Prediction of the tertiary structure of the beta-secretase zymogen

beta-Secretase, also known as BACE, is a transmembrane aspartyl protease, which generates the N terminus of Alzheimer's disease amyloid beta-peptide. The activity of beta-secretase is the rate-limiting step of brain plaques production in vivo, and hence is a potential target for disease modifying drugs for Alzheimer's disease. To better understand the mechanism of action of beta-secretase and help explore novel strategies for drug discovery for Alzheimer's disease, it is important to elucidate the three-dimensional structure of its zymogen. Based on the X-ray structure of the enzyme's protease domain and the X-ray structure of pepsinogen, a model of the three-dimensional structure of the beta-secretase zymogen has been constructed. Comparison of the computed structure of pro-BACE with X-ray structures of pepsinogen and progastricsin (two other pro-aspartyl proteases) reveals a significant difference in the relationship of the pro-segment to the catalytic aspartates. In both pepsinogen and progastricsin a lysine side-chain in the pro-segment forms a salt bridge to the two catalytic aspartates, occupying the position normally occupied by a catalytic water. In the pro-BACE model there is no salt bridge, and the corresponding residue-a proline-does not interact at all with the catalytic residues. These findings can be used to elucidate the recent observations that the pro-domain of beta-secretase does not suppress activity as in a strict zymogen but does appear to facilitate proper folding of an active protease domain. The predicted three-dimensional structure of beta-secretase zymogen and the relevant findings might also provide useful insights for rational design of effective drugs against Alzheimer's disease.     

Using subsite coupling to predict signal peptides

Given a nascent protein sequence, how can one predict its signal peptide or "Zipcode" sequence? This is a first important problem for scientists to use signal peptides as a vehicle to find new drugs or to reprogram cells for gene therapy. Based on a model that takes into account the coupling effect among some key subsites, the so-called [-3, -1, +1] coupling model, a new prediction algorithm is developed. The overall rate of correct prediction for 1939 secretory proteins and 1440 non-secretary proteins was over 92%. It has not escaped our attention that the new method may also serve as a useful tool for helping investigate further many unclear details regarding the molecular mechanism of the ZIP code protein-sorting system in cells.     

Hemodynamic effects of Salvia miltiorrhiza on cirrhotic rats

Salvia miltiorrhiza (Sm) administration has been shown to reduce hepatic fibrosis in rats. We investigated the hemodynamic effects of Sm on bile duct ligated (BDL) rats. Hemodynamic, histological, and vascular contractile studies were conducted in rats 4 weeks after bile duct ligation. An aqueous extract of Sm (0.2 g twice per day) or vehicle was administered for 4 weeks to BDL rats. Sm treatment in BDL rats significantly reduced histological grades of fibrosis and ameliorated the portal hypertensive state (including portal venous pressure, superior mesenteric artery blood flow, cardiac index, and total peripheral resistance) as compared with vehicle treatment. Moreover, Sm treatment enhanced the vascular sensitivity of mesenteric arteries to phenylephrine in BDL rats. Sm treatment had no effect on plasma biochemical profiles of either BDL or normal rats. Our results suggest that 4-week Sm treatment ameliorates the portal hypertensive state in BDL rats.     

The catalytic mechanism of 1-aminocyclopropane-1-carboxylic acid oxidase

It has been proposed that 1-aminocyclopropane-1-carboxylic acid (ACC) oxidase catalyzes the oxidation of ACC to ethylene via N-hydroxyl-ACC as an intermediate. However, due to its chemical instability the putative intermediate has never been isolated. Here, we have shown that a purified recombinant ACC oxidase can utilize alpha-aminoisobutyric acid (AIB), an analog of ACC, as an alternative substrate, converting AIB into CO2, acetone, and ammonia. We chemically synthesized the putative intermediate compound, N-hydroxyl-AIB (HAIB), and tested whether it serves as an intermediate in the oxidation of AIB. When [1-(14)C]AIB was incubated with ACC oxidase in the presence of excess unlabeled HAIB as a trap, no labeled HAIB was detected. By comparing the acetone production rates employing HAIB and AIB as substrates, the conversion of HAIB to acetone was found to be much slower than that of using AIB as substrate. Based on these observations, we conclude that ACC oxidase does not catalyze via the N-hydroxylation of its amino acid substrate. ACC oxidase also catalyzes the oxidation of other amino acids, with preference for the D-enantiomers, indicating a stereoselectivity of the enzyme.     

Prediction of protein signal sequences and their cleavage sites

Protein signal sequences play a central role in the targeting and translocation of nearly all secreted proteins and many integral membrane proteins in both prokaryotes and eukaryotes. The knowledge of signal sequences has become a crucial tool for pharmaceutical scientists who genetically modify bacteria, plants, and animals to produce effective drugs. However, to effectively use such a tool, the first important thing is to find a fast and effective method to identify the "zipcode" entity; this is also evoked by both the huge amount of unprocessed data available and the industrial need to find more effective vehicles for the production of proteins in recombinant systems. In view of this, a sequence-encoded algorithm was developed to identify the signal sequences and predict their cleavage sites. The rate of correct prediction for 1,939 secretory proteins and 1,440 nonsecretory proteins by self-consistency test is 90.14% and that by jackknife test is 90.13%. The encouraging results indicate that the signal sequences share some common features although they lack similarity in sequence, length, and even composition and that they are predictable to a considerably accurate extent.     

The adsorption of Congo red and vacuum pump oil by rice hull ash

Rice hull ash (RHA) of large surface area was obtained by acid wash and then calcination at 600 degrees C for 4 h. The white ash was then mixed with kaolin and starch to make pellet adsorbents with reasonable strength to be utilized in a packed column. Both ash and pellet samples showed good adsorption capacities toward the organic substances in wastewater. Furthermore, the surface nature of the white ash and pellet adsorbent could be modified through either hydration or esterification reactions. Corresponding changes in silanol concentrations were successfully correlated to changes in adsorption capacity toward either Congo red or vacuum pump oil molecules.     

The 300-kDa intermediate filament-associated protein (IFAP300) is a hamster plectin ortholog

Plectin is a high-molecular-weight cytoskeleton-associated protein that was initially identified in intermediate filament (IF)-enriched fractions of rat C6 glioma cells. At the cellular level, plectin has been found to associate with IF networks and IF-associated structures that are involved in cell-cell and cell-substrate adhesions. IFAP300 is an IF-associated protein that was initially identified in hamster cells by a monoclonal antibody directed against a high molecular weight protein present in IF-enriched cytoskeletal preparations. Plectin and IFAP300 display similar distribution patterns within cells as determined by immunofluorescence. Based upon this and the finding that their biochemical properties are similar, it has been suggested that they may actually be orthologous proteins. In this paper we demonstrate that this is the case. Cloning and sequencing of most of the hamster plectin cDNA demonstrates that plectin is found in hamster cells and that its sequence is highly conserved between species. Using immunological cross-reactivity, epitope mapping, and immunoelectron microscopy, we show that IFAP300 is actually the hamster ortholog of plectin.     

补增UV—B辐射对香蕉叶片光合作用和叶氮在光合碳循环组分中分配 …

补增UV -B辐射的香蕉叶片光下呼吸速率 (Rd)和不包括光下呼吸的CO2 补偿点 (г ) ,分别为0 .33μmol·m- 2 ·s- 1 和 46.5μl·L- 1 ,较对照植株分别高 5.6%和 1 0 .0 %。在较高CO2 浓度 (>340 μl·L- 1 )条件下的An/θp关系最初直线部分斜率 ,即表观量子产率 (αA)为 0 .0 2 3± 0 .0 0 7,而补增UV B辐射处理的植株则降低 1 3.0 % ,光能转换效率 (δ)亦降低 2 8.6% ,表明UV B辐射明显降低αA 和δ。在高θp(1 1 0 0 μmol·m- 2 ·s- 1 )和Ci<2 0 0 μl·L- 1 条件下 ,对照植株的An/Ci关系为An =0 .0 2 8Ci 1 .44,补增UV B辐射处理的植株则为An =0 .0 2 1Ci 1 .0 1 ,UV B辐射降低羧化限制速率。最大羧化速率 (Vcmax)和电子传导速率的光饱和值 (Jmax)亦较低 ,补增UV B辐射的叶片 ,叶氮在Rubisco的分配系数 (PR)和叶氮在生物力能学组分的分配系数 (PB)分别较对照低 8.1 %和 3.0 % ,叶氮分配到类囊体膜捕光色素蛋白组分的则略见增高 ,UV B辐射降低叶氮在光合循环组分的分配     

活性氧对外源IAA诱导的ACC合酶活性的影响

本文试图从活性氧的角度阐明外源IAA诱导ACC合酶活性的机制.绿豆(Phaseolus radiatus L.)幼苗的乙烯产生及ACC合酶活性从萌发的第5天开始上升,到第10天达到高峰,接着下降.10 μmol/L的外源IAA能明显促进绿豆幼苗乙烯的产生及ACC合酶的活性,同时也促进了超氧阴离子自由基(O(-)/(*)2)、过氧化氢(H2O2)的产生.显示外源IAA诱导的ACC合酶的活性与其诱导的活性氧的产生具有某种相关性.外源O(-)/(*)2处理能明显提高绿豆幼苗的乙烯产生速率及ACC合酶的活性,而外源H2O2无论对乙烯产生或ACC合酶的活性均没有明显的作用.外加O(-)/(*)2的清除剂SOD对绿豆幼苗乙烯的产生及ACC合酶活性的提高有一定的抑制作用,而外源过氧化氢酶却没有明显的作用.为此我们可以得出结论:外源IAA诱导的绿豆幼苗ACC合酶活性的提高可能是由于其诱导的O(-)/(*)2产生的升高引起的,这可能也是高等植物中调控乙烯生物合成的机制之一;而IAA诱导的H2O2产率的升高并不是其诱导ACC合酶活性升高的原因.