槲皮素与DNA的相互作用

有机小分子与DNA相互作用机理研究已经成为药物作用机理研究与新药筛选的重要手段之一。槲皮素 (Quercetin) 是一种多羟基黄酮类化合物,具有抗癌、抗炎、抗菌、抗病毒、降糖降压、免疫调节及保护心血管的作用。实验研究的目的是发现与确认槲皮素与DNA之间是否具有相互作用,以及确定其相互作用的类型。根据荧光光谱法和共振散射荧光光谱法的分析结果,发现槲皮素与鲱鱼精DNA之间存在相互作用;使用紫外-可见分光光度法和荧光偏振分析,发现槲皮素与鲱鱼精DNA之间的相互作用模式不属于嵌插作用,而是沟槽嵌合或者静电相互作用;最后通过分子对接实验,成功佐证槲皮素与鲱鱼精DNA之间的相互作用模式是沟槽结合。该工作有利于理解槲皮素与DNA之间的体外作用方式,助力于相应疾病的药物开发。     

利用荧光寿命变化定量分子内和分子间相互作用的方法

荧光寿命是指荧光分子在回到基态前在激发态停留的平均时间. 本文发展了基于荧光寿命测量来定量分子内和分子间相互作用的方法：通过G碱基猝灭对于荧光寿命的影响定量DNA二级结构的形成；通过荧光共振能量传递（FRET）中荧光寿命的变化来定量分子间的相互作用. 第一种方法巧妙利用了G碱基会猝灭临近的染料分子的性质，结合荧光寿命的变化，可以判断DNA二级结构的形成以及形成的比率. FRET是用于研究生物分子相互作用的一个重要手段. 传统的FRET方法主要是基于强度的变化，但这种变化容易受到荧光表达水平变动、样品中分子扩散以及荧光串色的影响，因此经常存在着实验比较复杂和重复性差的问题. 而基于荧光寿命的FRET研究则可以很好地克服上述缺点. 通过检测供体荧光寿命的变化，我们能够方便快捷地判断是否发生FRET，并通过建立系统的数据分析方法，得到FRET的效率以及分子之间相互作用的信息.     

NF-κBp50参与IL-4在THP-1细胞中诱导DC-SIGN的表达

树突状细胞表面特异的胞间黏附分子3捕获非整合素(DC-specific intercellular adhesion molecule-3-grabbing nonintegrin,DC-SIGN)是树突状细胞表面特异的蛋白,在抗原呈递过程中起关键作用.这种特异性的表达和DC-SIGN的调节机制有关.到目前为止,DC-SIGN表达调控的机制还不是很清楚.IL-4是诱导DC-SIGN表达的最重要的细胞因子之一,而NF-κB是调控细胞信号转导的一个重要调控因子,两者都和DC-SIGN的表达调节相关.研究了IL-4和NF-κB对DC-SIGN启动子活性、对DC-SIGN表达的影响以及IL-4和NF-κB之间相互作用的关系.发现:DC-SIGN启动子中NF-κB位点缺失可以使DC-SIGN启动子活性下降大约50%,NF-κBp50可以促进DC-SIGN在THP-1细胞的表达,IL-在THP-1细胞诱导DC-SIGN表达的同时,也促进了NF-κBp50的表达.这些结果显示,在THP-1细胞中NF-κBp50参与IL-4诱导的DC-SIGN表达.     

分子伴侣HdeA与底物蛋白SurA作用机制的模拟研究

分子伴侣HdeA与底物蛋白间的相互作用可帮助底物蛋白复性,这是肠道致病菌得以在酸性环境中幸存的重要原因之一.为探究HdeA发挥伴侣活性的作用机制,本研究采用分子对接和分子动力学的方法,模拟了HdeA与底物蛋白SurA间的相互作用,计算了二者的结合自由能.通过分析HdeA-SurA复合物体系的作用模式、氢键作用以及能量分解的结果,确定了HdeA与底物蛋白SurA结合时发挥重要作用的关键氨基酸残基.该研究结果为以后采用实验手段探究HdeA与底物蛋白之间的作用提供了重要的理论参考,同时为今后设计与开发HdeA的抑制剂提供了理论指导依据.     

生物大分子溶液三维结构及分子间相互作用的波谱研究

生物大分子溶液三维结构及分子间相互作用的波谱研究吴厚铭（中国科学院上海有机化学研究所生命有机化学国家重点实验室２０００３２）生物活性分子的溶液空间结构及分子间作用（如蛋白质与核酸,信息分子,各种调节剂,拮抗剂,以及核酸与药物分子等相互作用）的研究是发...     

DC-SIGN与mCEACAM1a分子相互作用调控鼠冠状病毒复制

树突细胞特异性细胞间黏附分子-3结合非整合素分子(dendritic cell-specific intercellular adhesion molecule-3-grabbing non-integrin,DC-SIGN)和肝/淋巴结特异性细胞间黏附分子-3结合非整合素分子(liver/lymph node-specific intercellular adhesion molecules-3-grabbing non-integrin,L-SIGN)是钙离子依赖的C型凝集素受体,通过识别病毒粒子表面含甘露聚糖或果糖寡聚糖的分子介导病毒进入细胞,但其在调节病毒复制中的作用较少被关注。本研究通过建立稳定表达DC-SIGN和L-SIGN及其功能域嵌合体的细胞系,分析两者过表达对鼠冠状病毒复制的影响。结果显示,L-SIGN比DC-SIGN更能显著抑制病毒复制,这种差异与两者胞内区序列和基序组成不同有关;鼠冠状病毒感染导致细胞外信号调节激酶(extracellular signal-regulated kinase,ERK)信号通路分子磷酸化下调,过表达DC-SIGN和L-SIGN可抑制这种下调趋势。在没有鼠癌胚抗原相关细胞黏附分子1(mouse carcinoembryonic antigen-related cell adhesion molecule 1,mCEACAM1)存在时,DC-SIGN不能介导病毒感染。这些结果提示,DC-SIGN通过与mCEACAM1a分子相互作用和调节细胞信号通路分子功能以调控鼠冠状病毒复制。     

生物大分子相互作用检测技术新进展———三色荧光级联荧光共振能量转移技术

荧光共振能量转移(fluorescenceresonanceenergytransfer,FRET),是指能量从一种受激发的荧光基团(fluorophore)以非辐射的方式转移到另一种荧光基团的物理现象.FRET的能量转移效率是两个荧光基团间距离的函数,并对此距离十分敏感,它的有效响应距离一般在1～10nm之间,因而可被用于测定原子间及分子间的距离.这一特点使FRET技术在大分子构象变化、大分子之间相互作用、细胞信号通路等研究中发挥重要作用,成为生物医学研究中的重要方法.但细胞内的生物学过程常常涉及多于两个的大分子间相互作用,二色荧光基团的FRET技术不能满足这种生物学研究的需求.最近,两个研究小组在这方面取得突破,建立了分别基于共聚焦显微镜和流式细胞仪的三色荧光级联FRET技术.这一技术的出现将会极大地促进生物学及相关研究领域的发展.     

单分子荧光检测技术的发展及其在植物生物学研究中的应用

单分子荧光检测技术是利用荧光基团对目的分子标记后,在单分子水平成像并追踪分子的构象变化、动力学特征以及分子之间相互作用的研究方法.相较于传统分子生物学和遗传学的研究手段,单分子检测技术可以对单个分子的动态和特性进行分析,特别是瞬时或偶发性的事件,从而更加深入地挖掘在群体测量中被掩盖的信息.该技术已广泛应用于动物细胞生物...     

基于密度泛函理论方法的核酸碱基拉曼光谱研究

核酸碱基是核酸的重要组成部分,而拉曼光谱是研究分子结构的一种重要技术,利用拉曼光谱对核酸碱基分子进行研究对于研究核酸大分子的结构变化,以及核酸分子与小分子之间的作用具有重要的意义.本研究以表征核酸碱基的拉曼光谱为目的,利用密度泛函理论(density functional theory,DFT)的方法优化腺嘌呤、鸟嘌呤、胞嘧啶、胸腺嘧啶和尿嘧啶的分子结构,对这5种核酸碱基的分子内化学键振动进行了量化计算并获得了理论拉曼光谱结果.利用计算结果对实验获得的碱基的固体拉曼光谱进行了表征,并且结合前人的研究结果对每种碱基的一些重要特征拉曼谱峰进行了细致的阐释,为进一步利用拉曼光谱研究核酸分子的结构信息奠定了理论基础.     

DC-SIGN与肿瘤关系的研究进展

树突状细胞特异性细胞间黏附分子-3结合非整合素因子(dendritic cell specific intercellular-adhesionmolecule-3 grabbing non-integrin,DC-SIGN)是一种主要表达于树突状细胞(dendritic cell,DC)表面的特异性受体,属于C型凝集素超分子家族。DC-SIGN不仅能与细胞间黏附分子-2(intercellular adhesion molecule-2,ICAM-2)和细胞间黏附分子-3(intercellular adhesion molecule-3,ICAM-3)等结合,还能识别HIV、登革病毒、巨细胞病毒等病原微生物,从而参与了这些病原体的感染过程,与多种感染性疾病的发病机制密切相关。近年来,有学者发现DC-SIGN还与肿瘤的发生、免疫、易感性有关,也因此受到了更广泛的关注。对DC-SIGN与肿瘤之间的关系进行更深一步的研究将有助于了解相关肿瘤疾病的发生机制,为促进其诊疗进展奠定基础。     

The cell surface receptor DC-SIGN discriminates between Mycobacterium species through selective recognition of the mannose caps on lipoarabinomannan

Interactions between dendritic cells (DCs) and Mycobacterium tuberculosis, the etiological agent of tuberculosis, most likely play a key role in anti-mycobacterial immunity. We have recently shown that M. tuberculosis binds to and infects DCs through ligation of the DC-specific intercellular adhesion molecule-3-grabbing nonintegrin (DC-SIGN) and that M. tuberculosis mannose-capped lipoarabinomannan (ManLAM) inhibits binding of the bacilli to the lectin, suggesting that ManLAM might be a key DC-SIGN ligand. In the present study, we investigated the molecular basis of DC-SIGN ligation by LAM. Contrary to what was found for slow growing mycobacteria, such as M. tuberculosis and the vaccine strain Mycobacterium bovis bacillus Calmette-Guérin, our data demonstrate that the fast growing saprophytic species Mycobacterium smegmatis hardly binds to DC-SIGN. Consistent with the former finding, we show that M. smegmatis-derived lipoarabinomannan, which is capped by phosphoinositide residues (PILAM), exhibits a limited ability to inhibit M. tuberculosis binding to DC-SIGN. Moreover, using enzymatically demannosylated and chemically deacylated ManLAM molecules, we demonstrate that both the acyl chains on the ManLAM mannosylphosphatidylinositol anchor and the mannooligosaccharide caps play a critical role in DC-SIGN-ManLAM interaction. Finally, we report that DC-SIGN binds poorly to the PILAM and uncapped AraLAM-containing species Mycobacterium fortuitum and Mycobacterium chelonae, respectively. Interestingly, smooth colony-forming Mycobacterium avium, in which ManLAM is capped with single mannose residues, was also poorly recognized by the lectin. Altogether, our results provide molecular insight into the mechanisms of mycobacteria-DC-SIGN interaction, and suggest that DC-SIGN may act as a pattern recognition receptor and discriminate between Mycobacterium species through selective recognition of the mannose caps on LAM molecules.     

Survey of the year 2009: applications of isothermal titration calorimetry

Isothermal titration calorimetry (ITC) is now an established and invaluable method for determining the thermodynamic constants, association constant and stoichiometry of molecular interactions in aqueous solutions. The technique has become widely used by biochemists to study protein interaction with other proteins, small molecules, metal ions, lipids, nucleic acids and carbohydrates; and nucleic acid interaction with small molecules. The drug discovery industry has utilized this approach to measure protein (or nucleic acid) interaction with drug candidates. ITC has been used to screen candidates, guide the design of potential drugs and validate the modelling used in structure-based drug design. Emerging disciplines including nanotechnology and drug delivery could benefit greatly from ITC in enhancing their understanding and control of nano-particle assembly, and drug binding and controlled release.     

Interaction between mannosylated lipoarabinomannan and dendritic cell-specific intercellular adhesion molecule-3 grabbing nonintegrin influences dendritic cells maturation and T cell immunity

The aim of the study was to investigate the interaction between manLAM and DC-SIGN influencing DCs maturation and downstream immune response using small interfering RNA-expressing lentiviral vectors to specifically knockdown DC-SIGN. Our data indicated that DC-SIGN knockdown alone in DCs did not affect the maturation or the immunological function of lipopolysacharide (LPS)-activated DCs. Surface molecules were dramatically down-regulated in DCs primed with manLAM but not in mock control DCs (P < 0.05). Meanwhile, manLAM enhanced the production of the immunosuppressive cytokine IL-10 in DCs (P < 0.05). The level of IFN-γ was significantly down-regulated in the supernatants of naive T cells after co-cultured with DCs primed with manLAM (P < 0.05). We demonstrated that DCs primed with manLAM may partially impair maturation phenotypes and immune response in LPS-activated DCs. However, the alterations of DCs function and downstream immune response caused by manLAM were reversed by the knockdown of DC-SIGN.     

Functional and antigenic characterization of human, rhesus macaque, pigtailed macaque, and murine DC-SIGN

DC-SIGN, a type II membrane protein with a C-type lectin binding domain that is highly expressed on mucosal dendritic cells (DCs) and certain macrophages in vivo, binds to ICAM-3, ICAM-2, and human and simian immunodeficiency viruses (HIV and SIV). Virus captured by DC-SIGN can be presented to T cells, resulting in efficient virus infection, perhaps representing a mechanism by which virus can be ferried via normal DC trafficking from mucosal tissues to lymphoid organs in vivo. To develop reagents needed to characterize the expression and in vivo functions of DC-SIGN, we cloned, expressed, and analyzed rhesus macaque, pigtailed macaque, and murine DC-SIGN and made a panel of monoclonal antibodies (MAbs) to human DC-SIGN. Rhesus and pigtailed macaque DC-SIGN proteins were highly similar to human DC-SIGN and bound and transmitted HIV type 1 (HIV-1), HIV-2, and SIV to receptor-positive cells. In contrast, while competent to bind virus, murine DC-SIGN did not transmit virus to receptor-positive cells under the conditions tested. Thus, mere binding of virus to a C-type lectin does not necessarily mean that transmission will occur. The murine and macaque DC-SIGN molecules all bound ICAM-3. We mapped the determinants recognized by a panel of 16 MAbs to the repeat region, the lectin binding domain, and the extreme C terminus of DC-SIGN. One MAb was specific for DC-SIGN, failing to cross-react with DC-SIGNR. Most MAbs cross-reacted with rhesus and pigtailed macaque DC-SIGN, although none recognized murine DC-SIGN. Fifteen of the MAbs recognized DC-SIGN on DCs, with MAbs to the repeat region generally reacting most strongly. We conclude that rhesus and pigtailed macaque DC-SIGN proteins are structurally and functionally similar to human DC-SIGN and that the reagents that we have developed will make it possible to study the expression and function of this molecule in vivo.     

Human immunodeficiency virus envelope (gp120) binding to DC-SIGN and primary dendritic cells is carbohydrate dependent but does not involve 2G12 or cyanovirin binding sites: implications for structural analyses of gp120-DC-SIGN binding

The calcium-dependent lectin, DC-SIGN, binds to human immunodeficiency virus (HIV) (and simian immunodeficiency virus) gp120 and mediates the binding and transfer of HIV from monocyte-derived dendritic cells (MDDCs) to permissive T cells. However, it has been recently reported that DC-SIGN binding to HIV gp120 may be carbohydrate independent. Here, we formally demonstrate that gp120 binding to DC-SIGN and MDDCs is largely if not wholly carbohydrate dependent. Endo-beta-N-glucosaminidase H (EndoH) treatment of gp120-Fc under conditions that maintained wild-type CD4 binding-and the full complement of complex glycans-significantly decreased (>90%) binding to DC-SIGN expressing cell lines, as well as to MDDCs. Any residual binding of EndoH-treated gp120-Fc to DC-SIGN was completely competed off with mannan. Mutational analysis indicated that no single glycosylation site affected the ability of gp120-Fc to bind DC-SIGN. To further guide our efforts in mapping the DC-SIGN binding sites on gp120, we used two well-characterized HIV inhibitory agents (2G12 monoclonal antibody and cyanovirin) that bind to high-mannose sugars on gp120. We showed that 2G12 and DC-SIGN bound to nonoverlapping sites in gp120 because (i) 2G12 did not block soluble gp120 or virion binding to DC-SIGN, (ii) 2G12 bound to gp120-Fc that was prebound to cell surface DC-SIGN, and (iii) gp120-Fc mutants that lack glycosylation sites involved in 2G12's epitope were also fully capable of binding DC-SIGN. These data were substantiated by the inability of cyanovirin to block gp120-Fc binding to DC-SIGN. Cyanovirin has been shown to effectively compete for 2G12 binding to gp120. Indeed, high concentrations of cyanovirin dramatically enhanced gp120-Fc binding to cell surfaces in the presence or absence of DC-SIGN. We provide evidence that this enhancement may be due to cyanovirin's ability to bridge gp120 to mannosylated cell surface proteins. These results have implications for antiviral therapeutics and for ongoing efforts to finely map the glycan structures on gp120 responsible for DC-SIGN binding.     

A hierarchical method for molecular docking using cloud computing

Discovering small molecules that interact with protein targets will be a key part of future drug discovery efforts. Molecular docking of drug-like molecules is likely to be valuable in this field; however, the great number of such molecules makes the potential size of this task enormous. In this paper, a method to screen small molecular databases using cloud computing is proposed. This method is called the hierarchical method for molecular docking and can be completed in a relatively short period of time. In this method, the optimization of molecular docking is divided into two subproblems based on the different effects on the protein–ligand interaction energy. An adaptive genetic algorithm is developed to solve the optimization problem and a new docking program (FlexGAsDock) based on the hierarchical docking method has been developed. The implementation of docking on a cloud computing platform is then discussed. The docking results show that this method can be conveniently used for the efficient molecular design of drugs.     

Molecular design of new aggrecanases-2 inhibitors

Aggrecanases-2 is a very important potential drug target for the treatment of osteoarthritis. In this study, a series of known aggrecanases-2 inhibitors was analyzed by the technologies of three-dimensional quantitative structure–activity relationships (3D-QSAR) and molecular docking. Two 3D-QSAR models, which based on comparative molecular field analysis (CoMFA) and comparative molecular similarity analysis (CoMSIA) methods, were established. Molecular docking was employed to explore the details of the interaction between inhibitors and aggrecanases-2 protein. According to the analyses for these models, several new potential inhibitors with higher activity predicted were designed, and were supported by the simulation of molecular docking. This work propose the fast and effective approach to design and prediction for new potential inhibitors, and the study of the interaction mechanism provide a better understanding for the inhibitors binding into the target protein, which will be useful for the structure-based drug design and modifications.     

Increasingly accurate dynamic molecular models of G-protein coupled receptor oligomers: Panacea or Pandora's box for novel drug discovery?

For years, conventional drug design at G-protein coupled receptors (GPCRs) has mainly focused on the inhibition of a single receptor at a usually well-defined ligand-binding site. The recent discovery of more and more physiologically relevant GPCR dimers/oligomers suggests that selectively targeting these complexes or designing small molecules that inhibit receptor–receptor interactions might provide new opportunities for novel drug discovery. To uncover the fundamental mechanisms and dynamics governing GPCR dimerization/oligomerization, it is crucial to understand the dynamic process of receptor–receptor association, and to identify regions that are suitable for selective drug binding. This minireview highlights current progress in the development of increasingly accurate dynamic molecular models of GPCR oligomers based on structural, biochemical, and biophysical information that has recently appeared in the literature. In view of this new information, there has never been a more exciting time for computational research into GPCRs than at present. Information-driven modern molecular models of GPCR complexes are expected to efficiently guide the rational design of GPCR oligomer-specific drugs, possibly allowing researchers to reach for the high-hanging fruits in GPCR drug discovery, i.e. more potent and selective drugs for efficient therapeutic interventions.