Receptor-mediated endocytosis of aldehyde-modified proteins by sinusoidal liver cells

Formaldehyde-treated serum albumin (f-Alb) is known to be endocytosed by sinusoidal lever cells via a receptor-mediated mechanism. The receptor purified from rat livers exhibited a molecular weight of 125,000, consisting of two glycoprotein components with molecular weights of 53,000 and 30,000, respectively. Experiments using antireceptor antibody demonstrated that the f-Alb receptor is distinct from the receptor that mediates endocytotic uptake of acetylated low-density lipoprotein, but they share a common property of being inhibited by several polyanions, suggesting that polyanion-sensitivity might play an important role in the scavenger function of simusoidal liver cells. Studies on the ligand specificity of this receptor revealed that a covalent modification by formaldehyde of a limited number of lysine residues in albumin has led to the formation of a receptor-recognition domain(s). Furthermore, in addition to formaldehyde, the ligand activity was also generated with albumin modified by other aliphatic aldehydes, such as glycoaldehyde and glyceraldehyde. This phenomenon was extended to several proteins other than albumin. These data suggest therefore that the f-Alb receptor originally described as being specific for albumin modified by formaldehyde may play a general role as a scavenger receptor for aldehyde-modified proteins.This article was presented during the proceedings of the International Conference on Macromolecular Structure and Function, held at the National Defence Medical College, Tokorozawa, Japan, December 1985.     

Analysis of nitrated proteins by nitrotyrosine-specific affinity probes and mass spectrometry

Tyrosine nitration is a well-established protein modification that occurs in disease states associated with oxidative stress and increased nitric oxide synthase activity. Nitration of specific tyrosine residues has been reported to affect protein structure and function, suggesting that 3-nitrotyrosine formation may not only be a disease marker but may also be involved in the pathogenesis of some diseases and in normal regulatory processes. It has been, however, difficult to identify sites of nitration. We describe a method that combines specific isolation of nitrated proteins with mass spectrometric determination of the amino acid sequence and the site of nitration of individual proteins. A complex protein mixture, e.g., serum or cell lysate, was enriched for nitrotyrosine-containing proteins by immunoprecipitation with antinitrotyrosine antibodies. The nitrotyrosines were then reduced to aminotyrosines with a strong reducing agent in parallel in-gel and in-solution procedures. Using nitrated human serum albumin as a model, we reduced the disulfide bonds with dithiothreitol and alkylated the free sulfhydryl groups with iodoacetamide. The nitrotyrosines were next reduced to aminotyrosines with sodium dithionite, and-at pH 5.0-cleavable biotin tags were selectively attached to the aminotyrosines and the albumin was then digested with trypsin. The biotinylated tryptic peptides were purified on a streptavidin affinity column and identified by mass spectrometry. We have also purified nitrated human serum albumin from an enriched sample of SJL mouse plasma and confirmed its identity by peptide mass fingerprinting and MASCOT.     

Uptake and secretion of host proteins by Taenia crassiceps metacestodes

Although the presence of intact host proteins in the cyst fluid of cyclophyllidean metacestodes has been well documented, the underlying reason for protein uptake is poorly understood. To investigate this discrepancy, both the cyst fluid (CF) and excreted/secreted (E/S) proteins were collected in vitro from Taenia crassiceps metacestodes 16 wk postinfection in Balb/cJ female mice. The CF and E/S were subsequently immunoblotted using rabbit anti-mouse whole serum antibodies as a probe. The results show that whole host proteins were not only internalized by metacestodes but also secreted as well. The predominant secreted host protein was 66 kDa and was confirmed to be mouse serum albumin. The amount of secreted albumin decreased daily, whereas the concentration of albumin in the cyst fluid remained consistent. This suggests that the secretion of albumin is a coordinated function rather than a random event. It is probable that albumin cycling may be an evolved mechanism providing multiple benefits for the larvae, including osmoregulation and protection from innate immune responses.     

Kinetics of amine modification of proteins

A simple kinetic model for coupling small molecules such as biotin to proteins with amine-reactive reagents such as N-hydroxysuccinimide esters is developed. It predicts the reagent concentration required to modify a protein at a given concentration to a specified number of modified amines per molecule. By optimizing the model's three adjustable kinetic parameters, its predictions can be brought into close agreement with empirical data for modification of IgG, serum albumin, and other proteins over a wide range of protein and reagent concentrations. Data for modification of one protein can be used to approximate the results for modification of another protein with the same reagent under the same reaction conditions.     

Albumin-like proteins from the pituitary glands of Dahl salt-resistant rats.

Dahl selectively bred rats for susceptibility (S strain) or resistance (R strain) to the hypertensive effect of high salt (NaCl) diet. Pituitary glands of R rats accumulate large amounts of four unique proteins not seen in S rats. These proteins were called R1, R2, R3, and R4 in order of decreasing electrophoretic mobility. Albumin, R4, R2, and R1 all bound to an affinity column for albumin (Cibacron blue 3G-A dye coupled to agarose) and were eluted in that order by a KSCN gradient. It was shown by crossed immunoelectrophoresis that R1 and R2 cross-react with plasma albumin. Peptide maps or tryptic digest of R1 and albumin showed that the majority of peptides generated were identical. It was not possible to incorporate labeled amino acid into albumin or the albumin-like R proteins with pituitary incubates, indicating that albumin-like proteins were not synthesized de novo by pituitary glands. R rat pituitary glands showed much greater protease (arginine esterase) activity than did S. This suggests that R proteins are formed locally in the pituitary gland of R proteins are formed locally in the pituitary gland of R rats by cleavabe of specific peptide bonds in albumin. The function of these endogenous albumin fragments is unknown, but albumin fragments produced in vitro by other investigators are known to potentiate bradykinin, a hypotensive peptide.     

On-gel fluorescent visualization and the site identification of S-nitrosylated proteins

Mounting evidence indicates that S-nitrosylation of critical cysteine residues in a protein represents a common feature of protein function regulation and cell signaling. However, the progress in studying the exact role of S-nitrosylation has been hampered by a lack of rapid and accurate methods for the detection of these S-nitrosylated proteins and the exact modification sites. In this article, we report a fluorescence-based method in which the S-nitrosylated cysteines are converted into 7-amino-4-methylcoumarin-3-acetic acid (AMCA) fluorophore-labeled cysteines—termed the AMCA switch method. The labeled proteins are then analyzed by nonreducing SDS-PAGE, and the S-nitrosylated proteins can be readily detected as brilliant blue bands after the activation of ultraviolet light. Furthermore, the sites of modification can be determined by liquid chromatography-tandem mass spectrometry (LC-MS/MS) after in-gel tryptic digestion of the fluorescent band, and the recognizable AMCA tag in the MS spectra ensures the accurate site identification of the nitrosocysteines. Therefore, our method offers some apparent advantages by direct visualization of on-gel image of S-nitrosylated proteins, shorter experiment time by skipping the anti-biotin immunoblotting step, and elimination of the potential interference of endogenous biotinylated proteins. Based on this method, we detected the S-nitrosylation and the modified site in bovine serum albumin and gankyrin after in vitro S-nitrosylation. Overall, our results indicate that the AMCA switch method is a fast and accurate method to identify the S-nitrosylated protein and the modification sites.     

Dynamisches Epigenom als Vermittler zwischen Umwelt und Genom

The epigenome serves as an interface between the dynamic environment and the inherited static genome. It is comprised of chromatin and a covalent modification of DNA by methylation. The epigenome is sculpted during development to shape the diversity of gene expression programs in the organism’s different cell types by a highly organized process. Epigenetic aberrations have consequences similar to those of genetic polymorphisms, resulting in variations in gene function. Recent data suggest that the epigenome is dynamic and is therefore responsive to environmental signals, not only during the critical periods in development but also later in life. It is postulated here that not only chemicals but also exposure to social behavior, such as maternal care, may affect the epigenome. It is proposed that exposure to different environmental agents could lead to interindividual phenotypic diversity as well as to varying susceptibility to disease and behavioral pathologies. Interindividual differences in the epige­netic state could also affect susceptibility to xenobiotics.     

Kinetic analysis of glycation as a tool for assessing the half-life of proteins

Glycation of proteins, a common postribosomal modification, proceeds via Amadori rearrangement to yield a stable ketoamine linkage of glucose with the protein. Kinetic analysis of the reaction shows that the amount of glycation at steady state is proportional to the glucose concentration, to protein half-life and to the rate of glycation. Thus, when the rate of glycation is determined in vitro and the extent of glycation of a given protein isolated from euglycemic subjects is measured, the half-life may be calculated. As the in vivo situation may not be simulated accurately in vitro, the calculated values may be considered as approximation. When the calculated values were compared with values reported in the literature fairly good agreement was found except for hemoglobin. Studies on stability of glycated albumin show that ketoamine decreases by about 20% when incubated under physiological conditions for 20 days. The method described by us is especially valuable when turnover of proteins in normal and pathophysiological states are compared. The half-life of plasma low-density lipoprotein is longer in patients with hypothyroidism or a high plasma low-density lipoprotein level than in normal subjects. Extending our studies to tissue proteins we did not find a significant increase in half-life of tendon collagen with age. Basement membrane collagen turnover is faster in diabetic patients in bad metabolic control. Thus, the procedure using fructosylamine as endogenous label of protein offers a method of great potential to study the turnover of human body proteins.     

Detection of oxidized methionine in selected proteins, cellular extracts and blood serums by novel anti-methionine sulfoxide antibodies

Methionine sulfoxide (MetO) is a common posttranslational modification to proteins occurring in vivo. These modifications are prevalent when reactive oxygen species levels are increased. To enable the detection of MetO in pure and extracted proteins from various sources, we have developed novel antibodies that can recognize MetO-proteins. These antibodies are polyclonal antibodies raised against an oxidized methionine-rich zein protein (MetO-DZS18) that are shown to recognize methionine oxidation in pure proteins and mouse and yeast extracts. Furthermore, mouse serum albumin and immunoglobulin (IgG) were shown to accumulate MetO as function of age especially in serums of methionine sulfoxide reductase A knockout mice. Interestingly, high levels of methionine-oxidized IgG in serums of subjects diagnosed with Alzheimer’s disease were detected by western blot analysis using these antibodies. It is suggested that anti-MetO-DZS18 antibodies can be applied in the identification of proteins that undergo methionine oxidation under oxidative stress, aging, or disease state conditions.     

Isoprenoid modification of proteins distinct from membrane acyl proteins in the prokaryote Acholeplasma laidlawii.

Isoprenylation is an important posttranslational modification that affects the activity, subunit interactions and membrane anchoring of different eukaryotic proteins. The small, cell-wall-less prokaryote Acholeplasma laidlawii has more than 20 membrane acyl-proteins enriched in myristoyl and palmitoyl chains. Radioactive mevalonate, a precursor to isoprenoids, was incorporated into several specific membrane proteins of 20 to 45 kDa and two soluble proteins of 23-25 kDa, respectively. No acyl proteins and none of the polar acyl lipids became labelled but these are all labelled by radioactive fatty acids. Mevalonate was incorporated mainly into a minor neutral, non-saponifiable lipid which migrated just above a C30-isoprenoid (squalene) on TLC-plates. The isoprenoid chains could not be released by mild alkaline hydrolysis from most of the isoprenylated proteins, although this procedure releases acyl chains from lipids and all acylated proteins. Isoprenylated proteins were enriched in the detergent phase upon partition with the non-ionic detergent Triton X-114. This behaviour is similar to the acyl proteins of this organism and indicates that the isoprenoid chains give the proteins a hydrophobic character.     

Tyrosine specific sequential labeling of proteins

We report (a) on the synthesis of a long-wavelength fluorescent coumarin containing an allyloxy acetate moiety, (b) the synthesis of two linkers containing an allyloxy acetate and an alkyne or azide function, respectively, and (c) the selective modification human serum albumin by a sequential method involving Pd(II) catalyzed modification of the phenolic side chain of tyrosine residues with an alkyne bearing linker and a subsequent azide–alkyne click reaction with an azide functionalized long-wavelength emitting coumarin dye. The method is likely to be applicable to various kinds of azido-modified fluorophores, and the Pd(II)-catalyzed modification of the tyrosines may also be used to introduce other kinds of tags. With these reagents, tyrosine specific modulation of proteins and peptides becomes possible either directly or in a sequential manner.     

Post-synthetic modification of proteins

Process of postsynthetic modifications of proteins in norm are considered. Two basic groups of modification processes are singled out: 1) processes which promote appearance of derivatives for 20 basic amino acids, i.e. change in the primary structure; 2) processes which are not associated with appearance of new amino acids but are responsible mainly for the changes in the polypeptide chain conformation and size. Modification processes of amino acid variations by means of methylation, acetylation, acylation, phosphorylation, ADP-ribosylation, glycosylation, amidation, hydroxylation and metal addition are described as referred to the first group. Proteolysis reactions are characterized in detail. Their significance for formation of biologically active peptides is considered. A notion "one gene--one protein" is thought to be incompetent because formation of a number of proteins necessitates participation of tens and hundreds of genes, coding enzymes of postsynthetic modification.     

Association of fibronectin with carboxy-group-modified proteins in vitro

Treatment of human immunoglobulin G, albumin and fibronectin with water-soluble carbodi-imide at pH4.75 in the presence of glycine ethyl ester resulted in an avid binding of ¹²⁵I-labelled native fibrinectin to the modified proteins. Succinoylation, reduction and alkylation or heat-denaturation had no such effect. In affinity chromatography under physiological conditions, serum was depleted of fibronectin when run through columns of the carbodi-imide-treated proteins coupled to agarose. Fractions eluted from such columns with urea were enriched in fibronectin. The binding of radiolabelled fibronectin to the carbodi-imide-treated proteins was inhibited by unlabelled fibronectin in relatively low concentrations, but also by albumin in higher concentrations. Heat-denatured albumin inhibited at concentrations approx. 10–30 times lower than native albumin. The binding reaction had a pH optimum of 6–8. It was inhibited at high ionic strength and in the presence of urea. Anionic detergents inhibited at millimolar concentrations, but non-ionic detergents did not inhibit the binding reaction. The results were interpreted as showing that: (1) fibronectin is capable of binding to itself, to immunoglobulin G and to albumin after a reduction of the negative surface charge of these proteins, and may have a general ability to bind such modified proteins; (2) this binding can take place under physiological conditions; (3) carboxy-group-modified proteins selectively bind fibronectin from serum. This novel binding phenomenon could be important in terms of the opsonin function of circulatory fibronectin. We propose that fibronectin may recognize modified (denatured) proteins and mediate their uptake by the reticuloendothelial system.     

Specific reduction of carboxyl groups in peptides and proteins by diborane

1. The reaction of several peptides and proteins with diborane was studied under different conditions to determine those most suitable for the specific reduction of carboxyl groups. 2. In the reaction of model peptides and the cyclic peptides bacitracin and tyrocidin, reduction at 0 degrees was entirely specific for the carboxyl groups without affecting the peptide bonds. Acid amide residues were not reduced. Some tripeptides showed anomalous results in that the C-terminal residue was quite resistant to reduction. 3. Specific reduction of carboxyl groups was achieved in each of the following proteins: human serum albumin, egg albumin, adult human haemoglobin, sperm-whale apomyoglobin, horse heart cytochrome c and egg-white lysozyme. The C-terminal amino acid was usually reduced. 4. Conditions for specific reduction of all available carboxyl groups are not easily found and may vary from one substance to another. Specific reduction of a limited number of available carboxyl groups may be generally accomplished by reactions at -10 degrees . 5. It is suggested that this chemical modification, which has the advantage of permanence, may be useful in studying the role of carboxyl groups in the conformation of proteins and in the biological properties of peptides and proteins.     

植物同源结构域指蛋白在拟南芥等十字花科植物春化作用途径中的功能

春化低温处理可以使拟南芥等十字花科植物提前开花,该过程中涉及到一个重要的植物同源结构域指(PHD-finger)蛋白VERNALIZATION INSENSITIVE3(VIN3)。PHD-finger结构域是真核生物中一种进化保守的锌指结构域,通常参与蛋白质之间的相互作用,特别是对核小体组蛋白进行甲基化、乙酰化、磷酸化等修饰。在春化处理过程中,VIN3及其同源基因编码的蛋白都具有PHD-finger结构域,该结构域通过对开花抑制基因FLOWERING LOCUS C染色质组蛋白进行H3K9、H3K27甲基化、H3K9和H3K14去乙酰化等修饰,调节FLC染色质结构状态,使其从松弛状态转变为高度凝缩状态而关闭其功能,从而影响FLC转录活性进而促进开花。以下综述了拟南芥等十字花科植物春化作用途径中PHD-finger蛋白的功能,并且概述了春化作用机制。     

Arginine methylation of RNA-binding proteins regulates cell function and differentiation

Arginine methylation is a post-translational modification that regulates protein function. RNA-binding proteins are an important class of cell-function mediators, some of which are methylated on arginine. Early studies of RNA-binding proteins and arginine methylation are briefly introduced, and the enzymes that mediate this post-translational modification are described. We review the most common RNA-binding domains and briefly discuss how they associate with RNAs. We address the following groups of RNA-binding proteins: hnRNP, Sm, Piwi, Vasa, FMRP, and HuD. hnRNPs were the first RNA-binding proteins found to be methylated on arginine. The Sm proteins function in RNA processing and germ cell specification. The Piwi proteins are largely germ cell specific and are also required for germ cell production, as is Vasa. FMRP participates in germ cell formation in Drosophila, but is more widely known for its neuronal function. Similarly, HuD plays a role in nervous system development and function. We review the effects of arginine methylation on the function of each protein, then conclude by addressing remaining questions and future directions of arginine methylation as an important and emerging area of regulation.     

Electrodecantation of serum proteins.

The sedimentation of albumin under the action of the electric and gravitational fields was determined as a function of time in discontinuous experiments in a rectangular cell, using serum with the albumin fraction stained blue. It was shown that even under the influence of strong electric fields, the upper boundary of the albumin layer fell no further than the mid-point of the cell. In continuous single-stage separation of gamma-globulin from other serum proteins, only about half the gamma-globulins can be obtained from the solution because it remains homogeneously distributed throughout the solution and is only free from albumin and other proteins in the upper half of the cell. In experiments with continuously operated triangular cells, the process was optimized to give gamma-globulin of 97.5% purity in a yield of 80%, at serum flow-through rates of up to 0.5 l/h in a block composed of 40 cells.     

Patterns of proteins synthesized during development of Caenorhabditis elegans.

Two-dimensional gel electrophoresis has been used to analyze proteins synthesized during postembryonic development of the nematode Caenorhabditis elegans. This organism is favorable for these studies because it has a limited number of cells, it is genetically well-defined, and its development is currently under investigation in several laboratories. ³⁵S-Labeled E. coli was used for continuous and pulse labeling of C. elegans during its four juvenile larval stages and as a gravid adult. After continuous labeling or pulse labeling for 1 hr, 600–800 individual spots can be resolved on a 2D gel using fluorography and 2 weeks of exposure. Proteins that represent 0.0017% of the total sample can be detected. Exposure for 12 weeks reveals only 100 additional spots even though the films are not saturated. It therefore appears that the frequency distribution of proteins decreases significantly beyond these 800 most abundant proteins that can be fractionated on an O'Farrell gel. When the patterns of pulse-labeled proteins of the five developmental stages were compared, 113 proteins could be seen to undergo modulation at one or more of the developmental stages. A maximum number of changes was seen in the transition from the L4 to the adult stages when 11% of the total spots either appeared, disappeared, or changed in intensity. As controls, different preparations of the same developmental stage were compared and revealed considerable fluctuation, 2.6–4.8%. These fluctuations are presumed to be due to variations in growth conditions during culture of the organism. Continuous label experiments reveal a distinct set of proteins that undergo turnover and/or modification during development. Some of these proteins are absent in only one stage, indicating that stable proteins are also modulated. But nearly all of the proteins seen in a continuous label are also seen in a pulse label indicating that most of the major proteins are always present and always synthesized.     

Subcellular location prediction of apoptosis proteins

Apoptosis proteins have a central role in the development and homeostasis of an organism. These proteins are very important for understanding the mechanism of programmed cell death. Many efforts in pharmaceutical research have been aimed at understanding their structure and function. Unfortunately, thus far, very few apoptosis protein structures have been determined. In contrast, many apoptosis protein sequences are known, and many more are expected to come in the near future. Because of the extremely unbalanced state, it would be worthwhile to develop a fast sequence-based method to identify their subcellular location so as to gain some insight about their biological function. In view of this, a study was initiated in an attempt to identify the subcellular location of apoptosis proteins according to their sequences by means of the covariant discriminant function, which was established based on the Mahalanobis distance and Chou's invariance theorem (Chou, Proteins 1995;21:319-344). The results were quite promising, indicating that the subcellular location of apoptosis proteins are predictable to a considerably accurate extent if a good training data set can be established. It is expected that, with a continuous improvement of the training data set by incorporating more and more new data, the current method might eventually become a useful tool in this area because the function of an apoptosis protein is closely related to its subcellular location.     

Fluorescent labeling of cysteinyl residues to facilitate electrophoretic isolation of proteins suitable for amino-terminal sequence analysis

A protein labeling procedure which enables detection of subpicomole quantities of proteins on sodium dodecyl sulfate (SDS)-polyacrylamide gels is described. Proteins are rendered fluorescent by reduction of disulfide bonds with dithiothreitol followed by alkylation with 5-N-[(iodoacetamidoethyl)amino]naphthalene-1-sulfonic acid (5-I-AEDANS) or 5-iodoacetamido-fluorescein. Labeling is performed prior to electrophoresis, thus eliminating the need for staining with dyes and destaining after electrophoresis. As little as 375 fmol (25 ng) of prelabeled bovine serum albumin can be readily visualized after electrophoresis. Bands are still visible after electrophoretic transfer to nitrocellulose. Simultaneous labeling of proteins in complex mixtures is possible using this technique. This includes cysteine containing proteins of disrupted Newcastle disease virus. The magnitudes of the molecular weight increases which occur upon labeling reflect the cysteine contents of proteins. The mode of chemical modification for the prelabeling procedure was chosen because of its compatibility with analytical techniques, such as amino acid analysis, peptide mapping, or sequence analysis, which may be applied to the protein after electroelution from SDS-acrylamide gels. It replaces the need for reduction and carboxymethylation prior to these analytical procedures. Protein-sequence analysis of prelabeled bovine serum albumin, including samples electroeluted from SDS-acrylamide gels, has justified the choice of this method to facilitate isolation of proteins for sequence analysis. Equivalent sequence data were obtained with reduced bovine serum albumin S-alkylated with iodoacetic acid or 5-I-AEDANS.