A common theme in the amino acid sequences of actin and many actin-binding proteins?

The amino acid sequences of several actin regulatory proteins have recently been determined. Do these proteins function by mimicking actin-actin interaction sites?     

An improved method for the determination of γ-carboxyglutamic acid in proteins,bone, and urine

A method of high-performance liquid chromatographic separation of the fluorescence derivative of γ-carboxyglutamic acid (Gla) is presented. Alkaline hydrolysates of protein samples were reacted with o-phthalaldehyde in the presence of ethanethiol for 2 min, and the fluorescence derivative of γ-carboxyglutamic acid was resolved from the other amino acids by a short column packed with silica-based anion exchanger under isocratic conditions. By this method, as low as 200 fmol of γ-carboxyglutamic acid can be quantitatively analyzed within 10 min. The method presented here shortened the analysis time for Gla and was at least 10 times more sensitive than the method we described previously (Anal. Biochem.117, 259–265, 1981). The application of this method to the formic acid-soluble or insoluble γ-carboxyglutamic acid-containing proteins in chicken bone and the concomitant increase of γ-carboxyglutamic acid content in chicken bone with age are reported.     

Covalent binding of 17β-estradiol and retinoic acid to proteins in the human breast cancer cell line MCF-7

Summary Both retinoic acid and 17β-estradiol formed covalent bonds with proteins of the human breast cancer cell line MCF-7. Two-dimensional gel patterns of the labeled proteins were unique for each ligand. There were four major retinoylated proteins in MCF-7 consisting of two doublets with molecular masses of 37 kDa and 20 kDa. These proteins were designated 37a, 37b, 37c, and 20d. The extent of retinoylation was very low in a 55 kDa protein that we previously identified in the human myeloid leukemia cell line HL60 [Takahashi, N. and Breitman, T. R. (1989) J. Biol. Chem. 264, 5159–5163]. These results indicated that the protein substrates for retinoylation may vary among cell-types. About 10 proteins were labeled from 17β-estradiol. Two of these proteins had mobilities that were identitied to the retinoylated proteins 37a and 20c. These results indicate that in MCF-7 cells there are two proteins that can be retinoylated and labeled from estradiol. The demonstration that some ligands of the steroid/thyroid receptor family are covalently linked to cellular proteins suggests new mechanisms for the many effects of these agents on cells. This study is the first report showing that estradiol or one of its metabolic products covalently binds to proteins in the human breast cancer cell line MCF-7. Two of the proteins labeled from radioactive estradiol comigrate with proteins labeled from radioactive retinoic acid. These results suggest new mechanisms of action for the steroid and thyroid hormones. EDITOR’S STATEMENT This study is the first report showing that estradiol or one of its metabolic products covalently binds to proteins in the human breast cancer cellline MCF-7. Two of the proteins labeled from radioactive estradiol comigrate with proteins labeled from radioactive retinoic acid. These results suggest new mechanisms of action for the steroid and thyroid hormones.     

Fluorescence spectroscopic study of α-chymotrypsin relevant to the enantioselectivity for optical resolution of amino acid esters in organic solvents

The fluorescence emission wavelength of alpha-chymotrypsin (CT) correlated with its enantioselectivity (E value) for the resolution of DL-tyrosine ethyl ester. The changes in the E value of the CT due to the changes in the solvent composition were closely related to its fluorescence properties (delta lambda(em)), which were most probably associated with the structural modification of the enzyme. A linear relationship was established between E value and delta lambda(em) in aqueous acetonitrile with high correlation coefficients (r = 0.94).     

The carbohydrate–polypeptide linkages, the amino acid sequences of the peptides adjacent to some of these bonds, and the composition and size of the carbohydrate units of α1-acid glycoprotein

1. The glycopeptides derived from a proteolytic digest of sialic acid-free α₁-acid glycoprotein were separated on a DEAE-cellulose column into five main fractions. 2. The average molecular weight of these glycopeptides was 2400, except for one fraction whose molecular weight was 3100. The average molecular weight of the sialic acid-free carbohydrate units was found to be 2200. From these data and the carbohydrate content of the native protein and the assumed molecular weight of 44000, it was concluded that α₁-acid glycoprotein probably possesses five carbohydrate units. The sialic acid-containing carbohydrate units of this glycoprotein have an average molecular weight of 3000, except for one unit the molecular weight of which is significantly higher. 3. The N-, non-N- and C-terminal amino acids of the main glycopeptides were determined. Aspartic acid and threonine occur in most peptides. Alanine, glycine, proline, serine and lysine were present in varying amounts. Traces of other amino acids were also found. 4. The amino acid sequence of three main glycopeptides was established and indicated that these glycopeptides are located at different positions of the polypeptide chain of the glycoprotein. These sequences are: Asp(NH₂)-Pro-Lys; Thr-Asp(NH₂)-Ala; Asp(NH₂)-Gly-Thr. 5. From the results of a series of chemical reactions (periodate oxidation, hydrazinolysis, dinitrophenylation, mild acid hydrolysis) it was shown that the hydroxyl group of the N-terminal threonine and the -amino group of lysine are free and that the β-carboxyl group of aspartic acid is present as amide. It was concluded that this amide group is involved in the carbohydrate–polypeptide linkages of at least four carbohydrate units of α₁-acid glycoprotein. 6. The carbohydrate composition of the sialic acid-free glycopeptides was determined in terms of moles of neutral hexoses, glucosamine and fucose/mole. 7. Fucose, at least to the larger part, is not linked to sialic acid, and its (glycosidic) linkage is significantly more stable toward acid hydrolysis than the bond of the sialyl residues. 8. Heterogeneity of the carbohydrate units of α₁-acid glycoprotein was found with regard to size and to content of fucose and sialic acid.     

Identification of amino acids involved in the binding of hMIP-1α to CC-CKR1, a MIP-lα receptor found on neutrophils

Human macrophage inflammatory protein-1 (hMIP-1) and human macrophage inflammatory protein-1 (hMIP-1) are chemokines involved in a diverse range of immunological effects. Both hMIP-1 and hMIP-1 are involved in the activation of monocytes and THP-1 cells probably through a common receptor(s). However, only hMIP-1 can bind to neutrophils with high affinity, presumably through CC-CKR1 (CKR1). Since the structure of these two proteins is highly conserved, non-conserved amino acids must define the disparate binding patterns that these two proteins exhibit. Measurements of binding, chemotaxis and calcium influx conducted with hMIP-1 and hMIP-1 chimeric proteins and mutants show that two amino acids (37K and 43L) are important in the binding and signaling of hMIP-1 through CKR1. Furthermore, we also show that mutations of the three charged amino acids at the C-terminus of hMIP-1 and hMIP-1 (amino acids 61, 65 and 67), do not adversely affect the binding to THP-1 cells.     

Structure of cytochromec oxidase from baker's yeast—a progress report. Preparation of four subunits for amino acid sequence determination and attempts to localize the cytochromec binding site

Summary Cytochromec oxidase from the inner membrane of yeast mitochondria consists of seven nonidentical protein subunits, three being synthesized on mitochondrial ribosomes (molecular weights I: 43 K, II: 34 K, and III: 24 K) and four being made on cytoplasmic ribosomes (molecular weights IV: 14 K, V: 12 K, VI: 12 K, and VII: 4.5 K).In the present study all four cytoplasmically synthesized subunits of the enzyme were isolated on a large scale using ion exchange chromatography and gel filtartion. Their amino acid composition as well as their amino- and carboxy-terminal amino acid residues have been determined. Sequence determinations of sub-units IV and VI are already in an advanced state. The sequence of subunit VI is characterized by a large amino-terminal stretch dominated by charged amino acid residues followed by a cluster of hydrophobic amino acids.The binding site of yeast cytochrome oxidase for cytochromec was studied by chemical crosslinking experiments. The formation of a disulfide bridge between the two proteins was observed by using cytochromec from yeast modified with 5-thionitrobenzoate at the cysteinyl residue in position 107. Alternatively, a disulfide between yeast cytochromec and the oxidase could be formed directly by oxidation with copper phenanthroline. Gel electrophoresis of the crosslinked complexes in sodium dodecyl sulfate revealed a new protein band with an apparent molecular weight of 38 K. This new band appears to be derived from cytochromec and from subunit III of cytochrome oxidase.Recipient of a fellowship from the Swiss National Science Foundation. Present address: Department of Biology, University of California at San Diego, La Jolla, Calif. 92037 (USA).     

Application of amino acid type-specific 1H- and 14N-labeling in a 2H-, 15N-labeled background to a 47 kDa homodimer: Potential for NMR structure determination of large proteins

NMR investigations of larger macromolecules (>20 kDa) are severely hindered by rapid 1H and 13C transverse relaxation. Replacement of non-exchangeable protons with deuterium removes many efficient 1H-1H and 1H-13C relaxation pathways. The main disadvantage of deuteration is that many of the protons which would normally be the source of NOE-based distance restraints are removed. We report the development of a novel labeling strategy which is based on specific protonation and 14N-labeling of the residues phenylalanine, tyrosine, threonine, isoleucine and valine in a fully deuterated, 15N-labeled background. This allows the application of heteronuclear half-filters, 15N-editing and 1H-TOCSY experiments to select for particular magnetization transfer pathways. Results from investigations of a 47 kDa dimeric protein labeled in this way demonstrated that the method provides useful information for the structure determination of large proteins.     

Substitutions of amino acids in the pore domain of homomeric α7 nicotinic receptors for analogous residues present in heteromeric receptors modify gating, rectification and binding properties

We have studied the role of different amino acids in the M2 transmembrane domain of the α7 neuronal nicotinic receptor by mutating residues that differ from the ones located at the same positions in other α (α2-α10) or β (β2-β4) subunits. Our aim was to investigate the contribution of these amino acids to the peculiar kinetic and inward rectification properties that differentiate the homomeric α7 receptor from other nicotinic receptors. Mutations of several residues strongly modified receptor function. We found that Thr245 had the most profound effect when mutated to serine, an amino acid present in all heteromeric receptors composed of α and β subunits, by dramatically increasing the maximal current, decreasing the decaying rate of the currents and decreasing receptor rectification. Some mutants also showed altered agonist-binding properties as revealed by shifts in the dose-response curves for acetylcholine. We conclude that residues in the M2 segment and flanking regions contribute to the unusual properties of the α7 receptor, especially to its characteristic fast kinetic behavior and strong inward rectification and furthermore to the potency of agonists.     

An improved method for the measurement of total lipid-bound sialic acids after cleavage of α2,8 sialic acid linkage withVibrio cholerae sialidase in the presence of cholic acid,SDS and Ca2+

In the measurement of total lipid-bound sialic acids involving periodic acid oxidation, as in the periodate-resorcinol assay, the inner sialic acids of disialoglycolipids (such as GD₃ and GD₂) are not involved because their 2,8 ketosidic linkages are resistant to periodic acid oxidation, even after acid/enzyme hydrolysis or alkali pretreatment. However, the sialic acids from these glycolipids can be recovered completely after cleavage of 2,8 linkages byV. cholerae sialidase in the presence of cholic acid, sodium dodecyl sulphate and calcium. Interestingly, removal of calcium or detergent(s) or both significantly minimizes the sialidase action on the disialyl residues of these gangliosides. Therefore, we recommend sialidase (Vibrio cholerae) pretreatment of the glycolipids in the presence of cholic acid, SDS and Ca²⁺ for complete recovery of sialic acids from di- and polysialogangliosides and for accurate measurement of total lipid-bound sialic acids by periodate-resorcinol assay.Presented at the Second International Glycobiology Symposium which was held in San Francisco, CA, USA (14 February 1994).     

Structure,chaperone activity,and aggregation of wild-type and R12C mutant αB-crystallins in the presence of thermal stress and calcium ion – Implications for role of calcium in cataract pathogenesis

The current study was performed with the aim to evaluate the chaperoning ability, structural features, and aggregation propensity of wild-type and R12C mutant αB-crystallins (αB-Cry) under thermal stress and in the presence of calcium ion. The results of different spectroscopic analyses suggest that wild-type and mutant αB-Cry have dissimilar secondary and tertiary structures. Moreover, αB-Cry indicates slightly improved chaperone activity upon the R12C mutation. Thermal stress and calcium, respectively, enhance and reduce the extent of solvent-exposed hydrophobic surfaces accompanying formation of ordered and non-ordered aggregate entities in both proteins. Compared to the wild-type protein, the R12C mutant counterpart shows significant resistance against thermal and calcium-induced aggregation. In addition, in the presence of calcium, significant structural variation was accompanied by reduction in the solvent-exposed hydrophobic patches and attenuation of chaperone activity in both proteins. Additionally, gel mobility shift assay indicates the intrinsic propensity of R12C mutant αB-Cry for disulfide bridge-mediated protein dimerization. Overall, the results of this study are of high significance for understanding the molecular details of different factors that are involved in the pathomechanism of cataract disorders.     

Domoic acid in a marine pelagic food web: Exposure of southern right whales Eubalaena australis to domoic acid on the Península Valdés calving ground,Argentina

The gulfs that surround Península Valdés (PV), Golfo Nuevo and Golfo San José in Argentina, are important calving grounds for the southern right whale Eubalaena australis. However, high calf mortality events in recent years could be associated with phycotoxin exposure. The present study evaluated the transfer of domoic acid (DA) from Pseudo-nitzschia spp., potential producers of DA, to living and dead right whales via zooplanktonic vectors, while the whales are on their calving ground at PV. Phytoplankton and mesozooplankton (primary prey of the right whales at PV and potential grazers of Pseudo-nitzschia cells) were collected during the 2015 whale season and analyzed for species composition and abundance. DA was measured in plankton and fecal whale samples (collected during whale seasons 2013, 2014 and 2015) using liquid chromatography coupled to tandem mass spectrometry (LC–MS/MS). The genus Pseudo-nitzschia was present in both gulfs with abundances ranging from 4.4 × 10² and 4.56 × 10⁵ cell l⁻¹. Pseudo-nitzschia australis had the highest abundance with up to 4.56 × 10⁵ cell l⁻¹. DA in phytoplankton was generally low, with the exception of samples collected during a P. australis bloom. No clear correlation was found between DA in phytoplankton and mesozooplankton samples. The predominance of copepods in mesozooplankton samples indicates that they were the primary vector for the transfer of DA from Pseudo-nitzschia spp. to higher trophic levels. High levels of DA were detected in four whale fecal samples (ranging from 0.30 to 710 μg g⁻¹ dry weight of fecal sample or from 0.05 and 113.6 μg g⁻¹ wet weight assuming a mean water content of 84%). The maximum level of DA detected in fecal samples (710 μg DA g⁻¹ dry weight of fecal sample) is the highest reported in southern right whales to date. The current findings demonstrate for the first time that southern right whales, E. australis, are exposed to DA via copepods as vectors during their calving season in the gulfs of PV.     

Atmospheric Phosphorus Deposition in Ashiu, Central Japan – Source Apportionment for the Estimation of True Input to a Terrestrial Ecosystem

Atmospheric bulk depositions of soluble reactive phosphorus (SRP), soluble unreactive phosphorus (SUP), particulate inorganic phosphorus (PIP), particulate organic phosphorus (POP), total phosphorus (TP) and some other dissolved and particulate components were monitored for 3 years in Ashiu, Central Japan. The mean bulk depositions of SRP, SUP, PIP, POP, TP, dissolved components (Na, Mg, nss-Ca, K, V, Mo, nss-SO₄) and particulate components (Al, Fe, Ti, Ca, Mg, Mn, Ba, Sr, Zn) were 175, 76, 136, 397, 783, 156,000, 10,900, 7450, 5470, 10.3, 1.52, 40,100, 13,200, 3590, 2630, 576, 624, 42.3, 30.2, 17.4, 8.2 μmol m⁻² year⁻¹, respectively. The value for TP deposition was in the lower range of previous literature. The low P deposition probably reflected the method applied to reduce the contribution of local particles, including (1) placement of samplers off the ground surface, (2) installation of multiple samplers, and (3) rejection of contaminated samples. Al data suggested that 15 ± 5% of TP was brought by lithogenic dust from East Eurasia. Nss-SO₄ and Mo data and air-mass backward trajectories suggested that 39 ± 4% of TP was derived from coal combustion in China. It was speculated that the rest (47 ± 6%) of the TP deposition might be predominantly attributed to the contribution of local biogenic particles. Net atmospheric TP input (lithogenic dust and fossil fuel combustion) was almost equal to the TP outflow from Japanese forests on granitic soils.     

Development,validation of a GC–MS method for the simultaneous measurement of amino acids,their PTM metabolites and AGEs in human urine,and application to the bi-ethnic ASOS study with special emphasis to lysine

A gas chromatography-mass spectrometry (GC–MS) method was developed and validated in relevant concentration ranges for the simultaneous measurement of l-lysine (Lys, L) and its N^ε- and N^α-methylated (M), N^ε- and N^α-acetylated (Ac), N^ε-carboxymethylated (CM) and N^ε-carboxyethylated (CE) metabolites in human urine. Analyzed Lys metabolites were the post-translational modification (PTM) products N^ε-mono-, di- and trimethyllsine, N^ε-MML, N^ε-DML, N^ε-TML, respectively, N^α-ML, N^ε-AcL, N^α-AcL, and its advanced glycation end-products (AGEs) N^ε-CML, N^ε-CM-[2,4,4-²H₃]Lys (d₃-CML), N^ε-CEL and furosine. AGEs of arginine (Arg) and cysteine (Cys) were also analyzed. De novo synthesized trideutero-methyl esters (R-COOCD₃) from unlabelled amino acids and derivatives were used as internal standards. Native urine samples (10 µL aliquots) were evaporated to dryness under a stream of nitrogen. Analytes were esterified using 2 M HCl in methanol (60 min, 80 °C) and subsequently amidated by pentafluoropropionic anhydride in ethyl acetate (30 min, 65 °C). The generated methyl ester-pentafluoropropionyl (Me-PFP) derivatives were reconstituted in borate buffer and extracted immediately with toluene. GC–MS analyses were performed by split-less injection of 1-µL aliquots, oven-programmed separation and negative-ion chemical ionization (NICI). Mass spectra were generated in the scan mode (range, m/z 50–1000). Quantification was performed in the selected-ion monitoring (SIM) mode using a dwell time of 50 or 100 ms for each ion. The GC–MS method was suitable for the measurement of Lys and all of its metabolites, except for the quaternary ammonium cation N^ε-TML. The Me-PFP derivatives of Lys, Arg and Cys and its metabolites eluted in the retention time window of 9 to 14 min. The derivatization of N^ε-CML, d₃-CML and N^ε-CEL was accompanied by partial N^ε-decarboxylation and formation of the Me-PFP Lys derivative. The lowest derivatization yield was observed for N^ε-DML, indicating a major role of the N^ε-DML group in Lys derivatization. The GC–MS method enables precise (relative standard deviation, RSD?<?20%) and accurate (bias,?<?±?20%) simultaneous measurement of 33 analytes in human urine in relevant concentration ranges. We used the method to measure the urinary excretion rates of Lys and its PTM metabolites and AGEs in healthy black (n?=?39) and white (n?=?41) boys of the Arterial Stiffness in Offspring Study (ASOS). No remarkable differences were found indicating no ethnic-related differences in PTM metabolites and AGEs except for N^ε-monomethyllysine and S-(2-carboxymethylcysteine).

     

In silico evidence for the horizontal transfer of gsiB, a σ(B)-regulated gene in gram-positive bacteria, to lactic acid bacteria

gsiB, coding for glucose starvation-inducible protein B, is a characteristic member of the σ(Β) stress regulon of Bacillus subtilis and several other Gram-positive bacteria. Here we provide in silico evidence for the horizontal transfer of gsiB in lactic acid bacteria that are devoid of the σ(Β) factor.     

Effects of UV radiation on five marine microphytobenthic Wadden sea diatoms,isolated from the Solthörn tidal flat (Lower Saxony,southern North Sea) – Part II: changes in carbohydrate,amino acid and fatty acid composition

Benthic diatoms inhabiting intertidal flats face highly variable environmental conditions, due to changing water levels and exposure during low tide. The present study is the second part of a more extensive study of the adaptive potential of these species in response to varying UV radiations in the Solthörn tidal flat (Lower Saxony, southern North Sea). Five isolates (Achnanthes exigua, Amphora exigua, Cocconeis peltoides, Diploneis littoralis and Navicula digitoradiata), which were found in this area in high cell numbers in summer 2008, were used in semi-continuous cultures to study the physiological effects of UV-radiation (PAR [photosynthetically active radiation], PAR+UV-A, PAR+UV-B, PAR+UV-B+UV-A). For short- and long-term exposures (6 h, 30 days), the composition of intercellular carbohydrates, amino and fatty acids were analysed in exponential-phase cultures grown at a salinity of 30 in a 12?:?12 h light?:?dark cycle at 20?°C. Although all tested species showed distinct differences in their initial carbohydrate, amino and fatty acid compositions and in their responses to the different UV treatments, general response patterns could be identified. Overall physiological responses to short- and long-term UV treatments included the accumulation of proline as well as an increase in total carbohydrates and lipids, whereas significant differences in the composition of carbohydrates, amino and fatty acids occurred after long-term exposure to the UV treatments (P < 0.05). While UV-A exposure led to higher accumulations of phenylalanine, aspartic acid and saturated fatty acids, the response to UV-B long-term exposure included increases of galactose, mannose and unsaturated fatty acids in the cells. In both UV experiments there was a noteworthy accumulation of the amino acid tryptophan in most species. The combined UV-A+UV-B experiment showed a significant (P < 0.05) increase of aspartic acid, phenylalanine, galactose and saturated fatty acids in a majority of species. Overall, the results indicated significant differences in the physiological responses of the five diatom taxa during UV exposure, which suggests species-specific acclimation strategies that may explain the growth insensitivity towards at least short-term UV.     

Plant growth, metabolism and adaptation in relation to stress conditions. XXVII. Can ascorbic acid modify the adverse effects of NaCl and mannitol on amino acids, nucleic acids and protein patterns in Vicia faba seedlings?

The adverse effects of either NaCl or mannitol on amino acids, protein patterns and nucleic acids in Vicia faba seeds were investigated. The exogenous addition of 4 mM ascorbic acid to the stressing media in which the broad bean seeds were germinated in combination with either the ionic (NaCl) or osmotic (mannitol) stressor induced significant protective changes in the total amount and in the relative composition of amino acids in general and in proline, glycine, glutamic, aspartic, alanine and serine in particular. It also induced changes in nucleic acids (RNA and DNA) content. These changes occurred throughout the entire period of the experiments (12 days). Separate administration of NaCl or mannitol enhanced the occurrence of particular novel proteins that were not detected in control bean seeds (water medium). Protein banding patterns of broad bean seedlings treated with NaCl or mannitol in combination with 4 mM ascorbic acid showed different de novo protein bands, with different molecular weights, at different stages of seedlings growth, with lower levels or a nearly complete absence of the major stress proteins. The pattern of changes for amino acids and nucleic acids and the range of protein bands extracted from the variously treated broad bean seedlings indicate a positive role of ascorbic acid in the alleviation of the damage effects induced by NaCl and mannitol. The importance of this role in the stress tolerance of broad beans is discussed.