Impact of Stable Protein-protein Interaction on Protein Conformational Space

Backbone dihedral angle based clustering approach was applied to investigate the effect of protein complexation on backbone conformational space and the effect on protein dynamics. Three representative enzyme-inhibitor complexes and their comprised proteins were used as models for small-and moderate-sized globular proteins to compare available backbone conformational space before and after complexation. Microsecond time scale molecular dynamic simulations were generated to ensure sufficient statistics. The result suggests that stable protein-protein interactions lead to redistribution of protein backbone mobility and restriction of the protein backbone conformational space, especially for short time scale motions. Surprisingly, these effects are found to be uncorrelated with protein-protein interaction surface. Consistent with many experimental and computational observations, our results indicate that both induced-fit and conformational selection models play roles in stable protein complexation process, with the dominant role being different for different protein complexes.     

NLIP and HAD-like Domains of Pah1 and Lipin 1 Phosphatidate Phosphatases Are Essential for Their Catalytic Activities

Saccharomyces cerevisiae Pah1 phosphatidate phosphatase (PAP) catalyzes the dephosphorylation of phosphatidate to yield diacylglycerol, controlling phospholipids and triacylglycerol metabolisms. Pah1 and human Lipin 1 are intrinsically disordered proteins with 56% and 43% unfolded regions, respectively. Truncation analysis of the conserved and non-conserved regions showed that N- and C-conserved regions are essential for the catalytic activity of Pah1. PAP activities can be detected in the conserved N-terminal Lipin (NLIP) domain and C-terminal Lipin (CLIP)/haloacid dehalogenase (HAD)-like domain of Pah1 and Lipin 1, suggesting that the evolutionarily conserved domains are essential for the catalytic activity. The removal of disordered hydrophilic regions drastically reduced the protein solubility of Pah1. Thioredoxin is an efficient fusion protein for production of soluble NLIP–HAD recombinant proteins in Escherichia coli.     

肝素与HIV-1膜表面蛋白gp120相互作用的预测和模拟

用分子模拟软件研究肝素与HIV-1膜表面蛋白gp120的相互作用.将肝素中的单糖、二糖和三糖片段作为探针对gp120蛋白进行搜索,统计分析确定肝素结合区域.用肝素六糖片段和结合区域进行反应分子对接,获得两种结合模式.最终建立的模型能够很好地解释肝素体外抑制HIV-1的现象,同时对其机理进行了推测.     

晶状体蛋白识别互作与白内障的研究进展

白内障是全球致盲率最高的眼科疾病, 发病组织为晶状体. 晶状体内纤维细胞含有高浓度的晶状体蛋白, 晶状体蛋白家族分α?, β?和γ?3大亚家族. α-晶状体蛋白具有小分子伴侣功能, 可识别错误折叠蛋白质, 维持晶状体内蛋白质稳态; β?/γ?晶状体蛋白通过分子内或分子间相互作用, 主要发挥结构蛋白功能. 晶状体蛋白在晶状体纤维细胞内呈瞬时有序排列, 精准分子识别及动态相互作用在维持晶状体透明度中发挥关键作用. 晶状体内蛋白质稳态失衡是白内障的主要致病因素. 晶状体蛋白半衰期长, 且翻译合成后不再更新, 广泛受pH值、 金属离子、 辐射损伤和蛋白质翻译后修饰等细胞内外环境因素和化学因素的干扰, 影响晶状体蛋白间的分子识别和相互作用, 诱发白内障. 理清化学调控的晶状体蛋白分子识别及互作调控, 有助于阐明白内障发病机理, 并发掘防治白内障的创新策略. 本文基于晶状体蛋白识别互作与白内障研究进展, 综合评述了晶状体蛋白的分子识别、 相互作用方式、 调控因素及研究技术创新, 并探讨了晶状体蛋白识别互作调控网络在白内障药物研发的应用价值与挑战.     

脂多糖与生物分子的相互作用及动力学分析

脂多糖(LPS)是构成革兰氏阴性细菌细胞外壁的主要成分,是一种热稳定的毒素。脂多糖与某些生物分子形成复合物,从而引发毒性反应。本研究应用基于表面等离子体共振(SPR)原理的生物传感技术,对脂多糖与几种生物分子之间的相互作用进行了动力学分析。采用氨基偶联法在CM5传感片上固定生物分子,LPS溶液注射于固定的传感片上,测得脂多糖与人血清白蛋白、血红蛋白、壳聚糖以及溶菌酶的亲和常数kA分别为2.36×107、2.03×108、7.58×106、2.82×104L/mol,而与铁蛋白之间没有结合。     

Structure and Dynamics of Confined Polymer Melts from Attractive Interaction to Repulsive Interaction Between Polymer and Smooth Wall

We studied the static and dynamic properties of unentangled polymer chains which have a variable strength of interaction with the confining smooth walls by means of the lattice Monte Carlo simulation based on the bond-fluctuation model, that is, investigated the wall-polymer interactions which systematically vary from attraction to repulsion. A critical value of attractive potential(ε_wc) is found to be -0.6k_BT, and only below it can the adsorption layer of monomers be formed near the wall. At the critical point of attraction ε_wc, attractive interaction counterba- lances the wall-polymer excluded volume effect, which minimizes the confinement effects on both chain dimension and mobility. Influences on both chain dimension and mobility increase with the increasing of either attraction or repulsion imposed by the walls. Despite of the nature and strength of the wall-polymer interaction, with the decrease of film thickness, configurations more parallelly aligned and flattened are adopted by confined chains, and a systematic trend of deceleration is found. Variations of chain dynamics with both film thickness and wall-polymer interaction can be well explained by the corresponding changes in the confinement of the nearest-neighboring particles that surround the chains. Besides, the thickness of the interfacial layer inside polymer films, where chains adopt a flattened “pancake” shape, is about two times the bulk radius of gyration and independent of the wall-polymer interaction.     

光谱法研究黄曲霉毒素B1与人血清白蛋白的结合反应

黄曲霉毒素B1(AFB1)是目前发现的致癌能力最强的真菌毒素,严重危害人畜健康.人血清白蛋白(Human serum albumin,HSA)在结合、运输内源性和外源性等小分子物质方面具有重要的生理功能.研究AFB1与HSA的相互作用机理和作用过程,在分子毒理学上具有重要意义.本研究模拟在人体血液pH条件(pH7.4,离子强度0.1 mol/L),通过荧光淬灭、3D荧光法和圆二色谱(Circular dichroism,CD)等光谱方法研究AFB1与人血清蛋白的相互作用.结果表明,AFB1与HSA的内源荧光淬灭属于静态淬灭,AFB1-HSA在298,303,308和313 K4个温度条件下,结合常数均为104数量级,结合位点都约为l.根据Van't Hoff方程,AFB1-HSA体系是熵增焓减的自发过程,分子间主要作用力为疏水作用和氢键.基于F(o)rster's能量转移,得知AFB1与HSA结合距离为3.31 nm.竞争结合实验表明,AFB1结合在HSA的siteI位点上,靠近色氨酸Trp-214.通过3D荧光分析,AFB1的结合作用导致了HSA氨基酸残基微环境和二级构象发生变化.圆二色谱的分析结果表明,二者的结合使得HSA的α-螺旋含量增加.     

气相色谱法研究聚辛烯-1与不同溶剂的热力学相互作用

用气相色谱法测定了聚辛烯－１与８种溶剂的Ｆｌｏｒｙ－Ｈｕｇｇｉｎｓ相互作用参数χ１和聚辛烯－１的溶解度参数,确定了χ１与温度的数学关系式。测定结果表明聚辛烯－１溶于正辛烷是一个放热过程。     

石墨烯材料与模拟生物膜界面相互作用的研究进展

石墨烯材料在生物领域的蓬勃发展使其纳米生物界面研究已成为纳米生物学研究的热点方向。生物膜是石墨烯材料进入生物体系环境中的第一道屏障,深入理解石墨烯材料与磷脂膜间的相互作用,对于石墨烯基生物材料的功能界面优化设计和生物学效应控制具有极为重要的意义。本文对石墨烯材料进行了简要介绍,系统总结了近几年石墨烯材料与模拟生物膜相互作用的研究进展,并对其研究方向进行了展望。     

黄曲霉毒素B1抗体和纳米金颗粒的相互作用机理

研究了纳米金标黄曲霉毒素B1单克隆抗体(McAb)探针的制备及其标记机理, 确定了稳定标记5种不同粒径金溶胶(10.7~67.4 nm)所需McAb的最适质量浓度, 分别为0.07, 0.051, 0.033, 0.019, 0.012 mg/mL, 作用时间为5 min, pH为7.4. 对金标探针复合物进行透射电镜、红外光谱和免疫反应性鉴定的结果表明, 与未标记抗体相比, 抗体探针的免疫亲和常数、效价和常温贮藏稳定性得到了明显提高. 通过荧光光谱和圆二色谱研究纳米金与AFB1单抗McAb的相互作用机理, 发现纳米金对McAb产生静态猝灭, 猝灭的速率常数随着温度升高而降低. 确定了结合位点数和结合常数. 结果显示, 表明McAb的色氨酸残基与纳米金颗粒之间发生了Förster偶极-偶极无辐射能量转移. 初步确定反应前后McAb构象组成发生了变化是McAb探针亲和力和稳定性提高的原因.     

脱氧核糖核酸与双苯甲亚胺相互作用的荧光特性研究

采用荧光光谱法对脱氧核糖核酸（ＤＮＡ）与双苯甲亚胺（Ｈｏｃｅｈｓｔ ３３２５８）相互作用的方式及其作用机理进行了研究,证实了Ｈｏｅｃｈｓｔ ３３２５８与ＤＮＡ的相互作用除嵌入作用时,还存在持异性的静电作用;Ｈｏｅｃｈｓｔ３３２５８与ＤＮＡ主要作用在Ａ－Ｔ匹配,同时,在磷酸根的存在下可以减弱Ｈｏｅｃｈｓｔ３３２５８与ＤＮＡ的非特异性作用。另外,根据荧光峰增强与Ｈｏｅｃｈｓｔ３３２５８浓度的线性关系,     

Interaction between bovine serum albumin and Indo-1 using fluorescence spectroscopic method

This work attempts to calculate the binding-site number using fluorescence spectroscopic method with bovine serum albumin (BSA) and Indo-1 as protein and ligand models, respectively. The method for calculating the binding-site number in BSA for Indo-1 was developed based on the relationships between changes in Indo-1 fluorescence intensity and the analytical concentration of BSA. The interaction between BSA with Indo-1 was investigated comprehensively using fluorescence techniques as well as fluorescence resonance energy transfer, and the thermodynamic parameters were calculated according to the effect of enthalpy on temperature. Three binding sites in BSA for Indo-1 were revealed, and the distances from Trp212 in BSA to the three binding sites were 2.93, 2.57 and 2.40 nm, respectively. It was also proven that Indo-1 embedded into the three hydrophobic cavities of BSA by hydrophobic association. This paper provides a reference on calculating the binding-site number in proteins for ligands and studying their interactions by fluorescence spectroscopic methods. In fluorescent quenching experiments, fluorescence changes were automatically recorded in real time by combining the Microlab 500 Series Dispenser and PTI fluorescence apparatus. __________ Translated from Chemical Journal of Chinese Universities, 2007, 28(2): 227–233 [译自: 高等学校化学学报]     

Voltammetric and Impedimetric Detection of Interaction Between Dacarbazine and Nucleic Acids

Dacarbazine (DTIC) is a chemotherapy drug that is used for the treatment of Hodgkin's lymphoma, malignant melanoma, childhood solid tumors and soft tissue sarcoma. The surface confined interaction between DTIC and nucleic acids was investigated for the first time in this study by using both differential pulse voltammetry (DPV) and electrochemical impedance spectroscopy (EIS) in combination with disposable pencil graphite electrodes. The oxidation signals of DTIC and guanine were measured before and after interaction process using DPV technique. The interaction of DTIC with nucleic acids; poly[A], poly[G], or double stranded of poly[A]‐poly[T] and poly[G]‐poly[C] was also examined using DPV. Furthermore, EIS technique was utilized for detection of the interaction between DTIC and nucleic acids; ssDNA/dsDNA, poly[A], poly[G], or double stranded poly[A]‐poly[T] and poly[G]‐poly[C].     

Electrochemical Behavior of Calcein and the Interaction Between Calcein and DNA

The electrochemical behavior of calcein (CA) has been investigated by using a conductive carbon black paste electrode (CCBPE) as working electrode. It exhibits a single well‐defined redox peak in phosphate buffered saline in the range of pH 5.5–8.0, which attributes to the irreversible oxidation with 2 electrons and 2 protons participation. Under the optimized analytical conditions, the proposed linear sweep voltammetry (LSV) method allows the determination of CA in a linear concentration range of 0.64–9.60 µM, with a limit of detection of 0.32 µM. Further, the interaction between CA and DNA were studied by voltammetric and spectrometric methods. Both studies have shown that CA can bind to DNA by the intercalation binding mode. Under the present experimental condition, the binding constant β of CA and dsDNA is 1.10×10⁷. Meanwhile, in the loop‐mediated isothermal amplification (LAMP) reaction mixture there is obvious interaction between CA and dsDNA, resulting in a nonignorable decrease of the indicating sensitivity.     

维生素B_1与氯酚红的分子吸收光谱及应用

建立了简便、快速测定维生素B1(VB1)的分光光度法。在弱酸性条件下,适量的VB1与氯酚红(CHR)反应生成具有明显正、负吸收峰的红色离子缔合物,最大正、负吸收波长分别为428nm、572nm,表观摩尔吸光系数(ε)分别为2.33×104 L/(mol·cm)(正吸收)和6.79×104 L/(mol·cm)(负吸收)。VB1的浓度在0~6.0mg/L范围内遵从比尔定律。该方法简便、快速、有较高的准确度和灵敏度,可用于市售奶粉中VB1的测定。     

Volumetric Study of the Interaction Between Chloride Salts and Polyvinylpyrrolidone in Aqueous Solution

We are interested in polyvinylpyrrolidone as an analog for the D-state proteins. In a volumetric study, the interactions between polyvinylpyrrolidone (PVP) and sodium-, potassium-, calcium-, and tetrabutylammonium chloride at 35°C in a series of aqueous PVP solutions over a concentration range of PVP up to 20 wt.% was performed. The volumes of transfer at infinite dilution _tr V ₂ ⁰ from water to the PVP solutions were determined for the salts; their decreasing order showed a parallel relation to the Hoffmeister series. The _tr V ₂ ⁰ data were analyzed by applying the McMillan–Mayer method to obtain the volumetric interaction coefficients between the ions and the polymer unit.     

N-(1-萘基)琥珀酰亚胺分子间相互作用的计算机模拟

对分子间相互作用比较复杂的N-(1-萘基)琥珀酰亚胺进行理论计算时, 提出了将溶液构建和随机构象搜索相结合的多分子相互作用体系构建方法, 可以简单而准确地得到二聚体和三聚体结构, 其中二聚体结构和采用分子对接方法得到的结果完全一致. 经密度泛函理论计算, 得到了在真空条件下二聚体结构的最低能量构象. 对较大体系的三聚体结构采用高精度分子力学进行了理论计算. 通过分子间相互作用对分子构象的影响讨论了溶液结晶过程中N-(1-萘基)琥珀酰亚胺分子构象变化, 为该化合物结晶机理的深入研究提供重要依据.     

Electroanalytical Study of the Interaction Between Double Stranded DNA and Antitumor Agent Curcumin

Curcumin, the major active component of the spice turmeric, which is considered to be a very useful compound in health matters, is recognized as a safe component with great potential for cancer chemoprevention and cancer therapy. For the first time, an interaction between the non-toxic agent curcumin and double stranded (ds) calf thymus DNA has been demonstrated by using voltammetry. The interaction of curcumin (CU) with dsDNA was studied using a carbon paste electrode (CPE) and a hanging mercury drop electrode (HMDE). Significant changes in the characteristic peaks of dsDNA were observed after addition of curcumin to a solution containing dsDNA.