丝组二肽对牛血清白蛋白的切割作用研究

肽与蛋白质的切割作为生物化学中的热点之一 ,具有非常广泛的应用 .长期以来 ,天然存在的多种蛋白酶如胰蛋白酶 (Trypsin)、糜蛋白酶 (Chymotrypsin)由于其高活性及区域选择性 ,一直是蛋白切割的主要工具 .但是这些酶只能在某些特定的条件 (如 p H值和温度等 )下使用 ,而且由于蛋白酶对底物的特异性要求高 ,因而切割蛋白的断裂位点相对较少 ,有一定的局限性 .而现代生物化学及分子生物学的发展在蛋白切割方面提出了越来越多的要求 [1,2 ] ,如蛋白部分合成 ,大蛋白的序列测定 ,蛋白区域结构与功能的分析 ,蛋白与其它蛋白、核酸、膜形成复合…     

丝组二肽所含基团在其切割DNA反应中的作用

近 2 0年来 ,人工核酸切割试剂的研究一直是化学、生物化学和分子生物学中最为活跃的前沿领域之一[1,2 ] .人工核酸切割试剂可以在足迹技术和核酸高级结构的研究中用作高分辨率的化学探针 ,还可以用于合成定点切割试剂[3] .后者又被称为人工工具酶 ,是一种非常重要的分子生物学工具 ,在疾病的基因治疗、反义 PCR技术等领域中都具有重要的应用 .人工核酸切割试剂的切割机理主要有自由基机理和磷酸酯水解机理两大类 .相对于自由基机理 ,水解机理具有许多优点 ,使得水解型切割试剂具有更为广泛的应用 .对于 DNA,目前文献报道的水解型人工切…     

结合丝组二肽的树状多肽对λDNA的切割

以Fmoc手工固相合成法合成了以多聚赖氨酸为骨架, 表面结合丝组二肽的四分支和二分支树状多肽, 以高效液相色谱提纯, 电喷雾电离质谱表征, 并通过凝胶电泳法研究了其对λDNA的切割活性.     

丝组二肽对DNA的切割作用的研究

近20年来,人工核酸切割试剂的研究一直是生物化学中最为活跃的前沿领域之一,研究人工核酸切割试剂的主要目的是合成定点切割试剂,后者是一种重要的分子生物学工具,在疾病的基团治疗、反义PCR技术等领域中有着重要的应用价值。此外,人工核酸切割试剂还可以在足迹技术和核酸高级结构的研究中用作高分辨率的化学探针。     

从磷酰化氨基酸到丝组二肽

Phosphorus is one of the important elements for life, which participates in various biochemical processes. L-Amino acids are the basic structural units of proteins. N-phosphorylation of amino acids makes them be activated and become one kind of "micro activating enzyme", which possesses a variety of biochemical reaction activities, such as peptide formation. Based on the peptide formation reaction of N-phosphoryl amino acids, L-seryl-L-histidine dipeptide (Seryl-histidine dipeptide) is produced and found that it is the smallest functional peptide with a variety of biological enzyme activities. Seryl-histidine dipeptide could be regarded as the original evolution prototype of modern hydrolytic enzyme. This paper reviews the research process from N-phosphoryl amino acids to the discovery of seryl-histidine dipeptide in detail. There are pain, confusion and joy, which fully embodies the charm of scientific exploration.     

丝组二肽对DNA切割作用的QM-MM研究

运用QM-MM方法对丝组二肽切割DNA作用的机理进行了研究．通过计算得到了丝组二肽与DNA形成多氢键作用的有效分子识别模型及相关分子结构参数,从理论上解释了丝组二肽与DNA通过形成五配位磷中间体而使磷酸二酯键发生水解,从而使得DNA被切断的作用机理。     

具有DNA切割功能的新型多聚酰胺/丝组缀合物

为得到具有核酸切割功能的人工核酸酶, 设计合成了一种新型多聚酰胺/丝组缀合物, 并研究了其DNA切割活性. 合成的目标化合物在pH=6.0的BR缓冲溶液中对pBR322 DNA切割活性的初步实验结果表明, 于37 ℃保温6 h后, pBR322 DNA基本上被完全从Form Ⅰ切割为Form Ⅱ, 保温36 h后, pBR322 DNA几乎被切割完全.     

HIV蛋白酶抑制剂——利迪链菌素的分子对接研究

用分子对接的方法, 对利迪链菌素的抗HIV蛋白酶活性进行了研究. 为了更准确地反映利迪链菌素分子与酶蛋白结合的情况, 充分考虑受体活性部位的柔性, 采用了FlexX(初步对接)和Flexidock(精确对接)分两步将配体与受体进行对接. 在初步对接中, 设计了不同的受体活性部位来考察是否有结合水分子参与抑制剂与酶的结合. 对一种作用方式已知的非肽类HIV蛋白酶抑制剂Aha006进行的对接研究显示, 分子模拟的结果与实际情况吻合得较好, 证明了本文所采用的方法的可靠性. 利迪链菌素与蛋白酶活性部位的对接结果显示, 配体分子与受体之间的结合没有结合水分子的参与, 两者通过5对氢键作用结合成为稳定的复合物. 利迪链菌素占据结合腔, 覆盖了蛋白酶的活性三联体Asp25-Thr26-Gly27, 从而起到抑制其生物活性的作用.     

膀胱癌分子标志物基质金属蛋白酶1的可溶性表达和尿液中的活性分析

通过分离人胚胎肾细胞(HEK293)中基质金属蛋白酶1(MMPl)基因序列,利用基因工程技术在大肠杆菌中表达并纯化了包涵体复性的MMP1;采用融合表达硫氧还蛋白(Thioredoxin,TrxA)的方法获得了可溶性的MMPl-TrxA复合蛋白,在TrxA蛋白和MMP1活性中心之间引入了一个肠激酶切割位点,通过酶切作用获得可溶性MMP1.明胶酶谱分析法对体外表达的MMP1和体内(尿液中)MMP1进行了分析比较.结果表明,TrxA蛋白能够显著提高MMP1的可溶性,且可溶性MMP1的明胶降解活性是复性的MMP1降解活性的1.54倍,与尿液中的MMP1的明胶酶降解活性相当.因此,明胶酶谱法是一种有效的、高灵敏的MMP1检测方法,所表达的可溶性MMP1为小分子探针筛选提供了更可靠的分子靶点.     

Using pseudo amino acid composition to predict protein structural class: approached by incorporating 400 dipeptide components

The proteins structure can be mainly classified into four classes: all-alpha, all-beta, alpha/beta, and alpha + beta protein according to their chain fold topologies. For the purpose of predicting the protein structural class, a new predicting algorithm, in which the increment of diversity combines with Quadratic Discriminant analysis, is presented to study and predict protein structural class. On the basis of the concept of the pseudo amino acid composition (Chou, Proteins: Struct Funct Genet 2001, 43, 246; Erratum: Proteins Struct Funct Genet 2001, 44, 60), 400 dipeptide components and 20 amino acid composition are, respectively, selected as parameters of diversity source. Total of 204 nonhomologous proteins constructed by Chou (Chou, Biochem Biophys Res Commun 1999, 264, 216) are used for training and testing the predictive model. The predicted results by using the pseudo amino acids approach as proposed in this paper can remarkably improve the success rates, and hence the current method may play a complementary role to other existing methods for predicting protein structural classification.     

High-throughput single molecule screening of DNA and proteins

We report a novel imaging technology for real time comprehensive analysis of molecular alterations in cells and tissues appropriate for automation and adaptation to high-throughput applications. With these techniques it should eventually be possible to perform simultaneous analysis of the entire contents of individual biological cells with a sensitivity and selectivity sufficient to determine the presence or absence of a single copy of a targeted analyte (e.g., DNA region, RNA region, protein), and to do so at a relatively low cost. The technology is suitable for DNA and RNA through sizing or through fluorescent hybridization probes, and for proteins and small molecules through fluorescence immunoassays. This combination of the lowest possible detection limit and the broadest applicability to biomolecules represents the final frontier in bioanalysis. The general scheme is based on novel concepts for single molecule detection (SMD) and characterization recently demonstrated in our laboratory. Since minimal manipulation is involved, it should be possible to screen large numbers of cells in a short time to facilitate practical applications. This opens up the possibility of finding single copies of DNA or proteins within single biological cells for disease markers without performing polymerase chain reaction or other biological amplification.     

应用ABEEM/MM蛋白质力场模型研究半胱氨酸二肽构象的性质

ABEEM/MM蛋白质力场模型是应用于蛋白质体系的原子-键电负性均衡方法(ABEEM)与力场(MM)相结合的浮动电荷模型.该模型能够准确地描述分子在环境变化时的静电极化,并能快速计算气态和溶液多肽的结构和能量.首次应用ABEEM/MM蛋白质力场模型研究半胱氨酸二肽构象的性质,如构象能、氢键等.此外,应用从头计算HF/6-31G**方法对其性质进行计算.ABEEM/MM蛋白质力场模型可以快速准确地得到半胱氨酸二肽分子不同稳定构象的性质,其结果可以和从头计算相媲美.以上研究有助于加深对半胱氨酸二肽构象性质的了解,从而也为进一步验证ABEEM/MM蛋白质力场模型的正确性以及参数的合理性提供可靠的依据.     

Computational design of novel cyclic urea as HIV-1 protease inhibitor

A series of novel cyclic urea molecules 5,6-dihydroxy-1,3-diazepane-2,4,7-trione as HIV-1 protease inhibitors were designed using computational techniques. The designed molecules were compared with the known cyclic urea molecules by performing docking studies, calculating their ADME (Absorption, Distribution, Metabolism, and Excretion) properties and protein ligand interaction energy. These novel molecules were designed by substituting the P ₁/P′ ₁ positions (4 ^th and 7 ^th position of 1, 3-diazepan-2-one) with double bonded oxygens. This reduces the molecular weight and increases the bioavailability, indicating better ADME properties. The docking studies showed good binding affinity towards HIV-1 protease. The biological activity of these inhibitors were predicted by a model equation generated by the regression analysis between biological activity (log 1/K ⁱ ) of known inhibitors and their protein ligand interaction energy. The synthetic studies are in progress.      

On the contribution of higher-order excitations to correlation energies: The ground state of the water molecule

Using the results of a configuration interaction calculation reported by Rosenberg and Shavitt, we derive an approximation to the correlation energy which may be associated with the sum to infinite order of all linked diagrams involving singly- and doubly-excited states. This result is compared with that obtained by calculation of the energy through third-order. The fourth-order linked diagrams involving quadruply-excited states are computed. It is shown that there is a considerable degree of cancellation between the fourth-order linked diagram energy terms involving doubly-excited intermediate states only and those which contain quadruply-excited states.     

Theoretical study of the role of low-barrier hydrogen bonds in enzyme catalysis: a model of proton transfer in serine protease

 A model of low-barrier hydrogen bonds (LBHBs) in enzymes has been studied by ab initio quantum mechanical calculations including the self-consistent reaction field solvent model. The hydrogen-bond strengths and the deprotonation energies for the hydrogen-bonded and non-hydrogen-bonded cis-urocanic acid were calculated at the HF/6-31 + G(d,p) level at various dielectric constants. The same calculations were performed for the α,β-dihydrourocanic acid to model the catalytic dyad of serine protease. The deprotonation energy of N^ɛ2 in α,β-dihydrourocanic acid is increased by formation of LBHBs and depends very much on the dielectric constant. This study suggests that the formation of LBHBs increases the basicity of the dyad, and the polarity change near the reaction center in the active site could help the proton abstraction from Ser 195 and the donation to the leaving group. Both the LBHBs and the environment can play crucial roles in the enzyme catalysis. Received: 8 March 2000 / Accepted: 3 January 2001 / Published online: 3 May 2001     

An efficient green catalyst comprising 12-tungstophosphoric acid and MCM-41: synthesis characterization and diesterification of succinic acid,a potential bio-platform molecule

An efficient green catalyst comprising 12-tungstophosphoric acid (TPA) and MCM-41 was synthesized. The catalytic activity was evaluated for liquid phase solvent free diesterification of succinic acid. The support and the synthesized catalyst were characterized by various physico-chemical techniques. Fourier transform infrared, diffuse reflectance spectroscopy, and ³¹P NMR spectra indicate that the Keggin structure of TPA was not destroyed after anchoring to MCM-41. X-ray diffraction, scanning electron microscopy, and transmission electron microscopy show that TPA is uniformly dispersed inside the channels without disturbing the hexagonal array of MCM-41. The present contribution reports solvent free diesterification of succinic acid with alcohols under mild reaction conditions. The catalyst shows higher activity toward diester, especially for dioctyl succinate 99% yield was obtained with very high turnover number, 12.43×10⁴. Also the catalyst shows potential of being used as recyclable catalytic material after simple regeneration without loss of any catalytic activity.     

DNA/BSA binding interactions and VHPO mimicking potential of vanadium(IV) complexes: Synthesis,structural characterization and DFT studies

Vanadium(IV) Schiff base complexes (VOL¹‐VOL³) were synthesized and characterized by elemental analysis, various spectral methods and single crystal XRD studies. Structural analysis of VOL² reveals that the central vanadium ion in the complex is six coordinate with distorted octahedral geometry. Density functional theory (DFT) and time dependent (TD‐DFT) studies were used to understand the electronic transitions observed in the complexes in UV–Vis spectra. The electrochemical behavior of the complexes was investigated in acetonitrile medium exhibit quasi‐reversible one electron transfer. The DNA and BSA protein binding interaction of vanadium complexes has been explored by UV–Vis and fluorescence spectral methods and viscosity measurements reveal that the complexes interact with CT‐DNA through intercalation mode and follows the order VOL¹ < VOL³ < VOL². The complexes exhibit binding interactions with BSA protein. The complexes act as chemical nuclease and cleave DNA in the presence of H₂O₂. The 2,2‐diphenyl‐1‐picrylhydrazyl (DPPH) assay was used to evaluate the radical scavenging activity demonstrate the antioxidant property of the complexes. The antimicrobial activity was screened for several microorganisms, Staphylococcus aureus, Bacillus subtilis, Pseudomonas aeruginosa, Escherichia coli. The mimicking of vanadium haloperoxidase was investigated by the bromination of the organic substrate phenol red by vanadium complexes in the presence of bromide and H₂O₂.