Structural studies on bovine γ-crystallin

The amino acid sequences around the cysteine residues in the lens protein, γ-crystallin, were studied. Fraction II of the γ-crystallin from calf lens (Björk, 1964) was used. The protein was oxidized with performic acid and then hydrolysed with trypsin. Six peptides containing cysteic acid were isolated. One of the peptides contained three residues of cysteic acid and the others contained one residue of cysteic acid. We conclude that there are eight unique residues of cysteic acid in the oxidized protein. Amino acid analysis suggests that there are also eight residues of cysteic acid in the molecule, which thus contains only one polypeptide chain.     

Relaxed specificity of endoproteinase Asp-N: this enzyme cleaves at peptide bonds N-terminal to glutamate as well as aspartate and cysteic acid residues

Asp-N, an endoproteinase specific for cleavage of protein or polypeptide bonds N-terminal to aspartate or cysteic acid residues, has been shown to possess a similar affinity for certain glutamate residues. Of 18 glutamate residues present in 2 cyanogen bromide fragments of apolipoprotein A-I, 5 residues were cleaved at rates comparable to that of cleavage at the 12 internal aspartate residues present in these polypeptides (all of which were cleaved). Cleavage of these 5 glutamate residues was obtained under standard enzyme digestion conditions, and the identities of all peptides obtained by Asp-N digestion were determined by amino acid sequencing of peaks obtained from reversed-phase high performance liquid chromatography.     

The amino acid sequence of cysteic acid-containing peptides from performic acid-oxidized ovotransferrin

1. The half-cystine content of ovotransferrin, measured as cysteic acid, was 31mol/80000g of protein. 2. The amino acid sequences of cysteic acid-containing peptides from performic acid-oxidized ovotransferrin were studied. 3. 34 unique cysteic acid residues were identified. 4. It is concluded that hen ovotransferrin does not consist of two identical halves or subunits.     

A bacterial virulence factor with a dual role as an adhesin and a solute-binding protein: the crystal structure at 1.5 A resolution of the PEB1a protein from the food-borne human pathogen Campylobacter jejuni

The PEB1a protein is an antigenic factor exposed on the surface of the food-borne human pathogen Campylobacter jejuni, which has a major role in adherence and host colonisation. PEB1a is also the periplasmic binding protein component of an aspartate/glutamate ABC transporter essential for optimal microaerobic growth on these dicarboxylic amino acids. Here, we report the crystal structure of PEB1a at 1.5 A resolution. The protein has a typical two-domain alpha/beta structure, characteristic of periplasmic extracytoplasmic solute receptors and a chain topology related to the type II subfamily. An aspartate ligand, clearly defined by electron density in the interdomain cleft, forms extensive polar interactions with the protein, the majority of which are made with the larger domain. Arg89 and Asp174 form ion-pairing interactions with the main chain alpha-carboxyl and alpha-amino-groups, respectively, of the ligand, while Arg67, Thr82, Lys19 and Tyr156 co-ordinate the ligand side-chain carboxyl group. Lys19 and Arg67 line a positively charged groove, which favours binding of Asp over the neutral Asn. The ligand-binding cleft is of sufficient depth to accommodate a glutamate. This is the first structure of an ABC-type aspartate-binding protein, and explains the high affinity of the protein for aspartate and glutamate, and its much weaker binding of asparagine and glutamine. Stopped-flow fluorescence spectroscopy indicates a simple bimolecular mechanism of ligand binding, with high association rate constants. Sequence alignments and phylogenetic analyses revealed PEB1a homologues in some Gram-positive bacteria. The alignments suggest a more distant homology with GltI from Escherichia coli, a known glutamate and aspartate-binding protein, but Lys19 and Tyr156 are not conserved in GltI. Our results provide a structural basis for understanding both the solute transport and adhesin/virulence functions of PEB1a.     

Aspartate taxis mutants of the Escherichia coli tar chemoreceptor.

The Tar protein of Escherichia coli belongs to a family of methyl-accepting inner membrane proteins that mediate chemotactic responses to a variety of compounds. These transmembrane signalers monitor the chemical environment by means of specific ligand-binding sites arrayed on the periplasmic side of the membrane, and in turn control cytoplasmic signals that modulate the flagellar rotational machinery. The periplasmic receptor domain of Tar senses two quite different chemoeffectors, aspartate and maltose. Aspartate is detected through direct binding to Tar molecules, whereas maltose is detected indirectly when complexed with the periplasmic maltose-binding protein. Saturating levels of either aspartate or maltose do not block behavioral responses to the other compound, indicating that the detection sites for these two attractants are not identical. We initiated structure-function studies of these chemoreceptor sites by isolating tar mutants which eliminate aspartate or maltose taxis, while retaining the ability to respond to the other chemoeffector. Mutants with greatly reduced aspartate taxis are described and characterized in this report. When present in single copy in the chromosome, these tar mutations generally eliminated chemotactic responses to aspartate and structurally related compounds, such as glutamate and methionine. Residual responses to these compounds were shifted to higher concentrations, indicating a reduced affinity of the aspartate-binding site in the mutant receptors. Maltose responses in the mutants ranged from 10 to 80% of normal, but had no detectable threshold shifts, indicating that these receptor alterations may have little effect on maltose detection sensitivity. The mutational changes in 17 mutants were determined by DNA sequence analysis. Each mutant exhibited a single amino acid replacement at residue 64, 69, or 73 in the Tar molecule. The wild-type Tar transducer contains arginines at all three of these positions, implying that electrostatic forces may play an important role in aspartate detection.     

Location of disulphide bridges by diagonal paper electrophoresis: The disulphide bridges of bovine chymotrypsinogen A

1. A new method is described for `fingerprinting' cysteic acid peptides derived from the disulphide bridges of proteins. Cystine peptides are separated by paper electrophoresis and oxidized on paper by performic acid vapour. Electrophoresis at right angles to the first direction produces parallel groups of cysteic acid peptides lying off a diagonal. This `fingerprint' reveals the way in which the cysteic acid peptides were originally joined in the protein. 2. The method allows a very easy selective purification of cysteic acid peptides. 3. By applying this method to bovine chymotrypsinogen A, we found that the half-cystine residues were linked 1–122, 42–58, 136–201, 168–182 and 191–220.     

Chemotactic responses of Escherichia coli to small jumps of photoreleased L-aspartate

Computer-assisted motion analysis coupled to flash photolysis of caged chemoeffectors provides a means for time-resolved analysis of bacterial chemotaxis. Escherichia coli taxis toward the amino acid attractant L-aspartate is mediated by the Tar receptor. The physiology of this response, as well as Tar structure and biochemistry, has been studied extensively. The beta-2, 6-dinitrobenzyl ester of L-aspartic acid and the 1-(2-nitrophenyl)ethyl ether of 8-hydroxypyrene-1,3,6-tris-sulfonic acid were synthesized. These compounds liberated L-aspartate and the fluorophore 8-hydroxypyrene 1,3,6-tris-sulfonic acid (pyranine) upon irradiation with near-UV light. Photorelease of the fluorophore was used to define the amplitude and temporal stability of the aspartate jumps employed in chemotaxis experiments. The dependence of chemotactic adaptation times on aspartate concentration, determined in mixing experiments, was best fit by two Tar aspartate-binding sites. Signal processing (excitation) times, amplitudes, and adaptive recovery of responses elicited by aspartate jumps producing less than 20% change in receptor occupancy were characterized in photorelease assays. Aspartate concentration jumps in the nanomolar range elicited measurable responses. The response threshold and sensitivity of swimming bacteria matched those of bacteria tethered to glass by a single flagellum. Stimuli of similar magnitude, delivered either by rapid mixing or photorelease, evoked responses of similar strength, as assessed by recovery time measurements. These times remained proportional to change in receptor occupancy close to threshold, irrespective of prior occupancy. Motor excitation responses decayed exponentially with time. Rates of excitation responses near threshold ranged from 2 to 7 s-1. These values are consistent with control of excitation signaling by decay of phosphorylated pools of the response regulator protein, CheY. Excitation response rates increased slightly with stimulus size up to values limited by the instrumentation; the most rapid was measured to be 16 +/- 3 (SE) s-1. This increase may reflect simultaneous activation of CheY dephosphorylation, together with inhibition of its phosphorylation.     

Covalent bonding of protein to polyamine in the cyst coat of the protozoan Colpoda steinii

1. High-voltage electrophoresis and chromatography before and after reaction with 5-dimethylaminonaphthalene-1-sulphonyl chloride have identified putrescine and spermidine in hydrolysates of cyst coat proteins from the protozoan Colpoda steinii. 2. Amounts present varied with putrescine up to 19.7 and spermidine up to 16.9 residues per 1000 amino acid residues. 3. The amines were not, in the main, removed by acid or alkaline extraction or by reprecipitation. They were present in hydrolysates of peptides isolated electrophoretically from acid-degraded coat protein. 4. Proteolysis of oxidised coat protein produced a soluble core polypeptide to which the major proportion of the amines were attached and which had a simple composition. It was composed almost entirely of glutamic acid or glutamine, glycine, serine and cysteic acid, these residues being present in the approximate ratio of 10:2:1:1. 5. When coat protein was treated with 5-dimethylaminonaphthalene-1-sulphonyl chloride and hydrolysed no fully substituted amines could be detected but putrescine with one group substituted and spermidine derivatives with one and two groups substituted were present.     

Solubilization of Chicken Feather Keratin by Ammonium Copper Hydroxide (Schweitzer’s Reagent)

Chicken feather powder was solubilized by Schweitzer’s reagent with shaking in the presence of air and the soluble feather keratin was prepared by dialyzing this extract against running water. Cystine residues in the starting feather keratin was converted to cysteic acid residues in the solubilized derivatives by air oxygen. Copper was bound fairly tightly to the solubilized protein and this copper-protein complex was separated into four fractions by CM- and DEAE-cellulose column chromatography. Each fraction had varied amount of bound copper, having a broad distribution of the molecular weight between 10,000 and 60,000 Sephadex column chromatographically. Although the amino acid composition of all separated feather keratin fractions were quite similar, the different electrophoretic patterns were observed among them by DISC electrophoresis.     

Ligand specificity determined by differentially arranged common ligand-binding residues in bacterial amino acid chemoreceptors Tsr and Tar

Escherichia coli has closely related amino acid chemoreceptors with distinct ligand specificity, Tar for l-aspartate and Tsr for l-serine. Crystallography of the ligand-binding domain of Tar identified the residues interacting with aspartate, most of which are conserved in Tsr. However, swapping of the nonconserved residues between Tsr and Tar did not change ligand specificity. Analyses with chimeric receptors led us to hypothesize that distinct three-dimensional arrangements of the conserved ligand-binding residues are responsible for ligand specificity. To test this hypothesis, the structures of the apo- and serine-binding forms of the ligand-binding domain of Tsr were determined at 1.95 and 2.5 Å resolutions, respectively. Some of the Tsr residues are arranged differently from the corresponding aspartate-binding residues of Tar to form a high affinity serine-binding pocket. The ligand-binding pocket of Tsr was surrounded by negatively charged residues, which presumably exclude negatively charged aspartate molecules. We propose that all these Tsr- and Tar-specific features contribute to specific recognition of serine and aspartate with the arrangement of the side chain of residue 68 (Asn in Tsr and Ser in Tar) being the most critical.     

A single amino acid substitution in the active site of Escherichia coli aspartate transcarbamoylase prevents the allosteric transition

Modeling of the tetrahedral intermediate within the active site of Escherichia coli aspartate transcarbamoylase revealed a specific interaction with the side-chain of Gln137, an interaction not previously observed in the structure of the X-ray enzyme in the presence of N-phosphonacetyl-L-aspartate (PALA). Previous site-specific mutagenesis experiments showed that when Gln137 was replaced by alanine, the resulting mutant enzyme (Q137A) exhibited approximately 50-fold less activity than the wild-type enzyme, exhibited no homotropic cooperativity, and the binding of both carbamoyl phosphate and aspartate were extremely compromised. To elucidate the structural alterations in the mutant enzyme that might lead to such pronounced changes in kinetic and binding properties, the Q137A enzyme was studied by time-resolved, small-angle X-ray scattering and its structure was determined in the presence of PALA to 2.7 angstroms resolution. Time-resolved, small-angle X-ray scattering established that the natural substrates, carbamoyl phosphate and L-aspartate, do not induce in the Q137A enzyme the same conformational changes as observed for the wild-type enzyme, although the scattering pattern of the Q137A and wild-type enzymes in the presence of PALA were identical. The overall structure of the Q137A enzyme is similar to that of the R-state structure of wild-type enzyme with PALA bound. However, there are differences in the manner by which the Q137A enzyme coordinates PALA, especially in the side-chain positions of Arg105 and His134. The replacement of Gln137 by Ala also has a dramatic effect on the electrostatics of the active site. These data taken together suggest that the side-chain of Gln137 in the wild-type enzyme is required for the binding of carbamoyl phosphate in the proper orientation so as to induce conformational changes required for the creation of the high-affinity aspartate-binding site. The inability of carbamoyl phosphate to create the high-affinity binding site in the Q137A enzyme results in an enzyme locked in the low-activity low-affinity T state. These results emphasize the absolute requirement of the binding of carbamoyl phosphate for the creation of the high-affinity aspartate-binding site and for inducing the homotropic cooperativity in aspartate transcarbamoylase.     

Cysteine Sulfinic Acid in the Central Nervous System: Specific Binding of [35S]Cysteic Acid to Cortical Synaptic Membranes-An Investigation of Possible Binding Sites for Cysteine Sulfinic Acid

Abstract: Specific binding sites for cysteine sulfinic acid, an excitatory amino acid, in crude synaptic membrane fractions of rat cerebral cortex were examined, using L-[³⁵S]cysteic acid as a ligand. Two specific binding systems of [³⁵S] cystec acid were found, one Na⁺-dependent and the other Na⁺-independent. The Na⁺-independent specific binding of [³⁵S]Cysteic acid was saturable, with a K_d of 474 n M and B_max of 3.29 pmol/mg protein. The binding was optimal at pH 7.4 and at 37°C. Treatment of the membranes with proteases, concanavalin A, or Triton X-100 markedly reduced the binding. Of various compounds related to cysteic acid, L-cysteine sulfinic acid was the most effective competitor of this binding. These results indicate the existence of an Na⁺-independent specific binding site for cysteic acid in the synaptic membrane of rat cerebral cortex, which may be different from that for glutamate. Possible involvement of cysteine sulfinic acid as an endogenous ligand for this binding site is discussed.     

Transport of Cysteate by Synaptosomes Isolated from Rat Brain: Evidence that It Utilizes the Same Transporter as Aspartate, Glutamate, and Cysteine Sulfinate

Synaptosomes isolated from rat brain accumulated cysteic acid by a high-affinity transport system (Km = 12.3 +/- 2.1 microM; Vmax = 2.5 nmol mg protein-1 min-1). This uptake was competitively inhibited by aspartate (Ki = 13.3 +/- 1.8 microM) and cysteine sulfinate (Ki = 13.3 +/- 2.3 microM). Addition of extrasynaptosomal cysteate, aspartate, or cysteine sulfinate to synaptosomes loaded with [35S]cysteate induced rapid efflux of the cysteate. This efflux occurred via stoichiometric exchange of amino acids with half-maximal rates at 5.0 +/- 1.1 microM aspartate or 8.0 +/- 1.3 microM cysteine sulfinate. Conversely, added extrasynaptosomal cysteate exchanged for endogenous aspartate and glutamate with half-maximal rates at 5.0 +/- 0.4 microM cysteate. In the steady state after maximal accumulation of cysteate, the intrasynaptosomal cysteate concentrations exceeded the extrasynaptosomal concentrations by up to 10,000-fold. The measured concentration ratios were the same, within experimental error, as those for aspartate and glutamate. Depolarization, with either high [K+] or veratridine, of the plasma membranes of synaptosomes loaded with cysteate caused parallel release of cysteate, aspartate, and glutamate. It is concluded that neurons transport cysteate, cysteine sulfinate, aspartate, and glutamate with the same transport system. This transport system catalyzes homoexchange and heteroexchange as well as net uptake and release of all these amino acids.     

Ribonuclease inhibitor from human placenta. Purification and properties

A soluble ribonuclease inhibitor from the human placenta has been purified 4000-fold by a combination of ion exchange and affinity chromatography. The inhibitor has been isolated in 45% yield (about 2 mg/placenta) as a protein that is homogeneous by sodium dodecyl sulfate-gel electrophoresis. In common with the inhibitors of pancreatic ribonuclease from other tissues that have been studied earlier, the placental inhibitor is an acidic protein of molecular weight near 50,000; it forms a 1:1 complex with bovine pancreatic RNase A and is a noncompetitive inhibitor of the pancreatic enzyme, with a Ki of 3 X 10(-10) M. The amino acid composition of the protein has been determined. The protein contains 30 half-cystine plus cysteine residues determined as cysteic acid after performic acid oxidation. At pH 8.6 the nondenatured protein alkylated with iodoacetic acid in the presence of free thiol has 8 free sulfhydryl groups. The inhibitor is irreversibly inactivated by sulfhydryl reagents and also by removal of free thiol from solutions of the protein. Inactivation by sulfhydryl reagents causes the dissociation of the RNase - inhibitor complex into active RNase and inactive inhibitor.     

Cysteine sulfinic acid decarboxylase activity of Aedes aegypti aspartate 1-decarboxylase: the structural basis of its substrate selectivity

Insect aspartate 1-decarboxylase (ADC) catalyzes the decarboxylation of aspartate to β-alanine. Insect ADC proteins share high sequence identity to mammalian cysteine sulfinic acid decarboxylase (CSADC), but there have been no reports indicating any CSADC activity in insect ADC or any ADC activity in mammalian CSADC. Substrate screening of Aedes aegypti ADC (AeADC), however, demonstrates that other than its activity to aspartate, the mosquito enzyme catalyzes the decarboxylation of cysteine sulfinic acid and cysteic acid as efficiently as those of mammalian CSADC under the same testing conditions. Further analysis of Drosophila melanogaster ADC also demonstrated its CSADC activity, suggesting that all insect ADC likely has CSADC activity. This represents the first identification of CSADC activity of insect ADC. On the other hand, HuCSADC displayed no detectable activity to aspartate. Homology modeling of AeADC and substrate docking suggest that residue Q377, localized at the active site of AeADC, could better interact with aspartate through hydrogen bonding, which may play a role in aspartate selectivity. A leucine residue in mammalian CSADC occupies the same position. A mutation at position 377 from glutamine to leucine in AeADC diminished its decarboxylation activity to aspartate with no major effect on its CSADC activity. Comparison of insect ADC sequences revealed that Q377 is stringently conserved among the available insect ADC sequences. Our data clearly established the CSADC activity of mosquito and Drosophila ADC and revealed the primary role Q377 plays in aspartate selectivity in insect ADC.     

Proteolytic fragments identified with domains of the aspartate chemoreceptor

Two proteolytic fragments generated during the preparation of the aspartate receptor from Salmonella typhimurium have been purified. These fragments are the products of a single cleavage by an endogenous protease after amino acid 259 in the sequence of the intact receptor. Proteolytic fragment 1 (PF1) represents amino acids 1-259 (Mr = 29,000); this unit retains the aspartate-binding function of the intact receptor. The second fragment (PF2) includes residues 260-552 (Mr = 31,000) and has the normal sites of reversible methylation for the receptor. Like the purified intact receptor, this fragment can be methylated in vitro, although at a much slower rate. Circular dichroic measurements suggest that both proteolytic fragments contain substantial alpha-helical structure, approximately 95 and 53% for PF1 and PF2, respectively. No beta-structure could be detected in either fragment. Molecular sieve chromatography in the presence of detergent suggests that PF1 occurs as a stable multimer of an order equivalent to that observed for the detergent-solubilized aspartate receptor, i.e. a tetramer (+/- 1). PF2 is found to have a multimeric form which is sensitive to the removal of detergent. It is proposed that these fragments represent structural and functional domains of the aspartate receptor.     

Alteration in the Amino Acid Content of Yeast During Growth Under Various Nutritional Conditions

Yeast cells grown under optimal and suboptimal concentrations of biotin were analyzed for the amino acid content of their soluble pool and cellular protein. Optimally grown yeast cells exhibited a maximum amino acid content after 18 hr of growth. Biotin-deficient cells were depleted of all amino acids at 26 and 43 hr, with alanine, arginine, aspartate, cysteine, glutamate, isoleucine, leucine, lysine, methionine, serine, threonine, and valine being present in less than half the concentration observed in biotin-optimal cells. At early time intervals, the amino acid pool of biotin-deficient yeast contained lower concentrations of all amino acids except alanine. After more prolonged incubation, several amino acids accumulated in the pool of biotin-deficient yeast, but citrulline and ornithine accumulated to appreciable levels. The addition of aspartate to the growth medium resulted in a decrease in the amino acid content of biotin-optimal cells but caused a marked increase in the concentration of amino acids in biotin-deficient cells. The pools of biotin-deficient yeast grown in the presence of aspartate displayed a marked reduction in every amino acid with the exception of aspartate itself. These data provide evidence that the amino acid content of yeast cells and their free amino acid pools are markedly affected by biotin deficiency as well as by supplementation with aspartate, indicating that aspartate plays a major role in the nitrogen economy of yeast under both normal as well as abnormal nutritional conditions.     

温和过甲酸氧化辅助酶解结合液质联用技术鉴定大鼠大脑皮层质膜蛋白质

由于膜蛋白质尤其是内在膜蛋白的强疏水性,分析和鉴定质膜蛋白质仍然是以质谱为基础的蛋白质组学的方法中的一个难点.过甲酸氧化是一种应用广泛的打开二硫键的方法,温和的过甲酸试剂能完全的将半胱氨酸转化为半胱磺酸,将甲硫氨酸转化为甲硫氨酸砜,从而使目的蛋白更易溶于水介质.采用蔗糖密度梯度离心法纯化得到大鼠大脑皮层质膜,提取的质膜蛋白质经温和过甲酸氧化处理后经胰酶酶解消化得到肽段,利用LC-MS/MS对所得肽段进行质谱分析,采集的原始数据用Mascot软件进行库搜寻鉴定.此方法是研究质膜蛋白质的新方法,温和过甲酸氧化显示出很好的氧化效果却避免其它不利于鉴定的副反应.从大鼠大脑皮层膜提取物共鉴定出220种蛋白质,其中73种为整合膜蛋白,证明对质膜蛋白质直接进行温和过甲酸氧化然后酶解的方法辅助酶解可以有效的鉴定质膜蛋白质.     

Effect of Depolarizing Agents on the Incorporation of Amino Acids into Soluble Cytoplasmic and Membrane-Bound Proteins of Synaptosome Fractions

Abstract: The incorporation of [U-¹⁴C] protein hydrolysate and [U-¹⁴C]leucine into the trichloroacetic acid (TCA)-insoluble membrane and the soluble synaptoplasm proteins of synaptosomes was studied. Following treatment with the depolarizing agents veratrine, Tityus toxin, or potassium, the specific radioactivity of both precursor pool and proteins was measured to examine the link between protein labeling and the fall in the free amino acid pool due to depolarization-induced release of glutamate and aspartate. By reducing the size of the fall in precursor pool due to depolarization by using a nontransmitter amino acid such as leucine (as compared with the usual use of protein hydrolysate), it was shown that the amount by which the pool is reduced is proportional to the change in the protein labeling observed. These results confirm that membrane depolarization causes a large increase in the labeling of membrane-bound proteins as compared with the soluble synaptosomal proteins.