UPLC-TSQ-Endure质谱分析Rg_3对2型糖尿病大鼠P450酶活性的影响

应用超高效液相色谱-质谱联用法(UPLC-MS)结合多探针底物法建立了同时定量测定5个细胞色素P450酶探针底物的方法,同时考察正常大鼠和2型糖尿病大鼠CYP亚型酶活性的变化,分析人参皂苷Rg_3对CYP亚型酶的调控作用。结果表明,与正常组比较,2型糖尿病大鼠肝微粒体酶中P3A4和P2E1活性被诱导,P2D6,P1A2和P2C9活性被抑制。人参皂苷Rg_3诱导2型糖尿病大鼠P3A4和P1A2活性,抑制P2E1和P2C9活性,对P2D6活性无明显影响。人参皂苷Rg_3能够使糖尿病大鼠CYP2E1和CYP1A2亚型酶活性趋于恢复到正常生理状态,其在CYP450酶中的代谢产物为人参皂苷Rh2。方法适用于评价P450酶诱导或抑制的酶活性测定,在临床上指导2型糖尿病患者合理用药。     

鹰嘴豆β-半乳糖苷酶的分离纯化与表征

从鹰嘴豆中分离得到了三种β－半乳糖苷酶（酶Ⅰ、酶Ⅱ和酶Ⅲ）。将酶Ⅰ和酶Ⅱ进一步纯化,其比活力分别提高了19倍和48倍．酶活力回收率分别为16％和18％,测得它们的表观分子里分别为2．4×104和5.8×104;最适pH分别5.9和5.0,最适温度分别为55℃和45℃．酶Ⅰ水解ONPG和PNPG的KM分别为33×10-2mol·dm-3和60×10-3mol·dm－3;酶Ⅱ水解ONPG和PNPG的KM分别为30×10－3mol·dm－3和60×10－4mol·dm－3.乳糖和半乳糖为该酶的竞争性可逆抑制剂,棉子糖为非竞争性可逆抑制剂．该酶受Hg2＋和PCMB强烈抑制和NEM明显抑制,而Mg2＋、Zn2＋和Ca2＋具有激活作用,推知巯基（－SH)是酶活性中心必须基团．     

SARS 3CL蛋白酶同源二聚化与底物结合互为别构调控因素

研究了严重急性呼吸系统综合症(SARS)冠状病毒3C-Like蛋白酶(3CLpro)在存在底物或抑制剂时的二聚体形成情况. 通过测定酶活性随酶浓度的变化, 拟合出在底物存在下酶二聚体的解离常数约为0.94 μmol·L-1, 小于纯蛋白酶的二聚体解离常数(14.0 μmol·L-1), 表明底物对二聚体的形成具有增强作用. 选用与底物具有类似结合方式的靛红类抑制剂N-萘甲基靛红-5-甲酰胺(5f), 利用超速离心沉降速率方法定量测定了SARS 3CL蛋白酶单体和二聚体在不同浓度5f时的含量, 发现5f同样具有诱导二聚体形成的能力. 在3 μmol·L-1蛋白酶浓度下测定得到诱导二聚的EC50 值(半数有效浓度)约为1 μmol·L-1, 说明二聚体中只有一个单体与抑制剂结合. 研究结果表明, 随着底物浓度的升高, SARS 3CL蛋白酶会形成更多的二聚体, 而二聚体含量的提高又反过来提高酶的活性, 这种双向别构调控机制有可能是病毒用来调控多聚蛋白水解速率和组装时机的一种方法.     

猪肉中过氧化物酶活性的TMB法研究

以3,5,3',5'-四甲基联苯胺(TMB)为底物对猪肉过氧化物酶(POD)的酶学特性以及猪肉不同部位过氧化物酶活性水平进行了较为系统的研究,并以辣根过氧化物酶(HRP)为标准酶获得了酶活性标准曲线.猪肉过氧化物酶在温度38℃,pH 4.80时活性最高.酶浓度与酶反应初始阶段的酶活性有较好的线性关系,氢供体底物TMB的最佳浓度为2.80×10-4 mol/L,浓度过大则会抑制酶的活性,氢受体底物过氧化氢的浓度与酶活性有较好的线性关系和较宽的线性范围(0～4.20×10-3 mol/L).猪肉不同部位如腰条(指外腰条)、里脊(指内腰条)、后腿、前腿、三层、腱子中POD活性大小不同,前三者的POD活性相近且活性较小,而后三者活性较为相近且活性较大.通过辣根过氧化物酶标准曲线可以求估待测样品中POD的活性值.     

新型SARS-CoⅤ 3CL蛋白酶荧光多肽底物的设计、制备及其酶动力学研究

以邻氨基苯甲酸(Abz)为荧光发射基团、2,4-二硝基苯基乙二胺(Eddnp)为荧光猝灭基团,设计合成了SARS-CoⅤ3CL蛋白酶的新型荧光多肽底物:H2N-E(Eddnp)STLQSGLK(Abz)-CONH2.用液相色谱-质谱(LC-MS)联用技术进行了表征,表明该多肽底物能被SARS-CoⅤ3CL蛋白酶识别,并在QS之间被专一性酶解.另外,利用该多肽底物的荧光共振能量转移(FRET)特性,对SARS-CoⅤ3CL蛋白酶的酶解动力学性质进行了研究,结果表明,此荧光多肽底物可以作为荧光探针,应用于SARS-CoⅤ3CL蛋白酶活性的测定及其抑制剂的筛选.     

靛红类双功能抑制剂: 调控SARS-3CL蛋白酶聚集状态与活性

1-(2-萘甲基)靛红-5-甲酰胺类化合物通过与底物口袋结合来抑制SARS-3CL 蛋白酶的活性, 而SARS-3CL蛋白酶自身的N端8 肽是作用于蛋白二聚界面的抑制剂. 本文设计同时占据SARS-3CL蛋白酶底物口袋和二聚界面的双功能抑制剂, 通过固相多肽合成方法制备由1-(2-萘甲基)靛红-5-甲酸和N端8肽组成的化合物, 得到不同长度连接链的6 个目标产物. 用显色底物方法测定化合物对SARS-3CL蛋白酶的抑制活性,其中化合物3的活性最高, IC₅₀值(半抑制率)为3.8 μmol·L^-1, 连接偶数甘氨酸的活性明显要好于连接奇数甘氨酸的化合物. 用超速离心沉降速率方法研究了化合物3对SARS-3CL蛋白酶聚集状态与活性的调控作用, 其同时具有诱导与抑制二聚的双重能力, 综合调控结果是抑制SARS-3CL蛋白酶的二聚. 这项研究给应用合成的化合物研究酶活性调节机制提供了一个示例.     

化学修饰法表征Bacillus smithii T7产耐热菊粉酶催化活性中心的必需氨基酸残基

采用化学修饰法研究了史氏芽胞杆菌Bacillus smithiiT7产耐热菊粉酶活性中心氨基酸残基,发现该酶活性中心存在一个组氨酸残基和一个谷氨酸(或天冬氨酸)残基.修饰前后的酶动力学参数变化表明组氨酸残基参与了底物的结合和催化过程,而谷氨酸(或天冬氨酸)的羧基亲核攻击促使底物分解.邹氏作图法证明酶活性中心存在两个必需的色氨酸残基,荧光和圆二色光谱研究表明色氨酸残基在酶的催化和酶的耐热性方面起重要作用.     

金属离子抑制剂对酶法测定的影响

基于乳酸脱氢酶(LDH)催化乳酸和氧化型烟酰胺腺嘌呤二核苷酸(NAD)的反应,在最佳酶反应条件下,研究了金属离子对酶催化的抑制作用.发现Cu2 对LDH的酶促反应有显著的抑制,抑制常数KQS为9.1靘ol/L,属非竞争性抑制.根据在抑制剂作用下的米氏方程,可以利用酶法对铜离子进行定量测定,通过加入金属离子络合剂乙二胺四乙酸(EDTA)可有效消除一定浓度的Cu2 对LDH酶促反应测定底物的干扰.     

神经氨酸酶与3-(3-戊氧基)安息香酸作用机制的理论研究

运用柔性分子对接和分子动力学方法, 深入研究了4-(氮乙酰氨基)-5-胍基-3-(3-戊氧基)安息香酸(BA)与各类型神经氨酸酶(N1, N2, N9亚型和B型)间的作用机制. 结果显示, BA与各类型神经氨酸酶结合模式存在差异, 但作用机制比较相似: 与它们的活性腔均匹配良好, 并形成稳定的复合体系, 最大结合能分别等于－1233.62, －1385.72, －663.11, －1058.87 kJ•mol^－1. 这表明BA对各类型神经氨酸酶均有良好的抑制效果. 进一步分析发现, BA与各类型神经氨酸酶活性腔内保守关键氨基酸残基发生较强的静电和氢键作用, 而与易突变氨基酸残基作用较弱, 表明了活性腔内易突变氨基酸残基发生突变也不会对抑制效果造成明显影响. 因此, BA是一种极具应用前景的新型抗流感病毒药物. 结合以前的研究结果, 我们提出了以BA为底物的抗流感病毒药物的修饰方向.     

以透明质酸为骨架的新型谷胱甘肽过氧化物酶(GPX)模拟酶的制备及性质研究

用修饰法合成以透明质酸为骨架的两种新型GPX模拟酶: 硒化透明质酸SeHA及碲化透明质酸TeHA. 用红外光谱和核磁共振波谱对模拟酶的结构进行研究, 证明其修饰位点位于透明质酸的N-乙酰氨基葡萄糖的—CH2OH. 用二硫代双硝基苯甲酸(DTNB)法测定模拟酶的硒含量为1.2%. 通过模拟酶对3种不同底物过氧化氢(H2O2)、过氧化氢正丁烷(t-BuOOH)和过氧化氢异丙苯(CuOOH)的催化活性的研究结果表明CuOOH为该反应的最佳底物. 研究模拟酶催化谷胱甘肽(GSH)还原3种过氧化物的动力学发现, 反应速率与底物浓度的双倒数曲线均为平行的直线, 说明模拟酶反应的动力学机制与天然GPX相同, 为乒乓机制. 用2,4-二叔丁基甲基苯酚(BHT)法证明了该催化反应为非自由基机理, 且模拟酶不易被碘乙酸抑制.     

Mechanistic Analysis of Fluorescence Quenching of Reduced Nicotinamide Adenine Dinucleotide by Oxamate in Lactate Dehydrogenase Ternary Complexes

Fluorescence of Reduced Nicotinamide Adenine Dinucleotide (NADH) is extensively employed in studies of oxidoreductases. A substantial amount of static and kinetic work has focused on the binding of pyruvate or substrate mimic oxamate to the binary complex of lactate dehydrogenase (LDH)‐NADH where substantial fluorescence quenching is typically observed. However, the quenching mechanism is not well understood limiting structural interpretation. Based on time‐dependent density functional theory (TDDFT) computations with cam‐B3LYP functional in conjunction with the analysis of previous experimental results, we propose that bound oxamate acts as an electron acceptor in the quenching of fluorescence of NADH in the ternary complex, where a charge transfer (CT) state characterized by excitation from the highest occupied molecular orbital (HOMO) of the nicotinamide moiety of NADH to the lowest unoccupied molecular orbital (LUMO) of oxamate exists close to the locally excited (LE) state involving only the nicotinamide moiety. Efficient quenching in the encounter complex like in pig heart LDH requires that oxamate forms a salt bridge with Arg‐171 and hydrogen bonds with His‐195, Thr‐246 and Asn‐140. Further structural rearrangement and loop closure, which also brings about another hydrogen bond between oxamate and Arg‐109, will increase the rate of fluorescence quenching as well.     

Synthesis and characterisation of a ligand that forms a stable tetrahedral intermediate in the active site of the Aureobacterium species (-) gamma-lactamase

The crystal structure of a (-) gamma-lactamase from an Aureobacterium species showed a molecule bound covalently to the active site serine residue. This enzyme complex represented the first structure of a stably bound tetrahedral intermediate for an alpha/beta hydrolase fold enzyme. The structural elucidation of tetrahedral intermediates is important for the understanding of enzymatic mechanism, substrate recognition and enzyme inhibition. In this paper, we report the synthesis and subsequent characterisation of (3aR,7aS)-3a,4,7,7a-tetrahydrobenzo-[1,3]-dioxol-2-one (BD1), the molecule modelled into the Aureobacterium (-) gamma-lactamase active site. This molecule has been confirmed to be an inhibitor and to be displaced from the enzyme by the racemic gamma-lactam substrate.     

Enzymatic membranes for the selective transport of neutral molecules by electrophoresis

The active and selective transport of glucose and glycerol was carried out using electrophoresis and artificial enzymatic membranes. These positively charged composite membranes carry, on the face adjacent to the donor compartment of an electrophoresis module, a specific kinase (hexokinase or glycerokinase) and, on the opposite face, an alkaline phosphatase (ALP). Phosphorylation of the neutral substrate (glucose or glycerol) on the donor side by the kinase generates a negatively charged phosphorylated substrate, whose transmembrane migration is promoted by an electric field and by the membrane's positive charge. Dephosphorylation of the phosphorylated substrate by ALP on the opposite face regenerates the neutral substrate, which accumulates in the receiver compartment of the electrophoresis module. Using an electrophoresis module specifically designed for this study, our experiments were carried out enabling glucose and glycerol to be concentrated approximately eight- and twelve-fold, respectively, in 8 h.     

Hybrid QM/MM and DFT investigations of the catalytic mechanism and inhibition of the dinuclear zinc metallo-beta-lactamase CcrA from Bacteroides fragilis

Based on hybrid QM/MM molecular dynamics simulation and density functional theoretical (DFT) calculations, we investigate the mechanistic and energetic features of the catalytic action of dizinc metallo-beta-lactamase CcrA from Bacteroides fragilis. The 200 ps QM/MM simulation of the CcrA enzyme in complex with nitrocefin shows that the substrate beta-lactam moiety is directed toward the active site dizinc center through the interactions of aminocarbonyl and carboxylate groups with the two active site zinc ions and the two conserved residues, Lys167 and Asn176. From the determination of the potential energy profile of a relevant enzymatic reaction model, it is found that the nucleophilic displacement reaction step proceeds with a low-barrier height, leading to the formation of an energetically favored reaction intermediate. The results also show that the high catalytic activity of the CcrA enzyme stems from a simultaneous operation of three catalytic components: activation of the bridging hydroxide nucleophile by zinc-coordinated Asp86; polarization of the substrate aminocarbonyl group by the first zinc ion; stabilization of the negative charge developed on the departing amide nitrogen by the second zinc ion. Consistent with the previous experimental finding that the proton-transfer reaction step is rate-limiting, the activation energy of the second step is found to be 1.6 kcal/mol higher than that of the first step. Finally, through an examination of the structural and energetic features of binding of a thiazolidinecarboxylic acid inhibitor to the active site dizinc center, a two-step inhibition mechanism involving a protonation-induced ligand exchange reaction is proposed for the inhibitory action of a tight-binding inhibitor possessing a thiol group.     

High turnover remote catalytic oxygenation of alkyl groups: how steric exclusion of unbound substrate contributes to high molecular recognition selectivity

H-bonding mediated molecular recognition between substrate and ligand -COOH groups orients the substrate so that remote, catalyzed oxygenation of an alkyl C-H bond by a Mn-oxo active site can occur with very high (>98%) regio- and stereoselectivity. This paper identifies steric exclusion-exclusion of non H-bonded substrate molecules from the active site-as one requirement for high selectivity, along with the entropic advantage of intramolecularity. If unbound substrate molecules were able to reach the active site, they would react unselectively, degrading the observed selectivity. Both of the faces of the catalyst are blocked by two ligand molecules each with a -COOH group. The acid p-(t)BuC6H4COOH binds to the ligand -COOH recognition site but is not oxidized and merely blocks approach of the substrate therefore acting as an effective inhibitor for ibuprofen oxidation in both free acid and ibuprofen ester form. Dixon plots show that inhibition is competitive for the free acid ibuprofen substrate, no doubt because this substrate can compete with the inhibitor for binding to the recognition site. In contrast, inhibition is uncompetitive for the ibuprofen-ester substrate, consistent with this ester substrate no longer being able to bind to the recognition site. Inhibition can be reversed with MeCOOH, an acid that can competitively bind to the recognition site but, being sterically small, no longer blocks access to the active site.     

Synthesis of modified peptidoglycan precursor analogues for the inhibition of glycosyltransferase

The peptidoglycan glycosyltransferases (GTs) are essential enzymes that catalyze the polymerization of glycan chains of the bacterial cell wall from lipid II and thus constitute a validated antibacterial target. Their enzymatic cavity is composed of a donor site for the growing glycan chain (where the inhibitor moenomycin binds) and an acceptor site for lipid II substrate. In order to find lead inhibitors able to fill this large active site, we have synthesized a series of substrate analogues of lipid I and lipid II with variations in the lipid, the pyrophosphate, and the peptide moieties and evaluated their biological effect on the GT activity of E. coli PBP1b and their antibacterial potential. We found several compounds able to inhibit the GT activity in vitro and cause growth defect in Bacillus subtilis . The more active was C16-phosphoglycerate-MurNAc-(L-Ala-D-Glu)-GlcNAc, which also showed antibacterial activity. These molecules are promising leads for the design of new antibacterial GT inhibitors.     

Transient pockets as mediators of gas molecules routes inside proteins: The case study of dioxygen pathway in homogentisate 1,2-dioxygenase and its implication in Alkaptonuria development

Alkaptonuria (AKU) is an ultra-rare disease caused by mutations in homogentisate 1,2-dioxygenase (HGD) enzyme, characterized by the loss of enzymatic activity and the accumulation of its substrate, homogentisic acid (HGA) in different tissues, leading to ochronosis and organ degeneration. Although the pathological effects of HGD mutations are largely studied, less is known about the structure of the enzyme, in particular the pathways for dioxygen diffusion to the active site, required for the enzymatic reaction, are still uninvestigated. In the present project, the combination of two in silico techniques, Molecular Dynamics (MD) simulation and Implicit Ligand Sampling (ILS), was used to delineate gas diffusion routes in HGD enzyme. A route from the central opening of the hexameric structure of the enzyme to the back of the active site trough the protein moiety was identified as the path for dioxygen diffusion, also overlapping with a transient pocket, which then assumes an important role in dioxygen diffusion. Along the route the sequence location of the missense variant E401Q, responsible for AKU development, was also found, suggesting such mutation to be conducive of enzymatic activity loss by altering the flow dynamics of dioxygen. Our in silico approach allowed also to delineate the route of HGA substrate to the active site, until now only supposed.     

Probing single-molecule enzyme active-site conformational state intermittent coherence

The relationship between protein conformational dynamics and enzymatic reactions has been a fundamental focus in modern enzymology. Using single-molecule fluorescence resonance energy transfer (FRET) with a combined statistical data analysis approach, we have identified the intermittently appearing coherence of the enzymatic conformational state from the recorded single-molecule intensity-time trajectories of enzyme 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) in catalytic reaction. The coherent conformational state dynamics suggests that the enzymatic catalysis involves a multistep conformational motion along the coordinates of substrate-enzyme complex formation and product releasing, presenting as an extreme dynamic behavior intrinsically related to the time bunching effect that we have reported previously. The coherence frequency, identified by statistical results of the correlation function analysis from single-molecule FRET trajectories, increases with the increasing substrate concentrations. The intermittent coherence in conformational state changes at the enzymatic reaction active site is likely to be common and exist in other conformation regulated enzymatic reactions. Our results of HPPK interaction with substrate support a multiple-conformational state model, being consistent with a complementary conformation selection and induced-fit enzymatic loop-gated conformational change mechanism in substrate-enzyme active complex formation.     

壳聚糖固定化乳酸脱氢酶的制备及酶学性质研究

以磁性壳聚糖作为载体,戊二醛作为交联剂,对乳酸脱氢酶(LDH)进行固定化.固定化的最适条件为:戊二醛浓度6%,pH值7.5,酶的偶联时间2 h.对游离及固定化LDH酶学性质的研究表明,酶促反应的最适pH值为9.2,最适温度分别为37℃和50℃,对乳酸的表观米氏常数分别为1.6 mmol/L和0.9 mmol/L.游离酶和固定化酶在40℃放置150 min后,其活力分别为最初的56.5%和76.1%.固定化酶在4℃贮存4周后,活力仍保留50%以上.固定化酶在室温下与底物重复反应6次后,活力仍保留60%以上,说明固定化酶具有较好的热稳定性、贮存稳定性和复用性.     

聚羟基烷酸酯酶降解动力学研究

研究了羟基丁酸 羟基戊酸共聚物 (PHBV)在脂肪酶中的降解行为 ,用滴定法测定降解速度并进行酶促反应动力学研究 .探讨了降解速度与酶浓度和底物浓度的数学关系和Michaelis Menten常数 ,从实验上和理论上证实了PHBV的物理形态和几何尺寸对酶降解过程的影响 ,以及实验数据与非均相动力学模型的拟合