Structure and Function of the Catalytic Domain of the Dihydrolipoyl Acetyltransferase Component in Escherichia coli Pyruvate Dehydrogenase Complex

The Escherichia coli pyruvate dehydrogenase complex (PDHc) catalyzing conversion of pyruvate to acetyl-CoA comprises three components: E1p, E2p, and E3. The E2p is the five-domain core component, consisting of three tandem lipoyl domains (LDs), a peripheral subunit binding domain (PSBD), and a catalytic domain (E2pCD). Herein are reported the following. 1) The x-ray structure of E2pCD revealed both intra- and intertrimer interactions, similar to those reported for other E2pCDs. 2) Reconstitution of recombinant LD and E2pCD with E1p and E3p into PDHc could maintain at least 6.4% activity (NADH production), confirming the functional competence of the E2pCD and active center coupling among E1p, LD, E2pCD, and E3 even in the absence of PSBD and of a covalent link between domains within E2p. 3) Direct acetyl transfer between LD and coenzyme A catalyzed by E2pCD was observed with a rate constant of 199 s⁻¹, comparable with the rate of NADH production in the PDHc reaction. Hence, neither reductive acetylation of E2p nor acetyl transfer within E2p is rate-limiting. 4) An unprecedented finding is that although no interaction could be detected between E1p and E2pCD by itself, a domain-induced interaction was identified on E1p active centers upon assembly with E2p and C-terminally truncated E2p proteins by hydrogen/deuterium exchange mass spectrometry. The inclusion of each additional domain of E2p strengthened the interaction with E1p, and the interaction was strongest with intact E2p. E2p domain-induced changes at the E1p active site were also manifested by the appearance of a circular dichroism band characteristic of the canonical 4′-aminopyrimidine tautomer of bound thiamin diphosphate (AP).     

乳腺癌易感蛋白2的结构和功能

乳腺癌易感蛋白2是由乳腺癌易感基因2编码的一种在维持哺乳动物细胞染色体的稳定及DNA损伤生物应答中发挥重要作用的蛋白质。文章通过介绍近几年来对乳腺癌易感蛋白2的结构研究,阐述其在双链DNA损伤修复中的作用模型及其在肿瘤抑制中的功能。     

Solution Structure and Characterisation of the Human Pyruvate Dehydrogenase Complex Core Assembly

Mammalian pyruvate dehydrogenase complex (PDC) is a key multi-enzyme assembly that is responsible for glucose homeostasis maintenance and conversion of pyruvate into acetyl-CoA. It comprises a central pentagonal dodecahedral core consisting of two subunit types (E2 and E3BP) to which peripheral enzymes (E1 and E3) bind tightly but non-covalently. Currently, there are two conflicting models of PDC (E2 + E3BP) core organisation: the ‘addition’ model (60 + 12) and the ‘substitution’ model (48 + 12). Here we present the first ever low-resolution structures of human recombinant full-length PDC core (rE2/E3BP), truncated PDC core (tE2/E3BP) and native bovine heart PDC core (bE2/E3BP) obtained by small-angle X-ray scattering and small-angle neutron scattering. These structures, corroborated by negative-stain and cryo electron microscopy data, clearly reveal open pentagonal core faces, favouring the ‘substitution’ model of core organisation. The native and recombinant core structures are all similar to the truncated bacterial E2 core crystal structure obtained previously. Cryo-electron microscopy reconstructions of rE2/E3BP and rE2/E3BP:E3 directly confirm that the core has open pentagonal faces, agree with scattering-derived models and show density extending outwards from their surfaces, which is much more structurally ordered in the presence of E3. Additionally, analytical ultracentrifugation characterisation of rE2/E3BP, rE2 (full-length recombinant E2-only) and tE2/E3BP supports the substitution model. Superimposition of the small-angle neutron scattering tE2/E3BP and truncated bacterial E2 crystal structures demonstrates conservation of the overall pentagonal dodecahedral morphology, despite evolutionary diversity. In addition, unfolding studies using circular dichroism and tryptophan fluorescence spectroscopy show that the rE2/E3BP is less stable than its rE2 counterpart, indicative of a role for E3BP in core destabilisation. The architectural complexity and lower stability of the E2/E3BP core may be of benefit to mammals, where sophisticated fine-tuning is required for cores with optimal catalytic and regulatory efficiencies.     

植物COP1蛋白的结构与功能

组成型光形态建成 1 (constitutivelyphotomorphogenic 1 ,COP1 )蛋白是一个分子量为 76kD的核蛋白 ,它由 3个特殊的结构域组成即环形锌指结合域、卷曲螺旋形结构域和WD_40重复序列 ,并含有一个核定位信号和一个新型细胞质定位信号 ,它是一个光形态建成的抑制子 ,是一个光调控植物发育的分子开关。当植物在暗环境下生长时 ,COP1蛋白聚集在细胞核内 ,抑制光形态的建成 ,而在光环境下 ,COP1蛋白则分散到细胞质中 ,解除其抑制作用 ,恢复光形态建成。COP1蛋白在细胞内的核质分布受多个因素的影响 ,核内COP1通过与特异转录因子相互作用来调节光形态建成。继从植物中分离鉴定出COP1蛋白之后 ,动物体内也发现有COP1蛋白的存在 ,提示COP1蛋白可能在调节动物和植物的发育及信号转导等方面具有共同作用模式。     

蛋白质二硫键异构酶家族的结构与功能

蛋白质二硫键异构酶（protein disulfide isomerase,PDI）家族是一类在内质网中起作用的巯基-二硫键氧化还原酶.它们通常含有CXXC（Cys-Xaa-Xaa-Cys,CXXC）活性位点,活性位点的两个半胱氨酸残基可催化底物二硫键的形成、异构及还原.所有PDI家族成员包含至少一个约100个氨基酸残基的硫氧还蛋白同源结构域.PDI家族的主要职能是催化内质网中新生肽链的氧化折叠,另外在内质网相关的蛋白质降解途径（ERAD）、蛋白质转运、钙稳态、抗原提呈及病毒入侵等方面也起重要作用.     

蛋白激酶Cα相互作用蛋白的结构与功能

蛋白激酶Cα相互作用蛋白（protein interacting with Cα kinase,PICK1）是蛋白激酶Cox（protein kinase Cα,PKCα）的靶蛋白之一,也是在PKCα和突触后膜受体蛋白间起重要作用的衔接蛋白。PICK1分别由PDZ结构域、BAR结构域以及卷曲螺旋区和酸性氨基酸区组成。PICK1中的PDZ结构域和受体蛋白、转运蛋白、衔接蛋白的相互作用报道较多,BAR结构域则与支架蛋白、质膜等相互作用。PICK1在突触可塑性、神经递质传递、外周神经感觉、细胞生长和黏连等方面发挥重要作用。本文对PICK1的结构和功能进行综述。     

植物中钙依赖蛋白激酶（CDPKs）的结构与功能

在植物细胞中,钙离子作为第二信使,通过钙依赖蛋白激酶（CDPKs)发挥功能是其传递信号的主要途径之一。CDPKs广泛存在于植物体中,是目前植物体内研究最深入的蛋白激酶,在简要阐述CDPKs于植物体内的分布定位的基础上,介绍了CDPKs的结构特点,生化性质及其在植物细胞生理功能中的作用,并就该领域的研究前景作了展望。     

接头蛋白Gab1的结构及功能研究进展

Gab1蛋白属于接头蛋白Gab家族,该家族蛋白因能与生长因子受体结合蛋白2（Grb2）相结合而得名。作为接头蛋白,Gab1蛋白能被多种受体酪氨酸激酶或非受体酪氨酸激酶激活,接受胞外多种生长因子、细胞因子和一些T/B细胞抗原受体的刺激,介导PI3K/Akt和Ras/MAPK等多条信号转导途径,具有促进细胞生长、迁移、调节免疫等多种生物学功能,与糖尿病、肿瘤、心血管疾病等的发生发展密切相关。     

高等植物中蛋白磷酸酶2C的结构与功能

蛋白质磷酸化／去磷酸化是生物信号级联传递的重要方式之一,主要通过生化性质互为对立的蛋白激酶和蛋白磷酸酶实现。蛋白磷酸酶2C(PP2C)是蛋白磷酸酶的一个分支,其生化性质、蛋白质组成与结构都和其他磷酸酶显著不同,但都在生物信号传递中扮演重要角色。高等植物中PP2C广泛参与脱落酸(ABA)的各种信号途径,包括ABA诱导的种子萌发／休眠、保卫细胞及离子通道调控和气孔关闭、逆境胁迫等。PP2C也多样地参与植物创伤反应、生长发育以及抗病性等各个途径。作为大多数信号途径的负调控因子,PP2C能直接与激酶结合,与其他调控蛋白结合,以及直接与DNA结合调控相关基因的表达。     

蛋白激酶R分子结构与激活机制研究进展

双链RNA依赖型蛋白激酶(PKR)是由干扰素诱导的、具有抗病毒活性的蛋白激酶。本文介绍了PKR的分子结构特征,并对PKR激活机制进行探讨。     

The Solution Structure of the Lantibiotic Immunity Protein NisI and Its Interactions with Nisin

Many Gram-positive bacteria produce lantibiotics, genetically encoded and posttranslationally modified peptide antibiotics, which inhibit the growth of other Gram-positive bacteria. To protect themselves against their own lantibiotics these bacteria express a variety of immunity proteins including the LanI lipoproteins. The structural and mechanistic basis for LanI-mediated lantibiotic immunity is not yet understood. Lactococcus lactis produces the lantibiotic nisin, which is widely used as a food preservative. Its LanI protein NisI provides immunity against nisin but not against structurally very similar lantibiotics from other species such as subtilin from Bacillus subtilis. To understand the structural basis for LanI-mediated immunity and their specificity we investigated the structure of NisI. We found that NisI is a two-domain protein. Surprisingly, each of the two NisI domains has the same structure as the LanI protein from B. subtilis, SpaI, despite the lack of significant sequence homology. The two NisI domains and SpaI differ strongly in their surface properties and function. Additionally, SpaI-mediated lantibiotic immunity depends on the presence of a basic unstructured N-terminal region that tethers SpaI to the membrane. Such a region is absent from NisI. Instead, the N-terminal domain of NisI interacts with membranes but not with nisin. In contrast, the C-terminal domain specifically binds nisin and modulates the membrane affinity of the N-terminal domain. Thus, our results reveal an unexpected structural relationship between NisI and SpaI and shed light on the structural basis for LanI mediated lantibiotic immunity.     

The Influence of CO2 Concentration and pH on Two Chlorella Species Grown in Continuous Light

Both Chlorella pyrenoidosa and Chlorella vulgaris grow equally well at 20°C aerated with ordinary air or mixtures of air with 5 or 12 per cent CO₂ (5 klux continuous light). Whereas C. vulgaris relatively rapidly adapts to a higher CO₂ tension, adaptation takes about 24 hours for C. pyrenoidosa. In Chlorella vulgaris pH in the range 3.6–7.6 has no apparent influence on the rate of photosynthesis in experiments having a duration of two hours. This is true both for algae grown aerated by ordinary air and for algae grown with a mixture of 5 per cent CO₂ in air. The adaptation time must be short. In Chlorella pyrenoidosa the same is found for algae in ordinary air, whereas an influence of pH is seen in some experiments where the aeration was by 5 per cent CO₂ in air. As is to be expected, the rate of photosynthesis in C. pyrenoidosa during the first two hours is very much influenced by the concentration of free CO₂. The highest rate is found at the CO₂ concentration at which the algae had been growing previously. The influence on the rate of photosynthesis in C. vulgaris is very much less, although in principle the same. The investigation of the corresponding influence on the rate of respiration is complicated by considerable variation from one series to another. In C. vulgaris this is particularly of importance. In C. pyrenoidosa, the highest rate of respiration is generally found at the CO₂-concentration at which the alga had been growing before the experiment. It seems probable that variations between similar series is due to the fact that the algae were grown in continuous light but with dilution with fresh culture medium when the optical density had reached a certain magnitude. Algae grown in this way are neither synchronized nor non-synchronized.Our thanks are due to the Danish State Research Foundation for financial support.     

Effect of Mg2+ on the Structure and Function of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase

Mg²⁺ in various concentrations was added to purified Rubisco in vitro to gain insight into the mechanism of molecular interactions between Mg²⁺ and Rubisco. The enzyme activity assays showed that the reaction between Rubisco and Mg²⁺ was two order, which means that the enhancement of Rubisco activity was accelerated by low concentration of Mg²⁺ and slowed by high concentration of Mg²⁺. The kinetics constant (K _m) and V _max was 1.91 μM and 1.13 μmol CO₂ mg⁻¹ protein∙min⁻¹, respectively, at a low concentration of Mg²⁺, and 3.45 μM and 0.32 μmol CO₂∙mg⁻¹ protein∙min⁻¹, respectively, at a high concentration of Mg²⁺. By UV absorption and fluorescence spectroscopy assays, the Mg²⁺ was determined to be directly bound to Rubisco; the binding site of Mg²⁺ to Rubisco was 0.275, the binding constants (K _A) of the binding site were 6.33 × 10⁴ and 5.5 × 10⁴ l·mol⁻¹. Based on the analysis of the circular dichroism (CD) spectra, it was concluded that the binding of Mg²⁺ did not alter the secondary structure of Rubisco, suggesting that the observed enhancement of Rubisco carboxylase activity was caused by a subtle structural change in the active site through the formation of the complex with Mg²⁺.     

Design and Structure of an Equilibrium Protein Folding Intermediate: A Hint into Dynamical Regions of Proteins

Partly unfolded protein conformations close to the native state may play important roles in protein function and in protein misfolding. Structural analyses of such conformations which are essential for their fully physicochemical understanding are complicated by their characteristic low populations at equilibrium. We stabilize here with a single mutation the equilibrium intermediate of apoflavodoxin thermal unfolding and determine its solution structure by NMR. It consists of a large native region identical with that observed in the X-ray structure of the wild-type protein plus an unfolded region. Small-angle X-ray scattering analysis indicates that the calculated ensemble of structures is consistent with the actual degree of expansion of the intermediate. The unfolded region encompasses discontinuous sequence segments that cluster in the 3D structure of the native protein forming the FMN cofactor binding loops and the binding site of a variety of partner proteins. Analysis of the apoflavodoxin inner interfaces reveals that those becoming destabilized in the intermediate are more polar than other inner interfaces of the protein. Natively folded proteins contain hydrophobic cores formed by the packing of hydrophobic surfaces, while natively unfolded proteins are rich in polar residues. The structure of the apoflavodoxin thermal intermediate suggests that the regions of natively folded proteins that are easily responsive to thermal activation may contain cores of intermediate hydrophobicity.     

胰岛素受体底物PH结构域相互作用蛋白结构和功能研究进展

PHIP是一种与胰腺β细胞中胰岛素受体底物（IRS）的PH结构域相互作用的蛋白。根据小鼠PHIP（mPHIP）mRNA翻译的不同起始位点,除全长的PHIP1外,mPHIP基因还编码其他3种不同变异体。在胰岛素诱导的信号途径中,主要分布于细胞核的PHIP1和IRS-1的PH结构域相互作用,介导IRS蛋白酪氨酸的磷酸化。IRS-2和PHIP1的共表达能诱导IRS在细胞膜上的定位,促进葡萄糖转运蛋白4（GLUT4）向细胞质膜的转移。PHIP1的表达能提高β-细胞内细胞周期蛋白D2的表达,促进β细胞的生长。PHIP1的表达活化蛋白激酶B（PKB）,活化的PKB能明显抑制β细胞的凋亡。PHIP与胰岛素信号传导途径中其他信号分子的相互作用机制尚不明确。     

Influence of Perfusate Glucose Concentration on Dialysate Lactate, Pyruvate, Aspartate, and Glutamate Levels Under Basal and Hypoxic Conditions: A Microdialysis Study in Rat Brain

Abstract: The aim of this study was to evaluate the influence of perfusion media with different glucose concentrations on dialysate levels of lactate, pyruvate, aspartate (Asp), and glutamate (Glu) under basal and hypoxic conditions in rat brain neocortex. Intracerebral microdialysis was performed with the rat under general anesthesia using bilateral probes (o.d. 0.3 mm; membrane length, 2 mm) perfused with artificial CSF containing 0.0 and 3.0 m M glucose, respectively. Basal dialysate levels were obtained 2 h after probe implantation in artificially ventilated animals. Dialysate levels of glucose were also measured for the two different perfusion fluids. The mean absolute extracellular concentration of glucose was estimated by a modification of the no-net-flux method to be 3.3 mmol/L, corresponding to an average in vivo recovery of 6% for glucose. Hypoxia was induced by lowering the inspired oxygen concentration to 3%. Hypoxia caused a disturbance of cortical electrical activity, evidenced by slower frequency and lower amplitudes on the electroencephalogram compared with prehypoxic conditions. This was associated with significant elevations of lactate, Asp, and Glu levels. There were no statistically significant differences in dialysate metabolite levels between the two perfusion fluids, during either normal or hypoxic conditions. We conclude that microdialysis with glucose-free perfusion fluid does not drain brain extracellular glucose in anesthetized rats to the extent that the dialysate lactate, pyruvate, Asp, and Glu levels during basal or hypoxic conditions are altered.     

Influence of gag and RRE Sequences on HIV-1 RNA Packaging Signal Structure and Function

The packaging signal (Ψ) and Rev-responsive element (RRE) enable unspliced HIV-1 RNAs' export from the nucleus and packaging into virions. For some retroviruses, engrafting Ψ onto a heterologous RNA is sufficient to direct encapsidation. In contrast, HIV-1 RNA packaging requires 5′ leader Ψ elements plus poorly defined additional features. We previously defined minimal 5′ leader sequences competitive with intact Ψ for HIV-1 packaging, and here examined the potential roles of additional downstream elements. The findings confirmed that together, HIV-1 5′ leader Ψ sequences plus a nuclear export element are sufficient to specify packaging. However, RNAs trafficked using a heterologous export element did not compete well with RNAs using HIV-1's RRE. Furthermore, some RNA additions to well-packaged minimal vectors rendered them packaging-defective. These defects were rescued by extending gag sequences in their native context. To understand these packaging defects' causes, in vitro dimerization properties of RNAs containing minimal packaging elements were compared to RNAs with sequence extensions that were or were not compatible with packaging. In vitro dimerization was found to correlate with packaging phenotypes, suggesting that HIV-1 evolved to prevent 5′ leader residues' base pairing with downstream residues and misfolding of the packaging signal. Our findings explain why gag sequences have been implicated in packaging and show that RRE's packaging contributions appear more specific than nuclear export alone. Paired with recent work showing that sequences upstream of Ψ can dictate RNA folds, the current work explains how genetic context of minimal packaging elements contributes to HIV-1 RNA fate determination.