Oxidation of buried cysteines is slow and an insignificant factor in the structural destabilization of staphylococcal nuclease caused by H<Subscript>2</Subscript>O<Subscript>2</Subscript> exposure

Summary. The oxidation of buried cysteine or methionine residues can destroy the enzyme activity of a protein by disrupting structure. Engineering in such an oxidatively triggered switch for enzyme activity would only be useful if the effects of substitution are relatively minor, while the effects of the oxidized side chain upon structure are significant and the oxidation relatively easy. To assess the feasibility of this strategy for controlling enzyme activity, the effects of such substitutions and their oxidation were studied in a well characterized model protein, staphylococcal nuclease. Stability and enzyme activity of the oxidized proteins was assessed and compared to the stability and enzyme activity of the unoxidized proteins. Cysteines were found to be generally well tolerated in buried positions but these mutants were not more destabilized than wild-type when oxidized. This shows that buried cysteines are difficult enough to oxidize that this is not likely to be a useful protein engineering strategy or a commonly used regulatory modification. Similar effects were observed for methionine.     

Dityrosine as a product of oxidative stress and fluorescent probe

Summary. Dityrosine can be a natural component of protein structure, a product of environmental stress, or a product of in vitro protein modification. It is both a cross-link and a fluorescent probe that reports structural and functional information on the cross-linked protein molecule. Diverse reactions produce tyrosyl radicals, which in turn may couple to yield dityrosine. Identification and quantitation of dityrosine in protein hydrolysates usually employs reversed phase high pressure liquid chromatography (RP-HPLC) or gas chromatography. RP-HPLC of protein hydrolysates that have been derivatized with dabsyl chloride gives a complete amino acid analysis that includes dityrosine and 3-nitrotyrosine. Calmodulin, which contains a single pair of tyrosyl residues, undergoes both photoactivated and enzyme-catalyzed dityrosine formation. Polarization measurements, employing the intrinsic fluorescence of dityrosine, and catalytic activity determinations show how different patterns of inter- and intramolecular cross-linking affect the interactions of calmodulin with Ca²⁺ and enzymes.     

Free radical-mediated oxidation of free amino acids and amino acid residues in proteins

Summary. We summarize here results of studies designed to elucidate basic mechanisms of reactive oxygen (ROS)-mediated oxidation of proteins and free amino acids. These studies have shown that oxidation of proteins can lead to hydroxylation of aromatic groups and aliphatic amino acid side chains, nitration of aromatic amino acid residues, nitrosylation of sulfhydryl groups, sulfoxidation of methionine residues, chlorination of aromatic groups and primary amino groups, and to conversion of some amino acid residues to carbonyl derivatives. Oxidation can lead also to cleavage of the polypeptide chain and to formation of cross-linked protein aggregates. Furthermore, functional groups of proteins can react with oxidation products of polyunsaturated fatty acids and with carbohydrate derivatives (glycation/glycoxidation) to produce inactive derivatives. Highly specific methods have been developed for the detection and assay of the various kinds of protein modifications. Because the generation of carbonyl derivatives occurs by many different mechanisms, the level of carbonyl groups in proteins is widely used as a marker of oxidative protein damage. The level of oxidized proteins increases with aging and in a number of age-related diseases. However, the accumulation of oxidized protein is a complex function of the rates of ROS formation, antioxidant levels, and the ability to proteolytically eliminate oxidized forms of proteins. Thus, the accumulation of oxidized proteins is also dependent upon genetic factors and individual life styles. It is noteworthy that surface-exposed methionine and cysteine residues of proteins are particularly sensitive to oxidation by almost all forms of ROS; however, unlike other kinds of oxidation the oxidation of these sulfur-containing amino acid residues is reversible. It is thus evident that the cyclic oxidation and reduction of the sulfur-containing amino acids may serve as an important antioxidant mechanism, and also that these reversible oxidations may provide an important mechanism for the regulation of some enzyme functions.     

Genetic manipulation of the γ‐aminobutyric acid (GABA) shunt in rice: overexpression of truncated glutamate decarboxylase (GAD2) and knockdown of γ‐aminobutyric acid transaminase (GABA‐T) lead to sustained and high levels of GABA accumulation in rice kernels

Gamma‐aminobutyric acid (GABA) is a non‐protein amino acid commonly present in all organisms. Because cellular levels of GABA in plants are mainly regulated by synthesis (glutamate decarboxylase, GAD) and catabolism (GABA‐transaminase, GABA‐T), we attempted seed‐specific manipulation of the GABA shunt to achieve stable GABA accumulation in rice. A truncated GAD2 sequence, one of five GAD genes, controlled by the glutelin (GluB‐1) or rice embryo globulin promoters (REG) and GABA‐T‐based trigger sequences in RNA interference (RNAi) cassettes controlled by one of these promoters as well, was introduced into rice (cv. Koshihikari) to establish stable transgenic lines under herbicide selection using pyriminobac. T₁ and T₂ generations of rice lines displayed high GABA concentrations (2–100 mg/100 g grain). In analyses of two selected lines from the T₃ generation, there was a strong correlation between GABA level and the expression of truncated GAD2, whereas the inhibitory effect of GABA‐T expression was relatively weak. In these two lines both with two T‐DNA copies, their starch, amylose, and protein levels were slightly lower than non‐transformed cv. Koshihikari. Free amino acid analysis of mature kernels of these lines demonstrated elevated levels of GABA (75–350 mg/100 g polished rice) and also high levels of several amino acids, such as Ala, Ser, and Val. Because these lines of seeds could sustain their GABA content after harvest (up to 6 months), the strategy in this study could lead to the accumulation GABA and for these to be sustained in the edible parts.     

Histidine and lysine as targets of oxidative modification

Summary. Histidine and lysine are two representative targets of oxidative modifications. Histidine is extremely sensitive to a metal-catalyzed oxidation, generating 2-oxo-histidine and its ring-ruptured products, whereas the oxidation of lysine generates carbonyl products, such as aminoadipic semialdehyde. On the other hand, both histidine and lysine are nucleophilic amino acids and therefore vulnerable to modification by lipid peroxidation-derived electrophiles, such as 2-alkenals, 4-hydroxy-2-alkenals, and ketoaldehydes, derived from lipid peroxidation. Histidine shows specific reactivity toward 2-alkenals and 4-hydroxy-2-alkenals, whereas lysine is a ubiquitous target of aldehydes, generating various types of adducts. Covalent binding of reactive aldehydes to histidine and lysine is associated with the appearance of carbonyl reactivity and antigenecity of proteins.     

Isolation and characterization of a polymorphic stigma-specific class III peroxidase gene from <Emphasis Type="Italic">Senecio squalidus</Emphasis> L. (Asteraceae)

A novel stigma-specific class III peroxidase gene, SSP (Stigma-Specific Peroxidase), has been isolated from the self-incompatible daisy Senecio squalidus L. (Asteraceae). Expression of SSP in flower buds is developmentally regulated, with maximal levels of expression coinciding with anthesis, when stigmas are most receptive to pollen and when self-incompatibility is fully developed. In situ hybridization revealed SSP expression to be localized exclusively to the specialized secretory epidermal cells (papillae) of the stigma, which receive and discriminate pollen. SSP is therefore the first tissue-specific and cell-specific peroxidase gene identified in a plant. SSP belongs to a distinct clade of class III plant peroxidases that possess two introns, instead of the more normal situation of three conserved introns. The deduced amino acid sequence of SSP revealed a 27 amino acid signal peptide, suggesting that the SSP protein is secreted to the cell wall of the stigmatic papillae. In-gel peroxidase activity assays showed that SSP has relatively low peroxidase activity compared to other, as yet uncharacterized, peroxidases present in stigmatic extracts. Six SSP alleles have been cloned from different lines of S. squalidus carrying a range of self-incompatibility (S)-alleles but there was no consistent association between the presence of a particular SSP allele and S-genotype indicating that SSP is not the female determinant of SSI in S. squalidus. Nevertheless, the precise expression of SSP in stigmatic papillae suggests that it may have a more general function in pollen–stigma interactions, or alternatively in protection of stigmas from pathogen attack. Extensive database screens have identified homologues of SSP in other plant species, but available expression data for these genes indicates that none are flower-specific, suggesting that SSP represents a new functional type of class III peroxidase specific to the stigma. We discuss the possible function(s) of S. squalidus SSP in pollen–stigma interactions and in protection of stigmas from pathogen attack.     

Biotin tagging coupled with amino acid‐coded mass tagging for efficient and precise screening of interaction proteome in mammalian cells

In mammalian cells, when tandem affinity purification approach is employed, the existence of untagged endogenous target protein and repetitive washing steps together result in overall low yield of purified/stable complexes and the loss of weakly and transiently interacting partners of biological significance. To avoid the trade‐offs involving in methodological sensitivity, precision, and throughput, here we introduce an integrated method, biotin tagging coupled with amino acid‐coded mass tagging, for highly sensitive and accurate screening of mammalian protein–protein interactions. Without the need of establishing a stable cell line, using a short peptide tag which could be specifically biotinylated in vivo, the biotin‐tagged target/bait protein was then isolated along with its associates efficiently by streptavidin magnetic microbeads in a single step. In a pulled‐down complex amino acid‐coded mass tagging serves as “in‐spectra” quantitative markers to distinguish those bait‐specific interactors from non‐specific background proteins under stringent criteria. Applying this biotin tagging coupled with amino acid‐coded mass tagging approach, we first biotin‐tagged in vivo a multi‐functional protein family member, 14‐3‐3ε, which was expressed at close to endogenous level. Starting with approximately 20 millions of 293T cells which were significantly less than what needed for a tandem affinity purification run, 266 specific interactors of 14‐3‐3ε were identified in high confidence.     

Pollen S–locus F–box proteins of Petunia involved in S–RNase‐based self‐incompatibility are themselves subject to ubiquitin‐mediated degradation

Many flowering plants show self‐incompatibility, an intra‐specific reproductive barrier by which pistils reject self‐pollen to prevent inbreeding and accept non‐self pollen to promote out‐crossing. In Petunia, the polymorphic S–locus determines self/non‐self recognition. The locus contains a gene encoding an S–RNase, which controls pistil specificity, and multiple S‐locus F‐box (SLF) genes that collectively control pollen specificity. Each SLF is a component of an SCF (Skp1/Cullin/F‐box) complex that is responsible for mediating degradation of non‐self S‐RNase(s), with which the SLF interacts, via the ubiquitin–26S proteasome pathway. A complete set of SLFs is required to detoxify all non‐self S‐RNases to allow cross‐compatible pollination. Here, we show that SLF1 of Petunia inflata is itself subject to degradation via the ubiquitin–26S proteasome pathway, and identify an 18 amino acid sequence in the C‐terminal region of S₂‐SLF1 (SLF1 of S₂ haplotype) that contains a degradation motif. Seven of the 18 amino acids are conserved among all 17 SLF proteins of S₂ haplotype and S₃ haplotype involved in pollen specificity, suggesting that all SLF proteins are probably subject to similar degradation. Deleting the 18 amino acid sequence from S₂‐SLF1 stabilized the protein but abolished its function in self‐incompatibility, suggesting that dynamic cycling of SLF proteins is an integral part of their function in self‐incompatibility.     

Threonine is the best substrate for <Emphasis Type="SmallCaps">D</Emphasis>-lactate formation in octopus tentacle

Summary. Carbon sources for D-lactate and enzyme activities related to D-lactate formation were investigated using cell-free homogenates of Octopus vulgaris tentacle tissue. The results are as follows: a) The best precursor for D-lactate formation was threonine and second best precursors were glycine and fructose-1,6-bisphosphate. Threonine and glycine served as precursors only in presence of glutathione. b) Both amino acids were precursors for methylglyoxal from which D-lactate was synthesized. Alanine, cysteine and serine were not precursors. We present a metabolic map for D-lactate formation in octopus in order to explain these experimental results.     

Allosteric mechanisms in ACT domain containing enzymes involved in amino acid metabolism

Summary. An important sequence motif identified by sequence analysis is shared by the ACT domain family, which has been found in a number of diverse proteins. Most of the proteins containing the ACT domain seem to be involved in amino acid and purine synthesis and are in many cases allosteric enzymes with complex regulation enforced by the binding of ligands. Here we explore the current understanding of the ACT domain function including its role as an allosteric module in a selected group of enzymes. We will further describe in more detail three of the proteins where some understanding is available on function and structure: i) the archetypical ACT domain protein E. coli 3PGDH, which catalyzes the first step in the biosynthesis of L-Ser, ii) the bifunctional chorismate mutase/prephenate dehydratase (P-protein) from E. coli, which catalyzes the first two steps in the biosynthesis of L-Phe, and iii) the mammalian aromatic amino acid hydroxylases, with special emphasis on phenylalanine hydroxylase, which catalyzes the first step in the catabolic degradation of L-phenylalanine (L-Phe). The ACT domain is commonly involved in the binding of a small regulatory molecule, such as the amino acids L-Ser and L-Phe in the case of 3PGDH and P-protein, respectively. On the other hand, for PAH, and probably for other enzymes, this domain appears to have been incorporated as a handy, flexible small module with the potential to provide allosteric regulation via transmission of finely tuned conformational changes, not necessarily initiated by regulatory ligand binding at the domain itself.Current address: Protein Biophysics & Delivery, Novo Nordisk A/S, Novo Allé, 2880 Bagsværd, Denmark.     

Vitamin C protects low-density lipoprotein from homocysteine-mediated oxidation

Homocysteine, an atherogenic amino acid, promotes iron-dependent oxidation of low-density lipoprotein (LDL). We investigated whether vitamin C, a physiological antioxidant, could protect LDL from homocysteine-mediated oxidation. LDL (0.2 mg of protein/ml) was incubated at 37 degrees C with homocysteine (1000 microM) and ferric iron (10-100 microM) in either the absence (control) or presence of vitamin C (5-250 microM). Under these conditions, vitamin C protected LDL from oxidation as evidenced by an increased lag time preceding lipid diene formation (> or = 5 vs. 2.5 h for control), decreased thiobarbituric acid-reactive substances accumulation (< or = 19 +/- 1 nmol/mg when vitamin C > or = 10 microM vs. 32 +/- 3 nmol/mg for control, p <.01), and decreased lipoprotein anodic electrophoretic mobility. Near-maximal protection was observed at vitamin C concentrations similar to those in human blood (50-100 microM); also, some protection was observed even at low concentrations (5-10 microM). This effect resulted neither from altered iron redox chemistry nor enhanced recycling of vitamin E in LDL. Instead, similar to previous reports for copper-dependent LDL oxidation, we found that vitamin C protected LDL from homocysteine-mediated oxidation through covalent lipoprotein modification involving dehydroascorbic acid. Protection of LDL from homocysteine-mediated oxidation by vitamin C may have implications for the prevention of cardiovascular disease.     

Measurement of 5-hydroxy-2-aminovaleric acid as a specific marker of iron-mediated oxidation of proline and arginine side-chain residues of low-density lipoprotein apolipoprotein B-100

An alteration of apolipoprotein (apo) B-100 structure by direct oxidative modification is supposed to be an important mechanism involved in atherogenesis. There is difficulty in quantifying this type of modification owing to a lack of specific assays. We evaluated a methodology based on the oxidation of protein arginine and proline to gamma-glutamyl semialdehyde which by reduction forms 5-hydroxy-2-aminovaleric acid (HAVA). We determined HAVA by using derivatization to N(O)-ethoxycarbonyl ethyl esters and gas chromatography-mass spectrometry in different low-density lipoprotein preparations subjected to oxidative damage in the presence of iron. Results suggest that apoB-100 proline and arginine residues are highly reactive toward oxygen radicals ex vivo. Femtomole levels of HAVA can be reproducible measured. HAVA determination compares well with the measurement of carbonyl group formation used as a generally accepted but nonspecific index of protein oxidation. Thus, HAVA could prove to be a sensitive assay for studying specific modification of apoB-100.     

Patterns of diversification in two species of short‐tailed bats (Carollia Gray, 1838): the effects of historical fragmentation of Brazilian rainforests

The small‐sized frugivorous bat Carollia perspicillata is an understory specialist and occurs in a wide range of lowland habitats, tending to be more common in tropical dry or moist forests of South and Central America. Its sister species, Carollia brevicauda, occurs almost exclusively in the Amazon rainforest. A recent phylogeographic study proposed a hypothesis of origin and subsequent diversification for C. perspicillata along the Atlantic coastal forest of Brazil. Additionally, it also found two allopatric clades for C. brevicauda separated by the Amazon Basin. We used cytochrome b gene sequences and a more extensive sampling to test hypotheses related to the origin and diversification of C. perspicillata plus C. brevicauda clade in South America. The results obtained indicate that there are two sympatric evolutionary lineages within each species. In C. perspicillata, one lineage is limited to the Southern Atlantic Forest, whereas the other is widely distributed. Coalescent analysis points to a simultaneous origin for C. perspicillata and C. brevicauda, although no place for the diversification of each species can be firmly suggested. The phylogeographic pattern shown by C. perspicillata is also congruent with the Pleistocene refugia hypothesis as a likely vicariant phenomenon shaping the present distribution of its intraspecific lineages. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102 , 527–539.     

Cloning and Functional Expression of the Mucrosobin Protein, a β-Fibrinogenase of Trimeresurus mucrosquamatus (Taiwan Habu)

A venom-specific cDNA encoding for a thrombin-like enzyme designated as mucrosobin has been cloned and sequenced from the cDNA library of the venomous gland of Trimeresurus mucrosquamatus. The full-length cDNA of mucrosobin was assembled by oligonucleotide screening and 5′-rapid amplification of cDNA ends. The amino acid sequence deduced from the cDNA consists of 257 amino acid residues with a putative signal peptide of 24 residues. It is highly homologous to the other thrombin-like enzymes (batroxobin, mucofirase, and calobin), suggesting that it is a serine proteinase with a conserved catalytic triad of His⁴¹, Asp⁸⁴ and Ser¹⁷⁹ in the deduced form of mucrosobin protein. Northern blot analysis revealed that the mucrosobin gene encodes an mRNA of 1.5 kb and suggested a tissue-specific expression in the venomous gland. In an effort to study the biological property of mocrosobin, we have expressed the 28-kDa protein as inclusion bodies in Escherichia coli. For analyzing enzymatic activity, the inclusion bodies were solubilized and the recombinant protein was refolded with a two-step dialysis protocol. The refolded recombinant protein exhibited a specific β-fibrinogenolytic activity. This study offers a possibility of using genetic engineering to acquirie a functional snake venom protein with therapeutic potential.     

Syntheses,Receptor Bindings,in vitro and in vivo Stabilities and Biodistributions of DOTA‐Neurotensin(8–13) Derivatives Containing β‐Amino Acid Residues – A Lesson about the Importance of Animal Experiments

Neurotensin(8–13) (NTS(8–13)) analogs with C‐ and/or N‐terminal β‐amino acid residues and three DOTA derivatives thereof have been synthesized (i.e., 1 – 6 ). A virtual docking experiment showed almost perfect fit of one of the 1,4,7,10‐tetraazacyclododecane‐1,4,7,10‐tetraacetic acid (DOTA) derivatives, 6a , into a crystallographically identified receptor NTSR1 (Fig. 1). The affinities for the receptors of the NTS analogs and derivatives are low, when determined with cell‐membrane homogenates, while, with NTSR1‐exhibiting cancer tissues, affinities in the single‐digit nanomolar range can be observed (Table 2). Most of the β‐amino acid‐containing NTS(8–13) analogs (Table 1 and Fig. 2), including the ⁶⁸Ga complexes of the DOTA‐substituted ones ( 6 ; Figs. 2 and 5), are stable for ca. 1 h in human serum and plasma, and in murine plasma. The biodistributions of two ⁶⁸Ga complexes (of 6a and 6b ) in HT29 tumor‐bearing nude mice, in the absence and in the presence of a blocking compound, after 10, 30, and 60 min (Figs. 3 and 4) lead to the conclusion that the amount of specifically bound radioligand is rather low. This was confirmed by PET‐imaging experiments with the tumor‐bearing mice (Fig. 6). Comparison of the in vitro plasma stability (after 1 h) with the ex vivo blood content (after 10–15 min) of the two ⁶⁸Ga complexes shows that they are rapidly cleaved in the animals (Fig. 5).     

The use of N-urethane-protected N-carboxyanhydrides (UNCAs) in amino acid and peptide synthesis

N-Urethane-protected N-carboxyanhydrides (UNCAs) are very reactives. They have been successfully used in peptide synthesis, in both solution and solid phase. We have demonstrated that UNCAs are interesting starting materials for the synthesis of various amino acid derivatives. Chemoselective reduction of UNCAs with sodium borohydride led the corresponding N-protected β amino alcohols. Reaction of UNCAs with Meldrum's acid, followed by cyclisation, yielded enantiomerially pure tetramic acid derivatives. Diastereoselective reduction of tetramic acid derivatives produced (4S,5S)-N-alkoxycarbonyl-4-hydroxy-5-alkylpyrrolidin-2-ones derived from amino acids, which after hydrolysis yielded statine and statine analogues. Tetramic acid derivatives could also be obtained by reaction of UNCAs with benzyl ethyl followed by hydrogenolytic deprotection and decarboxylation. UNCAs also reacted with phosphoranes to produce the ketophosphorane in excellent yields. Subsequent oxidation with oxone or with [bis(acetoxy)-iodol]-benzene produced vicinal tricarbonyl derivatives. These reactions usually proceeded smoothly and with high yields.     

Genetic differentiation of populations of Iberian rock‐lizards Iberolacerta (Iberolacerta) sensuArribas (1999)

The genetic structure and relationships of five populations of the Iberian group of Iberolacerta (sensu 6 ) were analysed by protein electrophoresis. In this study we confirmed the differentiation between the group of populations from Galicia/Cantabrian/S. Estrela versus the group of populations from de Spanish Central System, Gredos and Guadarrama that are included in the two different species by Arribas (Herpetozoa 9(1/2), 31–56, 1996; Russian J. Herpetol. 6, 1–22, 1999), Iberolacerta (I.) monticola and Iberolacerta (I.) cyreni, respectively. However, the differentiation level is not high enough to clearly prove their specific discrimination. On the other hand, we did not confirm the subspecific discrimination of the Gredos –Iberolacerta (I.) cyreni castiliana, and Guadarrama –Iberolacerta (I.) cyreni cyreni populations, proposed by 5 ). These two populations are genetically almost homogeneous. Interestingly, we found an unexpected high genetic similarity between the Galician and the Serra da Estrela populations, presently included into two different subspecies, Iberolacerta (I.) monticola cantabrica and Iberolacerta (I.) monticola monticola, respectively. Their genetic similarity is even higher than that between the populations of Galicia and the Cantabrian Mountains, which are both included in the same subspecies, cantabrica. This result suggests that the populations of Galicia and Serra da Estrela would have maintained contacts, possibly through the north of Portugal, until relatively recent times. Their separation is thus probably post‐glacial. Some evidence also points to the existence of relatively recent contacts between the population of Serra da Estrela and those of the Central System, particularly, with the neighbouring Peña de Francia population. With the cautions imposed by the reduced sample size of our analysis, the significant differentiation of the populations from Galicia and the Cantabrian Mountains allow us to suggest that this last population may not be the result of a recent expansion of the Galician population as 5 ) suggests, but, more likely, the result of a fragmentation process of a more ancient and wider north‐eastern distribution area of this group of rock‐lizards.