胆碱酯酶催化反应的量子化学研究 活性部位残基间氢键的形成及残基氧化的影响

采用量子化学的CNDO/2法,探讨了胆碱酯酶活性部位的组氨酸、丝氨酸等残基问氢键的形成和氢迁移问题,从理论上阐明了酸催化乙酸胆碱反应中何者作为亲核基团向底物进攻。考虑到氧化对酶生物活性的丧失有较大影响,对组氨酸残基氧化前后的氢键构成和催化机理进行了理论比较。为研究酶催化过程提供了有用的信息。     

结合分子模拟探讨共聚酯PBSH在不同溶剂中的PC脂肪酶催化降解

采用固定化洋葱假单胞菌(PC)脂肪酶为催化剂,研究了在氯仿和四氢呋喃(THF)中不同摩尔比的聚(丁二酸丁二醇-co-丁二酸己二醇酯)(PBSH)的酶促降解规律及其差异性.通过PBSH降解前后的相对分子质量变化、降解产物的MALDI-TOF-MS分析研究了共聚酯降解规律,并以分子动力学(MD)及分子对接模拟分别研究了PC酶的溶剂效应及酶与底物的结合机制.研究结果表明,PC酶在2种溶剂中均可催化PBSH降解,但在氯仿中酶的活性较大,PBSH降解率大.分子动力学模拟数据表明,在THF中,PC酶整体氨基酸残基的涨落比氯仿中大,且THF会进入酶活性口袋中与催化残基Ser87结合,破坏了催化残基Ser87和His286之间的相互作用.分子对接结果分析发现,含丁二酸己二醇酯(HS)单元底物与PC酶活性位点的对接比含丁二酸丁二醇酯(BS)单元的更为稳定.     

白喉毒素活性中心的量子化学计算与149位突变体的酶学动力学

通过量子化学计算确定白喉毒素分子催化区活性中心的关键氨基酸残基, 评价其取代后的酶活性的改变, 为导向性抗癌药物研究提供高效杀伤细胞工具. 结合目前关于白喉毒素结构与功能的研究状况和量子化学计算结果, 将白喉毒素催化区的第149位酪氨酸突变为苯丙氨酸, 对其酶活性和与底物的结合能力进行评价. Y149位酪氨酸位于正电中心, 起受电子作用, 与野生白喉毒素相比, 苯丙氨酸突变体的酶催化活性增加约一倍, 而与底物结合能力没有变化. Y149是酶活性中心的关键氨基酸残基, 对其取代能够影响蛋白质的生物活性.     

麦芽酸性磷酸酶的化学修饰及紫外光谱

本文研究化学修饰剂2,3-丁二酮(Butanedione)、β-巯基乙醇(Mercaptoethanol)、对硝基苯磺酰氟(4-Nitrobenzensulfonyl fluoride,NBSF)和焦碳酸二乙酯(Diethyl pyrocarhonate,DEPC)在不同浓度、不同时间条件下对麦芽酸性磷酸酶(ACPase,E.C.3.1.3.2)相互作用后的活力及紫外光谱的变化。结果表明:色氨酸和精氨酸可能是维系麦芽酸性磷酸酶催化功能的必需基团,酶分子中二硫键和组氨酸残基不参与该酶分子活性中心的构成。     

L-乳酸脱氢酶抑制剂抑制成因的探讨

应用HF/3 21G研究了抑制剂H2N－CO－COO－对L 乳酸脱氢酶的抑制成因.结果表明,酶被抑制的主要原因有:(1)抑制剂与底物的稳定构象态在结构上极为相似,导致酶不能有效识别底物;(2)模型抑制剂各原子所带净电荷的优势使抑制剂更易与酶活性中心结合;(3)抑制剂通过对酶的诱导契合作用使酶活性中心的空间被缩小;(4)对活性中心有关结构的分析表明,底物的甲基分子片以及酶的氨基酸残基Gln 102,对催化反应能否顺利进行,影响极大.     

基于快速定点突变研究含硒人Zeta型谷胱甘肽硫转移酶1c-1c的催化活性

先将人Zeta型谷胱甘肽硫转移酶1c-1c(hGSTZ1c-1c)中非催化中心的Cys-137,Cys-154,Cys-165和Cys-205突变为Ser,然后将催化中心14,15和17位的3个氨基酸残基突变为Cys,再利用半胱氨酸缺陷型大肠杆菌表达系统将其特定地转化为Sec,即把GPx的催化基团引入到hGSTZ1c-1c中,高效地获得了具有谷胱甘肽过氧化物酶(GPx)活力的模拟酶.其中制备的3个含硒突变体15C,14C/15C和17C均显示出明显的GPx活力.对非含硒突变体性质研究发现,Ser-14或Ser-15任何一个残基发生突变都会导致hGSTZ1c-1c的GST活力几乎丧失,表明Ser-14和Ser-15在催化反应中发挥着重要作用,但前者主要参与底物结合,后者更侧重于催化.     

长白山白眉蝮蛇蛇毒精氨酸酯酶1的研究Ⅱ.酶学性质和荧光光谱研究(续Ⅰ)

测得了长白山白眉蝮蛇毒精氨酸酯酶 1的最适反应的pH范围为 7.0～ 8.0 ,且与酶反应底物对甲苯磺酰-L -精氨酸甲酯 (TAME)的反应无明显的最适应反应温度 .荧光光谱的研究结果表明 :该酶的酪氨酸残基的荧光被色氨酸残基的荧光所掩盖 ;同步荧光光谱结果表明 :当发射波长与激发波长差Δλ分别为 2 0nm和 75nm时 ,精氨酸酯酶 1的荧光光谱分别由酪氨酸 (Tyr)和色氨酸 (Trp)残基所贡献 ,且处于亲水性环境中 ;精氨酸酯酶 1的荧光发射强度受溶液酸度变化的影响 .I- ,Acr和NBS对精氨酸酯酶 1的荧光淬灭结果表明这种酶中含有多个色氨酸残基 ,且处于不同的微环境中。     

酶蛋白直接修复嘧啶二聚体机理的模型研究

去辅基的DNA光解酶在280 nm光辐照下, 能高效修复底物嘧啶二聚体(Φ＝0.56). 为了模拟酶蛋白的这一修复过程, 合成了色氨酸(Trp)和/或酪氨酸(Tyr)与胸腺嘧啶二聚体(D)共价连接的化合物, 作为酶-底物复合物的模型, 研究了它们在295 nm光照射下氨基酸残基光敏化二聚体裂解的性质, 测定了二聚体裂解量子产率(Φ), 获得一些新的结果并对其进行了分析.     

酶催化过程的全程模拟

酶催化包括底物到活性区的输运、选择催化化学反应及产物释放等复杂过程,由于复杂的蛋白质环境效应,任一化学和非化学过程都有可能是决定酶活性的关键步骤。为了全面认识酶催化活性,我们对几类酶催化过程进行了广泛的组合量子/分子力学(QM/MM)和经典分子力学(MM)动力学模拟(MD)研究,详细地讨论了整个酶催化过程的分子机制、关键残基的作用和蛋白质环境效应,丰富了对酶催化活性的认识。随着多尺度模型和计算模拟方法的进一步完善与发展,有望实现超大复杂生物酶催化过程的全程模拟研究,为酶工程领域的相关研究提供支持。     

盐酸拓扑替康与人血清白蛋白的相互作用及分子模拟

用荧光光谱法、分光光度法研究了盐酸拓扑替康(topotecan hydrochloride, 简记为THC)与人血清白蛋白(human serum albumins, HSA)的相互结合反应. 计算了反应的结合常数、结合位点数和热力学常数. 盐酸拓扑替康在人血清白蛋白上的结合位置与色氨酸残基间的距离为3.63 nm. 分子模型研究表明, 盐酸拓扑替康与人血清白蛋白的亚结构域IIA结合, 二者间的作用力主要为疏水作用, 此外, 蛋白质的丙氨酸(Ala-291)残基和天冬氨酸(Asp-256)残基与盐酸拓扑替康之间还存在氢键作用力.     

Spectroscopic and computational studies of α-keto acid binding to Dke1: understanding the role of the facial triad and the reactivity of β-diketones

The O(2) activating mononuclear nonheme iron enzymes generally have a common facial triad (two histidine and one carboxylate (Asp or Glu) residue) ligating Fe(II) at the active site. Exceptions to this motif have recently been identified in nonheme enzymes, including a 3His triad in the diketone cleaving dioxygenase Dke1. This enzyme is used to explore the role of the facial triad in directing reactivity. A combination of spectroscopic studies (UV-vis absorption, MCD, and resonance Raman) and DFT calculations is used to define the nature of the binding of the α-keto acid, 4-hydroxyphenlpyruvate (HPP), to the active site in Dke1 and the origin of the atypical cleavage (C2-C3 instead of C1-C2) pattern exhibited by this enzyme in the reaction of α-keto acids with dioxygen. The reduced charge of the 3His triad induces α-keto acid binding as the enolate dianion, rather than the keto monoanion, found for α-keto acid binding to the 2His/1 carboxylate facial triad enzymes. The mechanistic insight from the reactivity of Dke1 with the α-keto acid substrate is then extended to understand the reaction mechanism of this enzyme with its native substrate, acac. This study defines a key role for the 2His/1 carboxylate facial triad in α-keto acid-dependent mononuclear nonheme iron enzymes in stabilizing the bound α-keto acid as a monoanion for its decarboxylation to provide the two additional electrons required for O(2) activation.     

Possible Role of Carboxyl and Imidazole Groups in the Catalysis of Pummelo Limonoid Glucosyltransferase

 Limonoid bitterness is a serious problem in the citrus industry worldwide. Limonoid glucosyltransferase is an enzyme that catalyzes the conversion of bitter limonoid into non-bitter limonoid glucoside while retaining the health benefit of limonoids in the juice. The immobilization of this enzyme in a column can solve the juice bitterness problem. More information about the catalytic residues of the en-zyme is needed in this immobilization process. Glutamate/aspartate, histidine, lysine, tryptophan, serine, and cysteine residues were chemi-cally modified to investigate their roles in the catalytic function of limonoid glucosyltransferase. Inactivation of the enzyme following modi-fication of carboxyl and imidazole moieties was a consequence of a loss in substrate binding and catalysis in the glucosyltransfer reaction. The modification of a single histidine residue completely destroyed the ability of limonoid glucosyltransferase to transfer the D-glucopyranosyl unit. Tryptophan seemed to have some role in maintaining the active conformation of the catalytic site. Lysine also seemed to have some direct or indirect role in this catalysis but the modification of serine and cysteine did not have any effect on catalysis. There-fore, we conclude that the carboxyl and imidazole groups contain amino acids are responsible for the catalytic action of the enzyme.     

Quercetin 2,4‐Dioxygenase Activates Dioxygen in a Side‐On O2–Ni Complex

Quercetin 2,4‐dioxygenase (quercetinase) from Streptomyces uses nickel as the active‐site cofactor to catalyze oxidative cleavage of the flavonol quercetin. How this unusual active‐site metal supports catalysis and O₂ activation is under debate. We present crystal structures of Ni‐quercetinase in three different states, thus providing direct insight into how quercetin and O₂ are activated at the Ni²⁺ ion. The Ni²⁺ ion is coordinated by three histidine residues and a glutamate residue (E⁷⁶) in all three states. Upon binding, quercetin replaces one water ligand at Ni and is stabilized by a short hydrogen bond through E⁷⁶, the carboxylate group of which rotates by 90°. This conformational change weakens the interaction between Ni and the remaining water ligand, thereby preparing a coordination site at Ni to bind O₂. O₂ binds side‐on to the Ni²⁺ ion and is perpendicular to the C2?C3 and C3?C4 bonds of quercetin, which are cleaved in the following reaction steps.     

Histidine in enzyme active centers.

The presence of histidine in the active center of an enzyme can be demonstrated by kinetic measurements, chemical modification, NMR spectroscopy or X-ray structure analysis. Histidine is the only naturally occurring amino acid to contain an imidazole residue as a side chain. The role of histidine in enzyme catalysis depends, inter alia, upon the special features of the imidazole residue: it thus tends to form hydrogen bonds, combines donor and acceptor properties and can take part in either nucleophilic or base catalysis. In some of these enzymes the position of each atom is known; however, the theories as to how the catalysis proceeds at a molecular level are controversial.     

Residue-specific radical-directed dissociation of whole proteins in the gas phase

The rapid identification of proteins from biological samples is critical for extracting useful information in proteomics studies. Mass spectrometry is one among the various methods of choice for achieving this task; however, current approaches are limited by a lack of chemical control over proteins in the gas phase. Herein, it is shown that modification of tyrosine to iodo-tyrosine followed by UV photodissociation of the carbon-iodine bond can be used to generate a radial site specifically at the modified residue. The subsequent dissociation of the protein is largely dominated by radical-directed reactions, including dominant backbone fragmentation at the modified tyrosine. If iodination of the protein is carried out under natively folded conditions, the modification and ultimate fragmentation can typically be isolated to a single tyrosine residue. Some secondary backbone cleavage in the immediate vicinity of the modified tyrosine also occurs, especially if proline is present. In the absence of a reactive tyrosine residue, similar chemistry occurs via iodination at histidine. Possible mechanisms which would lead to the observed a-type fragments at tyrosine and the secondary fragments at proline are discussed. A method for using this type of site-specific information to reduce database searching times in proteomics experiments by several orders of magnitude is outlined.     

Studies on the Chemical Modification of the Essential Groups of <Emphasis Type="Italic">N</Emphasis>-Acetyl-β-<Emphasis Type="SmallCaps">d</Emphasis>-Glucosaminidase from Viscera of Green Crab (<Emphasis Type="Italic">Scylla Serrata</Emphasis>)

The chemical modification of N-acetyl-β-d-glucosaminidase (EC3.2.1.30) from viscera of green crab (Scylla serrata) has been first studied. The modification of indole groups of tryptophan of the enzyme by N-bromosuccinimide can lead to complete inactivation, accompanying the absorption decreasing at 275 nm and the fluorescence intensity quenching at 338 nm, indicating that tryptophan is essential residue to the enzyme. The modification of histidine residue, the carboxyl groups, and lysine residue inactivates the enzyme completely or incompletely. The results show that imidazole groups of histidine residue or sulfhydryl residues, the carboxyl groups of acidic amino acid, amino groups of lysine residue, and indole groups of tryptophan were essential for the catalytic activity of enzyme, while the results demonstrate that the disulfide bonds and the carbamidine groups of arginine residues are not essential to the enzyme’s function.     

Singlet oxygen generation versus O–O homolysis in phenyl-substituted anthracene endoperoxides investigated by RASPT2, CASPT2, CC2, and TD-DFT methods

Peptidylarginine deiminase 4 (PAD4), also known as protein arginine deiminase 4, performs a post-translational deimination that converts arginine to citrulline. The dysregulation of PAD4 has been implicated in a number of diseases, including rheumatoid arthritis (RA) and cancer. This makes PAD4 an important therapeutic target. To develop small-molecule inhibitors as potential treatments, it is advantageous if the catalytic mechanism is well understood. The protonation states of the active site residues, which have long been under controversy, have a direct impact on the catalytic mechanism. Two competing mechanisms are under investigation in the current literature. The first is a reverse protonation mechanism that depends on the active site histidine and cysteine existing as an ion pair. The second is a substrate-assisted mechanism that depends on the active site histidine and cysteine being neutral. This study uses the semimicroscopic protein dipoles Langevin dipoles (PDLD/S) linear response approximation method in the MOLARIS software package to calculate the change in solvation energy of moving the residue from water to the protein interior, and then using that information to assess the protonation states of the active site residues of PAD4. Results from these calculations suggest that in the enzyme–substrate complex of PAD4, the cysteine and histidine are protonated and deprotonated, respectively, and are therefore both neutral, analogous to the proposed protonation states of the active site residues in the Michaelis complex in the substrate-assisted mechanism.     

Positional ordering of reacting groups contributes significantly to the efficiency of proton transfer at an antibody active site

Catalytic antibody 34E4 accelerates the conversion of benzisoxazoles to salicylonitriles with surprising efficiency, exploiting a carboxylate base with an elevated pKa for proton abstraction. Mutagenesis of this antibody, produced as a chimeric Fab, confirms the prediction of a homology model that GluH50 is the essential catalytic residue. Replacement of this residue by glutamine, alanine, or glycine reduces catalytic activity by more than 2.6 x 10(4)-fold. By comparing the chemical proficiencies of the parent antibody with the chemical proficiencies of acetate and the mutants, the effective concentration of the catalytic side chain was estimated to be >51 000 M. The 2.1 kcal/mol destabilization of the transition state observed when GluH50 is replaced by aspartate suggests that positional ordering imposed by the antibody active site contributes significantly to the efficiency of proton transfer. The observation that the GluH50Ala and GluH50Gly variants could not be chemically rescued by exogenous addition of high concentrations of formate or acetate further underscores the advantage the antibody derives from covalently fixing its base at the active site. Although medium effects also play an important role in 34E4, for example in enhancing the reactivity of the carboxylate side chain through desolvation, comparison of 34E4 with less proficient antibodies shows that positioning a carboxylate in a hydrophobic binding pocket alone is insufficient for efficient general base catalysis. Our results demonstrate that structural complementarity between the antibody and its substrate in the transition state is an important and necessary component of 34E4's high activity. By harnessing an additional catalytic group that could serve as a general acid to stabilize developing negative charge in the leaving group, overall efficiencies rivaling those of highly evolved enzymes should be accessible.     

Discovery of a substrate selectivity switch in tyrosine ammonia-lyase, a member of the aromatic amino acid lyase family

Tyrosine ammonia-lyase (TAL) is a recently described member of the aromatic amino acid lyase family, which also includes phenylalanine (PAL) and histidine ammonia-lyases (HAL). TAL is highly selective for L-tyrosine, and synthesizes 4-coumaric acid as a protein cofactor or antibiotic precursor in microorganisms. In this report, we identify a single active site residue important for substrate selection in this enzyme family. Replacing the active site residue His89 with Phe in TAL completely switched its substrate selectivity from tyrosine to phenylalanine, thereby converting it into a highly active PAL. When a corresponding mutation was made in PAL, the enzyme lost PAL activity and gained TAL activity. The discovered substrate selectivity switch is a rare example of a complete alteration of substrate specificity by a single point mutation. We also show that the identity of the amino acid at the switch position can serve as a guide to predict substrate specificities of annotated aromatic amino acid lyases in genome sequences.