The amino acid sequence of cytochrome c from niger-seed, Guizotia abyssinica

The amino acid sequence of cytochrome c from niger-seed has been determined by sequence analysis of chymotryptic and tryptic peptides using the dansyl-phenylisothiocyanate method and by qualitative analysis of peptide composition by the dansyl method. Although the spectral ratios indicated the protein was not completely pure, no indication of impurity was found during the sequence analysis and no peptides in addition to those given here were obtained. In certain cases the alignment of peptides was by homology with other cytochromes c. Four residues in the proposed sequence, alanine-1, cysteine-25, histidine-26 and lysine-61 were identified only from peptide compositions. The amino-terminus of the protein is acetylated. The sequence contains two residues of ϵ-N-trimethyllysine.     

Importance of protein quality versus quantity in alternative host plants for a leaf-feeding insect

The nutritional value of alternative host plants for leaf-feeding insects such as caterpillars is commonly measured in terms of protein quantity. However, nutritional value might also depend on the quality of the foliar protein [i.e., the composition of essential amino acids (EAAs)]. A lack of comparative work on the EAA compositions of herbivores and their host plants has hampered the testing of this hypothesis. We tested the “protein quality hypothesis” using the tree-feeding caterpillars of Lymantria dispar (gypsy moth) and two taxonomically unrelated host plants, red oak (Quercus rubra) and sugar maple (Acer saccharum). Because L. dispar has higher fitness on oak than on maple, support for the hypothesis would be found if protein were of higher quality from oak than from maple. The whole-body EAA composition of L. dispar larvae was measured to estimate its optimum dietary protein composition, which was compared with the EAA compositions of oak and maple leaves. Contrary to the protein quality hypothesis, the EAA compositions of oak and maple were not significantly different in the spring. The growth-limiting EAAs in both tree species were histidine and methionine. Similar results were observed in the summer, with the exception that the histidine composition of oak was between 10 and 15 % greater than in maple leaves. The two main factors that affected the nutritional value of protein from the tree species were the quantities of EAAs, which were consistently higher in oak, and the efficiency of EAA utilization, which decreased from 80 % in May to <50 % in August. We conclude that the relative nutritional value of red oak and sugar maple for L. dispar is more strongly affected by protein quantity than quality. Surveys of many wild herbaceous species also suggest that leaf-feeding insects would be unlikely to specialize on plants based on protein quality.     

Amino acid compositions and evolutionary relationships with protein families.

We have examined the merits of the three functions based on amino acid compositions which have been proposed to indicate the similarity in amino acid sequences of two proteins; the difference index, the composition divergence and the composition coefficient. We have taken the amino acid compositions and sequences of 41 cytochrome c's and used the 820 values from all possible comparisons in the evaluation. We conclude that the functions do have a limited value in predicting proteins which are closely related in sequence and that the three functions are equivalent in this predictive ability. We have used the composition divergence values obtained from available pyruvate kinase amino acid compositions to generate a phylogenetic tree for this glycolytic enzyme.     

Comparative composition of free,peptide and protein amino acids in symbiotic and aposymbiotic Sitophilus oryzae (coleoptera,curculionidae)

Free, peptide-bound and total amino acids were determined in symbiotic and aposymbiotic Sitophilus oryzae. The concentrations of free and peptide amino acids were higher, that of protein amino acids lower in aposymbiotic larvae (+30, +66 and −35%, respectively). In the free fraction, tyrosine concentration was the only one to be lower in aposymbiotic larvae (−41%) and could be a limiting factor for protein synthesis.In nymphs and adults, the compositions in symbiotic and aposymbiotic insects were very similar. A deficiency of tyrosine occurred however in aposymbiotic nymphs and of aspartate, glutamate, arginine, lysine and tyrosine in aposymbiotic adults. On the other hand, the composition in ovaries was unchanged.It is suggested that symbiotes could favour the synthesis of proteins in the larvae by increasing the efficiency of the conversion of phenylalanine in tyrosine.     

Selective constraints, amino acid composition, and the rate of protein evolution

What are the major forces governing protein evolution? A common view is that proteins with strong structural and functional requirements evolve more slowly than proteins with weak constraints, because a stringent negative selection pressure limits the number of substitutions. In contrast, Graur claimed that the substitution rate of a protein is mainly determined by its amino acid composition and the changeabilities of amino acids. In this paper, however, we found that the relative changeabilities of amino acids in mammalian proteins are different for transmembranal and nontransmembranal segments, which have very distinct structural requirements. This indicates that the changeability of a given residue is influenced by the structural and functional context. We also reexamined the relationship between substitution rate and amino acid composition. Indeed, the two kinds of segments exhibit contrasting amino acid compositions: transmembranal regions are made up mainly of hydrophobic residues (a total frequency of approximately 60%) and are very poor in polar amino acids (<5%), whereas nontransmembranal segments have frequencies of 30% and 22%, respectively. Interestingly, we found that within a given integral membrane protein, nontransmembranal segments accumulate, on average, twice as many substitutions as transmembranal regions. However, regression analyses showed that the variability in amino acid frequencies among proteins cannot explain more than 30% of the variability in substitution rate for the transmembranal and nontransmembranal data sets. Furthermore, transmembranal and nontransmembranal segments evolving at the same rate in different proteins have different compositions, and the compositions of slowly evolving and rapidly evolving segments of the same type are similar. From these observations, we conclude that the rate of protein evolution is only weakly affected by amino acid composition but is mostly determined by the strength of functional requirements or selective constraints.     

根据蛋白质的氨基酸组成实现其快速鉴定

常规进行蛋白质鉴定的方法是测定其氨基酸顺序,它需要蛋白质顺序分析仪,对蛋白质的纯度要求高,费时和花费大,与之相比,蛋白质的氨基酸组成和分子量是容易实验测定的。本文描述了一个基于蛋白质的组成和分子量进行其快速鉴定的方法。其基本出发点是,通过统计蛋白质序列数据库中每个序列的氨基酸组成和分子量,得到一个含蛋白质长度、组成和分子量的数据库,将靶蛋白质的组成等数据与该数据库进行对比,可以检出组成和分子量与之接近的蛋白质。从而对该蛋白质进行初步鉴定。在有些情况下,甚至能相当准确地确定靶蛋白质与数据库中的某个（些）蛋白质相关。根据这一原理本文设计了根据氨基酸组成检索蛋白质组成数据库的程序,通过对胰岛素原、细胞肿瘤抗原Ｐ５３和泛肽等多种蛋白质的组成分析,证实根据氨基酸组成能较好地进行蛋白质鉴定。     

The amino acid composition of secreted mouse prolactin,growth hormone,and hamster prolactin: The presence of one tryptophan in mouse prolactin

The amino acid compositions and the electrophoretic properties of secreted mouse prolactin (mPRL), mouse growth hormone (mGH), and hamster prolactin (haPRL) were determined. The amino acid compositions of secreted mPRL and haPRL were similar to the compositions of other rodent prolactins, except that secreted mPRL contained only one tryptophan residue rather than the usual two. The composition of secreted mGH was similar to that of rat growth hormone. On 10% alkaline polyacrylamide gels, mPRL, mGH, and haPRL migrated with R_f's of 0.54, 0.21, and 0.69, respectively. The molecular weights of mPRL, mGH, and haPRL, determined by SDS-gel electrophoresis, were 23,000, 21,000, and 22,000, respectively.     

Comparison of the protein fractions of finger millet

Sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) has been employed to resolve protein subunits of finger millet (Eleusine coracana) varieties according to their MW. These studies have established that varietal differences exist in the protein composition of finger millet varieties. The MW distribution of the protein subunits in the albumin-globulin, prolamin and glutelin fractions show many differences between the parental and cross-bred varieties and these differences are greater in the albumin-globulin and glutelin fractions than in the prolamin fraction. The amino acid compositions of the protein fractions show some differences between varieties.     

Exeristes,Itoplectis, Aphaereta,Brachymeria, and Hyposoter species: In vitro glyceride synthesis and regulation of fatty acid composition

Microsomes from two species of parasitic Hymenoptera, Exeristes roborator and Itoplectis conquisitor, exhibited little or no de novo glyceride synthesis but actively acylated endogenous mono- and diacylglycerides. It is suggested that this lack of de novo synthesis is related to the fact that the fatty acid composition of these parasitoid species closely resembles that of the hosts on which they are reared. Microsomes from three other species of parasitic Hymenoptera, Aphaereta pallipes, Brachymeria lasus, and Hyposoter exigua, whose fatty acid compositions are little influenced by the host species, exhibited active de novo glyceride synthesis as well as acylation of endogenous mono- and diacylglycerides. Radiotracer studies indicated that E. roborator microsomes and cytosol did not contain noncompetitive or uncompetitive inhibitors of glycerophosphate acyltransferase. E. roborator microsomes acylated exogenous phosphatidic acid but not dihydroxyacetone phosphate or glycerol. The maximum rate of glycerophosphate acylation was less than 0.1 nmole/min/mg microsomal protein after 15 min incubation. The incorporation was subject to rapid lipolysis on further incubation. The addition of bovine serum albumin (BSA) reduced the ability of E. roborator microsomes to acylate mono- and diacylglycerides with endogenous acyl groups. In the absence of BSA, palmitoyl-CoA was a more effective substrate than stearoyl-CoA for both mono- and diacylglyceride acyltransferases.     

Intra-specific diversity of the chemical composition of Ligularia lamarum in the Hengduan Mountains,China: The structures of four new eremophilanes and a new seco-eremophilane

Chemical compositions and internal transcribed spacer (ITS) sequences of five samples of Ligularia lamarum collected in Sichuan Province, China, were analyzed. Fourteen compounds, including four new eremophilanes and one new seco-eremophilane, were isolated and their structures were elucidated by spectroscopic methods. Intra-specific diversity in the chemical composition was found to be higher than previously known. The result of DNA analysis suggested that one of the samples was introgressed, although its chemical composition was typical of L. lamarum.     

Stable isotopic study of Oligocene-Miocene sediments from DSDP Site 354, Equatorial Atlantic

The oxygen- and carbon-isotope compositions of planktic and benthic foraminifera and calcareous nannofossils from Middle Oligocene-Early Miocene Equatorial Atlantic sediments (DSDP Site 354) indicate two important paleoceanographic changes, in the Late Oligocene (foraminiferal Zone P.21) and in the Early Miocene (foraminiferal Zone N.5). The first change, reflected by a δ¹⁸O increase of 1.45‰ inGlobigerina venezuelana, affected only intermediate pelagic and not surface, deep or bottom waters. The second change affected surface and intermediate waters, whereas deep and bottom waters showed only minor fluctuations. In the case of the former the isotope effect of the moderate ice accumulation on the Antarctic continent is amplified in the Equatorial Atlantic by changes in the circulation pattern. The latter paleoceanographic change, reflected by a significant increase in¹⁸O in both planktic and benthic forms (about 1.0‰ and 0.5‰, respectively), may have been caused by ice volume increase and temperature decrease. Both oxygen- and carbon-isotope compositions indicate a marked depth-habitat stratification for planktic foraminifera and calcareous nannofossils. Three different dwelling groups are recognized: shallowGlobigerinoides, Globoquadrina dehiscens, Globorotalia mayeri and nannofossils; intermediateGlobigerina venezuelana; and deepCatapsydrax dissimilis. The comparison of foraminifera and calcareous nannofossils suggests that the isotopic compositions of nannofossils are generally controlled by the same parameters which control the isotopic composition of shallow-dwelling foraminifera, but the former are more enriched in¹⁸O.     

Effect of sound and Lenzites-decayed wood on the amino acid composition of Reticulitermes flavipes

In hydrolysates of the eastern subterranean termite, Reticulitermes flavipes, the most abundant protein amino acids (μmoles) were glycine, alanine, and glutamic acid; the least abundant were methionine and histidine. Sawdust from both sound and Lenzites trabea-decayed sapwood blocks of sugar maple, loblolly pine, and slash pine was force-fed to termites. A diet of decayed rather than sound wood had little effect on protein amino acid composition of the termites; glycine content varied the most. In contrast, diet affected the free amino acid composition. Except for glutamic acid, the major protein amino acids of the termites were not the predominant free amino acids. Tyrosine and histidine were relatively more abundant as free than as protein amino acids. Greatest differences in protein amino acid compositions of sound and decayed wood were in contents of glycine, leucine, lysine, and arginine.     

Variation in protein intake induces variation in spider silk expression

Background

It is energetically expensive to synthesize certain amino acids. The proteins (spidroins) of spider major ampullate (MA) silk, MaSp1 and MaSp2, differ in amino acid composition. Glutamine and proline are prevalent in MaSp2 and are expensive to synthesize. Since most orb web spiders express high proline silk they might preferentially attain the amino acids needed for silk from food and shift toward expressing more MaSp1 in their MA silk when starved.

Methodology/Principal Findings

We fed three spiders; Argiope aetherea, Cyrtophora moluccensis and Leucauge blanda, high protein, low protein or no protein solutions. A. aetherea and L. blanda MA silks are high in proline, while C. moluccesnsis MA silks are low in proline. After 10 days of feeding we determined the amino acid compositions and mechanical properties of each species'' MA silk and compared them between species and treatments with pre-treatment samples, accounting for ancestry. We found that the proline and glutamine of A. aetherea and L. blanda silks were affected by protein intake; significantly decreasing under the low and no protein intake treatments. Glutmaine composition in C. moluccensis silk was likewise affected by protein intake. However, the composition of proline in their MA silk was not significantly affected by protein intake.

Conclusions

Our results suggest that protein limitation induces a shift toward different silk proteins with lower glutamine and/or proline content. Contradictions to the MaSp model lie in the findings that C. moluccensis MA silks did not experience a significant reduction in proline and A. aetherea did not experience a significant reduction in serine on low/no protein. The mechanical properties of the silks could not be explained by a MaSp1 expressional shift. Factors other than MaSp expression, such as the expression of spidroin-like orthologues, may impact on silk amino acid composition and spinning and glandular processes may impact mechanics.     

Prediction of protein structural class for low-similarity sequences using support vector machine and PSI-BLAST profile

Knowledge of structural class plays an important role in understanding protein folding patterns. In this study, a simple and powerful computational method, which combines support vector machine with PSI-BLAST profile, is proposed to predict protein structural class for low-similarity sequences. The evolution information encoding in the PSI-BLAST profiles is converted into a series of fixed-length feature vectors by extracting amino acid composition and dipeptide composition from the profiles. The resulting vectors are then fed to a support vector machine classifier for the prediction of protein structural class. To evaluate the performance of the proposed method, jackknife cross-validation tests are performed on two widely used benchmark datasets, 1189 (containing 1092 proteins) and 25PDB (containing 1673 proteins) with sequence similarity lower than 40% and 25%, respectively. The overall accuracies attain 70.7% and 72.9% for 1189 and 25PDB datasets, respectively. Comparison of our results with other methods shows that our method is very promising to predict protein structural class particularly for low-similarity datasets and may at least play an important complementary role to existing methods.     

P(700) Chlorophyll a-Protein : Purification, Characterization, and Antibody Preparation

The P₇₀₀ chlorophyll α-protein was purified by preparative sodium dodecyl sulfate (SDS) gel electrophoresis from SDS-solubilized barley (Hordeum vulgare L., cv Himalaya) chloroplast membranes. After elution from the gel in the presence of 0.05 to 0.1% Triton X-100, the recovered protein had a chlorophyll/P₇₀₀ ratio of 50 to 60/1 and contained no chlorophyll b or cytochromes. Analysis of the polypeptide composition of the chlorophyll-protein revealed a 58 to 62 kilodalton (kD) polypeptide component but no lower molecular weight polypeptides. The 58 to 62 kD component was further resolved into two distinct polypeptide bands which were subsequently mapped by partial cyanogen bromide digestion and Staphylococcus aureus proteolysis. Based on results from the mapping experiments and other data, we suggest that the two components are conformational variants of a single polypeptide. Measurement of the chlorophyll to protein ratio by quantitative amino acid analysis and consideration of the yield of P₇₀₀ in the protein isolate suggest that, contrary to previous models (Bengis and Nelson, 1975, 1977), P₇₀₀in vivo is associated with a minimum of four subunits of approximately 60 kD.

Antibodies raised against the photochemically active chlorophyll-protein complex from barley reacted specifically with the 58 to 62 kD apoprotein. The same preparative electrophoresis procedure was used to isolate photochemically active P₇₀₀ chlorophyll a-protein from soybean (Glycine max L.), tobacco (Nicotiana tobacum L.), petunia (Petunia × hybrida), tomato (Lycopersicum esculentum), and Chlamydomonas reinhardti. The isolated complex from all species exhibited identical polypeptide compositions and chlorophyll/P₇₀₀ ratios. Antibodies to the barley protein cross reacted with all species tested demonstrating the highly conserved structure of the apoprotein.

     

Characterization of cuticular proteins from the migratory locust,Locusta migratoria

Proteins were extracted from the still unhardened (teneral) cuticle of the migratory locust, Locusta migratoria. The proteins are soluble only at extreme pH-values and at low ionic strength, the solubility increases with decreasing temperature. The unhardened cuticle contains approx. 100 different proteins according to two-dimensional polyacrylamide gel electrophoresis. The majority of the proteins are very basic. The basicity and solubility properties of the proteins have necessitated development of modified electrophoretic procedures. The amino acid composition of the bulk protein shows that alanine, proline, glycine, valine and tyrosine constitute two thirds of the total amino acid content and that cysteine, methionine and tryptophan are absent.The proteins have been extracted from various parts of the cuticle and analysed by two-dimensional electrophoresis. Characteristic protein compositions were found for cuticle from the different body parts. Amino acid analyses of these extracts are strikingly similar. The only significant difference is in the glycine-alanine ratio. Cuticles that are destined to become hard are extremely rich in alanine, whereas the flexible parts of the cuticle are enriched in glycine. The results indicate that the proteins of locust cuticle constitute a group of structural proteins different from other known structural proteins.     

The proteinaceous components of the gum exudates from some phyllodinous Acacia species

Acacia gum exudates are proteinaceous polysaccharides; their protein content ranges from ca 0.2 to 45%.The data presented show that the amino acid compositions of the gums from 12 phyllodinous species (10 from Bentham's sub-series Uninerves racemosae, two from sub-series Juliflorae) also vary considerably, particularly in respect of their hydroxyproline content (55 residues per 1000 residues in A. aestivalis gum, 287 residues per 1000 in A. saliciformis gum). The proportions of some other amino acids, e.g. alanine, aspartic acid, proline and serine also vary considerably, but the proportions of others, e.g. cystine, methionine, histidine, threonine, tyrosine and valine, are remarkably constant. The amino acid composition of gums with a very low protein content (e.g. A. victoriae and A. mycrobotrya) is similar to that for a highly proteinaceous gum (A. tumida). There are, however, considerable differences between the amino acid compositions of the gums from A. saligna and A. pycnantha (South African and Western Australian specimens). This strengthens previous chemotaxonomic evidence, based on the polysaccharide parameters of their gums, that these two species are not as close taxonomically as was originally believed from morphological considerations.     

Comparison between the sclerotization of adult and larval cuticle in Schistocerca gregaria

Femur cuticle from fifth instar larvae of the desert locust, Schistocerca gregaria, has been characterized with respect to composition, rate of deposition, and rate of sclerotization. The results are compared with those from adult cuticle of the same species. The protein compositions of the two types of cuticle are very similar, but the rates of deposition of both protein and chitin are different. The main difference is, however, that sclerotization is restricted to the first day after ecdysis in larval cuticle, whereas in adult cuticle sclerotization continues for at least a couple of weeks. The result is that the endocuticle remains untanned in the larvae, whereas in the adults the whole cuticle becomes tanned.     

Comparative studies on S-adenosyl-l-methionine binding sites of protein N-methyltransferases,using 8-azido-S-adenosyl-l-methionine as photoaffinity probe

Employing a photoaffinity labeling procedure with 8-azido-S-adenosyl-l-[methyl-³H]methionine (8-N₃-Ado[methyl-³H]Met), the binding sites for S-adenosyl-l-methionine (AdoMet) of three protein N-methyltransferases [AdoMet:myelin basic protein-arginine N-methyltransferase (EC2.1.1.23); AdoMet:histone-arginin N-methyltransferase (EC2.1.1.23); and AdoMet:cytochromec-lysine N-methyltransferase (EC2.1.1.59)] have been investigated. The incorporation of the photoaffinity label into the enzymes upon UV irradiation was highly specific. In order to define the AdoMet binding sites, the photolabeled enzymes were sequentially digested with trypsin, chymotrypsin, and endoproteinase Glu-C. After each proteolytic digestion, radiolabeled peptide from each enzyme was resolved on HPLC first by gradient elution and further purified by an isocratic elution. Retention times of the purified radiolabeled peptides from the three enzymes from the corresponding proteolysis were significantly different, indicating that their sizes and compositions were different. Amino acid composition analysis of these peptides confirmed further that the AdoMet binding sites of these protein N-methyltransferases are quite different.     

Proteomic analysis of heart mitochondria from <Emphasis Type="Italic">Bos taurus:</Emphasis> I. Application of proteomic methods to identification of transmembrane domains of proteins of the internal mitochondrial membrane

This study is part of a large-scale investigation of the proteome of mitochondria from the heart muscle of Bos taurus. We developed a special approach to simplification of the protein mixture by separation of mitochondrial fractions with stable protein compositions. At the first stage of this approach, we isolated and purified internal mitochondrial membranes. The protein composition of this fraction was analyzed by the following proteomic methods: enzymatic or/and chemical cleavage of the proteins, chromatographic fractionation of the complex mixture of the resulting peptides, mass-spectrometric identification of these peptides, and a search for proteins in databases of amino acid sequences. We reliably identified 147 unique proteins with the use of the SwissProt database. The subcellular location and functions of these proteins were analyzed. Approaches to studies of transmembrane domains of integral membrane proteins of the internal mitochondrial membrane were proposed on the basis of proteomic methods of analysis. Considerable coincidence of the experimental data with the results of determination of the 3D structures of the proteins by X-ray analysis was shown.