关于植物光合作用的量子分析

以无限深势阱为模型,应用量子力学微扰理论计算了叶绿素中电子跃迁几率,并且求得电子对阱壁产生的压力以及所做的构像功。研究结果表明：只有外场频率与叶绿素的固有频率相等时电子才发生跃迁,从而导致叶绿素吸收中心波长432nm的蓝光和662nm红光。当电子跃迁到高能级,对阱壁的压力增大,阱壁被拓宽,激发电子做了构像功,激发了酶的活性,促使植物光合作用。     

藻胆素的构象变化及其对光吸收的影响

研究藻胆蛋白中藻胆素构象的变化对藻胆素光谱性质的影响,在光合作用原初过程的研究中有重要意义．由于四吡咯发色团构象的非同源性随机涨落,藻胆素的电子激发态能级呈类Boltzmann分布;藻胆素的电子－振动吸收跃迁谱带线型因子可描述为与构象随机分布因子有关的卷积形式;藻胆素构象的随机分布导致电子－振动吸收跃迁谱带的不对称增宽．     

蛋白质分子络合物的电子结构与氧化还原反应

本文用量子化学方法研究蛋白质分子格合物的电子能谱及电子转移和氧化还原反应的关系。本文的结果表明:当蛋白质分子和辅酶或其它有机分子形成电荷迁移络合物时,在蛋白质分子导带下面将出现一系列定域化的电子-空穴束缚态能级。络合物受激发时,首先由基态跃迁到束缚态最低能级,出现电荷迁移吸收光谱。再激发时,才能由束缚态最低能级跃迁到其它束缚态能级或导带,从而出现非定域化的电子和产生电子顺磁共振信号。极性介质的影响和化学反应有助于电子转移。而络合物中的电子转移又会导致电子施主分子被氧化,电子受主分子被还原。通过对辅酶等分子的电离能和电子亲合势的计算,说明辅酶和蛋白质分子可能以电荷迁移络合物的形式存在。一些半定量的计算和定性的结论能初步解释氧化还原酶在光激发和酶促反应中所产生的电荷迁移吸收光谱及电子顺磁其振信号的实验事实。     

神经细胞膜钠通道的门控电流和门控动力学

根据作者已提出的神经轴突钠离子通道蛋白质分子构象模型,组成通道闸门的极性氨基酸侧链可以有两种类型:偶极子和荷电离子基团.它们在两种构象间的跃迁导致通道呈现关闭或开放态,并产生了门控电流相应的两种组分.对两种侧链跃迁动力学参量的计算结果表明,门控电流曲线的时间常数、稳态开启几率及门控电荷随膜电位的变化是不同的.去极化脉冲引起通道状态的变化,可由关闭态经过活化态转变为失活态,也可由关闭态经部分关闭态转变为失活态,对不同膜电位条件下一个通道各种稳定状态几率的计算表明,活化和失活的耦联程度随膜电位而改变.     

东亚马氏钳蝎(Buthus martensi karsch)蝎毒神经毒素的园二色性研究

本文研究了从东亚马氏钳蝎中纯化的神经毒素BmKⅢ的园二色性,并对不同类型毒素的CD光谱进行了比较.BmKⅢ在水溶液中的近紫外CD谱在274和290nm处显示二正峰,279nm处显示一肩峰.远紫外CD谱在209nm处呈一强负峰,为典型的β-折迭图谱.在中性水溶液中,其主链构象参数分别为4.0%α-螺旋,63%B-折迭,33%无规卷曲和回折.溶液的pH对BmKⅢ的构象影响不大,但分子在碱性溶液中构象的变化较之中性及酸性溶液稍大.温度的升高对其分子的构象有影响,但这种温度诱导的构象变化是可逆的.SDS的加入可诱导β-折迭转变为α-螺旋.在同时存在β-疏基乙醇时,分子的有序结构完全消失.几种不同的哺乳动物神经毒素以及它们同甲壳动物神经毒素的比较研究指出,它们的远紫外CD谱很相似, 但其近紫外CD谱却有差异,尤其是哺乳动物类同甲壳动物类毒素之间差异更大.     

苹果锈果类病毒的温度梯度凝胶电泳

用温度梯度凝胶电泳技术研究了苹果锈果类病毒(ASSV)的变性行为,并与菊花矮化类病毒(CSV)的变性行为进行了比较。提纯的ASSV的温度梯度电泳示出了类病毒特有的从类似于棒状的分子到打开的环状分子的构象转变曲线,与CSV及报道的马铃薯纺锤块状类病毒(PSTV)相似。但ASSV的构象转变中点温度及转变的协同性均低于CSV。在8.9mol／LTBE缓冲液中,ASSV构象转变的中点温度和半辐值分别为41．5℃和2.4℃,而CSV的分别为46.0℃和1．0℃。在ASSV的温度梯度凝胶电泳图中,除了有代表单分子构象转变的曲线外,还观察到另一构象转变曲线,作者认为这代表了在提纯过程中由分子间碱基配对形成的双分子复合体的变性曲线。     

偏振光激发的单分子荧光纵向成像研究

本文从单分子的水平上,详细分析并模拟了不同偏振光下的单个荧光分子的成像,指出荧光成像强度的差别是由分子的纵向位置及跃迁偶极矩的取向共同决定的。给出了确定荧光分子偶极矩取向的方法,并在此基础上给出了重构分子间纵向间隔的公式。     

天冬氨酸酶在盐酸胍变性时的酶活性与构象变化

 本文应用荧光光谱法和CD光谱法测定了天冬氨酸酶在不同浓度盐酸胍中变性时的构象与活力变化,并测定了天冬氨酸酶在不同浓度盐酸胍中变性时的巯基暴露速度。发现一部分色氨酸残基位于分子疏水核内部,另一部分位于分子表面;至少一部分酪氨酸残基与其相邻近基团形成氢键。该酶的大部分巯基位于分子内部结构比较稳定的区域而不在分子表面。低浓度盐酸胍作用下,构象发生明显变化,而活力维持原水平;盐酸胍达到一定浓度后,活力才发生骤然下降。CD谱表明,α-螺旋构象维持整个分子构象,因而对于维持活性中心构象是重要的。     

磷脂分子链构象及相变的拉曼光谱研究

本文报导了几种纯磷脂的固态、分散体或脂质体的激光拉曼光谱特性.在室温条件下固态DMPC、DPPC和DSPC的拉曼光谱表明,它们的分子链的有序性呈现差别.DMPC分子链的有序性远较其它二者为低.研究了DSPC的热致相变,分别观察固态DSPC的Ⅰ_(1100)/Ⅰ_(1064).～温度关系特性曲线和它的分散体的Ⅰ_(2882)/Ⅰ_(2847)～温度关系特性曲线,并发现上述两种关系特性曲线在相变温度之前均出现预相变峰,这可能反映在磷脂分子的相变过程中除trans(?)gauche构象转变外还存在其它构象的变化.DPPC分散体和脂质体的拉曼光谱特性进行比较的结果表明,曲率效应可能是脂质体分子链的有序性不同于分散体的原因.     

构型与构象

构型和构象是表征分子结构特征的易混淆的两个概念,构型是指具有一定构造的分子中原子或基团的固有空间排列。广义的构象是指分子中原子或基团在三维空间的取向和定位,狭义的构象是指具有相同构造和构型分子中原子或基团在空间的取向和定位。构型和构象既相互区别,又相互联系。对分子构型和构象概念的正确认识是阐明生物大分子结构与功能复杂关系的重要前提,对其正确地理解和运用将有助于教师教学任务的完成和学生对相关知识的理解和掌握。     

A stochastic model for the sigmoidal behaviour of cooperative biological systems

A stochastic model for cooperative transitions in biological systems based on a Markov chain is proposed. This model requires only two parameters, the mean probability, p, and the coupling capacity, Deltap, which measure the probability of forming a new weak bond depending on the number of similar bonds already formed and it is also responsible for the transition. In this paper we show how the model works for a large number of identical molecules and how it can be useful for studying the noise around the centre of the transition where, increasing the degree of cooperativity, i.e. the number n in the well-known Hill equation, the width of the noise increases along with its fractal dimension. A simple relationship between the degree of cooperativity and the parameter Deltap is proposed, suggesting that the cooperativity of real biological transitions is related to the coupling capacity Deltap of the present model.     

Structural Dynamics of Glutamate Signaling Systems by smFRET

Single-molecule Förster resonance energy transfer (smFRET) is a powerful technique for investigating the structural dynamics of biological macromolecules. smFRET reveals the conformational landscape and dynamic changes of proteins by building on the static structures found using cryo-electron microscopy, x-ray crystallography, and other methods. Combining smFRET with static structures allows for a direct correlation between dynamic conformation and function. Here, we discuss the different experimental setups, fluorescence detection schemes, and data analysis strategies that enable the study of structural dynamics of glutamate signaling across various timescales. We illustrate the versatility of smFRET by highlighting studies of a wide range of questions, including the mechanism of activation and transport, the role of intrinsically disordered segments, and allostery and cooperativity between subunits in biological systems responsible for glutamate signaling.     

Tunnelling of electrons in biological processes

A new mechanism of energy conversion in biological systems (particularly for phosphorylation on intracellular membranes) is proposed. This mechanism involves electron tunnelling accompanied by relaxation type conformational changes in enzyme macromolecules. The membrane potential may be considered as a regulator of this process.Electron tunnelling is the most important mechanism of electron transfer between electron carriers in electron transport chains of chloroplasts and mitochondria. The requirements of energy balance are met due to excitation or changing of the normal vibrations of carriers or molecules in the medium.     

Cooperativity of the phase transition in single- and multibilayer lipid vesicles.

The effect of membrane morphology on the cooperativity of the ordered-fluid, lipid phase transition has been investigated by comparing the transition widths in extended, multibilayer dispersons of dimyristoyl phosphatidyl-choline, and also of dipalmitoyl phosphatidylcholine, with those in the small, single-bilayer vesicles obtained by sonication. The electron spin resonance spectra of three different spin-labelled probes, 2,2,6,6-tetramethylpiperdine-N-oxyl, phosphatidylcholine and stearic acid, and also 90 degrees light scattering and optical turbidity measurements were used as indicators of the phase transition. In all cases the transition was broader in the single-bilayer vesicles than in the multibilayer dispersions, corresponding to a decreased cooperativity on going to the small vesicles. Comparison of the light scattering properties of centrifuged and uncentrifuged, sonicated vesicles suggests that these are particularly sensitive to the presence of intermediate-size particles, and thus the spin label measurements are likely to give a more reliable measure of the degree of cooperativity of the small, single-bilayer vesicles. Application of the Zimm and Bragg theory ((1959) J. Chem. Phys. 31, 526-535) of cooperative transitions to the two-dimensional bilayer system shows that the size of the cooperative unit, 1/square root sigma, is a measure of the mean number of molecules per perimeter molecule, in a given region of ordered or fluid lipid at the centre of the transition. From this result it is found that it is the vesicle size which limits the cooperativity of the transition in the small, single-bilayer vesicles. The implications for the effect of membrane structure and morphology on the cooperativity of phase transitions in biological membranes, and for the possibility of achieving lateral communication in the plane of the membrane, are discussed.     

Hydrogen-bond cooperativity in protein secondary structure

Hydrogen bonding in the α-helix and β-sheet has been studied by ab initio molecular orbital calculations carried out on complexes of formamide. Hydrogen-bond geometries were taken from x-ray crystallography of polypeptides. Positive cooperativity is found in all cases. The limiting value for infinite chains is obtained by use of a double-reciprocal plot and indicates an increase in the effective bond strength of 25% over that of a single isolated bond. Parallel calculations based on a classical electrostatic model yield qualitatively similar trends but underestimate the cooperativity by half. Charge redistribution accompanying cooperativity is characterized by a new type of charge-density difference plot, the cooperativity map. The magnitude and distance over which cooperativity acts suggest several significant biological consequences. Thus the average of α-helices and the number of β-sheet strands found in protein may be influenced by cooperativity. Cooperativity in the interpeptide hydrogen bond may also be partly responsible for the rapid formation of secondary structure in renaturing proteins and help stabilize secondary structure relative to the random-coil conformation.     

Thermodynamics and the structure of biological macromolecules. Rozhinkes mit mandeln

In this review, I will discuss the role of thermodynamics in both the determination and evaluation of the structure of biological macromolecules. The presentation relates to the historical context, state-of-the-art and projection into the future. Fundamental features relate to the effect of charge, exemplified in the study of synthetic and natural polyelectrolytes. Hydrogen bonding and water structure constitute basic aspects of the medium in which biological reactions occur. Viscosity is a classical tool to determine the shape and size of biological macromolecules. The thermodynamic analysis of multicomponent systems is essential fo the correct understanding of the behavior of biological macromolecules in solution and for the evaluation of results from powerful experimental techniques such as ultracentrifugation, light, X-ray and neutron scattering. The hydration, shape and flexibility of DNA have been studied, as well as structural transitions in nucleosomes and chromatin. A particularly rewarding field of activity is the study of unusual structural features of enzymes isolated from the extreme halophilic bacteria of the Dead Sea, which have adapted to saturated concentrations of salt. Future studies in various laboratories will concentrate on nucleic-acid--protein interactions and on the so-called 'crowding effect', distinguishing the behavior in bacteria, or other cells, from simple test-tube experiments.     

Effect of intramolecular energetic barriers on conformation-non-equilibrium states of protein globules in ensemble

Within the Blumenfeld's model interpretation theoretical investigations of conformation relaxation of the protein globule were carried out. Analytical expressions describing the relaxation time and cyclic frequency of enzymes synchronization by arbitrary number of metastable states and unequal probabilities of transitions between them were found. It was shown that inequality of activation energies affects the frequency and number of cycles of enzymes synchronous work to a considerably greater degree, than the relaxation time of initial disturbance. The number of macromolecules in the definite conformation state was evaluated and conditions of experimental observation of synchronization were discussed.     

On thermal transitions in biological macromolecules

The thermal transitions shown by macromolecules are to be understood as an allosteric phenomenon. They can be dealt with in terms of the same linkage principles as those governing the binding of a chemical ligand. This provides a basis for analyzing the observed differences between the reversible heat denaturation of proteins and the melting of nucleic acids. It also adds to our understanding of cooperativity and heterotropic linkage.     

Solid interactions in statistical physics of biopolymers

A short survey is presented of the development of statistical physics of biological macromolecules and its modern state. The main attention is paid to the analysis of the manifestation of scale invariance and fractal properties of biopolymers--DNA and proteins. Phase transitions related to the phase structure of DNA are briefly analysed. A more detailed account is given of phase transitions in globular proteins, denaturation problem, two phases of the melted globule and the theory of heteropolymers included. Some unsolved problems of this field of science and its prospects are discussed.     

Gating mechanisms of mechanosensitive channels of large conductance, II: systematic study of conformational transitions

Part II of this study is based on the continuum mechanics-based molecular dynamics-decorated finite element method (MDeFEM) framework established in Part I. In Part II, the gating pathways of Escherichia coli-MscL channels under various basic deformation modes are simulated. Upon equibiaxial tension (which is verified to be the most effective mode for gating), the MDeFEM results agree well with both experiments and all-atom simulations in literature, as well as the analytical continuum models and elastic network models developed in Part I. Different levels of model sophistication and effects of structural motifs are explored in detail, where the importance of mechanical roles of transmembrane helices, cytoplasmic helices, and loops are discussed. The conformation transitions under complex membrane deformations are predicted, including bending, torsion, cooperativity, patch clamp, and indentation. Compared to atom-based molecular dynamics simulations and elastic network models, the MDeFEM framework is unusually well-suited for simulating complex deformations at large length scales. The versatile hierarchical framework can be further applied to simulate the gating transition of other mechanosensitive channels and other biological processes where mechanical perturbation is important.