高活性F1-ATP酶单分子旋转初步观察

从基因突变的F1 ATP酶 (基因突变质粒 ,α C193S ,γ S10 7C ,β亚基带有 10个组氨酸标记 (His Tag) ,转入到菌株大肠杆菌JM10 3)的菌株中筛选出一高表达菌株 .该菌株表达的F1 ATP酶经纯化后其水解活性明显高于文献值 .从单分子水平上进行观察 ,发现在水解ATP过程中 ,γ亚基上连接的荧光标记蛋白微丝 ,其旋转速度要比文献中同样条件下快约一倍     

猪心线粒体Fo的纯化、重建及其质子转运功能

比较了猪心线粒体F_oF₁-ATPase膜部分F_o的四种纯化方法.结果表明,用NaBr从亚线粒体除去F_oF₁-ATPase的水溶性部分F₁-ATPase后,再以CHAPS增溶,并经蔗糖梯度离心,可获得高纯度的F_o.SDS-聚丙烯酰胺凝胶电泳鉴定表明,纯化的F_o含有b、OSCP（寡霉素敏感授予蛋白）、d、a、e、F₆、IF₁、A6L和c等9种亚基.用去污剂稀释法将纯化的F_o在脂质体上重建后,重建F_o表现较高的被动转运质子活性.这为在体外深入研究F_o的活性、构象与膜脂的关系,以及F_o与F₁-ATPase的组装等提供了很好的实验模型.     

竹红菌乙素作猝灭剂研究Fo构象方法的建立

线粒体F₁F_o复合体F_o部分a亚基的色氨酸荧光可被竹红菌乙素(hypocrellin B, HB)猝灭.不同温度下测定Stern-Volmer图的结果显示,猝灭常数(K_sv)随温度的增加而加大,时间衰变荧光的结果显示,荧光寿命随HB浓度的增加而减小,加入不同浓度的HB, F₁F_o复合体的吸收峰没有位移.这些实验结果支持动态猝灭机理.HB还具有有效猝灭浓度低,不影响酶的活力;在脂相和水相的分布比率可高达16 560∶1;实验操作简便等优点.因此HB可作为理想的疏水相荧光猝灭剂,研究与膜结合的F₁F_o复合体中镶嵌于膜脂内F_o的构象变化.     

Mg2＋对阿霉素引起心肌线粒体F1F0变化的保护

抗肿瘤药物阿霉素(ADM)对心肌线粒体F₁F₀-复合体呈现抑制而对F₁-ATPase无抑制,这表明ADM可能是通过膜脂起作用的,适当浓度Mg²⁺能降低ADM对复合体的抑制.经 ³¹P-NMR和标记荧光探针NBD-PE,DPH,MC-540以及内源荧光等的测定,结果表明ADM可能首先通过诱导F₁F₀膜脂形成非双层脂结构,继而影响了膜脂的堆积程度和流动性,进而引起F₁F₀-复合体酶蛋白构象的改变,最终导致酶活力的降低.Mg^2＋则可能由于与ADM竞争与心磷脂的结合,而对ADM引起F₁F₀的变化产生保护作用.     

无机磷影响叠氮钠对ATP合成酶合成活性的抑制

利用ADP和放射性磷直接合成ATP的方法,研究了无机磷(P_i)和叠氮钠对猪心线粒体ATP合成酶（F₁F_O-ATPase）ATP合成活性的影响.结果发现无机磷除作为合成ATP的底物参与F₁F_O-ATPase的合成反应外,还对F₁F_O-ATPase的合成活性呈现抑制作用,在1 mmol/L ADP存在时,随着P_i浓度由0.01～10 mmol/L增加,抑制合成作用越来越强.与叠氮钠在低浓度时(小于1 mmol/L)只抑制ATP水解,不影响ATP合成的观点不同.实验结果显示0.1 mmol/L叠氮钠表观激活F₁F_O-ATPase的ATP合成活性,且激活程度与反应体系中所加P_i的浓度呈负相关.当固定P_i浓度（0.1 mmol/L）后,随着叠氮钠浓度的增加表观激活程度也在变化,叠氮钠与磷浓度相等时表观激活程度最大,直至叠氮钠浓度接近0.5 mmol/L时,开始呈现表观抑制现象,叠氮钠浓度高于1 mmol/L之后,就出现解偶联现象.     

ATP合成酶的结合变化机制和旋转催化——1997年诺贝尔化学奖的部分工作介绍

保罗.博耶(P.D.Boyer)教授为阐明ATP酶作用机制所提出的结合变化机制有两个基本要点：一是ATP合成所需要的能量原则上是用于促进酶上紧密结合的ATP的释放和无机磷、ADP的结合;二是在净ATP形成过程中,酶上的各催化部位是高度协同地顺序起作用的.γ亚基在F₁-ATP酶中的旋转运动使三个催化部位构象不对称是实现结合变化的基础.高分辨率牛心线粒体F₁-ATP酶的晶体结构发表以后,出现了一些支持旋转催化机制的直接实验证据.     

不同CO2浓度升高和氮肥水平对水稻叶绿素荧光特性的影响

为研究不同CO₂浓度升高和氮肥水平对水稻叶绿素荧光特性的影响,利用由开顶式气室（OTC）组成的CO₂浓度自动调控平台开展田间试验。以粳稻9108为试验材料,CO₂浓度设置CK（对照,环境大气CO₂浓度）、C₁（CO₂浓度比CK增加160 μmol/mol）和C₂（CO₂浓度比CK增加200 μmol/mol）3个水平;氮肥设置低氮（N₁：10 g/m²）、中氮（N₂：20 g/m²）和高氮（N₃：30 g/m²）3个水平。结果表明,在低氮条件下,与CK相比,C₁处理使拔节期的F_o上升4.8%（P=0.031）;C₂处理使拔节期的F_o上升6.3%（P=0.015）,F_v/F_m下降4.8%（P=0.003）,使孕穗期的F_o上升12.7%（P=0.039）,F_v/F_o下降18.2%（P=0.039）。在高氮条件下,与CK相比,C₂处理使灌浆期的F_m、F_v和F_v/F_m分别下降3.6%（P=0.039）、4.9%（P=0.013）和1.3%（P=0.039）。在中氮条件下,与CK相比,C₁和C₂处理的影响不明显。在整个生育期内,CO₂浓度升高与施氮处理交互作用对水稻叶绿素荧光特性的影响未到达显著水平。研究表明,大气CO₂浓度升高使水稻叶片光系统Ⅱ受损,抑制其电子传递能力、电子受体Q_A氧化还原情况、最大光化学效率和潜在活性,通过适量施氮可以有效地缓解其负面效应。     

亲和层析纯化肌质网Ca2+－ATP酶

建立了一种亲和层析纯化肌质网Ca²⁺-ATP酶的方法．用非离子型去污剂C₁₂E₈ 溶解肌质网,再通过反应红－120琼脂糖亲和层析柱使肌质网Ca²⁺-ATP酶纯度从粗品中的65％提高到99％,并具有较高ATP水解活性．经SDS－聚丙烯酰胺凝胶电泳检测,为电泳纯．     

过氧化氢对培养心肌细胞损伤作用的研究

氧化应激时产生大量的自由基,造成心肌细胞的损伤.过氧化氢(H₂O₂)是有机体氧化代谢产物,同时是一种活性氧.应用不同浓度的H₂O₂,分别于不同作用时间,动态观察其对心肌细胞的损伤作用.从实验结果看到,低浓度的H₂O₂（＜0.1 mmol/L）作用2 h,使心肌细胞产生早期的生物化学的改变,如MDA产生堆积和细胞周期时相改变（G1期细胞增加,G2期细胞减少）,此时心肌酶基本无泄漏,心肌细胞的死亡率很低,HE形态学观察基本无改变;随着H₂O₂浓度的增加（1～5 mmol/L）和作用时间的延长,进一步诱导细胞损伤加剧,LDH释放和MDA积累明显升高,细胞死亡率也明显增加,已具有统计学意义.同时可观察到其病理形态学的坏死性改变;当10 mmol/L H₂O₂作用时,细胞大量死亡,形态学可见细胞极度收缩、脱落,形成大面积的细胞脱失区.因此,H₂O₂作为一种活性氧自由基,依其浓度和作用时间不同可造成不同程度的心肌细胞的损伤.辣根过氧化物酶作为一种自由基清除剂,可明显减少H₂O₂活性氧自由基对心肌细胞的损伤作用.     

猪瘟病毒E2基因主要抗原区的克隆及原核表达

利用反转录PCR（RT-PCR）和套式PCR（nest Polymerase Chain Reaction ,nPCR）技术扩增出当前猪瘟流行毒（广西玉林株,GXYL）与中国猪瘟兔化弱毒（C-株）兔脾组织毒E₂基因的主要抗原区,将其克隆到表达载体pP_ROEX-HTb中,获得重组质粒pP_ROEX-GXYL和pP_ROEX-C,经PCR、酶切和序列分析鉴定表明,插入的位置、大小和读码框均正确。 SDS-PAGE检测表明,经重组质粒pP_ROEX-GXYL和pP_ROEX-C转化、诱导的受体菌能表达E₂基因主要抗原区蛋白,Western-blot检测表明,诱导表达的抗原蛋白能与猪瘟阳性血清发生特异性反应。      

Mutations within the P-loop of Kir6.2 modulate the intraburst kinetics of the ATP-sensitive potassium channel

The ATP-sensitive potassium (K(ATP)) channel exhibits spontaneous bursts of rapid openings, which are separated by long closed intervals. Previous studies have shown that mutations at the internal mouth of the pore-forming (Kir6.2) subunit of this channel affect the burst duration and the long interburst closings, but do not alter the fast intraburst kinetics. In this study, we have investigated the nature of the intraburst kinetics by using recombinant Kir6.2/SUR1 K(ATP) channels heterologously expressed in Xenopus oocytes. Single-channel currents were studied in inside-out membrane patches. Mutations within the pore loop of Kir6.2 (V127T, G135F, and M137C) dramatically affected the mean open time (tau(o)) and the short closed time (tauC1) within a burst, and the number of openings per burst, but did not alter the burst duration, the interburst closed time, or the channel open probability. Thus, the V127T and M137C mutations produced longer tau(o), shorter tauC1, and fewer openings per burst, whereas the G135F mutation had the opposite effect. All three mutations also reduced the single-channel conductance: from 70 pS for the wild-type channel to 62 pS (G135F), 50 pS (M137C), and 38 pS (V127T). These results are consistent with the idea that the K(ATP) channel possesses a gate that governs the intraburst kinetics, which lies close to the selectivity filter. This gate appears to be able to operate independently of that which regulates the long interburst closings.     

Investigation of the conformational dynamics of the apo A2A adenosine receptor

The activation/deactivation processes for G-protein coupled receptors (GPCRs) have been computationally studied for several different classes, including rhodopsin, the β2 adrenergic receptor, and the M2 muscarinic receptor. Despite determined cocrystal structures of the adenosine A_2A receptor (A_2AAR) in complex with antagonists, agonists and an antibody, the deactivation process of this GPCR is not completely understood. In this study, we investigate the convergence of two apo simulations, one starting with an agonist-bound conformation (PDB: 3QAK)¹⁴ and the other starting with an antagonist-bound conformation (PDB: 3EML)¹¹. Despite the two simulations not completely converging, we were able to identify distinct intermediate steps of the deactivation process characterized by the movement of Y288^7.53 in the NPxxY motif. We find that Y288^7.53 contributes to the process by forming hydrogen bonds to residues in transmembrane helices 2 and 7 and losing these interactions upon full deactivation. Y197^5.58 also plays a role in the process by forming a hydrogen bond only once the side chain moves from the lipid interface to the middle of the helical bundle.     

调控T型钙通道Cav3.1电压依赖性失活的分子结构域

T型钙通道(Cav3)广泛分布于各类细胞,其显著的电生理学特点是低电位激活和快速的电压依赖性失活.失活在通道的生理功能调节中起十分重要的作用,但具体参与通道失活的分子基础目前并不完全清楚.为明确Cav3.1通道中调控电压依赖性失活的结构域,用Cav1.2通道(无电压依赖性失活)结构域Ⅰ和Ⅱ中的S1~S4、S5~S6区及Ⅰ和Ⅱ间的联系区替换Cav3.1中的相应区域,构建嵌合通道,并在卵母细胞中表达,用电压钳技术分析通道的电生理学特性.结果表明,替换Ⅰ中的S1~S4或S5~S6区可使Cav3.1的失活特性显著改变,但这种改变主要是由激活-失活偶联所致.Ⅱ的替换使通道的失活曲线参数发生显著改变,表明结构域Ⅱ,包括S1~S4和S5~S6均参与Cav3.1失活过程的调控.Ⅰ、Ⅱ间的联系区及Ⅰ中的S5~S6主要调控Cav3.1的失活速率,Ⅰ和Ⅱ中的S1~S4对通道失活速率无影响.综上所述,结构域Ⅱ是调控Cav3.1电压依赖性失活的关键因素,结构域Ⅰ不参与该通道失活过程的调控.Ⅰ、Ⅱ间的联系区及Ⅰ中的S5~S6主要调控Cav3.1通道的失活速率,Ⅰ、Ⅱ中的S1~S4对通道失活速率无影响.     

Structural analysis by reductive cleavage with LiAlH4 of an allyl ether choline-phospholipid, archaetidylcholine, from the hyperthermophilic methanoarchaeon Methanopyrus kandleri

A choline-containing phospholipid (PL-4) in Methanopyrus kandleri cells was identified as archaetidylcholine, which has been described by Sprott et al. (1997). The PL-4 consisted of a variety of molecular species differing in hydrocarbon composition. Most of the PL-4 was acid-labile because of its allyl ether bond. The identity of PL-4 was confirmed by thin-layer chromatography followed by positive staining with Dragendorff reagent and fast-atom bombardment-mass spectrometry. A new method of LiAlH4 hydrogenolysis was developed to cleave allyl ether bonds and recover the corresponding hydrocarbons. We confirmed the validity of the LiAlH4 method in a study of the model compound synthetic unsaturated archaetidic acid (2,3-di-O-geranylgeranyl-sn-glycerol-1-phosphate). Saturated ether bonds were not cleaved by the LiAlH4 method. The hydrocarbons formed following LiAlH4 hydrogenolysis of PL-4 were identified by gas-liquid chromatography and mass spectrometry. Four kinds of hydrocarbons with one to four double bonds were detected: 47% of the hydrocarbons had four double bonds; 11% had three double bonds; 14% had two double bonds; 7% had one double bond; and 6% were saturated species. The molecular species composition of PL-4 was also estimated based on acid lability: 77% of the molecular species had two acid-labile hydrocarbons; 11% had one acid-labile and one acid-stable hydrocarbon; and 11% had two acid-stable hydrocarbons. To our knowledge, this is the first report of a specific chemical degradation method for the structural analysis of allyl ether phospholipid in archaea.     

A broader model for C₄ photosynthesis evolution in plants inferred from the goosefoot family (Chenopodiaceae s.s.)

C(4) photosynthesis is a fascinating example of parallel evolution of a complex trait involving multiple genetic, biochemical and anatomical changes. It is seen as an adaptation to deleteriously high levels of photorespiration. The current scenario for C(4) evolution inferred from grasses is that it originated subsequent to the Oligocene decline in CO(2) levels, is promoted in open habitats, acts as a pre-adaptation to drought resistance, and, once gained, is not subsequently lost. We test the generality of these hypotheses using a dated phylogeny of Amaranthaceae s.l. (including Chenopodiaceae), which includes the largest number of C(4) lineages in eudicots. The oldest chenopod C(4) lineage dates back to the Eocene/Oligocene boundary, representing one of the first origins of C(4) in plants, but still corresponding with the Oligocene decline of atmospheric CO(2). In contrast to grasses, the rate of transitions from C(3) to C(4) is highest in ancestrally drought resistant (salt-tolerant and succulent) lineages, implying that adaptation to dry or saline habitats promoted the evolution of C(4); and possible reversions from C(4) to C(3) are apparent. We conclude that the paradigm established in grasses must be regarded as just one aspect of a more complex system of C(4) evolution in plants in general.     

Designer proteins that competitively inhibit Gαq by targeting its effector site

During signal transduction, the G protein, Gα_q, binds and activates phospholipase C-β isozymes. Several diseases have been shown to manifest upon constitutively activating mutation of Gα_q, such as uveal melanoma. Therefore, methods are needed to directly inhibit Gα_q. Previously, we demonstrated that a peptide derived from a helix-turn-helix (HTH) region of PLC-β3 (residues 852–878) binds Gα_q with low micromolar affinity and inhibits Gα_q by competing with full-length PLC-β isozymes for binding. Since the HTH peptide is unstructured in the absence of Gα_q, we hypothesized that embedding the HTH in a folded protein might stabilize the binding-competent conformation and further improve the potency of inhibition. Using the molecular modeling software Rosetta, we searched the Protein Data Bank for proteins with similar HTH structures near their surface. The candidate proteins were computationally docked against Gα_q, and their surfaces were redesigned to stabilize this interaction. We then used yeast surface display to affinity mature the designs. The most potent design bound Gα_q/i with high affinity in vitro (K_D = 18 nM) and inhibited activation of PLC-β isozymes in HEK293 cells. We anticipate that our genetically encoded inhibitor will help interrogate the role of Gα_q in healthy and disease model systems. Our work demonstrates that grafting interaction motifs into folded proteins is a powerful approach for generating inhibitors of protein–protein interactions.     

Conformational features of cepacian: the exopolysaccharide produced by clinical strains of Burkholderia cepacia

Conformational energy calculations and molecular dynamics investigations, both in water and in dimethyl sulfoxide, were carried out on the exopolysaccharide cepacian produced by the majority of the clinical strains of Burkholderia cepacia, an opportunistic pathogen causing serious lung infection in patients affected by cystic fibrosis, The investigation was aimed at defining the structural and conformational features, which might be relevant for clarification of the structure-function relationships of the polymer. The molecular dynamics calculations were carried out by Ramachandran-type energy plots of the disaccharides that constitute the polymer repeating unit. The dynamics of an oligomer composed of three repeating units were investigated in water and in Me2SO, a non-aggregating solvent. Analysis of the time persistence of hydrogen bonds showed the presence of a large number of favourable interactions in water, which were less evident in Me2SO. The calculations on the cepacian chain indicated that polymer conformational features in water were affected by the lateral chains, but were also largely dictated by the presence of solvent. Moreover, the large number of intra-chain hydrogen bonds in water disappeared in Me2SO solution, increasing the average dimension of the polymer chains.     

Mechanism of tetrodotoxin block and resistance in sodium channels

Tetrodotoxin (TTX) has been used for many decades to characterize the structure and function of biological ion channels. Yet, the precise mechanism by which TTX blocks voltage-gated sodium (Na_V) channels is not fully understood. Here molecular dynamics simulations are used to elucidate how TTX blocks mammalian voltage-gated sodium (Nav) channels and why it fails to be effective for the bacterial sodium channel, Na_VAb. We find that, in Na_VAb, a sodium ion competes with TTX for the binding site at the extracellular end of the filter, thus reducing the blocking efficacy of TTX. Using a model of the skeletal muscle channel, Na_V1.4, we show that the conduction properties of the channel observed experimentally are faithfully reproduced. We find that TTX occludes the entrance of Na_V1.4 by forming a network of hydrogen-bonds at the outer lumen of the selectivity filter. The guanidine group of TTX adopts a lateral orientation, rather than pointing into the filter as proposed previously. The acidic residues just above the selectivity filter are important in stabilizing the hydrogen-bond network between TTX and Na_V1.4. The effect of two single mutations of a critical tyrosine residue in the filter of Na_V1.4 on TTX binding observed experimentally is reproduced using computational mutagenesis.     

A Conserved Protonation-Induced Switch can Trigger “Ionic-Lock” Formation in Adrenergic Receptors

The mechanism of signal transduction in G-protein-coupled receptors (GPCRs) is a crucial step in cell signaling. However, the molecular details of this process are still largely undetermined. Carrying out submicrosecond molecular dynamics simulations of β-adrenergic receptors, we found that cooperation between a number of highly conserved residues is crucial to alter the equilibrium between the active state and the inactive state of diffusible ligand GPCRs. In particular, “ionic-lock” formation in β-adrenergic receptors is directly correlated with the protonation state of a highly conserved aspartic acid residue [Asp(2.50)] even though the two sites are located more than 20 Å away from each other. Internal polar residues, acting as local microswitches, cooperate to propagate the signal from Asp(2.50) to the G-protein interaction site at the helix III-helix VI interface. Evolutionarily conserved differences between opsin and non-opsin GPCRs in the surrounding of Asp(2.50) influence the acidity of this residue and can thus help in rationalizing the differences in constitutive activity of class A GPCRs.     

Polymerase chain reaction: basic protocol plus troubleshooting and optimization strategies

In the biological sciences there have been technological advances that catapult the discipline into golden ages of discovery. For example, the field of microbiology was transformed with the advent of Anton van Leeuwenhoek''s microscope, which allowed scientists to visualize prokaryotes for the first time. The development of the polymerase chain reaction (PCR) is one of those innovations that changed the course of molecular science with its impact spanning countless subdisciplines in biology. The theoretical process was outlined by Keppe and coworkers in 1971; however, it was another 14 years until the complete PCR procedure was described and experimentally applied by Kary Mullis while at Cetus Corporation in 1985. Automation and refinement of this technique progressed with the introduction of a thermal stable DNA polymerase from the bacterium Thermus aquaticus, consequently the name Taq DNA polymerase.PCR is a powerful amplification technique that can generate an ample supply of a specific segment of DNA (i.e., an amplicon) from only a small amount of starting material (i.e., DNA template or target sequence). While straightforward and generally trouble-free, there are pitfalls that complicate the reaction producing spurious results. When PCR fails it can lead to many non-specific DNA products of varying sizes that appear as a ladder or smear of bands on agarose gels. Sometimes no products form at all. Another potential problem occurs when mutations are unintentionally introduced in the amplicons, resulting in a heterogeneous population of PCR products. PCR failures can become frustrating unless patience and careful troubleshooting are employed to sort out and solve the problem(s). This protocol outlines the basic principles of PCR, provides a methodology that will result in amplification of most target sequences, and presents strategies for optimizing a reaction. By following this PCR guide, students should be able to: ● Set up reactions and thermal cycling conditions for a conventional PCR experiment ● Understand the function of various reaction components and their overall effect on a PCR experiment ● Design and optimize a PCR experiment for any DNA template ● Troubleshoot failed PCR experiments