光合细菌Chromatium vinosum可溶性氢酶的分离提纯及特性

光合细菌 Chromatium vinosum可溶性氢酶经 4次柱层析 (Whatman DE- 52 ,TSK- DEAE,Ultragel Ac A- 44 ,Mono Q)分离提纯后被纯化 630倍 ,得率为 33.5% .可溶性氢酶催化放氢比活性为 7.5μmol· min-1· mg-1.SDS- PAGE结果显示 ,可溶性氢酶由 52 k D和 2 1 .5k D两个亚基组成 .大亚基 N端氨基酸序列为 :SRTITIEPVTRXEGHAR;小亚基 N端氨基酸序列为 :STQPKIT-VATXLDG.氧化态可溶性氢酶在 54K时产生了典型的 Ni( )电子顺磁共振 (EPR)信号 (gxyz=2 .37、2 .1 6、2 .0 1 6和 gxyz=2 .30、2 .2 3、2 .0 1 6) .研究结果表明 ,C.vinosum可溶性氢酶是一种新的催化放氢的 Ni Fe-氢酶 .     

二氢硫辛酰转乙酰基酶通过乙酰化磷酸葡糖酸脱氢酶促进核酸合成

丙酮酸脱氢酶复合物(pyruvate dehydrogenase complex,PDC)是位于线粒体内的多酶复合物,催化丙酮酸不可逆地氧化脱羧转为乙酰辅酶A,二氢硫辛酰转乙酰基酶(dihydrolipoyl acetyltransferase,DLAT)是PDC的1个亚基.PDC在细胞线粒体呼吸中发挥关键作用.但是D...     

2 呼吸链的组份

真核有机体的呼吸链位于线粒体的内膜上(3.1节),主要催化NAD(P)H和琥珀酸(同较小的底物,诸如3—磷酸甘油,脂肪乙酰辅酶A一起)做分子氧的氧化作用。它是四个彼此无关的氧化还原载体复合物(ⅠⅡⅢ和Ⅳ)、转氢酶、辅酶Q和细胞色素C的聚合体。氧化还原载体能藉各种分光技术监测,这些分光技术在历史上已被用作在原来位置上呼吸膜     

芳香族氨基酸羟化酶家族结构与催化功能

芳香族氨基酸羟化酶(AAAH）家族是一类单加氢酶,包括苯丙氨酸羟化酶(PAH)、酪氨酸羟化酶(TH)和色氨酸羟化酶(TPH). 在辅因子四氢生物蝶呤、铁原子及氧存在下,分别催化苯丙氨酸、酪氨酸、色氨酸的羟化反应. 多种疾病如苯丙酮尿症、帕金森氏病以及神经相关疾病的发病机制均与这类酶有关. 本文综述近年来对芳香族氨基酸羟化酶家族蛋白结构功能、底物特异性、催化机制等方面的研究进展,为该类酶的定向进化及功能应用提供新思路.     

tRNA转录后修饰的功能及其与人类疾病的关系

转移核糖核酸(tRNA)的转录后修饰对tRNA正常行使生物学功能具有重要意义,这些功能包括tRNA的正确折叠和维持其稳定性、在核糖体上正确解码。虽然tRNA转录后大部分核苷酸修饰形式在20世纪70年代已被鉴定出,但最近才在大肠杆菌及酵母中鉴定出催化这些tRNA核苷酸修饰的酶的绝大部分基因。这些修饰酶基因的鉴定为研究tRNA转录后修饰的生物功能开启了新的大门。人胞质tRNA和线粒体tRNA(mt tRNA)都存在大量核苷酸修饰,这些修饰的缺陷常常与多种人类疾病相关。因此,研究tRNA核苷酸修饰有助于我们了解相关疾病的发病机理。     

蓖麻蚕线粒体基因组细胞色素氧化酶亚基Ⅲ的序列及其分子进化分析

测定了蓖麻蚕Samia cynthia ricini线粒体基因组(mtDNA)含完整的细胞色素氧化酶亚基Ⅲ(COX3)、tRNA-Gly和部分的NADH亚基Ⅲ(ND3)基因的DNA片段序列。COX3基因编码框包含789个核苷酸,编码262个氨基酸的蛋白质。通过同源性比较,发现COX3基因的3′端比5′端要保守,其编码的蛋白在C端有两个保守序列存在。COX3的下游为66 bp的tRNA-Gly基因。蓖麻蚕的COX3与家蚕COX3同源性最高,核苷酸和氨基酸序列同源性分别是80.2%和85.6%。根据COX3氨基酸序列进行了12种无脊椎动物的分子进化树分析,认为在采用线粒体基因序列进行分子进化分析时,应该综合考虑物种的繁殖模式及生态特点。     

H2O2诱导的线粒体损伤神经元内硫氧还蛋白 mRNA水平的变化

线粒体缺陷和氧化应激参与了神经退行性疾病的发病机制.叠氮钠(NaN3)是线粒体细胞色素C氧化酶(COX)的特异性抑制剂,能诱导线粒体缺陷.本实验通过细胞活性检测(MTT法),形态学观察,分析H2O2对原代培养的正常神经元及NaN3诱导的线粒体缺陷神经元的损伤作用的差异.并通过RT-PCR半定量法检测H2O2损伤后两类神经元内硫氧还蛋白(Thioredoxin,Trx)mRNA水平的变化,以阐明细胞内这一重要氧化还原调节蛋白在神经元损伤时的作用机制.实验表明,在正常神经元内,H2O2的损伤对Trx表达量的改变似乎不明显;而线粒体缺陷神经元内Trx的表达量下降,且对于H2O2的损伤具有浓度、时间依赖性.提示在线粒体功能缺陷神经元中,Trx似乎发挥更重要的作用.     

丙酮酸脱氢酶活性缺失与疾病发生的研究进展

丙酮酸脱氢酶系(pyruvate dehydrogenase complex,PDH_C)主要由丙酮酸脱氢酶(E1)、二氢硫辛酸乙酰转移酶(E2)、二氢硫辛酸脱氢酶(E3)和E3结合蛋白(E3BP)组成,绝大多数的丙酮酸脱氢酶系缺失都是由丙酮酸脱氢酶E1α亚基突变或者磷酸化引起,仅有少数突变发生在E2、E3和E3BP上。本文就PDHC的结构与功能,PDHA1基因突变和E1α磷酸化与其功能的关系,及在相关疾病包括肿瘤的发生、发展和转移中的分子机制的研究进展做一总结,以期对因E1α功能丧失引起的疾病的诊断与治疗有所借鉴意义。     

肿瘤SDH基因突变的研究进展

线粒体琥珀酸脱氢酶(succinate dehydrogenase,SDH)是三羧酸循环和有氧电子传递呼吸链中的关键酶之一,包含A、B、C、D 4个亚基.4个亚基分别由4个基因编码,即SDHA、SDHB、SDHC和SDHD,4个基因突变可以诱发癌症,包括副神经节瘤(paraganglioma,PGL)、嗜铬细胞瘤(pheochromocytoma,PHEO)、肾细胞癌(renal cell carcinoma,RCC)、胃肠道间质瘤(gastrointestinal stromal tumors,GIST)、Leigh综合症等.近年来,突变的SDH已经被证实是一种重要的诊断与预后的生物标志物和治疗分子标靶.本文就SDH存在的各种突变以及在肿瘤发生、发展与转移的作用机理研究的进展进行全面的论述.     

Interaction of NADP(H) with oxidized and reduced P450 reductase during catalysis. Studies with nucleotide analogues

Previous studies have shown that the interaction of P450 reductase with bound NADP(H) is essential to ensure fast electron transfer through the two flavin cofactors. In this study we investigated in detail the interaction of the house fly flavoprotein with NADP(H) and a number of nucleotide analogues. 1,4,5,6-Tetrahydro-NADP, an analogue of NADPH, was used to characterize the interaction of P450 reductase with the reduced nucleotide. This analogue is inactive as electron donor, but its binding affinity and rate constant of release are very close to those for NADPH. The 2'-phosphate contributes about 5 kcal/mol of the binding energy of NADP(H). Oxidized nicotinamide does not interact with the oxidized flavoprotein, while reduced nicotinamide contributes 1.3 kcal/mol of the binding energy. Oxidized P450 reductase binds NADPH with a K(d) of 0.3 microM, while the affinity of the reduced enzyme is considerably lower, K(d) = 1.9 microM. P450 reductase catalyzes a transhydrogenase reaction between NADPH and oxidized nucleotides, such as thionicotinamide-NADP(+), acetylpyridine-NADP(+), or [(3)H]NADP(+). The reverse reaction, reduction of [(3)H]NADP(+) by the reduced analogues, is also catalyzed by P450 reductase. We define the mechanism of the transhydrogenase reaction as follows: NADPH binding, hydride ion transfer, and release of the NADP(+) formed. An NADP(+) or its analogue binds to the two-electron-reduced flavoprotein, and the electron-transfer steps reverse to transfer hydride ion to the oxidized nucleotide, which is released. Measurements of the flavin semiquinone content, rate constant for NADPH release, and transhydrogenase turnover rates allowed us to estimate the steady-state distribution of P450 reductase species during catalysis, and to calculate equilibrium constants for the interconversion of catalytic intermediates. Our results demonstrate that equilibrium redox potentials of the flavin cofactors are not the sole factor governing rapid electron transfer during catalysis, but conformational changes must be considered to understand P450 reductase catalysis.     

Mutation of conserved polar residues in the transmembrane domain of the proton-pumping pyridine nucleotide transhydrogenase of Escherichia coli

The pyridine nucleotide transhydrogenase carries out transmembrane proton translocation coupled to transfer of a hydride ion equivalent between NAD+ and NADP+. Previous workers (E. Holmberg et al. Biochemistry 33, 7691-7700, 1994; N. A. Glavas et al. Biochemistry 34, 7694-7702, 1995) had examined the role in proton translocation of conserved charged residues in the transmembrane domain. This study was extended to examine the role of conserved polar residues of the transmembrane domain. Site-directed mutagenesis of these residues did not produce major effects on hydride transfer or proton translocation activities except in the case of betaAsn222. Most mutants of this residue were drastically impaired in these activities. Three phenotypes were recognized. In betaN222C both activities were impaired maximally by 70%. The retention of proton translocation indicated that betaAsn222 was not directly involved in proton translocation. In betaN222H both activities were drastically reduced. Binding of NADP+ but not of NADPH was impaired. In betaN222R, by contrast, NADP+ remained tightly bound to the mutant transhydrogenase. It is concluded that betaAsn222, located in a transmembrane alpha-helix, is part of the conformational pathway by which NADP(H) binding, which occurs outside of the transmembrane domain, is coupled to proton translocation. Some nonconserved or semiconserved polar residues of the transmembrane domain were also examined by site-directed mutagenesis. Interaction of betaGlu124 with the proton translocation pathway is proposed.     

The crystal structure of an asymmetric complex of the two nucleotide binding components of proton-translocating transhydrogenase

BACKGROUND: Membrane-bound ion translocators have important functions in biology, but their mechanisms of action are often poorly understood. Transhydrogenase, found in animal mitochondria and bacteria, links the redox reaction between NAD(H) and NADP(H) to proton translocation across a membrane. Linkage is achieved through changes in protein conformation at the nucleotide binding sites. The redox reaction takes place between two protein components located on the membrane surface: dI, which binds NAD(H), and dIII, which binds NADP(H). A third component, dII, provides a proton channel through the membrane. Intact membrane-located transhydrogenase is probably a dimer (two copies each of dI, dII, and dIII). RESULTS: We have solved the high-resolution crystal structure of a dI:dIII complex of transhydrogenase from Rhodospirillum rubrum-the first from a transhydrogenase of any species. It is a heterotrimer, having two polypeptides of dI and one of dIII. The dI polypeptides fold into a dimer. The loop on dIII, which binds the nicotinamide ring of NADP(H), is inserted into the NAD(H) binding cleft of one of the dI polypeptides. The cleft of the other dI is not occupied by a corresponding dIII component. CONCLUSIONS: The redox step in the transhydrogenase reaction is readily visualized; the NC4 atoms of the nicotinamide rings of the bound nucleotides are brought together to facilitate direct hydride transfer with A-B stereochemistry. The asymmetry of the dI:dIII complex suggests that in the intact enzyme there is an alternation of conformation at the catalytic sites associated with changes in nucleotide binding during proton translocation.     

Structures of the dI2dIII1 complex of proton-translocating transhydrogenase with bound, inactive analogues of NADH and NADPH reveal active site geometries

Transhydrogenase couples the redox reaction between NADH and NADP+ to proton translocation across a membrane. The enzyme comprises three components; dI binds NAD(H), dIII binds NADP(H), and dII spans the membrane. The 1,4,5,6-tetrahydro analogue of NADH (designated H2NADH) bound to isolated dI from Rhodospirillum rubrum transhydrogenase with similar affinity to the physiological nucleotide. Binding of either NADH or H2NADH led to closure of the dI mobile loop. The 1,4,5,6-tetrahydro analogue of NADPH (H2NADPH) bound very tightly to isolated R. rubrum dIII, but the rate constant for dissociation was greater than that for NADPH. The replacement of NADP+ on dIII either with H2NADPH or with NADPH caused a similar set of chemical shift alterations, signifying an equivalent conformational change. Despite similar binding properties to the natural nucleotides, neither H2NADH nor H2NADPH could serve as a hydride donor in transhydrogenation reactions. Mixtures of dI and dIII form dI2dIII1 complexes. The nucleotide charge distribution of complexes loaded either with H2NADH and NADP+ or with NAD+ and H2NADPH should more closely mimic the ground states for forward and reverse hydride transfer, respectively, than previously studied dead-end species. Crystal structures of such complexes at 2.6 and 2.3 A resolution are described. A transition state for hydride transfer between dihydronicotinamide and nicotinamide derivatives determined in ab initio quantum mechanical calculations resembles the organization of nucleotides in the transhydrogenase active site in the crystal structure. Molecular dynamics simulations of the enzyme indicate that the (dihydro)nicotinamide rings remain close to a ground state for hydride transfer throughout a 1.4 ns trajectory.     

Functional interactions in cytochrome P450BM3. Evidence that NADP(H) binding controls redox potentials of the flavin cofactors

NADP(H) binding is essential for fast electron transfer through the flavoprotein domain of the fusion protein P450BM3. Here we characterize the interaction of NADP(H) with the oxidized and partially reduced enzyme and the effect of this interaction on the redox properties of flavin cofactors and electron transfer. Measurements by three different approaches demonstrated a relatively low affinity of oxidized P450BM3 for NADP(+), with a K(d) of about 10 microM. NADPH binding is also relatively weak (K(d) approximately 10 microM), but the affinity increases manyfold upon hydride ion transfer so that the active 2-electron reduced enzyme binds NADP(+) with a K(d) in the submicromolar range. NADP(H) binding induces conformational changes of the protein as demonstrated by tryptophan fluorescence quenching. Fluorescence quenching indicated preferential binding of NADPH by oxidized P450BM3, while no catalytically competent binding with reduced P450BM3 could be detected. The hydride ion transfer step, as well as the interflavin electron transfer steps, is readily reversible, as demonstrated by a hydride ion exchange (transhydrogenase) reaction between NADPH and NADP(+) or their analogues. Experiments with FMN-free mutants demonstrated that FAD is the only flavin cofactor required for the transhydrogenase activity. The equilibrium constants of each electron transfer step of the flavoprotein domain during catalytic turnover have been calculated. The values obtained differ from those calculated from equilibrium redox potentials by as much as 2 orders of magnitude. The differences result from the enzyme's interaction with NADP(H).     

Mitochondrial energy-linked nicotinamide nucleotide transhydrogenase: effect of substrates on the sensitivity of the enzyme to trypsin and identification of tryptic cleavage sites

The mitochondrial nicotinamide nucleotide transhydrogenase catalyzes hydride ion transfer between NAD(H) and NADP(H) in a reaction that is coupled to proton translocation across the inner mitochondrial membrane. The enzyme (1043 residues) is composed of an N-terminal hydrophilic segment (approximately 400 residues long) which binds NAD(H), a C-terminal hydrophilic segment (approximately 200 residues long) which binds NADP(H), and a central hydrophobic segment (approximately 400 residues long) which appears to form about 14 membrane-intercalating clusters of approximately 20 residues each. Substrate modulation of transhydrogenase conformation appears to be intimately associated with its mechanism of proton translocation. Using trypsin as a probe of enzyme conformation change, we have shown that NADPH (and to a much lesser extent NADP) binding alters transhydrogenase conformation, resulting in increased susceptibility of several bonds to tryptic hydrolysis. NADH and NAD had little or no effect, and the NADPH concentration for half-maximal enhancement of trypsin sensitivity of transhydrogenase activity (35 microM) was close to the Km of the enzyme for NADPH. The NADPH-promoted trypsin cleavage sites were located 200-400 residues distant from the NADP(H) binding domain near the C-terminus. For example, NADPH binding greatly increased the trypsin sensitivity of the K410-T411 bond, which is separated from the NADP(H) binding domain by the 400-residue-long membrane-intercalating segment. It also enhanced the tryptic cleavage of the R602-L603 bond, which is located within the central hydrophobic segment. These results, which suggest a protein conformation change as a result of NADPH binding, have been discussed in relation to the mechanism of proton translocation by the transhydrogenase.     

Glutamine 132 in the NAD(H)-binding component of proton-translocating transhydrogenase tethers the nucleotides before hydride transfer

Transhydrogenase, found in bacterial membranes and inner mitochondrial membranes of animal cells, couples the redox reaction between NAD(H) and NADP(H) to proton translocation. In this work, the invariant Gln132 in the NAD(H)-binding component (dI) of the Rhodospirillum rubrum transhydrogenase was substituted with Asn (to give dI.Q132N). Mixtures of the mutant protein and the NADP(H)-binding component (dIII) of the enzyme readily produced an asymmetric complex, (dI.Q132N)(2)dIII(1). The X-ray structure of the complex revealed specific changes in the interaction between bound nicotinamide nucleotides and the protein at the hydride transfer site. The first-order rate constant of the redox reaction between nucleotides bound to (dI.Q132N)(2)dIII(1) was <1% of that for the wild-type complex, and the deuterium isotope effect was significantly decreased. The nucleotide binding properties of the dI component in the complex were asymmetrically affected by the Gln-to-Asn mutation. In intact, membrane-bound transhydrogenase, the substitution completely abolished all catalytic activity. The results suggest that Gln132 in the wild-type enzyme behaves as a "tether" or a "tie" in the mutual positioning of the (dihydro)nicotinamide rings of NAD(H) and NADP(H) for hydride transfer during the conformational changes that are coupled to the translocation of protons across the membrane. This ensures that hydride transfer is properly gated and does not take place in the absence of proton translocation.     

Active-site conformational changes associated with hydride transfer in proton-translocating transhydrogenase

Transhydrogenase couples the redox (hydride-transfer) reaction between NAD(H) and NADP(H) to proton translocation across a membrane. The redox reaction is catalyzed at the interface between two components (dI and dIII) which protrude from the membrane. A complex formed from recombinant dI and dIII (the dI(2)dIII(1) complex) from Rhodospirillum rubrum transhydrogenase catalyzes fast single-turnover hydride transfer between bound nucleotides. In this report we describe three new crystal structures of the dI(2)dIII(1) complex in different nucleotide-bound forms. The structures reveal an asymmetry in nucleotide binding that complements results from solution studies and supports the notion that intact transhydrogenase functions by an alternating site mechanism. In one structure, the redox site is occupied by NADH (on dI) and NADPH (on dIII). The dihydronicotinamide rings take up positions which may approximate to the ground state for hydride transfer: the redox-active C4(N) atoms are separated by only 3.6 A, and the perceived reaction stereochemistry matches that observed experimentally. The NADH conformation is different in the two dI polypeptides of this form of the dI(2)dIII(1) complex. Comparisons between a number of X-ray structures show that a conformational change in the NADH is driven by relative movement of the two domains which comprise dI. It is suggested that an equivalent conformational change in the intact enzyme is important in gating the hydride-transfer reaction. The observed nucleotide conformational change in the dI(2)dIII(1) complex is accompanied by rearrangements in the orientation of local amino acid side chains which may be responsible for sealing the site from the solvent and polarizing hydride transfer.     

Cloning of the sth gene from Azotobacter vinelandii and construction of chimeric soluble pyridine nucleotide transhydrogenases

The gene encoding the soluble pyridine nucleotide transhydrogenase (STH) of Azotobacter vinelandii was cloned and sequenced. This is the third sth gene identified and further defines a new subfamily within the flavoprotein disulfide oxidoreductases. The three STHs identified all lack one of the redox active cysteines that are characteristic for this large family of enzymes, and instead they contain a conserved threonine residue at this position. The recombinant A. vinelandii enzyme was purified to homogeneity and shown to form filamentous structures different from those of Pseudomonas fluorescens and Escherichia coli STH. Chimeric STHs were constructed which showed that the C-terminal region is important for polymer formation. The A. vinelandii STH containing the C-terminal region of P. fluorescens or E. coli STH showed structures resembling those of the STH contributing the C-terminal portion of the protein.     

A change in ionization of the NADP(H)-binding component (dIII) of proton-translocating transhydrogenase regulates both hydride transfer and nucleotide release.

Transhydrogenase couples the transfer of hydride-ion equivalents between NAD(H) and NADP(H) to proton translocation across a membrane. The enzyme has three components: dI binds NAD(H), dIII binds NADP(H) and dII spans the membrane. Coupling between transhydrogenation and proton translocation involves changes in the binding of NADP(H). Mixtures of isolated dI and dIII from Rhodospirillum rubrum transhydrogenase catalyse a rapid, single-turnover burst of hydride transfer between bound nucleotides; subsequent turnover is limited by NADP(H) release. Stopped-flow experiments showed that the rate of the hydride transfer step is decreased at low pH. Single Trp residues were introduced into dIII by site-directed mutagenesis. Two mutants with similar catalytic properties to those of the wild-type protein were selected for a study of nucleotide release. The way in which Trp fluorescence was affected by nucleotide occupancy of dIII was different in the two mutants, and hence two different procedures for determining the rate of nucleotide release were developed. The apparent first-order rate constants for NADP(+) release and NADPH release from isolated dIII increased dramatically at low pH. It is concluded that a single ionisable group in dIII controls both the rate of hydride transfer and the rate of nucleotide release. The properties of the protonated and unprotonated forms of dIII are consistent with those expected of intermediates in the NADP(H)-binding-change mechanism. The ionisable group might be a component of the proton-translocation pathway in the complete enzyme.