SARS病毒蛋白中caveolin推测的结合位点

目的：获得SARS冠状病毒蛋白与caveolin-1蛋白相互作用的信息,识别病毒蛋白中可能的caveolin-1结合位点,为SARS冠状病毒蛋白的功能研究以及设计抗SARS病毒的药物和疫苗提供线索．方法：基于3个caveolin结合基序,采用氨基酸基序搜索方法预测SARS冠状病毒蛋白中可能与caveolin-1相互作用的区域,并用分子模拟和分子对接的方法进一步证实它们之间的相互作用。结果：通过生物信息学分析,在SARS冠状病毒蛋白中发现了36个caveolin结合基序。经过分子模拟和分子对接,获得了SARS冠状病毒蛋白与caveolin-1相互作用的8个结合位点。这些caveolin-1结合位点分别位于replicase 1AB、S蛋白、ofr3蛋白和M蛋白．结论：caveolin-1可能是SARS冠状病毒蛋白结合的一个靶点,它们之间的相互作用可能与SARS冠状病毒的感染、复制、装配和释放有关。     

基于蛋白质序列预测蛋白质-蛋白质相互作用位点研究进展

生物分子之间的相互作用是生命过程的分子基础,其中蛋白质分子之间的相互作用占有极其重要的地位。因此研究蛋白质相互作用对于理解生命的分子机理、探讨致病微生物的致病机理,以及研究新药提高人们的健康水平具有重要的作用。文章对蛋白质-蛋白质相互作用数据库和蛋白质-蛋白质相互作用位点的序列特征和蛋白质-蛋白质结合位点预测最先进的方法进行介绍。蛋白质-蛋白质相互作用位点的残基在调节物理结合过程中具有重要的意义,例如这些残基参与酶抑制剂相互作用的抑制效应,通过抗体-抗原相互作用的最初免疫反应,和细胞中信号蛋白的调节等。当前,各种各样的方法被用于预测蛋白质-蛋白质相互作用位点的预测中,并通过整体的构建蛋白质-蛋白质作用网络,从残基水平去理解蛋白质结合现象。     

作用于雄激素受体不同结合位点的前列腺癌治疗药物的研究进展

前列腺癌是最常见的男性泌尿生殖系统的恶性肿瘤。雄激素受体在前列腺癌的发生、发展中起着重要作用。目前,所有治疗前列腺癌的药物(包括第一代的氟他胺、比卡鲁胺、尼鲁米特和第二代的恩扎鲁胺)都与雄激素受体的配体结合口袋结合,并且这些药物有着相似的分子结构,这可能引起药物之间的交叉耐药。为了避免耐药性的产生,研究者们致力于发现雄激素受体上新的药物结合位点。除雄激素受体配体结合位点外,主要对作用于氮端结合位点上的第一活性功能区(AF1)、第二活性功能区(AF2)、AF2附近的第三结合功能区(BF3)和DNA结合位点(DBD)的药物进行综述。     

宁夏回族人群CYP2D6*10基因多态性及功能分析

目的 探讨基因突变对人CYP2D6蛋白结构与功能的影响.方法 采用等位基因特异扩增(ASA-PCR)及DNA测序技术分析宁夏网族人群CYP2D6*10(C188T)基因多态性,以生物信息学方法对突变造成的肝药酶活性的下降做出合理的解释.结果 蛋白质基本性质分析工具(ProtParam)分析显示,在溶液中CYP2D6*10突变型蛋白的不稳定指数高于野生型,都高于阈值40;二级结构预测软件(DNAStar/Protean)分析显示,突变型蛋白的二级结构在第33位多了一个转角(Gamier-Robson Turn);功能佗点预测程序(Motif Scan)对蛋白功能位点进行预测,结果显示CYP2D6*10野生型蛋白有2个P450酶激活位点.而突变型没有;信号肽预测程序(Signal P)分析显示.神经网络模型(NN)C-score计算结果为突变型蛋白没有信号肽,而野牛型有.结论 基因突变可引起CYP2D6蛋白结构与功能的改变;应用生物信息学方法对CYP2D6基因突变致使的酶活性的下降做出一些可能的解释是可行的.     

咔啉类衍生物与小牛胸腺DAN的结合——结合方式及结合强度的测定

研究了六个咔啉类衍生物（CB1－6）与DNA结合的方式，强度及与其抗肿瘤活性的关系。通过DNA双螺旋结构的变化，包括粘度、^31PNMR、CD谱的测定及CB1－6在用DNA滴定过程中，UV－Vis光谱的减色效应和化合物芳环质子的^HNMR谱的变化来阐明CB1－6与DNA的结合方式；通过光谱法及微量量热测定了与DNA的结合强度。测定数据表明结合强度与环的芳香性及取代基有很强的依赖性，此结果在生物测定中得到证实。     

核糖体展示小分子抗体的研究进展

核糖体展示技术是由Plückthun实验室[1]在多聚核糖体展示技术[2]的基础上改进而来的一种利用功能性蛋白相互作用进行筛选的新技术,它将正确折叠的蛋白及其mRNA同时结合在核糖体上,形成mRNA-核糖体-蛋白质三聚体,使目的蛋白的基因型和表型联系起来,可用于抗体及蛋白质文库选择、蛋白质体外改造等。运用此技术已成功筛选到一些与靶分子特异结合的高亲和力蛋白质,包括抗体、多肽、酶等,是蛋白质筛选的重要工具。1核糖体展示技术的基本原理及特点核糖体展示技术通过聚合酶链反应(PCR)扩增DNA文库,同时引入T7启动子、核糖体结合位点及茎-…     

药物小分子与DNA相互作用分析方法概述

DNA是生命活动中最基本的遗传物质,是基因表达和遗传变异的物质基础。DNA由平行堆积的碱基,聚合的阴离子磷酸骨架以及两条由核苷酸链形成的大沟、小沟共同组成了药物分子和蛋白质相互识别的位点。药物小分子与DNA相互作用的方式主要有三种：非共价结合、共价结合和剪切作用。非共价结合又以3种不同的方式进行：     

华支睾吸虫硫氧还蛋白跨膜蛋白基因的生物信息学分析

目的对华支睾吸虫硫氧还蛋白跨膜蛋白(Cs TMX)基因进行生物信息学分析。方法利用生物信息学方法(Inter Pro Scan、Signal P、TMHMM和SWISS-MODEL等相关软件)对Cs TMX基因及相应氨基酸序列的同源性、理化性质、保守结构域、信号肽、亲水性/疏水性、三级结构进行预测分析。结果 Cs TMX基因的开放阅读框(ORF)包含414 bp,编码137个氨基酸,理论分子质量为16.04×103,等电点为5.16。TMHMM和Signal P3.0分析结果显示Cs TMX含信号肽,其在第19~20位氨基酸之间有1个切割位点;Inter Pro Scan和SWISS-MODEL分析结果显示,TMX特征性结构域位于第21~27位氨基酸之间,并且具有高度保守的CPAC基因序列。结论利用生物信息学知识和各种分析软件对Cs TMX所编码的c DNA序列及理论蛋白质的理化性质、结构和功能域等进行预测和分析,能够为开展Cs TMX的表达及其功能研究提供理论依据。     

复制蛋白A功能研究进展

复制蛋白A(RPA)是目前国内外研究细胞DNA损伤应激反应的热点之一。RPA是真核细胞中主要的单链结合蛋白,包含70-,34-和14-ku 3个亚单位。RPA在DNA复制和修复过程中起着重要的作用。复制开始与延长阶段中,RPA具有解链、结合单链模板并维持DNA连续复制的功能;DNA损伤时,RPA与许多具有染色体结构维持、保护、修复功能的蛋白质簇集在DNA损伤位点,共同完成对DNA损伤的检测并进行修复。     

基于多芳环多吡啶配体的单功能铂配合物DNA结合研究

目的验证配体2,4,6-三[二(2-吡啶甲基)-氨甲基苯基]-1,3,5-三嗪(L4)配合物的DNA结合能力。方法合成一个多芳环多吡啶配体2,4,6-三[二(2-吡啶甲基)-氨甲基苯基]-1,3,5-三嗪(L4)。配体(L4)与Pt(DMSO)2Cl2反应得到配合物4,表征配合物,通过紫外、荧光和凝胶电泳的方法研究了配合物4的DNA结合能力。结果紫外和荧光实验表明该配合物均可与DNA嵌入结合,结合常数分别为2.1×104M-1、2.78×107M-1。凝胶电泳实验表明配合物可使DNA超螺旋形式完全解旋,有效扰乱DNA的二级结构。结论配体2,4,6-三[二(2-吡啶甲基)-氨甲基苯基]-1,3,5-三嗪(L4)配合物与DNA具有较强的结合能力,可以缓慢结合形成DNA的加合物,并且能够有效扰乱DNA构象。     

Kinetics of the DNA binding of 2-substituted anthraquinones

The DNA-binding properties of the 2-substituted-1,4-dihydroxyanthraquinones 5-12 were examined. Compounds 5 and 6 were synthesized in this study, 7-12 were already available. Spectral studies were consistent with intercalation of 5, 6 and 8 into DNA. Affinity constants were in the range of 3 x 10(4)M-1. Compounds 7 and 10-12 showed no DNA binding, presumably being sterically excluded from binding. The kinetics of the DNA interaction of 5, 6 and 8 were studied. There is a biphasic process. This may reflect an initial reaction, with drug from this first mode of binding moving into the second binding mode (a sequential process) or independent binding of drug in two sets of sites (a parallel process). The methods used in this study do not allow us to discriminate between these models. However, if the parallel binding model is correct, the compounds show sequence selectivity of binding, and provide a lead for further development of neutral DNA-binding ligands with sequence selectivity.     

Recognition of DNA modified by antitumor cisplatin by "latent" and "active" protein p53

Tumor suppressor protein p53 possesses two DNA-binding sites. One that is located within its core domain is responsible for sequence-specific DNA binding of the protein, non-specific binding to internal segments of single- or double-stranded DNA, and to certain kinds of non-B DNA structures. The other that is contained in the C-terminus of the protein binds to damaged DNA. Binding of active, latent, and in vitro-activated p53 protein to DNA fragments modified by antitumor cisplatin was studied using electrophoretic mobility shift assay in agarose gels and immunoblotting analysis. We found that both latent and active p53 forms bound to random sequences of DNA globally modified by cisplatin with a higher affinity than to unmodified DNA. Interestingly, the latent form exhibited a more pronounced selectivity for platinated DNA than the active p53. Consistently with this observation, the preference of the latent form for platinated DNA decreased as a consequence of the activation of latent p53 by phosphorylation at the protein kinase C site within its C-terminus or by binding of the monoclonal antibody Bp53-10.1. Competition experiments involving a 20-bp consensus sequence of p53 suggested that the p53 core domain was a primary binding site of the active p53 when it bound to DNA fragments lacking consensus sequence, but modified by cisplatin. In addition, the latent protein was found to selectively interact with DNA modified by cisplatin probably via its C-terminus.     

Steric constraints for DNA binding and biological activity in the amsacrine series

To determine the relation between DNA binding mode and biological activity in compounds related to the clinical anti-leukaemia drug amsacrine, a series of acridine-substituted derivatives has been synthesized and compared for lipophilicity, DNA-binding affinity, DNA-binding geometry and anti-leukaemia activity in vitro and in vivo. DNA-binding affinity, as estimated either by ethidium displacement or equilibrium dialysis, decreased progressively as the bulk of the substituent increased. Substitution at the 2 position provided the largest effects. The DNA unwinding angles, estimated by changes in viscosity of closed circular duplex DNA in the presence of drug, decreased significantly with ethyl and isopropyl substituents. However, with tertbutyl groups in the 2, 3 or 4 position of the acridine ring, unwinding was not observed even though DNA binding was measurable. Anti-leukaemia activity in vivo was also abolished when the acridine ring was substituted with a tertbutyl group. The results suggest that methyl substitution of the acridine ring inhibits DNA binding at the 2 position but not at the 3 and 4 positions, that ethyl and isopropyl substitution inhibits intercalative binding at all positions and that tertbutyl substitution abolishes intercalative binding. Biological activity in vitro is dependent on both lipophilicity and DNA binding and activity in vivo requires intercalative DNA binding.     

雄激素受体抑制剂的研究进展

雄激素受体与前列腺癌的发生、发展密切相关,是配体依赖的转录因子,其与雄激素结合后发生构象转化形成二聚体而活化,并进入细胞核中与相应的 DNA 反应元件结合,促进靶基因的转录,进而促进细胞的增殖。在前列腺癌组织中,雄激素受体的增殖或突变能使其对血清中较低含量的雄激素敏感,是前列腺癌恶化的主要原因。设计合成对野生型及突变型雄激素受体具有较好抑制活性的药物是治疗前列腺癌的首要策略。该文综述了雄激素受体的结构、功能及其抑制剂的研究进展,期望为新型抗前列腺癌药物的设计研究提供参考。     

Release of specific proteins from nuclei of HL-60 and MOLT-4 cells by antitumor drugs having affinity to nucleic acids

The binding sites for mitoxantrone (MIT), Ametantrone (AMT), doxorubicin (DOX), actinomycin D (AMD) and ethidium bromide (EB) in nuclei from exponentially growing and differentiating human promyelocytic HL-60 and lymphocytic leukemic MOLT-4 cells were studied by gel electrophoresis of proteins selectively released during titration of these nuclei with the drugs. Each drug at different drug: DNA binding ratios resulted in a characteristic pattern of protein elution and/or retention. For example, in nuclei from exponentially growing HL-60 cells, MIT affected 44 nuclear proteins that were different from those affected by EB; of these 29 were progressively released at increasing MIT:DNA ratios, 11 were transiently released (i.e. only at a low MIT:DNA ratio) and 4 entrapped. Patterns of proteins displaced from nuclei of exponentially growing HL-60 cells differed from those of cells undergoing myeloid differentiation as well as from those of exponentially growing MOLT-4 cells. The first effects were seen at a binding density of approximately one drug molecule per 10-50 base pairs of DNA. The observed selective displacement of proteins may reflect drug-altered affinity of the binding sites for those proteins, for example due to a change of nucleic acid or protein conformation upon binding the ligand. The data show that the binding site(s) for each of the ligands studied is different and the differences correlate with variability in chemical structure between the ligands. The nature of the drug-affected proteins may provide clues regarding antitumor or cytotoxic mechanisms of drug action.     

Patent Evaluation: Biotinylated nucleotide analogues as inhibitors of TNF hyperproduction

Novelty: Nucleotide analogues having a photoreactive group and a biotinyl group which covalently attach to nucleotide dependent protein binding sites are provided. Protein structurefunction studies are significantly facilitated by receptor binding site directed labelling. The invention has particular application to the characterisation of the active sites of nucleotide dependent enzymes. The use of the method for detection and removal of undesired DNA or RNA from cells (e.g. AIDS viral RNA) is briefly described.

Biology: Analogue modified proteins are detected by avidin-linked peroxidase or alkaline phosphatase methods. The modified protein can be purified by strepavidin-linked or avidinlinked affinity chromatography. After elution of unmodified protein, modified proteins are released and collected from the avidin column by raising the pH to hydrolyze the ester linkage by which the biotin is bound to the ribose hydroxyl group.

Chemistry: The biotin radical is attached to the ribose moiety of the nucleotide through an ester linkage. Upon photo irradiation the biotinylated photoaffinity analogues covalently bond to the nucleotide binding site.