rare. In this work an approach is presented to generate injury prone situations for noncontact ACL-injuries on a computer. The injury prone situations are generated by a musculoskeletal simulation model using kinematic data of a non-injury situation and the method of Monte Carlo simulation. The approach is successfully applied to generate injury prone landings in downhill ski racing. The characteristics of the obtained injury prone landings are consistent with video recordings of injury cases.     

Molecular dynamics simulations of peptides and proteins with a continuum electrostatic model based on screened Coulomb potentials

A continuum electrostatics approach for molecular dynamics (MD) simulations of macromolecules is presented and analyzed for its performance on a peptide and a globular protein. The approach incorporates the screened Coulomb potential (SCP) continuum model of electrostatics, which was reported earlier. The model was validated in a broad set of tests some of which were based on Monte Carlo simulations that included single amino acids, peptides, and proteins. The implementation for large-scale MD simulations presented in this article is based on a pairwise potential that makes the electrostatic model suitable for fast analytical calculation of forces. To assess the suitability of the approach, a preliminary validation is conducted, which consists of (i) a 3-ns MD simulation of the immunoglobulin-binding domain of streptococcal protein G, a 56-residue globular protein and (ii) a 3-ns simulation of Dynorphin, a biological peptide of 17 amino acids. In both cases, the results are compared with those obtained from MD simulations using explicit water (EW) molecules in an all-atom representation. The initial structure of Dynorphin was assumed to be an alpha-helix between residues 1 and 9 as suggested from NMR measurements in micelles. The results obtained in the MD simulations show that the helical structure collapses early in the simulation, a behavior observed in the EW simulation and consistent with spectroscopic data that suggest that the peptide may adopt mainly an extended conformation in water. The dynamics of protein G calculated with the SCP implicit solvent model (SCP-ISM) reveals a stable structure that conserves all the elements of secondary structure throughout the entire simulation time. The average structures calculated from the trajectories with the implicit and explicit solvent models had a cRMSD of 1.1 A, whereas each average structure had a cRMSD of about 0.8A with respect to the X-ray structure. The main conformational differences of the average structures with respect to the crystal structure occur in the loop involving residues 8-14. Despite the overall similarity of the simulated dynamics with EW and SCP models, fluctuations of side-chains are larger when the implicit solvent is used, especially in solvent exposed side-chains. The MD simulation of Dynorphin was extended to 40 ns to study its behavior in an aqueous environment. This long simulation showed that the peptide has a tendency to form an alpha-helical structure in water, but the stabilization free energy is too weak, resulting in frequent interconversions between random and helical conformations during the simulation time. The results reported here suggest that the SCP implicit solvent model is adequate to describe electrostatic effects in MD simulation of both peptides and proteins using the same set of parameters. It is suggested that the present approach could form the basis for the development of a reliable and general continuum approach for use in molecular biology, and directions are outlined for attaining this long-term goal.