Spectroscopic studies on the tyrosine residues of canavalin.

Canavalin is a tetramer with 6 tyrosines per subunit. In the work presented here, we have classified these tyrosines by their spectrophotometric and fluorometric pH titration and their ability to be quenched I-. Of the 6 residues, 2 were found to be exposed to the solvent. One (pK = 10.2) contributes 28% of the total fluorescence intensity; the second has a pK of 11.50, and a lower quantum yield, contributing only 16% of the total intensity. The remaining 4 residues (pK = 12.5, contributing 54% of fluorescence intensity) are buried; their titration is irreversible, requiring protein denaturation.     

Spectroscopic studies of the tyrosine residues of human plasma apolipoprotein A-II

Human apolipoprotein A-II (apo A-II) in solution and associated with 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) was investigated by a combination of absorbance and fluorescence methods. Each apo A-II polypeptide chain contains four tyrosine residues but no tryptophan residues. Two and three tyrosine residues, respectively, appear to be buried for apo A-II in aqueous solution and in the lipid-associated protein. The spectroscopic properties of the tyrosine residues of lipid-associated apo A-II were also investigated. Plots of fluorescence intensity against temperature revealed a discontinuity in the region of the phase transition; however, over the same temperature range, there was no change in the exposure of tyrosine residues to the aqueous environment or in their mobility as measured by fluorescence polarization. Near-ultraviolet circular dichroic measurements demonstrated that the environments of the tyrosine residues of lipid-associated apo A-II and nitrated apo A-II were different from that of the apo A-II in solution or in a denatured state. Similar measurements also revealed that the microenvironments around tyrosines of apo A-II bound to DMPC in the gel phase are different from those observed in the liquid crystalline phase. Using environmentally sensitive fluorescence lipid probes, we have previously demonstrated that the polarity of the lipid/water interface of DMPC changes through a phase transition. The observations presented here indicate that these environmental changes also occur at the lipid/protein interface.     

Photoreactivity of histidyl residues in subtilisins Novo and DY. Photooxidation of subtilisins

Subtilisins Novo and DY were photoinactivated in the presence of methylene blue according to first order kinetics. The competitive inhibitor N alpha-benzoyl-L-arginine protected significantly against inactivation. Under the conditions employed in this study a selective photooxidation of the active site histidine 64 was achieved. Rate constants of 0.32 X 10(-2), s-1 and 0.35 X 10(-2), s-1, were calculated for the Novo enzyme and subtilisin DY, respectively. Apparent pKa values of the catalytically important imidazole group of 7.0 +/- 0.1 (s. Novo) and 7.1 +/- 0.1 (s. DY) were directly determined. The histidyl residues in the two proteases, except the active site histidine, which is the first target of photooxidation, are "buried" in the interior of the protein globule. Conformational studies suggested that the photoreactive histidine is not involved in the stabilization of the protein conformation.     

Interactions of aromatic residues of proteins with nucleic acids. Fluorescence studies of the binding of oligopeptides containing tryptophan and tyrosine residues to polynucleotides.

The binding of oligopeptides of general structure Lys-X-Lys (where X is an aromatic residue) to several polynucleotides has been studied by fluorescence spectroscopy. Two types of complexes are formed, both involving electrostatic interactions between lysyl residues and phosphate groups as shown by the ionic strength and pH dependence of binding. The fluorescence quantum yield of the first complex is identical with that of the free peptide. The other complex involves a stacking of the nucleic acid bases with the aromatic amino acid whose fluorescence is quenched. Fluorescence data have been quantitatively analyzed according to a model involving these two types of complexes. Association constants and the size of binding sites have been determined. Stacking interactions are favored in single-stranded polynucleotides as compared to double-stranded ones. A short oligopeptide such as Lys-X-Lys is thus able to distinguish between single-stranded and double-stranded nucleic acids. Fluorescence results are compared to those obtained by proton magnetic resonance and circular dichroism.     

Conjugation of glutathione to oxidized tyrosine residues in peptides and proteins

Tyrosine residues are sensitive to oxidation and can be converted to hydroperoxides either by superoxide reacting with the Tyr radical or by singlet oxygen. These hydroperoxides rearrange to bicyclic derivatives that are readily reduced to more stable hydroxides. The aromatic character of tyrosine is lost, but the product contains an α-β unsaturated carbonyl group and is, therefore, an electrophile. We have generated hydroxide derivatives of several Tyr-containing peptides and shown using liquid chromatography/mass spectrometry that they undergo Michael addition with GSH. For Tyr-Gly, rate constants of 9.2 and 11.8 m(-1)min(-1) were measured for the two chromatographically distinct isomers. Unusual for GSH addition to an electrophile, the reaction is reversible, with a half-life of many hours for the reverse reaction. These kinetics indicate that with a typical cellular concentration of 5 mm GSH, >95% Tyr-Gly hydroxide would become conjugated with a half-life of ～15 min. Sperm whale myoglobin forms a hydroperoxide on Tyr-151 in a hydrogen peroxide/superoxide-dependent reaction. We show that its hydroxide derivative reacts with GSH to form a conjugate. Detection of the conjugate required stabilization by reduction; otherwise, the reverse reaction occurred during tryptic digestion and analysis. Our findings represent a novel mechanism for peptide or protein glutathionylation involving a carbon-sulfur cross-link between oxidized Tyr and Cys. As with other electrophiles, the oxidized Tyr should undergo a similar reaction with Cys residues in proteins to give intramolecular or intermolecular protein cross-links. This mechanism could give rise to protein cross-linking in conditions of oxidative stress.     

Comparison of two mass-selective detectors with special reference to the analysis of residues of anabolics

In the analysis of residues of anabolic agents the use of combined techniques, especially gas chromatography—mass spectrometry, is of increasing interest. When this method is used for the analysis of residues of anabolics it is very important to have a knowledge of the characteristics of the different types of apparatus on the market and to be sure that the results are not “apparatus-dependent”. In this study two mass-selective detectors, the Hewlett-Packard 5970 and the ion trap detector 800, were compared by injecting the same samples of derivatized anabolics (standard solutions) into the two systems.     

Hydroxyl radical mediated damage to proteins, with special reference to the crystallins.

Oxidative modification of the eye lens proteins, the crystallins, is known to cause protein cross-links and aggregates which lead to lens opacification or cataracts. We focus attention here on oxidative damage occurring in crystallins and some "control" proteins upon reaction with the hydroxyl radical (.OH) which, in the lens, is generated by photosensitization or by the Fenton reaction. In the present study, we have synthesized and used the bishydroperoxide I as a "photo-Fenton" reagent, in order to photolytically generate pure .OH, free of other oxyradicals. Our findings are the following: (i) Trp residues are oxidized by .OH to N-formylkynurenine and related compounds, but this in itself does not lead to covalent aggregation of the protein. (ii) Tyr residues react with .OH, but apparently do not produce dihydroxyphenylalanine or bityrosine. Nor do protein cross-links occur as a result. (iii) Oxidation of His residues appears to be obligatory for protein cross-linking. Histidine-free proteins do not form high molecular weight products upon reaction with .OH. Protection of His residues by adduct formation in other proteins inhibits cross-linking. (iv) Lys residues seem to participate in the cross-linking reaction. Protection of the Lys residues by maleylation of the protein inhibits cross-linking. (v) The oxidized protein is more acidic in nature than the parent, and it might have altered conformational features.     

Evolution of nested genes with special reference to cuticle proteins inDrosophila melanogaster

Summary One of the pupal cuticle protein (PCP) genes has been found within an intron of aDrosophila housekeeping gene (theGart locus) that encodes three enzymes involved in the purine pathway. This intronic gene has been described as a gene within a gene, and the gene is now called a “nested” gene. Because the intronic PCP gene has sequence similarity with the larval cuticle protein (LCP) gene, it may have been derived from one of the LCP genes or their ancestral gene. We have studied possible phylogenetic relationships among these five genes by comparing nucleotide sequences of four LCP genes with that of the PCP gene. The results obtained suggest that the PCP gene may have originated from an ancestral gene before duplication of the LCP genes occurred. Using the number of synonymous (silent) substitutions, we then estimated the divergence time between the PCP gene and the LCP genes to be about 70 million years (Myr). The divergence time estimated is much larger than that for the sibling species ofD. melanogaster (about 2.5 Myr), indicating that the “nested” gene structure can be seen not only inDrosophila melanogaster, but also in other distantly relatedDrosophila species.     

CLAP: A web-server for automatic classification of proteins with special reference to multi-domain proteins

Background

The function of a protein can be deciphered with higher accuracy from its structure than from its amino acid sequence. Due to the huge gap in the available protein sequence and structural space, tools that can generate functionally homogeneous clusters using only the sequence information, hold great importance. For this, traditional alignment-based tools work well in most cases and clustering is performed on the basis of sequence similarity. But, in the case of multi-domain proteins, the alignment quality might be poor due to varied lengths of the proteins, domain shuffling or circular permutations. Multi-domain proteins are ubiquitous in nature, hence alignment-free tools, which overcome the shortcomings of alignment-based protein comparison methods, are required. Further, existing tools classify proteins using only domain-level information and hence miss out on the information encoded in the tethered regions or accessory domains. Our method, on the other hand, takes into account the full-length sequence of a protein, consolidating the complete sequence information to understand a given protein better.

Results

Our web-server, CLAP (Classification of Proteins), is one such alignment-free software for automatic classification of protein sequences. It utilizes a pattern-matching algorithm that assigns local matching scores (LMS) to residues that are a part of the matched patterns between two sequences being compared. CLAP works on full-length sequences and does not require prior domain definitions.Pilot studies undertaken previously on protein kinases and immunoglobulins have shown that CLAP yields clusters, which have high functional and domain architectural similarity. Moreover, parsing at a statistically determined cut-off resulted in clusters that corroborated with the sub-family level classification of that particular domain family.

Conclusions

CLAP is a useful protein-clustering tool, independent of domain assignment, domain order, sequence length and domain diversity. Our method can be used for any set of protein sequences, yielding functionally relevant clusters with high domain architectural homogeneity. The CLAP web server is freely available for academic use at http://nslab.mbu.iisc.ernet.in/clap/.     

Some studies on Nigerian palm wine with special reference to yeasts

The identification and enumeration of yeasts and the effect of chemical preservatives on the yeast load in Nigerian palm wine have been studied. Yeast found largely belong to the genus Saccharomyces. Other genera found were Candida, Endomycopsis, Hansenula, Kloeckera, Pichia, Saccharomycoides and Schizosaccharomyces. The viable yeast count ranged from 0.5 × 10⁷ cfu/ml to 4.2 × 10⁹ in both fresh Elaeis and Raphia spp. of palms. Yeasts in palm wine were least sensitive to sodium nitrate and most sensitive to sodium benzoate. The addition of these two chemical preservatives amongst others reduced the yeast count to 3.2 × 10⁸ (in Raphia sp.), and 4.1 × 10⁹ (in Elaeis sp.) with 0.025% sodium nitrate and 1.2 × 10⁶ (in Raphia sp.) and 1.9 × 10⁷ (in Elaeis sp.) with 0.1% sodium benzoate. The values of the yeast count in bottled and fresh palm wine were between 1.3 × 10³ cfu/ml to 9.8 × 10⁶ and 0.5 × 10⁷ to 4.2 × 10⁹, respectively. Maximum values of actual dry and theoretical yeast weights were 1.09 and 42 mg/ml, respectively.