Protein Bodies from the Endosperm of Castor Bean: Subfractionation, Protein Components, Lectins, and Changes during Germination

Protein bodies from the storage endosperm of dry castor bean (Ricinus communis L.) were isolated by successive nonaqueous linear density gradient centrifugation. The isolated protein bodies were lysed by the addition of water, and the various structural components of the organelles were separated by sucrose gradient centrifugation. The matrix protein remained at the top of the gradient while the membrane, the crystalloids, and the globoids migrated to densities 1.15 g/cm³, 1.30 g/cm³, and > 1.46 g/cm³, respectively. The protein of the protein bodies was distributed evenly between the crystalloids and the matrix, and little protein was present in the globoids or the membrane.     

Protein co-evolution, co-adaptation and interactions

Co-evolution has an important function in the evolution of species and it is clearly manifested in certain scenarios such as host–parasite and predator–prey interactions, symbiosis and mutualism. The extrapolation of the concepts and methodologies developed for the study of species co-evolution at the molecular level has prompted the development of a variety of computational methods able to predict protein interactions through the characteristics of co-evolution. Particularly successful have been those methods that predict interactions at the genomic level based on the detection of pairs of protein families with similar evolutionary histories (similarity of phylogenetic trees: mirrortree). Future advances in this field will require a better understanding of the molecular basis of the co-evolution of protein families. Thus, it will be important to decipher the molecular mechanisms underlying the similarity observed in phylogenetic trees of interacting proteins, distinguishing direct specific molecular interactions from other general functional constraints. In particular, it will be important to separate the effects of physical interactions within protein complexes (‘co-adaptation') from other forces that, in a less specific way, can also create general patterns of co-evolution.     

Building Blocks,Hinge-Bending Motions and Protein Topology

Abstract

Here we show that the locations of molecular hinges in protein structures fall between building block elements. Building blocks are fragments of the protein chain which constitute local minima. These elements fold first. In the next step they associate through a combinatorial assembly process. While chain-linked building blocks may be expected to trial-associate first, if unstable, alternate more stable associations will take place. Hence, we would expect that molecular hinges will be at such inter-building block locations, or at the less stable, ‘unassigned’ regions.

On the other hand, hinge-bending motions are well known to be critical for protein function. Hence, protein folding and protein function are evolutionarily related. Further, the pathways through which proteins attain their three dimensional folds are determined by protein topology. However, at the same time the locations of the hinges, and hinge-bending motions are also an outcome of protein topology. Thus, protein folding and function appear coupled, and relate to protein topology. Here we provide some results illustrating such a relationship.     

Overexpression, Purification, and Characterization of Glutaminase-Interacting Protein, a PDZ-Domain Protein from Human Brain

A human brain cDNA clone coding for a novel PDZ-domain protein of 124 amino acids has been previously isolated in our laboratory. The protein was termed GIP (glutaminase-interacting protein) because it interacts with the C-terminal region of the human brain glutaminase L. Here we report the heterologous expression of GIP as a histidine-tagged fusion protein in Escherichia coli cells. The induction conditions (temperature and isopropyl beta-d-thiogalactopyranoside concentrations) were optimized in such a way that GIP accounted for about 20% of the total E. coli protein. A simple and rapid procedure for purification was developed, which yielded 17 mg of purified GIP per liter of bacterial cell culture. The apparent molecular mass of the protein by SDS-PAGE was 16 kDa, whereas in native form it was determined to be 28 kDa, which suggests dimer formation. The nature and integrity of the recombinant protein were verified by mass spectrometry analysis. The functionality of the GIP protein was tested with an in vitro activity assay: after being pulled down with glutathione S-transferase-glutaminase, GIP was revealed by Western blot using anti-GIP antibodies. Furthermore, the glutaminase activity in crude rat liver extracts was inhibited by the presence of recombinant purified GIP protein.     

Water Stress and Protein Synthesis: V. Protein Synthesis, Protein Stability, and Membrane Permeability in a Drought-sensitive and a Drought-tolerant Moss

The effects have been studied of water stress and desiccation on protein synthesis in the drought-tolerant moss Tortula ruralis and the drought-sensitive moss Hygrohypnum luridum. At any particular level of steady state water stress, the inhibition of protein synthesis was greater in H. luridum than in T. ruralis. Water stress-induced changes in the pattern of protein synthesis, as determined by the double label ratio technique, were minor in T. ruralis, but major in H. luridum. Proteins of both mosses were found to be stable during desiccation and subsequent rehydration. Changes in membrane permeability, as indicated by the leakage of amino acid, were observed during rehydration of desiccated moss and were dependent on the rate of desiccation. The leakage was small and reversible in T. ruralis but large and irreversible in H. luridum. Although H. luridum failed to recover from complete desiccation (80% loss in fresh weight), it was able to recover fully from steady state stress under conditions where a maximum loss of 55% in fresh weight was recorded.     

The Structure,Role, and Regulation of Type 1 Protein Phosphatases

Abstract

Type 1 protein phosphatases (PP-1) comprise a group of widely distributed enzymes that specifically dephosphorylate serine and threonine residues of certain phosphoproteins. They all contain an isoform of the same catalytic subunit, which has an extremely conserved primary structure. One of the properties of PP-1 that allows one to distinguish them from other serine/threonine protein phosphatases is their sensitivity to inhibition by two proteins, termed inhibitor 1 and inhibitor 2, or modulator. The latter protein can also form a 1:1 complex with the catalytic subunit that slowly inactivates upon incubation. This complex is reactivated in vitro by incubation with MgATP and protein kinase F_A/GSK-3. In the cell the type 1 catalytic subunit is associated with noncatalytic subunits that determine the activity, the substrate specificity, and the subcellular location of the phosphatase. PP-1 plays an essential role in glycogen metabolism, calcium transport, muscle contraction, intracellular transport, protein synthesis, and cell division. The activity of PP-1 is regulated by hormones like insulin, glucagon, α- and β-adrenergic agonists, glucocorticoids, and thyroid hormones.     

Protein misfolding, aggregation, and degradation in disease

Pathologies associated with protein misfolding have been observed in neurodegenerative diseases such as Alzheimer’s disease, metabolic diseases like phenylketonuria, and diseases affecting structural proteins like collagen or keratin. Misfolding of mutant proteins in these and many other diseases may result in premature degradation, formation of toxic aggregates, or incorporation of toxic conformations into structures. We review common traits of these diverse diseases under the unifying view of protein misfolding. The molecular pathogenesis is discussed in the context of protein quality control systems consisting of molecular chaperones and intracellular proteases that assist the folding and supervise the maintenance of the folded structure. Furthermore, genetic and environmental factors that may modify the severity of these diseases are underscored. The present article represents a partly revised and updated version of chapter 1 published earlier in volume 232 of the series Methods in Molecular Biology (Walker, J. M., ed., Humana Press, Totowa, NJ), Protein Misfolding and Disease: Principles and Protocols (Bross, P. & Gregersen, N., eds.), pp. 3–16 (2003).     

A Procedure for Isolation of Human Protein C and Protein S as by-Products of the Purification of Factors VII,IX, X and Prothrombin

Abstract

A DEAE-Sephadex column chromatography step utilized to purify human Factor VII consistently yields a protein peak between the factor VII activity peak and prothrombin, factor X and factor IX activity peak (S.P. Bajaj, S.I. Rapaport, and S.F. Brown: J. Biol. Chem. 251., 253-259, 1981). We now report that this protein peak contains protein C and protein S. Preparative disc polyacryla-mide gel electrophoresis of the proteins in this peak 'permitted a complete separation of protein C from protein S. Protein C at this step usually contained approximately 5-10% of Factor X, which could be removed by a goat anti-human Factor X antibody column. For a typical preparation, starting with 10L of plasma, the yield of Protein C was 5 mg and of protein S was 4 mg. Both proteins     

Structure and Calcium Binding Properties of a Neuronal Calcium-Myristoyl Switch Protein,Visinin-Like Protein 3

Visinin-like protein 3 (VILIP-3) belongs to a family of Ca²⁺-myristoyl switch proteins that regulate signal transduction in the brain and retina. Here we analyze Ca²⁺ binding, characterize Ca²⁺-induced conformational changes, and determine the NMR structure of myristoylated VILIP-3. Three Ca²⁺ bind cooperatively to VILIP-3 at EF2, EF3 and EF4 (K_D = 0.52 μM and Hill slope of 1.8). NMR assignments, mutagenesis and structural analysis indicate that the covalently attached myristoyl group is solvent exposed in Ca²⁺-bound VILIP-3, whereas Ca²⁺-free VILIP-3 contains a sequestered myristoyl group that interacts with protein residues (E26, Y64, V68), which are distinct from myristate contacts seen in other Ca²⁺-myristoyl switch proteins. The myristoyl group in VILIP-3 forms an unusual L-shaped structure that places the C₁₄ methyl group inside a shallow protein groove, in contrast to the much deeper myristoyl binding pockets observed for recoverin, NCS-1 and GCAP1. Thus, the myristoylated VILIP-3 protein structure determined in this study is quite different from those of other known myristoyl switch proteins (recoverin, NCS-1, and GCAP1). We propose that myristoylation serves to fine tune the three-dimensional structures of neuronal calcium sensor proteins as a means of generating functional diversity.     

Identification of a Novel Hypocholesterolemic Protein,Major Royal Jelly Protein 1, Derived from Royal Jelly

Royal jelly (RJ) intake lowers serum cholesterol levels in animals and humans, but the active component in RJ that lowers serum cholesterol level and its molecular mechanism are unclear. In this study, we set out to identify the bile acid-binding protein contained in RJ, because dietary bile acid-binding proteins including soybean protein and its peptide are effective in ameliorating hypercholesterolemia. Using a cholic acid-conjugated column, we separated some bile acid-binding proteins from RJ and identified the major RJ protein 1 (MRJP1), MRJP2, and MRJP3 as novel bile acid-binding proteins from RJ, based on matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Purified MRJP1, which is the most abundant protein of the bile acid-binding proteins in RJ, exhibited taurocholate-binding activity in vitro. The micellar solubility of cholesterol was significantly decreased in the presence of MRJP1 compared with casein in vitro. Liver bile acids levels were significantly increased, and cholesterol 7α-hydroxylase (CYP7A1) mRNA and protein tended to increase by MRJP1 feeding compared with the control. CYP7A1 mRNA and protein levels were significantly increased by MRJP1 tryptic hydrolysate treatment compared with that of casein tryptic hydrolysate in hepatocytes. MRJP1 hypocholesterolemic effect has been investigated in rats. The cholesterol-lowering action induced by MRJP1 occurs because MRJP1 interacts with bile acids induces a significant increase in fecal bile acids excretion and a tendency to increase in fecal cholesterol excretion and also enhances the hepatic cholesterol catabolism. We have identified, for the first time, a novel hypocholesterolemic protein, MRJP1, in RJ. Interestingly, MRJP1 exhibits greater hypocholesterolemic activity than the medicine β-sitosterol in rats.     

Interactive Effects of Indigestible Carbohydrates,Protein Type,and Protein Level on Biomarkers of Large Intestine Health in Rats

The effects of indigestible carbohydrates, protein type, and protein level on large intestine health were examined in rats. For 21 days, 12 groups of six 12-week-old male Wistar rats were fed diets with casein (CAS), or potato protein concentrate (PPC), providing 14% (lower protein level; LP), or 20% (higher protein level; HP) protein, and containing cellulose, resistant potato starch, or pectin. Fermentation end-products, pH, and β-glucuronidase levels in cecal digesta, and ammonia levels in colonic digesta were determined. Cecal digesta, tissue weights, cecal and colon morphology, and colonocyte DNA damage were also analyzed. Digesta pH was lower, whereas relative mass of cecal tissue and digesta were higher in rats fed pectin diets than in those fed cellulose. Cecal parameters were greater in rats fed PPC and HP diets than in those fed CAS and LP diets, respectively. Short-chain fatty acid (SCFA) concentrations were unaffected by protein or carbohydrate type. Total SCFA, acetic acid, and propionic acid concentrations were greater in rats fed LP diets than in those fed HP. Cecal pool of isobutyric and isovaleric acids was greater in rats fed PPC than in those fed CAS diets. PPC diets decreased phenol concentration and increased ammonia concentration in cecal and colonic digesta, respectively. Cecal crypt depth was greater in rats fed PPC and HP diets, and was unaffected by carbohydrates; whereas colonic crypt depth was greater in rats fed cellulose. Myenteron thickness in the cecum was unaffected by nutrition, but was greater in the colon of rats fed cellulose. Colonocyte DNA damage was greater in rats fed LP diets than in those fed HP diets, and was unaffected by carbohydrate or protein type. It was found that nutritional factors decreasing cecal digesta weight contribute to greater phenol production, increased DNA damage, and reduced ammonia concentration in the colon.     

Phosphorylation of B-50 Protein by Calcium-Activated, Phospholipid-Dependent Protein Kinase and B-50 Protein Kinase

B-50 is a brain-specific phosphoprotein, the phosphorylation state of which may play a role in the regulation of (poly)phosphoinositide metabolism. Several kinases were tested for their ability to phosphorylate purified B-50 protein. Only calcium-activated, phospholipid-dependent protein kinase (kinase C) and B-50 protein kinase were able to use B-50 protein as a substrate. Furthermore, kinase C specifically phosphorylates B-50 when added to synaptic plasma membranes. We further characterized the sensitivity of kinase C and B-50 kinase to ACTH (and various fragments), phospholipids, chlorpromazine, and proteolytic activation. Since the sensitivities of both kinases were similar, we conclude that B-50 protein kinase is a calcium-dependent, phospholipid-stimulated protein kinase of the same type as kinase C.     

Promoting Protein,a Silkworm Hemolymph Protein Promoting in Vitro Replication of Nucleopolyhedrovirus,Binds to β-Glucans

A protein which bound to ¹²⁵I-labeled peptidoglycan (PGN) was isolated from hemolymph of silkworm larvae. The N-terminal amino acid sequence and the molecular weight of the protein were in accord with those described for Promoting Protein (PP) from the silkworm. The binding of the protein to [¹²⁵I]PGN was competitively inhibited by various β-glucans. The binding kinetics of PGN and chitin to the protein were analyzed in a biosensor.     

Body Composition,and Utilization of Protein and Energy in Growing Rats at Different Dietary Protein to Energy Ratios by Use of Purified Whole Egg Protein

A study has been made on growing rats to investigate the effect of variation in percentage of dietary protein calories from 0 to 50% by the use of purified whole egg protein on the growth, food efficiency, protein efficiency ratio (PER), body composition, and efficiencies of protein and energy utilization.

Body weight gain and PER attained a maximum, and food efficiency reached a plateau at 10 PC% (protein calories percent) in the diet, having a constant metabolizable energy content (410 kcal). Body and liver compositions changed in systematic patterns, where liver lipid content showed a specific increase at 5 PC%.

Body protein retention reached a plateau at 15 PC% but with little difference from the value at 10 PC%, while body lipid retention give a maximum at 10 PC% showing a gradual decrease thereafter.

Throughout the given dietary protein to energy ratios, energy utilization was constant when expressed as the increment of body energy retention divided by the increment of metabolizable energy intake. At and above 12 or 13 PC%, the efficiency of net body protein energy retention against metabolizable energy intake was constant at about 12.5% on the average.     

Isolation, Purification, and Characterization of a Killer Protein from Schwanniomyces occidentalis

The yeast Schwanniomyces occidentalis produces a killer toxin lethal to sensitive strains of Saccharomyces cerevisiae. Killer activity is lost after pepsin and papain treatment, suggesting that the toxin is a protein. We purified the killer protein and found that it was composed of two subunits with molecular masses of approximately 7.4 and 4.9 kDa, respectively, but was not detectable with periodic acid-Schiff staining. A BLAST search revealed that residues 3 to 14 of the 4.9-kDa subunit had 75% identity and 83% similarity with killer toxin K2 from S. cerevisiae at positions 271 to 283. Maximum killer activity was between pH 4.2 and 4.8. The protein was stable between pH 2.0 and 5.0 and inactivated at temperatures above 40°C. The killer protein was chromosomally encoded. Mannan, but not β-glucan or laminarin, prevented sensitive yeast cells from being killed by the killer protein, suggesting that mannan may bind to the killer protein. Identification and characterization of a killer strain of S. occidentalis may help reduce the risk of contamination by undesirable yeast strains during commercial fermentations.     

Characterization of ATM Expression, Localization, and Associated DNA-dependent Protein Kinase Activity

Ataxia telangiectasia–mutated gene (ATM) is a 350-kDa protein whose function is defective in the autosomal recessive disorder ataxia telangiectasia (AT). Affinity-purified polyclonal antibodies were used to characterize ATM. Steady-state levels of ATM protein varied from undetectable in most AT cell lines to highly expressed in HeLa, U2OS, and normal human fibroblasts. Subcellular fractionation showed that ATM is predominantly a nuclear protein associated with the chromatin and nuclear matrix. ATM protein levels remained constant throughout the cell cycle and did not change in response to serum stimulation. Ionizing radiation had no significant effect on either the expression or distribution of ATM. ATM immunoprecipitates from HeLa cells and the human DNA-dependent protein kinase null cell line MO59J, but not from AT cells, phosphorylated the 34-kDa subunit of replication protein A (RPA) complex in a single-stranded and linear double-stranded DNA–dependent manner. Phosphorylation of p34 RPA occurred on threonine and serine residues. Phosphopeptide analysis demonstrates that the ATM-associated protein kinase phosphorylates p34 RPA on similar residues observed in vivo. The DNA-dependent protein kinase activity observed for ATM immunocomplexes, along with the association of ATM with chromatin, suggests that DNA damage can induce ATM or a stably associated protein kinase to phosphorylate proteins in the DNA damage response pathway.     

Cloning,Expression, and Assessment of Cytotoxic Effects of A-NGR Fusion Protein

Targeted drug delivery is an attractive field in cancer studies. In this study, a novel fusion protein consisting of Shiga toxin A subunit and NGR peptide has been constructed. The cytotoxic Shiga toxin A subunit has the ability to kill cancer cells while NGR is a well-known peptide that targets the whole molecule to cancer cells. Two forms of this novel fusion protein, one without linker (A-NGR) and one with linker (A-GGGGS-NGR) were studied. 3D structure prediction of the two forms carried out by I-TASSER and their validation and analysis were performed by ProSA web and RAMPAGE. Results showed that A-NGR is a better model than the one with linker. A-NGR was constructed by PCR method and cloned in pBAD/gIII A vector. Then, it was successfully expressed in Escherichia coli by induction with arabinose and subsequently purified by affinity chromatography under denaturing condition. Ultimately, the cytotoxic effect of the purified protein was evaluated on U937 cancer cells and MRC-5 normal cells by MTT assay. Conclusively, the fusion protein was successfully cloned and expressed and evaluated for its cytotoxic effects. The IC50 value of A-NGR fusion protein for U937 cell was about 26.86 µg/ml while no cytotoxic effect was observed on MRC-5 cells. Therefore, considering the promising cytotoxic effects of the fusion protein, further in vitro evaluations of this fusion protein on different cell lines are underway.     

Chloroplasts, Kinetin and Protein Synthesis

The effect of kinetin on protein synthesis of isolated chloroplasts was investigated by following the incorporation of ¹⁴C-leucine into isolated chloroplasts from Nicotiana tabacum. The incorporation activity varied greatly during the year, being largest in the winter and smallest in the summer. Conversely, the relative effect of kinetin on the incorporation of ¹⁴C-leucine, whether applied as a pretreatment to the leaves or directly in the incubation medium, was largest in the summer and smallest or absent altogether in the winter. Kinetin did not prolong the net incorporation period, which lasted about 40 min, but only enhanced the initial rate of the reaction. Chloroplasts extracted from leaves that had been detached for 24 or 48 h displayed very little of their original, pre-aged incorporation activity and treating the leaves with kinetin did not, essentially, prevent this loss. It was concluded that the major effect of kinetin upon chloroplasts may be related primarily to an effect upon hydration and permeability of the chloroplast and its membranes, and not to an effect directly upon its machinery for protein synthesis.     

Lifetime Trauma,Praying for Others,and C-Reactive Protein

Research indicates that praying for others may offset the effects of stress on self-rated health and psychological well-being. The purpose of the current study is to extend this literature by seeing whether praying for others moderates the effects of exposure to lifetime trauma on a key marker of inflammation: C-reactive protein. The data come from a recent nationwide survey of adults of all ages (N = 1,589). Levels of C-reactive protein were obtained from assays of blood spots drawn from a capillary fingerstick. The findings suggest that the magnitude of the relationship between lifetime trauma and C-reactive protein is completely offset for study participants who frequently pray for others. The theoretical implications of this research are discussed.     

YidC Protein,a Molecular Chaperone for LacY Protein Folding via the SecYEG Protein Machinery

To understand how YidC and SecYEG function together in membrane protein topogenesis, insertion and folding of the lactose permease of Escherichia coli (LacY), a 12-transmembrane helix protein LacY that catalyzes symport of a galactoside and an H⁺, was studied. Although both the SecYEG machinery and signal recognition particle are required for insertion of LacY into the membrane, YidC is not required for translocation of the six periplasmic loops in LacY. Rather, YidC acts as a chaperone, facilitating LacY folding. Upon YidC depletion, the conformation of LacY is perturbed, as judged by monoclonal antibody binding studies and by in vivo cross-linking between introduced Cys pairs. Disulfide cross-linking also demonstrates that YidC interacts with multiple transmembrane segments of LacY during membrane biogenesis. Moreover, YidC is strictly required for insertion of M13 procoat protein fused into the middle cytoplasmic loop of LacY. In contrast, the loops preceding and following the inserted procoat domain are dependent on SecYEG for insertion. These studies demonstrate close cooperation between the two complexes in membrane biogenesis and that YidC functions primarily as a foldase for LacY.