人类2-氨基3-羧基粘康酸6-半醛脱羧酶(ACMSD)与底物及抑制剂作用模型的理论研究

利用同源模建和分子动力学模拟方法构建了人类2-氨基3-羧基粘康酸6-半醛脱羧酶(hACMSD)的三维结构, 并利用Profile-3D和Procheck等方法评估了模型的可靠性. 在此基础上, 用分子对接程序(Affinity), 将其底物2-氨基3-羧基粘康酸6-半醛(ACMS)和抑制剂喹啉酸(QA)分别与hACMSD进行对接, 获得了复合物结构的理论模型. 通过配体与受体之间相互作用能和结构分析给出了底物和抑制剂的具体结合方式, 明确了hACMSD与底物和抑制剂结合时起重要作用的氨基酸残基.     

基于HPPD靶标酶的分子对接研究

对羟基苯丙酮酸双氧化酶(HPPD)是一类新型化学除草剂的重要靶标酶.首先研究了底物小分子与HPPD的对接模型,分析了不同价态铁离子对对接结果的影响,并最终确定铁离子是以二价的方式与底物发生作用.随后,采用类似方法,对文献报道的一系列环己二酮类HPPD抑制剂进行了对接研究,并得到了对接结合自由能与除草活性之间良好的线性关系,其相关性系数达到0.916.这一结果为设计新的HPPD抑制剂提供一定的理论指导.     

对羟基苯丙酮酸双加氧酶(HPPD)的结构及其吡唑类除草剂的最新研究进展

对羟基苯丙酮酸双加氧酶(EC 1.13.11.27,HPPD)是重要的除草剂靶标.以HPPD为靶标的除草剂具有高效、低毒、作物安全性高、不易产生抗性、环境相容性好及对后茬作物安全等一系列优点.结合最新的研究进展,详细综述了HPPD的结构,并针对吡唑类HPPD除草剂的作用模式、在生物体内的作用机制和代谢途径以及研究现状进行了总结与分析.     

人甲状腺旁素1型受体的结构特征

人甲状腺旁素1 型受体(PTH1R)是骨形成相关的B类G蛋白偶联受体, 其底物甲状腺旁腺素(PTH)及类似物具有抗骨质疏松作用. 由于此类受体的三维结构难以进行实验测定, 本文采用同源模建的方法, 完整构建了胞外区、跨膜区及其它相关区域, 并通过对接研究, 阐明复合物的氢键、疏水性相互作用及其与底物的相互作用关系和关键位点. 为进一步设计和发展此类药物提供理论依据.     

脂肪酶催化扁桃酸乙酯酯交换反应的研究

利用脂肪酶Novozym 435在正丁醇体系中催化酯交换反应,对(R,S)-扁桃酸乙酯进行了动力学拆分,考察了系统初始加水量,反应温度,振荡速度,底物浓度等因素对脂肪酶催化活性和对映体选择性的影响.研究结果表明,最适初始加水量为0.4%;在20℃~60℃范围内,酶催化活性随温度升高而增加,酶选择性随温度先升高后下降,最适温度45℃;底物扁桃酸乙酯浓度达5000 mmol/L时,未观察到底物抑制现象,反应初速度为2.78mmol.L-1.m in-1.     

大肠杆菌中高丝氨酸琥珀酰基转移酶的同源模建与对接研究

利用同源模建和分子动力学模拟方法,模建了大肠杆菌中高丝氨酸琥珀酰基转移酶的三维结构.分析了活性位点的组成,从结构上佐证了Cys142而不是Lys47为亲核进攻的残基,并通过与其天然底物琥珀酰-辅酶A的对接研究,从理论上确认了对复合物形成起到重要作用的氨基酸残基.     

PKA酶及其抑制剂balanol的计算化学*

蛋白激酶通过磷酸化蛋白底物来调节细胞内的信号转导途径,是重要的药物设计靶标。蛋白激酶A（PKA）是最早获得催化结构域X衍射晶体结构的激酶,是蛋白激酶家族中代表性结构。本文综述了PKA在计算化学领域的研究进展,包括PKA全酶以及它的催化（C）亚基和调节(R)亚基在水溶液中的分子动力学模拟研究,磷酰基转移机理和C亚基与其抑制剂balanol的结合自由能预测、柔性对接。分子动力学、分子对接、同源模建、QM/MM等计算机辅助设计方法在该体系中得到运用。     

棕榈酸维生素C酯的酶催化合成

以棕榈酸甲酯和维生素C为原料,以脂肪酶(LIPOZYM IM)为催化剂,催化合成了棕榈酸维生素C酯.详细研究了几种因素(维生素C与棕榈酸甲酯的摩尔比,反应温度,反应时间及脂肪酶用量)对合成反应的影响,确立了棕榈酸维生素C酯的较佳合成条件底物摩尔比为31,反应温度55℃,反应时间8h,脂肪酶用量为反应体系的3%(重量),产品一次收率为68.2%.     

睾丸酮丛毛单胞菌生物催化合成对苯二甲酸

 以对甲基苯甲酸为唯一碳源筛选能够生物催化合成对苯二甲酸的菌株,发现只有睾丸酮丛毛单胞菌DSM6577可以氧化对甲基苯甲酸生成对苯二甲酸. 对该菌株的细胞生长及其催化对甲基苯甲酸转化为对苯二甲酸的过程进行了研究. 结果表明,底物在8 h内即可完全转化,产物的生成时间为14～31 h, 其中在21 h时产量最大,为34 mg/L.     

Sirt1及Sirt2与活性分子INA的作用机制研究

应用分子模拟理论与方法研究了人类沉默信息调节因子2相关酶类Sirtuin家族成员Sirt1及Sirt2与一种活性分子(命名为INA)的作用机制.同源模建了Sirt1的三维结构,通过分子对接手段得到Sirt1(NAD+)-INA及Sirt2(NAD+)-INA的两种复合物体系,进行了分子动力学模拟.并且分别计算了两种体系中关键氨基酸残基与INA的结合自由能值,由此推测出Sirt1(NAD+)-INA、Sirt2(NAD+)-INA体系结合位点分别为Val72,Ser73和Arg272及Phe235,Leu264和Gly305,确证了两种体系的结合模式.模拟结果表明,在Sirt1(NAD+)-INA体系中,INA与催化底物NAD+距离较近,可以相互作用,具有较高活性;在Sirt2(NAD+)-INA体系中,INA与催化底物NAD+距离较远,与在Sirt1体系中比较,INA对Sirt2体系的活性较弱,结果与实验一致.本文的研究,对今后以去乙酰化酶Sirt1,Sirt2为靶点的新药开发具有一定指导意义.     

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.     

Computational exploration of the catalytic mechanism of dopamine beta-monooxygenase: modeling of its mononuclear copper active sites

Dopamine hydroxylation by the copper-superoxo, -hydroperoxo, and -oxo species of dopamine beta-monooxygenase (DBM) is investigated using theoretical calculations to identify the active species in its reaction and to reveal the key functions of the surrounding amino acid residues in substrate binding. A 3D model of rat DBM is constructed by homology modeling using the crystal structure of peptidylglycine alpha-hydroxylating monooxygenase (PHM) with a high sequence identity of 30% as a template. In the constructed 3D model, the CuA site in domain 1 is coordinated by three histidine residues, His265, His266, and His336, while the CuB site in domain 2 is coordinated by two histidine residues, His415 and His417, and by a methionine residue, Met490. The three Glu268, Glu369, and Tyr494 residues are suggested to play an important role in the substrate binding at the active site of DBM to enable the stereospecific hydrogen-atom abstraction. Quantum mechanical/molecular mechanical (QM/MM) calculations are performed to determine the structure of the copper-superoxo, -hydroperoxo, and -oxo species in the whole-enzyme model with about 4700 atoms. The reactivity of the three oxidants is evaluated in terms of density-functional-theory calculations with small models extracted from the QM region of the whole-enzyme model.     

The structure of 4-hydroxylphenylpyruvate dioxygenase complexed with 4-hydroxylphenylpyruvic acid reveals an unexpected inhibition mechanism

4-Hydroxyphenylpyruvate dioxygenase(HPPD) is an important target for both drug and pesticide discovery. As a typical Fe(II)-dependent dioxygenase, HPPD catalyzes the complicated transformation of 4-hydroxyphenylpyruvic acid(HPPA) to homogentisic acid(HGA). The binding mode of HPPA in the catalytic pocket of HPPD is a focus of research interests. Recently, we reported the crystal structure of Arabidopsis thaliana HPPD(At HPPD) complexed with HPPA and a cobalt ion, which was supposed to mimic the pre-reactive structure of At HPPD-HPPA-Fe(II). Unexpectedly, the present study shows that the restored At HPPD-HPPA-Fe(II) complex is still nonreactive toward the bound dioxygen. QM/MM and QM calculations reveal that the HPPA resists the electrophilic attacking of the bound dioxygen by the trim of its phenyl ring, and the residue Phe381 plays a key role in orienting the phenyl ring. Kinetic study on the F381 A mutant reveals that the HPPD-HPPA complex observed in the crystal structure should be an intermediate of the substrate transportation instead of the pre-reactive complex. More importantly, the binding mode of the HPPA in this complex is shared with several well-known HPPD inhibitors, suggesting that these inhibitors resist the association of dioxygen(and exert their inhibitory roles) in the same way as the HPPA. The present study provides insights into the inhibition mechanism of HPPD inhibitors.     

A DFT study on the formation of a phosphohistidine intermediate in prostatic acid phosphatase

Histidine phosphatases are a class of enzymes that are characterized by the presence of a conserved RHGXRXP motif. This motif contains a catalytic histidine that is being phosphorylated in the course of a dephosphorylation reaction catalyzed by these enzymes. Prostatic acid phosphatase (PAP) is one such enzyme. The dephosphorylation of phosphotyrosine by PAP is a two-step process. The first step involves the transfer of a phosphate group from the substrate to the histidine (His12). The present study reports on the details of the first step of this reaction, which was investigated using a series of quantum chemistry calculations. A number of quantum models were constructed containing various residues that were thought to play a role in the mechanism. In all these models, the transition state displayed an associative character. The transition state is stabilized by three active site arginines (Arg11, Arg15, and Arg79), two of which belong to the aforementioned conserved motif. The work also demonstrated that His12 could act as a nucleophile. The enzyme is further characterized by a His257-Asp258 motif. The role of Asp258 has been elusive. In this work, we propose that Asp258 acts as a proton donor which becomes protonated when the substrate enters the binding pocket. Evidence is also obtained that the transfer of a proton from Asp258 to the leaving group is possibly mediated by a water molecule in the active site. The work also underlines the importance of His257 in lowering the energy barrier for the nucleophilic attack.     

Two sequence elements of glycosyltransferases involved in urdamycin biosynthesis are responsible for substrate specificity and enzymatic activity.

BACKGROUND: Two deoxysugar glycosyltransferases (GTs), UrdGT1b and UrdGT1c, involved in urdamycin biosynthesis share 91% identical amino acids. However, the two GTs show different specificities for both nucleotide sugar and acceptor substrate. Generally, it is proposed that GTs are two-domain proteins with a nucleotide binding domain and an acceptor substrate site with the catalytic center in an interface cleft between these domains. Our work aimed at finding out the region responsible for determination of substrate specificities of these two urdamycin GTs. RESULTS: A series of 10 chimeric GT genes were constructed consisting of differently sized and positioned portions of urdGT1b and urdGT1c. Gene expression experiments in host strains Streptomyces fradiae Ax and XTC show that nine of 10 chimeric GTs are still functional, with either UrdGT1b- or UrdGT1c-like activity. A 31 amino acid region (aa 52-82) located close to the N-terminus of these enzymes, which differs in 18 residues, was identified to control both sugar donor and acceptor substrate specificity. Only one chimeric gene product of the 10 was not functional. Targeted stepwise alterations of glycine 226 (G226R, G226S, G226SR) were made to reintroduce residues conserved among streptomycete GTs. Alterations G226S and G226R restored a weak activity, whereas G226SR showed an activity comparable with other functional chimeras. CONCLUSIONS: A nucleotide sugar binding motif is present in the C-terminal moiety of UrdGT1b and UrdGT1c from S. fradiae. We could demonstrate that it is an N-terminal section that determines specificity for the nucleotide sugar and also the acceptor substrate. This finding directs the way towards engineering this class of streptomycete enzymes for antibiotic derivatization applications. Amino acids 226 and 227, located outside the putative substrate binding site, might be part of a larger protein structure, perhaps a solvent channel to the catalytic center. Therefore, they could play a role in substrate accessibility to it.     

Acyclic phenylalkanediols as substrates for the study of enzyme recognition. Regioselective acylation by porcine pancreatic lipase: a structural hypothesis for the enzymatic selectivity

The regioselective acylation of phenylalkanediols catalysed by porcine pancreatic lipase (PPL) was the reaction used for modelling different areas in the active site of the enzyme. With this aim, different racemic or prochiral (1,n)-diols, with n ranging from 2 to 6 were resolved via transesterification with vinyl acetate, and the results were explained according to microcrystalline enzyme structure. Thus, we describe a logical model for explaining the enzyme regio and stereoselectivity, based on three residues of the active site (Ser153, Phe216 and His264) which turned out to be crucial for the substrate binding and transformation.     

A novel genetic selection system for PLP-dependent threonine aldolases

Threonine aldolases are versatile pyridoxal-5′-phosphate (PLP)-dependent enzymes key to glycine, serine and threonine metabolism. Because they catalyze the reversible addition of glycine to an aldehyde to give β-hydroxy-α-amino acids, they are also attractive as biotechnological catalysts for the diastereoselective synthesis of many pharmaceutically useful compounds. To study and evolve such enzymes, we have developed a simple selection system based on the simultaneous inactivation of four genes involved in glycine biosynthesis in Escherichia coli. Glycine prototrophy in the deletion strain is restored by expression of a gene encoding an aldolase that converts β-hydroxy-α-amino acids, provided in the medium, to glycine and the corresponding aldehyde. Combinatorial mutagenesis and selection experiments with a previously uncharacterized l-threonine aldolase from Caulobacter crescentus CB15 (Cc-LTA) illustrate the power of this system. The codons for four active site residues, His91, Asp95, Glu96, and Asp176, were simultaneously randomized and active variants selected. The results show that only His91, which π-stacks against the PLP cofactor and probably serves as the catalytic base in the carbon-carbon bond cleavage step, is absolutely required for aldolase activity. In contrast, Asp176, one of the most conserved residues in this enzyme superfamily, can be replaced conservatively by glutamate, albeit with a >5000-fold decrease in efficiency. Though neither Asp95 nor Glu96 is catalytically essential, they appear to modulate substrate binding and His91 activity, respectively. The broad dynamic range of this novel selection system should make it useful for mechanistic investigations and directed evolution of many natural and artificial aldolases.     

Two-prong inhibitors for human carbonic anhydrase II

The enzyme inhibitors are usually designed by taking into consideration the overall dimensions of the enzyme's active site pockets. This conventional approach often fails to produce desirable affinities of inhibitors for their cognate enzymes. To circumvent such constraints, we contemplated enhancing the binding affinities of inhibitors by attaching tether groups, which would interact with the surface exposed amino acid residues. This strategy has been tested for the inhibition of human carbonic anhydrase II. Benzenesulfonamide serves as a weak inhibitor for the enzyme, but when it is conjugated to iminodiacetate-Cu2+ (which interacts with the surface-exposed His residues) via a spacer group, its binding affinity is enhanced by about 2 orders of magnitude. This "two-prong" approach is expected to serve as a general strategy for converting weak inhibitors of enzymes into tight-binding inhibitors.     

Substrate‐induced formation of a recognition structure in a four‐polypeptide–lipid monolayer system

Poly(γ‐methyl L ‐glutamate)s with Ser, His, Asp, and Glu residues at the amino terminal as the serine protease catalytic site were prepared. The number‐average degree of polymerization of the polypeptides was 51. A dipalmitoylphosphatidylcholine monolayer containing the polypeptides was formed at the air–water interface and was transferred onto gold‐deposited glass plates. The binding of N‐acetyltyrosine ethyl ester, a typical substrate of the serine protease, to the monolayer was characterized by surface plasmon resonance measurements. The four‐polypeptide–lipid monolayer system conditioned on an aqueous solution containing the substrate N‐acetyltyrosine ethyl ester exhibited Langmuir‐type binding of the substrate. Its binding constant of 6.1 × 10⁴ M⁻¹ was about 20 times larger than that observed for a monolayer prepared on pure water. The behavior may have arisen from a substrate‐induced rearrangement of the four kinds of polypeptides in the monolayer, forming a substrate‐binding structure similar to that found in serine protease. © 2000 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 38: 2186–2191, 2000