从多重定态到化学振荡

通过对化学反应体系动力学模型的分析, 论证了通过在多重定态体系中引入适当慢反馈步骤设计化学振荡体系的可能性, 提出了这类体系的动力学方程具有振荡解的判据以及在参数平面内划分振荡区域的方法。采用这种途径具体分析了一氧化碳在铂催化剂上氧化产生振荡现象的机理。     

蛋白质翻译后脂修饰的结构和功能分析:靶向细胞脂信号

蛋白质翻译后脂修饰是指蛋白质在核糖体合成后与疏水脂质分子的共价结合.在已知共价化学修饰中,脂质分子独特的物理化学性质赋予了蛋白质特殊的结构和功能,并极大地影响蛋白质的膜锚定能力、转运和定位途径、信号转导以及蛋白质相互作用等.多样化的脂质结构和结合方式决定了脂修饰蛋白功能的复杂性,这些脂修饰蛋白与其他已知或未知修饰蛋白一起,在细胞多层次交叉调控信号转导通路中互相影响,协同作用,从而实现对生理活动的精细调控.开展蛋白质翻译后脂修饰结构与功能分析是揭示微生物感染、免疫调节、肿瘤发生发展等机制的重要途径,对发现和筛选疾病标志物以及挖掘新型药物靶标具有重要意义.     

海洋芽孢杆菌酯酶BSE-1的催化动力学和热失活动力学研究

海洋芽孢杆菌发酵产生的酯酶BSE-1经分离纯化后,以对硝基苯磷酸酯(PNPP)为底物,对电泳纯BSE-1的催化性质、催化动力学和热失活动力学进行了研究.催化动力学研究表明,金属离子对BSE-1的活性影响显著,其中Ca2 的激活作用最强,为混合型激活作用;而Ba2 的抑制作用最为明显,为非竞争性抑制作用.BSE-1的酶促反应动力学符合米氏方程,其中Km=8.15mmol·L-1,Vmax=0.97mmol·mg-1·min-1.采用连续模型对BSE-1在70℃的热失活动力学进行模拟,求得酶的失活速率常数k1=1.41,k2=0.28.     

新型细胞外信号相关激酶(ERK)小分子抑制剂的设计、合成与抗肿瘤活性研究

细胞外信号相关激酶(ERK)是恶性肿瘤发生发展中的关键激酶,为了寻找新型结构的ERK抑制剂,采用拼合原理设计合成了两类共12个含有吗啉环的脲类化合物,其结构经¹H NMR、¹³C NMR和HRMS确证. ERK激酶活力和细胞增殖测试结果表明,大部分目标化合物对人结直肠癌细胞SW480和HCT-116具有中等强度的抑制作用,尤其是1-(4-氟苄基)-3-(5-(4-吗啉代苯基)吡啶-2-基)脲(18f)的IC₅₀分别达到0.36和0.55μmol/L,对正常细胞L02毒性较低(>10μmol/L).同时,18f能抑制ERK的激酶活力(IC₅₀=0.051μmol/L)和磷酸化水平,但不影响总ERK表达和上游丝裂原活化的细胞外信号调节激酶(MEK)的激活.上述结果为新型苄基吡啶基脲类ERK抑制剂的深入研究提供了重要参考信息.     

基于时间分辨方法的LicT蛋白荧光动力学特性

使用时间分辨荧光方法,结合紫外吸收光谱和稳态荧光光谱技术,测量了LicT蛋白中色氨酸残基的荧光动力学特性,进而对LicT蛋白质激活前后的局部微环境和结构变化进行了研究。LicT蛋白质的激活态使得有关糖类利用的基因转录过程继续进行,促进机体新陈代谢。通过色氨酸残基的荧光发射和寿命的差异判断出激活型蛋白AC 141和野生型蛋白Q 22不同的结构性质和微环境差异。在此基础上,通过衰减相关光谱(DAS)和时间分辨发射光谱(TRES)阐释了两种蛋白色氨酸残基和溶剂的相互作用,说明了激活型AC 141的比野生型Q 22的结构更加紧密。此外,TRES还说明了蛋白中的色氨酸残基存在连续光谱弛豫过程。各向异性结果则对残基和整个蛋白的构象运动进行了阐述,说明了色氨酸残基在蛋白质体系内有独立的局部运动,且在激活型蛋白中该运动更加强烈。     

动态细胞骨架网络的自组织与力学性能

细胞骨架是由微管、肌动蛋白丝和中间纤维三种蛋白丝为主要成分组成的复合动态网络结构，在结合蛋白、辅助调节蛋白和马达蛋白的参与下帮助细胞实现运动、分裂和生长等基本生命过程。研究体外纯化的细胞骨架蛋白和马达蛋白网络，可以深入了解控制自组织亚细胞结构动力学行为的基本原理，为设计类似生命的活性物质和机器提供方向。本文综述了近年来基于纯化蛋白在体外简化环境中实现的细胞骨架蛋白-马达蛋白网络，重点介绍其非平衡本质、活性应力和动态网络的产生，以及这种动态网络对亚细胞结构和宏观尺度活性材料自组织过程的影响。此外，还简要介绍了细胞骨架蛋白-马达蛋白网络在构建体外仿生系统中的应用。     

基于动态光散射技术的含乳糖组装体与蛋白质相互作用

采用非共价键合胶束(NCCM)的组装策略, 制备了表面为糖聚合物的纳米粒子, 利用动态光散射技术, 实时跟踪了在溶液中糖与蛋白相结合的动力学数据, 并以聚集体形成的速度来体现不同的蛋白对相同组装体的结合能力强弱. 实验结果表明, 对表面覆盖100%乳糖的组装体, 各蛋白的结合能力表现为SBA?LecA≈Galectin 3>ECA≈Galectin 1, 表明蛋白的糖结合位点个数及其空间分布对多价作用的动力学有较大影响. 基于此模型, 对人半乳凝素-3与糖结合的方式进行了初步探究.     

顺酐在负载型镍钼催化剂上高压液相加氢合成1,4-丁二醇本征动力学的研究

在电磁搅拌式高压反应釜中研究了顺酐在负载型镍钼催化剂上高压液相加氢本征动力学。建立了顺酐加氢的反应网络,考察了反应温度、氢气压力对反应速率的影响,用线性或非线性最小二乘法求取了动力学参数,得到了动力学模型。模型验证表明,模型对实验数据的拟合是有效的。     

甲基丙烯酸甲酯水溶性对其悬浮均聚动力学的影响

通过比较在大水油比下的甲基丙烯酸甲酯 (MMA)悬浮均聚的实验数据以及本体聚合实验结果 ,发现单体的水溶性对其聚合动力学有影响 ,不能用本体聚合动力学代替其悬浮聚合动力学 .为了能更好了解单体的水溶性对其悬浮聚合动力学的影响以及影响动力学的原因 ,在MMA本体聚合动力学模型基础上 ,进一步提出 3个假设 :扣除溶于水相部分的单体量、增长和终止速率参数降低、少部分的油溶性引发剂被带到水相中 ,得到改进的悬浮聚合动力学模型 .运用该模型能很好预测水油比、聚合温度、引发剂浓度等对MMA悬浮聚合动力学的影响 ,且与实验数据能较好吻合     

应用反向传播神经网络预测化合物脑血分配系数

选用27种三维结构性质描述符对脑血分配系数预测建立神经网络模型.网络模型选用典型的适合函数逼近的两层结构神经网络对脑血分配系数（lgBB，BB为脑血浓度比）进行预测,计算中采用的模型具有一个双曲正切型激活函数的隐含层和一个线性激活函数的输出层.计算表明,使用小心选择的反向传播神经网络模型对化合物脑血分配系数具有较好的预测能力.     

Controlling of explicit internal signal stochastic resonance by external signal

Explicit internal signal stochastic resonance (EISSR) is investigated in a model of energy transduction of molecular machinery when noise is added to the region of oscillation in the presence of external signal (ES). It is found that EISSR could be controlled, i.e., enhanced or suppressed by adjusting frequency (omega(e)) and amplitude (A) of ES, and that there exits an optimal frequency for ES, which makes EISSR strength reach the maximum. Meanwhile, a critical amplitude (A(c)) is found, which is a threshold of occurrence of EISSR. Finally, the difference and similarity between EISSR and IISSR (implicit internal signal stochastic resonance) are discussed.     

Modeling signal transduction networks: a comparison of two stochastic kinetic simulation algorithms

Computational efficiency of stochastic kinetic algorithms depend on factors such as the overall species population, the total number of reactions, and the average number of nodal interactions or connectivity in a network. These size measures of the network model can have a significant impact on computational efficiency. In this study, two scalable biological networks are used to compare the size scaling efficiencies of two popular and conceptually distinct stochastic kinetic simulation algorithms--the random substrate method of Firth and Bray (FB), and the Gillespie algorithm as implemented using the Gibson-Bruck method (GGB). The arithmetic computational efficiencies of these two algorithms, respectively, scale with the square of the total species population and the logarithm of the total number of active reactions. The two scalable models considered are the size scalable model (SSM), a four compartment reaction model for a signal transduction network involving receptors with single phosphorylation binding sites, and the variable connectivity model (VCM), a single compartment model where receptors possess multiple phosphorylation binding sites. The SSM has fixed species connectivity while the connectivity between species in VCM increases with the number of phosphorylation sites. For SSM, we find that, as the total species population is increased over four orders of magnitude, the GGB algorithm performs significantly better than FB for all three SSM compartment models considered. In contrast, for VCM, we find that as the overall species population decreases while the number of phosphorylation sites increases (implying an increase in network linkage) there exists a crossover point where the computational demands of the GGB method exceed that of the FB.     

A system for artificial light signal transduction via molecular translocation in a lipid membrane

Light signal transduction pathways are the central components of mechanisms that regulate plant development, in which photoreceptors receive light and participate in light signal transduction. Chemical systems can be designed to mimic these biological processes that have potential applications in smart sensing, drug delivery and synthetic biology. Here, we synthesized a series of simple photoresponsive molecules for use as photoreceptors in artificial light signal transduction. The hydrophobic structures of these molecules facilitate their insertion into vesicular lipid bilayers, and reversible photoisomerization initiates the reciprocating translocation of molecules in the membrane, thus activating or deactivating the hydrolysis reaction of a precatalyst in the transducer for an encapsulated substrate, resulting in a light controllable output signal. This study represents the first example of using simplified synthetic molecules to simulate light signal transduction performed by complex biomolecules.

Photoisomerization chemistry was used to simulate light signal transduction, in which the light-controlled reciprocating translocation of molecules in lipids activates or deactivates the hydrolysis reaction for an encapsulated substrate.     

Fluorescence signal transduction mechanism for immunoassay based on zinc ion release from ZnS nanocrystals

In this work, a fluorescence signal transduction mechanism based on cation release from ZnS nanocrystals was developed for sandwich immunoassay. In this mechanism, ZnS nanocrystals as labels in immunoassay are dissolved by acid to release zinc ions. After pH adjustment of the dissolving solution using a basic solution, zinc-ion sensitive fluorescence indicator Fluozin-3 is added to bind with the released zinc ions for sensitive fluorescence measurement. Using mouse IgG as a model analyte, the immunoassay adopting this signal transduction mechanism demonstrates a low detection limit around 1 pM and a detection range with two orders of magnitude (1 pM to 0.5 nM).     

Histidine kinases and two-component signal transduction systems.

The phosphorylation of histidine is the first step in many signal transduction cascades in bacteria, yeast and higher plants. The transfer of a very reactive phosphoryl group from phosphorylated histidine kinase to an acceptor is an essential step in many cellular signaling responses.     

Molecular mechanisms of phytochrome signal transduction in higher plants

Phytochromes in higher plants play a great role in development, responses to environmental stresses and signal transduction, which are the fundamental principles for higher plants to be adapted to changing environment. Deep and systematic understanding of the phytochrome in higher plants is of crucial importance to molecular biology, purposeful improvement of environment in practice, especially molecular mechanism by which higher plants perceive UV-B stress. The last more than 10 years have seen rapid progress in this field with the aid of a combination of molecular, genetic and cell biological approaches. No doubt, what is the most important, is the application of Arabidopsis experimental system and the generation of various mutants regarding phytochromes (phy A–E). Increasing evidence demonstrates that phytochrome signaling transduction constitutes a highly ordered multidimensional network of events. Some phytochromes and signaling intermediates show light-dependent nuclear-cytoplasmic partitioning, which implies that early signaling events take place in the nucleus and that subcellular localization patterns most probably represent an important signaling control point. The main subcellular localization includes nucleus, cytosol and chloroplasts, respectively. Additionally, proteasome-mediated degradation of signaling intermediates most possibly function in concert with subcellular partitioning events as an integrated checkpoint. What higher plants do in this way is to execute accurate responses to the changes in the light environment on the basis of interconnected subcellular organelles. By integrating the available data, at the molecular level and from the angle of eco-environment, we should be able to construct a solid foundation for further dissection of phytochrome signaling transduction in higher plants.     

Heme flattening is sufficient for signal transduction in the H-NOX family

The H-NOX family of nitric oxide (NO) sensing proteins has received considerable attention because its members include the mammalian NO sensor, soluble guanylate cyclase. Despite this attention, the mechanism of signal transduction has not been elucidated. Structural studies of bacterial members of the family have revealed that the H-NOX heme cofactor is extremely distorted from planarity. Furthermore, it has been determined that heme distortion is maintained primarily by a conserved proline residue located in the proximal heme pocket. It has been suggested that changes in heme planarity may contribute to signal transduction. Here we demonstrate that heme flattening is, indeed, sufficient for signal transduction in the H-NOX family. Using our previously described H-NOX/diguanylate cyclase functional partners from Shewanella woodyi, we demonstrate that mutation of the conserved proline (P117 in SwH-NOX) to alanine, which results in heme flattening, has the same affect on phosphodiesterase activity as NO binding to wildtype SwH-NOX. This study demonstrates, for the first time, that heme flattening mimics the activated, NO-bound state of H-NOX and suggests that NO binding induces heme flattening as part of the signal transduction mechanism in the H-NOX family.     

Link between allosteric signal transduction and functional dynamics in a multisubunit enzyme: S-adenosylhomocysteine hydrolase

S-adenosylhomocysteine hydrolase (SAHH), a cellular enzyme that plays a key role in methylation reactions including those required for maturation of viral mRNA, is an important drug target in the discovery of antiviral agents. While targeting the active site is a straightforward strategy of enzyme inhibition, evidence of allosteric modulation of active site in many enzymes underscores the molecular origin of signal transduction. Information of co-evolving sequences in SAHH family and the key residues for functional dynamics that can be identified using native topology of the enzyme provide glimpses into how the allosteric signaling network, dispersed over the molecular structure, coordinates intra- and intersubunit conformational dynamics. To study the link between the allosteric communication and functional dynamics of SAHHs, we performed Brownian dynamics simulations by building a coarse-grained model based on the holo and ligand-bound structures. The simulations of ligand-induced transition revealed that the signal of intrasubunit closure dynamics is transmitted to form intersubunit contacts, which in turn invoke a precise alignment of active site, followed by the dimer-dimer rotation that compacts the whole tetrameric structure. Further analyses of SAHH dynamics associated with ligand binding provided evidence of both induced fit and population shift mechanisms and also showed that the transition-state ensemble is akin to the ligand-bound state. Besides the formation of enzyme-ligand contacts at the active site, the allosteric couplings from the residues distal to the active site are vital to the enzymatic function.     

Determination of protein phosphorylation by extracellular signal-regulated kinase using capillary electrophoresis and matrix-assisted laser desorption ionization time-of-flight mass spectrometry

Extracellular signal-regulated kinase (ERK) is a key regulatory enzyme mediating cell responses to mitogenic stimulation and is one of the key components in linking growth factor receptor activation to serine/threonine protein phosphorylation processes. Phosphorylation reaction by ERK plays an important role in many signal transduction pathways. ERK phosphorylates numerous substrates such as MBP, microtubule-associated protein 2 (MAP2) and nuclear protein. In particular, MBP is a substrate commonly employed for the detection of ERK activity and contains the consensus primary sequence PRT97P. In this paper, we compared the degree of the phosphorylation reaction of MBP substrate peptides by ERK with the three different MBP substrate peptides, MBP1(KNIVTPRTPPPSQGK), MBP2(VPRTPGGRR) and MBP3(APRTPGGRR) in order to select an efficient substrate peptide for phosphorylation reaction by ERK. The results showed that the MBP3 peptide is the most efficient substrate for phosphorylation reaction by ERK. Using MBP3 peptide, the phosphorylation reaction of MBP by ERK was monitored with both matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and capillary electrophoresis (CE). Our results demonstrate the feasibility of the CE method, the method being a simple and reliable technique in determining and characterizing various kinds of enzyme reaction especially including kinase enzymes.