Protein modelling using a chimera reference protein derived from exons

Bovine pancreatic /S-trypsin (PDB ID-code: 1TPO) which is registeredin the Brookhaven Protein Data Bank (PDB) consists of four exons.The results of homology searches for each exon in the PDB showedthat homologous proteins were tonin (PDB ID-code: 1TON), ratmast cell protease (PDB ID-code: 3RP2_A), kaffikrein A (PDBID-code: 2PKA_B) and kallikrein A (2PKA_B) respectively. Thus,for the three-dimensional structure prediction of 1TPO, a chimeraprotein was constructed from the three proteins mentioned aboveand the 3-D structure prediction was performed using this chimerareference protein. The modelled structure of 1TPO was energeticallyoptimized by molecular mechanics and molecular dynamics simulationand was compared with its X-ray crystal structure registeredin the PDB. The root mean square deviations (r.m.s.d.) of mainchain atoms and the neighbouring active site (5 sphere fromHis57, AsplO2 and Serl95) between the modelled structure andthe X-ray structure were 1.66 and 0.94 respectively. Porcinepancreatic elastase (PDB ID-code: 3EST) which is registeredin the PDB was used as the reference protein and the modelledstructure from 3EST was also compared with the X-ray data. Ther.m.s.d. of main chain atoms and that of the active site were2.14 and 1.18 respectively. These results dearly support thepropriety of this method using the chimera reference protein.     

Quantification of secondary structure prediction improvement using multiple alignments

The use of multiple sequence alignments for secondary structurepredictions is analysed. Seven different protein families, containingonly sequences of known structure, were considered to providea range of alignment and prediction conditions. Using alignmentsobtained by spatial superposition of main chain atoms in knowntertiary protein structures allowed a mean of 8% in secondarystructure prediction accuracy, when compared to those obtainedfrom the individual sequences. Substitution of these alignmentsby those determined directly from an automated sequence alignmentalgorithm showed variations in the prediction accuracy whichcorrelated with the quality of the multiple alignments and distanceof the primary sequence. Secondary structure predictions canbe reliably improved using alignments from an automatic alignmentprocedure with a mean increase of 6.87percnt;, giving an overallprediction accuracy of 68.5%, if there is a minimum of 25% sequenceidentity between all sequences in a family.     

An evaluation of the performance of an automated procedure for comparative modelling of protein tertiary structure

A 3-D model of a protein can be constructed from its amino acidsequence and the 3-D structures of one or more homologues byannealing three sets of fragments: the structurally conservedregions, structurally variable regions and the side chains.The method encoded in the computer program COMPOSER was assessedby generating 3-D models of eight proteins whose crystal structuresare already known and for which 3-D structures of homologuesare available. In the structurally conserved regions, differencesbetween modelled and X-ray structures are smaller than the differencesbetween the X-ray structures of the modelled protein and thehomologues used to build the model. When several homologuesare used, the contributions of the known structures are weighted,preferably by the square of sequence similarity; this is especiallyimportant when the similarities of the homologues to the modelledstructure differ greatly. The ‘collar’ extensionapproach, in which a similar region of different length in ahomologue is used to extend the framework, can result in a moreaccurate model. If known homologues comprise more than one relatedgroup of proteins and they are both distantly related to theunknown, then alignment of the sequence to be modelled witheach group of homologues facilitates identification of structurallyconserved regions of the unknown and leads to an improved model.Models have root mean square differences (r.m.s.d.s) with thestructures defined by X-ray analysis of between 0.73 and 1.56Å for all C atoms, for seven of the eight models. Forthe model of mucor pepsin, where the closest homologue has 33%sequence identity and 20% of the residues are in structurallyvariable regions, the r.m.s.d. for the framework region is 1.71Å and the r.m.s.d. for all C atoms is 3.47 Â.     

应用免疫斑点法检测不同工艺灭活的乙肝血源疫苗中的前S_1和S_2蛋白

作者应用前 S_1、前 S_2和 HBsAg/a 单克隆抗体,用免疫斑点法(Immuno-spot)检测同一批的乙肝表面抗原分别经加热灭活和三步化学灭活后的前 S_1和前 S_2蛋白保留情况,比较了两种工艺对前 S_1和前 S_2蛋白的影响。结果表明;加热灭活可保留前 S_1和前 S_2蛋白,三步化学灭活使前 S_1和前 S_2蛋白丢失,从抗原组成上看,加热灭活后的抗原更接近自然抗原。首次报告了含有前 S_1蛋白的乙肝疫苗,并对前 S_1和前 S_2蛋白在乙肝血源疫苗中的可能作用进行了讨论。     

Increasing productivity and protein content using early-maturing rices and efficient nitrogen management

Germplasm with shorter duration than that of the currently grown varieties is being generated to maximize productivity of irrigated rice. However, short-duration varieties often produce yields lower than the medium- and long-duration varieties. Experiments were conducted during the 1980–82 dry and wet seasons to increase productivity through the use of very early-maturing rices and the improved management of nitrogen (N) fertilizers.Results over three years showed that IR58 and IR9729-67-3 (growth duration 100 ± 5 days) yield as well as or higher than IR36 although earlier maturing. They generally had a higher productivity (kg ha^–1 day^–1) than IR36 (110 ± 5 days).Three years' data suggest that the improved timing of broadcast applications of urea in split doses increased grain yield comparable with the basal incorporation of slow-release sulfur-coated urea (SCU) or deep point-placement of urea supergranules (USG).Results on elite breeding lines showed that the early-maturing IR9729-67-3 produced higher protein yield ha^–1 than longer duration varieties such as IR8 and IR42 in the dry season. Furthermore, contrary to earlier results, single basal incorporation of slow-release SCU increased the protein yield of rice by 53 kg ha^–1 and deep point-placement of USG by 43 kg ha^–1 over split application of prilled urea.     

Synthetic hydrogels: 3. Hydroxyalkyl acrylate and methacrylate copolymers: surface and mechanical properties

The surface and mechanical properties of copolymers of hydroxyalkyl acrylates and methacrylates have been examined by a variety of techniques. This work is complementary to earlier parts of this series which describe the effect of copolymer structure on water binding properties. Water structure has been demonstrated to exert a profound effect upon mechanical properties whether measured in compression or in tension. In particular, water that is characterized by differential scanning calorimetry as ‘freezing’ water is observed to have a marked plasticizing effect upon the gel, whereas ‘non-freezing’ water has little such effect. Similarly, the ‘freezing’ water produces a more marked effect on thermally induced transitions. Two distinct transition points are observed as a result of its presence. One corresponds to the freezing point of water and the other to a glass transition temperature, whose value depends upon the proportion of ‘freezing’ or ‘plasticizing’ water in the gel. Several predictive and direct measurement techniques have been used to study the surface properties of the copolymers in both hydrated and dehydrated states. Taken together they have established a sound understanding of the way in which polar and dispersive components of surface free energy vary as a function of copolymer composition and water content. Use of protein adsorption and fibroblast cell interaction techniques demonstrate that biological phenomena respond to changes at a molecular level which current macroscopic surface energy techniques are unable to discern.     

Thermoplastic extrusion—the mechanism of the formation of extrudate structure and properties

Systems processed by thermoplastic extrusion can be regarded as heterophase polymer melts of incompatible water-plasticized biopolymers. In the process of thermoplastic extrusion, proteins and polysaccharides are melted at high pressure and temperature below the temperature region of their thermal decomposition. Dispersed particles of these systems can be deformed in flow. The mixed-melt anisotropic structure, formed in flow, is fixed by rapid conversion of the melt jet that lets the extruder die from a viscous state to a rubber-like state and then to a glassy state caused by cooling and drying. Incompatibility of proteins and polysaccharides in their water-plasticized melt mixtures impacts on structure formation and texturization during thermoplastic extrusion. Presented at the 20th ISF World Congress and 83rd AOCS Annual Meeting and Expo, May 10–14, 1992, Toronto, Ontario, Canada.     

Solvent extraction of oil from soybean flour II— pilot plant and two-solvent extractions

The process of grinding soybeans to a fine flour and extracting the flour with hexane was studied on a pilot plant scale. The crude oil from the pilot plant study had 15 ppm phosphorus and was suitable for physical refining after a light acid pretreatment and bleaching. The refined oil showed a Lovibond color of 1.4 yellow and 0.3 red. The pilot plant study also showed that grinding of the soybeans and the separation of solid from miscella were the most difficult steps in solvent extraction with fine flour. A laboratory study on separation of miscella from meal by aqueous ethanol reduced the hold-up volume, but it did not remove all the miscella. A test with betacarotene showed that only the miscella outside the flour particles was displaced. Aqueous ethanol solutions used as a second solvent extracted additional nontriglyceride materials (primarily phospholipids) from the meal. Also, the free fatty acid content of the oil was increased with aqueous ethanol solution wash. The quality of the extracted crude oil was lowered by using a second solvent, but it had the advantage of needing only one centrifugation to separate miscella from meal.     

Effect of birch (Betula pendula) bark and food protein level on root voles (Microtus oeconomus): II. detoxification capacity

The effect of protein and birch bark powder (BBP) content of forage on detoxification capacity of root voles (Microtus oeconomus) was studied. Young voles were fed with eight different diets for two weeks. Individuals on low (3%) protein diets had significantly lighter livers and kidneys than those on moderate (6%) or high (12%) protein diets. Birch bark powder addition did not have significant effect on organ weight. Detoxification was significantly induced, apparently due to secondary compounds in BBP. The activity of ethoxyresorufin-O-dealkylase (EROD) was high when protein content or BBP concentration in forage was high as compared to low protein diets or diets containing no BBP. Glucuronidation, on the other hand, was not induced by BBP. High BBP content caused serious physiological stress to the voles. The only individuals surviving were those capable of sufficiently allocating energy and protein to detoxification.     

The role of heat-shock and chaperone proteins in protein folding: possible molecular mechanisms

Recently some heat-shock proteins have been linked to functionsof ‘chaperoning’ protein folding in vivo. Here currentexperimental evidence is reviewed and possible requirementsfor such an activity are discussed. It is proposed that onemode of chaperone action is to actively unfold misfolded orbadly aggregated proteins to a conformation from whkh they couldrefold spontaneously; that improperly folded proteins are recognizedby excessive stretches of solvent-exposed backbone, rather thanby exposed hydrophobic patches; and that the molecular mechanismfor unfolding is either repeated binding and dissociation (‘plucking’)or translocation of the protein backbone through a binding cleft(‘threading’), allowing the threaded chain to refoldspontaneously. The observed hydrolysis of ATP would providethe energy for active unfolding. These hypotheses can be appliedto both monomeric folding and oligomeric assembly and are sufficientlydetailed to be open to directed experimental verification.