On the cysteine and cystine content of proteins

Summary Analysis of published data on the cysteine and half-cystine content of proteins indicates that most intracellular proteins may be classified as sulfhydryl proteins (those containing cysteine but little or no half-cystine) and that such sulf-hydryl proteins have a low cysteine content. The mean cysteine content found for 32 intracellular mammalian proteins was 1.6 % and intracellular proteins of many bacteria have similar or lower values. Extracellular mammalian proteins are primarily disulfide proteins (those containing half-cystine but little or no cysteine) and have a high half-cystine content, the mean value found for some 34 extracellular mammalian proteins being 4.1 %. This is contrasted with many of the extracellular proteins from facultative bacteria which are cyst(e)ine-free proteins, being lacking in both cysteine and half-cystine. These and related observations are interpreted in terms of the evolution of life in a reducing atmosphere and the subsequent transition to an oxidizing environment. It is suggested that disulfide proteins evolved primarily after the accumulation of oxygen in the atmosphere.     

Influence of muscular activity on muscle proteins and sarcoplasmic reticulum content and binding of Ca2+

Training with an increase in intensity of loads causes muscle hypertrophy. The increase of myofibrillar proteins content and proteins of sarcoplasmic reticulum is greater after this training than after training with prolongation of duration of loads. The content of sarcoplasmic proteins is the same in the both kinds of training. The increase in the content of mitochondrial proteins is smaller. The myofibrillar and sarcoplasmic proteins content is the greatest with simultaneous increase in the intensity and duration of loads. Increase in the content of sarcoplasmic vesicles proteins in this case is the same as after training with an increase in the intensity of loads. An increase in the content of mitochondrial proteins is the same as in training with prolongation of duration of loads. The capacity of binding Ca2+ (per unit protein weight), Vmax and Km are not changed. When calculating per unit of muscle mass possibilities of Ca2+ binding under the effect of loads of the uncreasing intensity rise.     

Posttranslational deamidation of crystalline lens proteins during animal aging

The amide content of total proteins and protein fractions (alpha-, beta-, gamma-cristallins and albuminoid) from cortex and nuclear lens zones of cattle has been investigated. The amide content in proteins of cortex and nuclear lens of young animals (1,5-2 years old) is the same. The decrease of the amide content in the proteins of nuclear lenz zone of old animals (6-12 years old) is due to fraction of readily hydrolysed amides. The data obtained prove the posttranslational desamidation of lens proteins at ageing. beta-Cristallines--the proteins with the highest amides content is exposed to posttranslational desamidation most of all.     

Variation among species in proteomic sulphur content is related to environmental conditions

The elemental composition of proteins influences the quantities of different elements required by organisms. Here, we considered variation in the sulphur content of whole proteomes among 19 Archaea, 122 Eubacteria and 10 eukaryotes whose genomes have been fully sequenced. We found that different species vary greatly in the sulphur content of their proteins, and that average sulphur content of proteomes and genome base composition are related. Forces contributing to variation in proteomic sulphur content appear to operate quite uniformly across the proteins of different species. In particular, the sulphur content of orthologous proteins was frequently correlated with mean proteomic sulphur contents. Among prokaryotes, proteomic sulphur content tended to be greater in anaerobes, relative to non-anaerobes. Thermophiles tended to have lower proteomic sulphur content than non-thermophiles, consistent with the thermolability of cysteine and methionine residues. This work suggests that persistent environmental growth conditions can influence the evolution of elemental composition of whole proteomes in a manner that may have important implications for the amount of sulphur used by living organisms to build proteins. It extends previous studies that demonstrated links between transient changes in environmental conditions and the elemental composition of subsets of proteins expressed under these conditions.     

Proteins of normal hair and of cysteine-deficient hair from mentally retarded siblings

1. S-Carboxymethylkerateines extracted from normal hair can be fractionated into high-sulphur and low-sulphur proteins similar to those obtained from sheep's wool. Normal human hair gives a major high-sulphur protein of higher molecular weight and S-carboxymethylcysteine content than any isolated from normal sheep's wool. 2. The proteins from cystine-deficient hair can also be divided into high-sulphur and low-sulphur proteins. There is a lower proportion of high-sulphur protein in cystine-deficient hair than in normal hair. 3. The high-sulphur proteins from cystine-deficient hair have an abnormal amino acid composition and in particular are lower in S-carboxymethylcysteine content than the corresponding proteins from normal hair. New components are present and the content of very high-sulphur proteins of high molecular weight is much decreased. The low-sulphur proteins of cystine-deficient hair are probably also deficient in S-carboxymethylcysteine. 4. The proteins of cystine-deficient hair probably resemble those in the normal hair root, except that disulphide-bridge formation has occurred.     

The proteomics of sickle cell disease: profiling of erythrocyte membrane proteins by 2D-DIGE and tandem mass spectrometry

Quantitative changes in the red blood cell membrane proteome in sickle cell disease were analyzed using the two-dimensional fluorescence difference gel electrophoresis 2D-DIGE technique. From over 500 analyzed two-dimensional gel spots, we found 49 protein gel spots whose content in sickle cell membranes were changed by at least 2.5-fold as compared to control cells. In 38 cases we observed an increase and in 11 cases a decrease in content in the sickle cell membranes. The proteins of interest were identified by in-gel tryptic digestion followed by liquid chromatography in line with tandem mass spectrometry. From 38 analyzed gel spots, we identified 44 protein forms representing different modifications of 22 original protein sequences. The majority of the identified proteins fall into small groups of related proteins of the following five categories: actin accessory proteins--four proteins, components of lipid rafts--two proteins, scavengers of oxygen radicals--two proteins, protein repair participants--six proteins, and protein turnover components--three proteins. The number of proteins whose content in sickle RBC membrane is decreased is noticeably smaller, and most are either components of lipid rafts or actin accessory proteins. Elevated content of protein repair participants as well as oxygen radical scavengers may reflect the increased oxidative stress observed in sickle cells.     

How Prochlorococcus bacteria use nitrogen sparingly in their proteins

Organisms use proteins to perform an enormous range of functions that are essential for life. Proteins are usually composed of 20 different kinds of amino acids that each contain between one and four nitrogen atoms. In aggregate, the nitrogen atoms that are bound in proteins typically account for a substantial fraction of the nitrogen in a cell. Many organisms obtain the nitrogen that they use to make proteins from the environment, where its availability can vary greatly. These observations prompt the question: can environmental nitrogen scarcity lead to adaptive evolution in the nitrogen content of proteins? In this issue, Gilbert & Fagan (2011) address this question in the marine cyanobacteria Prochlorococcus, examining a variety of ways in which cells might be thrifty with nitrogen when making proteins. They show that different Prochlorococcus strains vary substantially in the average nitrogen content of their encoded proteins and relate this variation to nitrogen availability in different marine habitats and to genomic base composition (GC content). They also consider biases in the nitrogen content of different kinds of proteins. In most Prochlorococcus strains, a group of proteins that are commonly induced during nitrogen stress are poor in nitrogen relative to other proteins, probably reflecting selection for reduced nitrogen content. In contrast, ribosomal proteins are nitrogen rich relative to other Prochlorococcus proteins, and tend to be down‐regulated during nitrogen limitation. This suggests the possibility that decaying ribosomal proteins act as a source of nitrogen‐rich amino acids during periods of nitrogen stress. This work contributes to our understanding of how nutrient limitation might lead to adaptive variation in the composition of proteins and signals that marine microbes hold great promise for testing hypotheses about protein elemental costs in the future.     

Effects of salicylic acid on protein content and <Superscript>14</Superscript>C-amino acid incorporation into proteins of pea roots

Pea (Pisum sativum L.) root treatment with salicylic acid (SA) changed the content of some proteins and incorporation of ¹⁴C-amino acids into proteins. The analysis of changes in these indices allowed us to subdivide all proteins into the four groups: (1) most abundant SA-independent proteins; (2) SA-dependent proteins, which content and ¹⁴C-amino acids incorporation both increased; (3) SA-dependent proteins, which content and ¹⁴C-amino acids incorporation both decreased; and (4) SA-dependent proteins, which content was not essentially changed (referred earlier to SA-independent proteins) but ¹⁴C-amino acids incorporation into these proteins was strongly suppressed. It is very likely that proteolysis of the proteins referred to the fourth group is very low and even a strong inhibition of their synthesis (incorporation of ¹⁴C-amino acids) does not result in the substantial decrease in their contents. Some SA-dependent proteins were identified by means of modern methods of proteomics: phosphoglyceromutase, S-adenosylmethionine synthase 3, enolase, chalcone isomerase, nucleoside diphosphate kinase 1, and tioredoxin h.     

Kinetics of metallo-enzymatic paramagnetic centers and free radicals in the rat liver in lung carcinogenesis

Kinetics of the content of nonheme iron-sulphur-containing (iron-sulphur) proteins, free radicals of electron-transport mitochondrial system, as well as of microsome terminal oxidase cytochrome P-450 is studied in the liver of rats at early stages of carcinogenesis and in the process of tumour growth induced by intratracheal administration of various benz(a)pyrene doses. It is found that the content of iron-sulphur proteins increases after the first administration, then it falls against a background of higher concentration of free radicals. A degree of pronounced changes in the content of the studied iron-sulphur proteins correlates with carcinogen dose. The cytochrome P-450 content is lowered for almost the whole period of carcinogen administration. In later periods animals with morphologically determinable pretumour changes exhibit a much higher content of iron-sulphur proteins, somewhat increased concentration of free radicals and a tendency to an increased level of cytochrome P-450. The appearance and growth of malignant tumours is followed by a considerable decrease in the content of iron-sulphur proteins and cytochrome P-450. On the basis of the results obtained it is supposed that the changes in the content of iron-sulphur proteins in the rat liver is the earliest and most pronounced reaction which depends on the benz(a)pyrene dose and may be of prognostic significance.     

贝壳的有机质及生物矿化机制分析

以腹足纲贝壳香螺壳为研究对象,用弱酸去钙法进行蛋白提取,采用280纳米(A280)光吸收法测定蛋白含量,并通过聚丙烯酰胺(SDS-PAGE)凝胶电泳法对蛋白按照分子量大小的区别进行分离.实验结果表明香螺壳中蛋白含量和种类较少,其文石层比方解石层蛋白含量高的多,总量分别为0.89%和0.0533%;文石层分离出五种分子量的可溶性蛋白和四种分子量的不可溶性蛋白;而方解石层中分离出三种分子量的可溶性蛋白和三种分子量的不可溶性蛋白,且分子量不相同.正是这少量的蛋白质对贝壳的生物矿化过程和不同晶型的形成起着决定性作用.     

Differential Expression of Specific Proteins during In Vitro Tomato Organogenesis1

The cotyledons of tomato (Lycopersicon esculentum L., cv. Jia Fen-10) seedlings were induced to produce calli and regenerate plants via organogenesis. Utilizing this system, the composition and content of stage-specific proteins associated with organogenesis were analyzed. Moreover, a comparison of the protein composition and content between embryogenic and nonembryogenic calli was conducted. The SDS-PAGE results and laser densitometric scanning maps showed that there were different specific proteins expressed at different stages. Among them, six proteins (61, 54, 38, 37, 35, and 23 kD) were associated with the morphogenesis of organs, and two proteins (39 and 24 kD) were related to the morphogenesis of calli. Although no distinctive difference in protein components of embryogenic calli was noted, there were different trends of changes, both for the content of the proteins 39 and 24 kD, and for the content of the total proteins, at different developmental stages of embryogenic calli. The results obtained from the embryogenic and nonembryogenic calli indicated that these two materials were distinct in the protein components as well as in its content; for example, the protein 54 kD was detected in nonembryogenic but not in embryogenic calli. The total protein content in nonembryogenic calli was lower than that in the embryogenic calli.     

Calcium binding capacity and calcium sensitive protein content in denervated frog muscles

Total and ionic calcium content, calcium binding capacity of sarcoplasmic proteins and calcium insensitive proteins were examined in atrophying leg muscles of frog after 1-5 months period of denervation. Different muscles showed different levels of atrophy and the total calcium content varied with reference to the type of muscle. Ionic calcium levels doubled in the gastrocnemius muscle after three months denervation. Calcium binding capacity of proteins and calcium insensitive proteins decreased rapidly up to four months after denervation in the gastrocnemius muscle. However no significant changes in the levels of calcium binding capacity and calcium insensitive proteins were found with reference to the type of muscle. Since total calcium content remains constant and wet muscle mass (expressed as atrophy) decreased markedly, an apparent increase in calcium concentration occurs in each muscle on denervation.     

Changes in nucleus, nucleolus and cell size accompanying somatic embryogenesis of Theobroma cacao L. II. Relation between basic protein content and size of nucleus, nucleolus and cell

Embryo formation from callus of Theobroma cacao L. was associated with the changes in relationship between nuclear, nucleolar and cell sizes and the content of basic proteins (FG-FCF-stained). Together with the increase in nuclear size of callus and proembryo cells the increase in the amount of nuclear basic proteins was found. In the callus cells the increase in nucleolar protein content exceeded that in nucleolus size, which led to the rise in basic protein concentration in the nucleolus. However, in the early stage of embryogenesis the increase in protein content was not so marked as that in callus, which indicated that embryogenesis involved a decrease in concentration of nucleolar basic proteins. Differences between callus and proembryo cells were also observed in the concentration of cytoplasmic proteins. The increase in size of callus cells was the same as the increasing amount of cytoplasmic proteins. In proembryos a significant increase in cell size was accompanied by only slight changes in cytoplasmic proteins. The stimulation of embryogenesis by 2,4-D resulted in an increase of nuclear concentration of basic proteins in proembryos. The intensification of embryogenesis involved the decrease of the concentration of nucleolar proteins together with the increase in concentration of basic cytoplasmic proteins.     

Effect of sex and size on the protein composition in the tissues of the freshwater crab,Paratelphusa (Barytelphusa) guerini Milne Edwards

Soluble (enzymic) and insoluble (structural) proteins were estimated quantitatively in different tissues of the crab as a function of sex and size. The different protein fractions in the tissues of females decreased with weight. But the proteins in the tissues of males increased gradually with size up to 30–40 g and decreased later. In both sexes, the relative increase and decrease varied in different tissues.The insoluble protein content of the muscle was always greater than the soluble content in both sexes. However, the two fractions in other tissues showed different trends depending upon the sex. The soluble content was always greater than the insoluble content in gill, heart and hepatopancreas of males. The hepatopancreas of females had a higher soluble content at all weights, as in males. But the insoluble proteins of the gill and soluble proteins of the heart were more in smaller animals (below 25–30 g) and less in larger animals (above 25–30 g).The soluble proteins dominated in the males. This relation was maintained in the muscle throughout the weight range studed (10 to 75 g), while in other tissues this relation was seen for the the greater part of this weight range. The insoluble proteins in the different tissues tended to be more in smaller females (up to 25–30 g) and larger males (above 25–30 g).The total protein content of the muscle was always larger in males. The proteins of the gill and heart were larger in males at higher sizes (above 20–25 g). Hepatopancreatic proteins were larger only at the intermediate-sized males (between 25 and 60 g).     

Plant cell wall glycoproteins and their genes

At least two main groups of glycoproteins can be distinguished in plant cell walls: extensins which are insoluble cell wall proteins; and soluble arabinogalactan proteins (AGPs) which have a high carbohydrate content such that protein content constitutes in some cases only 5 % of the glycoprotein weight. These two groups of proteins together with other cell wall proteins more or less glycosylated, such as proline-rich proteins (PRPs), hybrid PRP (HyPRPs) and expansins, are reviewed and compared with similar proteins present in other cell compartments. Different patterns of N- or O-glycosylation are analysed. In some cases, these cell wall proteins or proteins related to them present patterns of glycosylation that act as epitopes recognizable by IgE in allergic responses.     

Not all secretory granules are created equal: Partitioning of soluble content proteins

Secretory granules carrying fluorescent cargo proteins are widely used to study granule biogenesis, maturation, and regulated exocytosis. We fused the soluble secretory protein peptidylglycine alpha-hydroxylating monooxygenase (PHM) to green fluorescent protein (GFP) to study granule formation. When expressed in AtT-20 or GH3 cells, the PHM-GFP fusion protein partitioned from endogenous hormone (adrenocorticotropic hormone, growth hormone) into separate secretory granule pools. Both exogenous and endogenous granule proteins were stored and released in response to secretagogue. Importantly, we found that segregation of content proteins is not an artifact of overexpression nor peculiar to GFP-tagged proteins. Neither luminal acidification nor cholesterol-rich membrane microdomains play essential roles in soluble content protein segregation. Our data suggest that intrinsic biophysical properties of cargo proteins govern their differential sorting, with segregation occurring during the process of granule maturation. Proteins that can self-aggregate are likely to partition into separate granules, which can accommodate only a few thousand copies of any content protein; proteins that lack tertiary structure are more likely to distribute homogeneously into secretory granules. Therefore, a simple "self-aggregation default" theory may explain the little acknowledged, but commonly observed, tendency for both naturally occurring and exogenous content proteins to segregate from each other into distinct secretory granules.     

Is there evidence of optimisation for carbon efficiency in plant proteomes?

Flowering plants, angiosperms, can be divided into two major clades, monocots and dicots, and while differences in amino acid composition in different species from the two clades have been reported, a systematic analysis of amino acid content and distribution remains outstanding. Here, we show that monocot and dicot proteins have developed distinct amino acid content. In Arabidopsis thaliana and poplar, as in the ancestral moss Physcomitrella patens, the average mass per amino acid appears to be independent of protein length, while in the monocots rice, maize and sorghum, shorter proteins tend to be made of lighter amino acids. An examination of the elemental content of these proteomes reveals that the difference between monocot and dicot proteins can be largely attributed to their different carbon signatures. In monocots, the shorter proteins, which comprise the majority of all proteins, are made of amino acids with less carbon, while the nitrogen content is unchanged in both monocots and dicots. We hypothesise that this signature could be the result of carbon use and energy optimisation in fast-growing annual Poaceae (grasses).     

Changes in the content of different nuclear proteins and DNA from diploid and polyploid hepatocytes in regenerating liver of mice]

The content of 4 fractions of nuclear proteins (histones, acid chromatin protein, globulins and chromatin-free acid protein) in diploid and polyploid hepatocytes from intact and regenerating liver of mice is studied. These types of nuclei are found to differ in the protein content and in the protein/DNA ratio. Synthesis of all classes of nuclear proteins was intensified at the G1-stage, and synthesis of DNP non-histone proteins at the end of S- and G2-stage. Possible role of different nuclear proteins in the regulation of cell multiplication is discussed.     

Fishing new proteins in the twilight zone of genomes: the test case of outer membrane proteins in Escherichia coli K12, Escherichia coli O157:H7, and other Gram-negative bacteria

We address the problem of clustering the whole protein content of genomes into three different categories-globular, all-alpha, and all-beta membrane proteins-with the aim of fishing new membrane proteins in the pool of nonannotated proteins (twilight zone). The focus is then mainly on outer membrane proteins. This is performed by using an integrated suite of programs (Hunter) specifically developed for predicting the occurrence of signal peptides in proteins of Gram-negative bacteria and the topography of all-alpha and all-beta membrane proteins. Hunter is tested on the well and partially annotated proteins (2160 and 760, respectively) of Escherichia coli K 12 scoring as high as 95.6% in the correct assignment of each chain to the category. Of the remaining 1253 nonannotated sequences, 1099 are predicted globular, 136 are all-alpha, and 18 are all-beta membrane proteins. In Escherichia coli 0157:H7 we filtered 1901 nonannotated proteins. Our analysis classifies 1564 globular chains, 327 inner membrane proteins, and 10 outer membrane proteins. With Hunter, new membrane proteins are added to the list of putative membrane proteins of Gram-negative bacteria. The content of outer membrane proteins per genome (nine are analyzed) ranges from 1.5% to 2.4%, and it is one order of magnitude lower than that of inner membrane proteins. The finding is particularly relevant when it is considered that this is the first large-scale analysis based on validated tools that can predict the content of outer membrane proteins in a genome and can allow cross-comparison of the same protein type between different species.