Amino acid sequences of ovomucoid third domain from 25 additional species of birds

Ovomucoids were isolated from 25 avian species other than the 101 studied in Laskowskiet al. (1987,Biochemistry 26, 202–221). These were subjected to limited proteolysis with an appropriate enzyme, and connecting peptide extended ovomucoid third domains were isolated and sequenced to the end in a protein sequencer. Of the 25 new sequences, 13 duplicate ones were already known, and 12 are unique. Probably the most striking findings are a Pro¹⁴ Ser¹⁴ replacement in weka, an Ala¹⁴Thr¹⁵ replacement in Bulwer's pheasant, the discovery of two additional amino acid residues Ile¹⁸ and Gly¹⁸ at the P₁ reactive site position in Kalij pheasant and tawny frogmouth, respectively, and the first finding of a negative (Glu³⁴) rather than positive (Lys³⁴ or Arg³⁴) amino acid residue at the NH₂ terminus of the helix in caracara ovomucoid third domain. These results complete the determination of all the sequences of ovomucoid third domains in the four species genusGallus, in the five species genusSyrmaticus, and in the two species generaAix andPavo.     

Specification of binding modes between a transmembrane peptide mimic of ATP6V0C and polytopic E5 of human papillomavirus-16

Interaction of E5 of papillomavirus-16 based on its three transmembrane domains (TMDs) with a peptide mimicking the fourth TMD (TMD-A) of the 16 kDa c subunit of the human vacuolar H⁺-ATPase, ATP6V0C, and one of its mutant is investigated. Docking reveals binding of the peptide between the second and third TMD of E5. A series of hydrophobic residues are responsible for the contact. Estimated weak binding energies based on potential of mean force calculations reveal marginal differences of the estimated binding energies between wild type (WT) and mutant peptide. Also differences in estimated binding energies of dimers of the individual TMDs of E5 with the WT peptide are marginal. Correlation of rotational data derived from coarse-grained molecular dynamics simulations of the peptides and the protein as well as from the principal component analysis reveal that the binding of TMD-A with TMD3 is enthalpy driven and binding with TMD2 is guided by entropic conditions.     

Effect of n-3 and n-6 fatty acids on hepatic microsomal lipid metabolism: a time course study

The present study examines the time dependent effects of n-6 and n-3 polyunsaturated fatty acids on liver microsomal lipid metabolism in FVB mice fed a diet supplemented with a mixture of free fatty acids (mainly 18:3n-6 and 20:5n-3) at 25 mg/g diet. Significant changes in the fatty acid composition of total liver and microsomal lipids were observed after 7 days on the diets. Thereafter, some animals remained on the same diet while others were fed a diet supplemented with hydrogenated coconut oil (HCO). With the exception of 20:5n-3 which showed a slower recovery, establishment of the HCO pattern was rapid indicating that the diet-induced changes could be easily reversed. The unsaturation index, the cholesterol/phospholipid ratio and the microviscosity of the microsomal membranes were not affected by these dietary manipulations. Unsaturated fatty acid supplementation reduced the activity of ⁹ desaturase by 50%. Feeding the HCO diet to mice previously fed the EPA/GLA diet led to a progressive increase in ⁹ desaturase activity, reaching 80% of the day zero values after 14 days. The monoene content of hepatic total lipids reflected, in most cases, the changes in enzyme activity. This study shows that a low dose of a n-3 and n-6 free fatty acid mixture increases the quantities of members of the n-3 family, without loss of n-6 fatty acids in microsomal membranes and modifies the activity of ⁹ desaturase without altering the microsome physicochemical parameters.     

The tryptic peptide composition of the beta chains of hemoglobins A and B of the domestic cat (Felis catus)

Summary The tryptic peptides from the ^A and ^B chains of cat hemoglobins A and B have been isolated and the amino acid compositions determined. Differences between the two chains were found in two peptides,T-1 (GlySer) andT-14 (AsnSer and LysArg). The GlySer and LysArg substitutions are placed at-1 and-144 respectively from earlier work, and the third substitution, AsnSer at-139 is suggested from this work. In addition, the presence of a blocked amino terminus in ^B has been confirmed. Tentative sequences constructed by homology with known-chain structures suggest the occurrence of substitutions at _{1 1} contacts in ^A and ^B that may be functionally significant. There are at least 18 differences in amino acid composition between cat ^A and dog-chains and 22 differences between cat ^A and normal adult human-chains.     

Conformational dynamics of the anticodon loop in yeast tRNAPhe as sensed by the fluorescence of wybutine

Conformational and dynamic properties of the anticodon loop of yeast tRNA^Phe were investigated by analyzing the time resolved fluorescence of wybutine serving as a local structural probe adjacent to the anticodon GmAA on its 3 side. The influence of Mg²⁺, important for stabilizing the tertiary structure of tRNA, and of the complementary anticodon s²UUC of E. coli tRNA ₂ ^Glu were investigated.Fluorescence lifetimes and anisotropies were measured with ps time resolution using time correlated single photon counting and a mode locked synchronously pumped and frequency doubled dye laser as excitation source. From the analysis of lifetimes () and rotational relaxation times ( _R ) we conclude that wybutine occurs in various structural states: (i) one stacked conformation where the base has no free mobility and the only rotational motion reflects the mobility of the whole tRNA molecule (=6 ns, _R =19 ns), (ii) an unstacked conformation where the base can freely rotate (=100 ps, _R = 370 ps) and (iii) an intermediary state (=2 ns, _R = 1.6 ns).Under biological conditions, i. e. in the presence of Mg²⁺ and neutral salts, wybutine is found in a stacked and immobile state which is consistent with the crystallographic picture. In the presence of the complementary codon however, as exemplified by the E. coli-tRNA ₂ ^Glu anticodon, our analysis indicates that the codon-anticodon complex exists in an equilibrium of structural states with different rotational mobility of wybutine. The conformation with wybutine freely mobile is the predominant one and suggests that this conformation of the codon-anticodon structure differs from the canonical 3–5 stack.     

Identification of a glutathione-S-transferase effector domain for inhibition of jun kinase, by molecular dynamics

We have recently found that the glutathione-S-transferase -isozyme (GST-), a cellular detoxification enzyme, potently and selectively inhibits activation of jun protein by its upstream kinase, jun kinase (JNK). This newly identified regulatory activity of GST- is strongly inhibited by a group of agents that inhibit its enzymatic activity. Since loss of enzymatic activity in general does not correlate with loss of regulatory activity, it is likely that inhibitor binding induces changes in the structure of one or more domains of GST that block its interaction with JNK. To identify regions of GST that change conformation on the binding of inhibitors, we have performed molecular dynamics calculations on GST- to compute its average structure in the presence and absence of the inhibitor, glutathione sulfonate. Superposition of the two average structures reveals that several regions change local structure depending upon whether the inhibitor is bound or not bound. Two of these regions, residues 36–50 and 194–201, are highly exposed. We have synthesized peptides corresponding to these two segments and find that the 194–201 sequence strongly inhibits the ability of GST- to block the in vitro phosphorylation of jun by JNK. These results suggest that this region of GST- is critical to its functioning as a newly discovered regulator of signal transduction.     

Cloning and expression of the α-amylase gene and oxytetracycline production in Streptomyces rimosus

An 8.4 kb Sau3AI DNA fragment containing the Streptomyces rimosus TM-55 -amylase gene (amy) was ligated to a vector pIJ702, named pCYL01, and cloned into amylase deficient mutant S. lividans M2 (amy ^–). Subcloning study showed that the amy gene was localized in 3.3 kbKpnI-PstI fragment. The molecular weight of the purified -amylases of S. lividans M2/pCYL01 and S. rimosus TM-55 were estimated to be 65.7 kDa. Different sizes of recombinant plasmids carrying the amy gene had been retransferred into the parental strain of S. rimosus TM-55. Among these S. rimosus transformants, TM-55/pCYL01, TM-55/pCYL12 and TM-55/pCYL36 showed amylase activity 1.36- to 2.05-fold at the seventh day (1.61 to 2.42 units vs 1.18 units), and oxytetracycline (OTC) production 2.00- to 2.50-fold at the ninth day (approximate 140 to 170 g ml^–1 vs 72 g ml^–1), higher than that of S. rimosus TM-55 alone, respectively. These results showed that industrial microorganisms could be improved by genetic and metabolic engineering.     

Fluorescence of 3-keto-steroids in aqueous solution

The physiologically important 3-keto-steroids are non-fluorescent or only weakly fluorescent in protic as well as in aprotic solvents. In contrast, the 4,6,8(14)-triene-3-one steroids are highly fluorescent in aqueous solution but they do not appreciably fluoresce in other solvents. Evidence is presented that the introduction of double bonds into the skeleton of the 3-keto-steroids leads to a decrease of the energy of the lowest – ^* state, bringing this level into the neighbourhood of the non-fluorescent n – ^* state. As a consequence, for two states of approximately the same energy, relatively small perturbations such as those due to solvent interactions, protein binding and micelle formation, will then determine whether a system will fluoresce ( – ^* state lowest) or not (n – ^* state lowest). When the fluorescent 3-keto-steroids, having three conjugated double bonds, bind to proteins, the fluorescence intensity becomes almost zero, making these compounds useful as probes for steroid-protein interactions. This quenching of the fluorescence is explained by a decrease in energy of the n – ^* state relative to the – ^* state of the steroids due to hydrophobic interactions with the proteins.Abbreviations 6,8-BDT 6,8-bisdehydrotestosterone; DMSO, dimethylsulfoxide - HPLC high pressure liquid chromatography This work was presented in part at the Annual Meeting of the Gesellschaft für Biologische Chemie, September 26–29, 1983, in Göttingen. For an abstract see: Hoppe-Seyler's Z. Physiol. Chem. (1983) 364: 1151–1152Dedicated to Prof. Dr. F.-W. Zilliken on the occasion of his 65th birthday     

Visualization ofπ − andπ + stopping density distributions in one and two dimensions

Summary A technique suitable for mapping ^± stopping density distributions in patients or phantoms is described. As a position sensitive detector a multiwire proportional chamber with a slit or a hole collimator in front was applied. Results using a water and a Rando phantom are presented for various momenta and momentum band widths of the ^± beam. To our knowledge the two-dimensional visualization of a ^– stopping density distribution was realized for the first time.     

High-resolution solution structure of two members of a conformationally homogeneous combinatorial peptide library based on the classical zinc-finger motif

Summary We describe the high-resolution structure by NMR of two peptides that belong to a combinatorial library based on the zinc-finger motif. The library represents, to the best of our knowledge, the first example of a conformationally homogeneous peptide library and was obtained by introducing random residues in five positions of the -helical portion of a 26-residue consensus peptide (CP1) belonging to the Cys²-Hys² zinc-finger family. The result was shown to be a highly homogeneous -helical library (Bianchi et al., 1995). The structures of the parent compound (CP1) and of a representative member (CP1m) that was selected by screening the library with a monoclonal antibody are compared in detail as an example of the very high stability of the zinc-finger scaffold upon sequence variability. The two peptides exhibit an extremely high degree of structural similarity. The use of this type of conformationally constrained combinatorial library might represent a step forward in the design of peptidomimetics, as it considerably accelerates the process of the identification of the spatial relationship among the pharmacophoric groups.Abbreviations t-Bu tert-butyloxycarbonyl - Fmoc 9-fluorenylmethoxycarbonyl     

Pre-clinical studies of the negative pi-meson beam at TRIUMF

Summary The ^– flux from the biomedical channel at TRIUMF increases with increasing channel momentum, while the contaminating electron flux decreases. Since the electrons appear to result from conversion of the high energy-rays produced by ⁰ decay in the production target, the electron contamination can be reduced further by target configurations which minimize gamma conversion.The attenuation of ^– beams by in-flight interactions was found to decrease from an initial value of 1.67 ± 0.02 % per g/cm² at zero depth to 1.48 ± 0.02 % per g/cm² near the stopping peak.The inactivation of cultured CHO cells by an extended-peak ^– dose distribution has been measured using the gel technique. The survival data have been fitted by a model which characterizes the physical quality of the dose profile by means of measured star densities. This model provides a convenient method of analysis for large sets of survival data and may be useful for prediction of the biological effect of new ^– dose distributions.The RBE value for 50% survival measured at the centre of a 7 cm extended peak was found to be approximately 1.4, in reasonable agreement with recent values obtained at LAMPF and SIN.     

Tyrosine group behaviour in bovine α-lactalbumin as revealed by its Raman effect

Side group behaviour is often used for conformational studies of proteins. We have performed Raman spectroscopic measurements on the tyrosine groups of bovine -lactalbumin. The 850/830 cm^-1 doublet intensity ratio is a direct measure of the negative charge state of the phenolic oxygen and of the tyrosine environment. pH measurements confirm the existence of an acid conformer of BLA, that is comparable to, but clearly distinguishable from the apo-conformer. Following the Siamwiza theory, the Tyr groups in this partially unfolded state are situated in a more hydrophobic environment. Observation of Tyr groups behaviour in the denaturated states obtained by thermal or chemical treatment leads us to the same conclusion. However, the behavior of tryptophan groups is quite different. In an unfolded sate, the Trp residues are mostly exposed to the solvent.The stabilizing role of Ca²⁺ and Na⁺ ions in BLA is also investigated.Abbreviations BLA bovine -lactalbumin - EGTA ethylene glycol bis (-aminoethyl ether) N,N-tetraacetic acid - Tyr tyrosine - Tris tris(hydroxymethyl)aminomethane     

Adventitious shoot regeneration from in vitro leaves of several pear cultivars (Pyrus communis L.)

An efficient adventitious shoot regeneration system was developed for pear (Pyrus communis L.), using leaves from in vitro proliferating shoots. Under optimal conditions, bud regeneration frequencies of Comice, Passe-Crassane, Williams and Conference ranged from 60% to 97%, with the mean number of shoots per regenerating leaf ranging from 3.2 to 6.6. Despite the great variability in responses of the different cultivars, in general an initial dark exposure of at least 20 days was required. Ammonium and total nitrogen proved to play an essential role: intermediate NH₄ ⁺ concentrations were suitable for regeneration. The balance between NH₄ ⁺ and NO₃ ^- also influenced regeneration; optimal regeneration occured on media with a 1:3 NH₄ ⁺/NO₃ ^- ratio. TDZ at 1 M was less efficient than higher concentrations, whatever the NAA level. Finally, length and growth regulator composition of the two phases (induction and expression) influenced the regeneration rate of Conference.Abbreviations BA 6-benzyladenine - EDFS ethylenediamine-tetraacetic acid ferric-sodium salt - IBA 4-indole-3yl-butyric acid - NAA -naphthaleneacetic acid - TDZ thidiazuron (N-phenyl-N-1,2,3-thidiazol-5-ylurea)     

Conformational changes induced by the transforming amino acid substitution in the transmembrane domain of the neu oncogene-encoded p185 protein

Theneu oncogene is frequently found in certain types of human carcinomas and has been shown to be activated in animal models by nitrosourea-induced mutation. The activating mutation in theneu oncogene results in the substitution of a glutamic acid for a valine at position 664 in the transmembrane domain of the encoded protein product of 185 kda (designated p185), which, on the basis of homology studies, is presumed to be a receptor for an as yet unidentified growth factor. It has been proposed that activating amino acid substitutions in this region of p185 lead to a conformational change in the protein which causes signal transduction via an increase in tyrosine kinase activity in the absence of any external signal. Using conformational energy analysis, we have determined the preferred three-dimensional structures for the transmembrane decapeptide (residues 658–667) of the p185 protein with valine and glutamic acid at the critical position 664. The results indicate that the global minimum energy conformation of the decapeptide from the normal protein with Val at position 664 is an -helix with a sharp bend (CD* conformation at residues 664 and 665) in this region, whereas the global minimum conformation for the decapeptide from the mutant transforming protein with Glu at position 664 assumes an all -helical configuration. Furthermore, the second highest energy conformation for the decapeptide from the normal protein is identical to the global minimum energy conformation for the decapeptide from the transforming protein, providing a possible explanation why overexpression of the normal protein also has a transforming effect. These results suggest there may be a normal and a transforming conformation for theneu-encoded p185 proteins which may explain their differences in transforming activity.     

Chydorus ‘mutilus’ Kreis, 1921 — a postephippial form of Chydorus sphaericus (O. F. Müller, 1785)

Since 1991 faunal collections have been made from the mountain lakes of NW Slovenia. These lakes are at altitudes of between 1250 and 2150 m a. s.l., and have rich biotas, both in terms of species-richness, and faunal abundance. Amongst the animals collected were hump-backed specimens of genus Chydorus. These are identical with Chydorus mutilus, a species described from Swiss mountain lakes by Kreis (1921). The abundance of specimen in the collections, coupled with the availability of data from four successive years of sampling, allowed the detailed analysis of these populations. This also includes an examination of chitinous remains preserved in subrecent sediments.The results show that C. mutilus Kreis, 1921 actually represents a postephippial form of C. sphaericus (O. F. Müller, 1785). From the data available, it appears that the hump-backed form only occurs under certain environmental conditions. Here I discuss environmental factors having the potential to trigger the formation of hump-backed Chydorus. These findings may prove significant in palaelimnological studies, and in the reconstruction of paleotemperatures.In addition, hump-backed animals, apparently identical to European C. mutilus, have also been found in a sample taken from Lake Titicaca (Peru) in 1954. This supports the hypothesis that the hump-backed morph is an environmentally-cued ecophenotype, and not an independent taxon.     

The identification of two mis-sense mutations at the PAH gene locus in a Turkish patient with phenylketonuria

Summary DNA sequence analysis of the 13 exons and intron/exon boundaries of the phenylalanine hydroxylase (PAH) gene has detected two base transitions, resulting in mis-sense mutations, in the genomic DNA of a Turkish patient (E1) with phenylketonuria (PKU). The Leu⁴⁸Ser amino acid substitution was associated with the mutant haplotype 3 allele and the Glu²²¹Gly amino acid substitution with the mutant haplotype 4 allele of this family. Allele-specific oligonucleotide (ASO) dotblot analysis subsequently detected the Leu⁴⁸Ser mutation in the haplotype 4 PKU alleles of nine (18.8%) of the 48 unrelated Caucasian PKU families investigated. This mutation results in mild PKU in the homozygous state. The Glu²²¹Gly mutation has only been detected within patient E1 and his father.     

α1-antitrypsin (Pi) phenotypes in a village population from the Gambia,West Africa

Summary A total of 701 individuals from a village in The Gambia, West Africa were tested for serum ₁ ^- antitrypsin phenotypes by isoelectric focusing in thinlayer polyacrylamide gels (pH 4-5). A new variant allele, Pi ^GAM , was discovered at a polymorphic frequency (0.0642), and the inheritance of the variant phenotype was confirmed by family studies. The variant was not found to be associated with any decrease in serum ₁ ^- concentration. The only other allele found within this population was the common allele Pi ^M (0.9358).     

Phylogeny and evolutionary rates of G protein α subunit genes

Summary Rooted phylogenetic trees for a total of 34 genes encoding the stimulatory (s), inhibitory (i), transducin (t), G_x (x), G_z (z), G₁₁ (11), G₁₂ (12), G₁₃ (13), G₁₆ (16), G_q (q), and other (o) G protein a subunits have been constructed. The analysis shows that the G₁₂ (12 and 13), G_q (11, 16, and q), and G_s (s genes) groups form one cluster, and the G_x (x and z genes), G_i (i genes), G_t (t1 and t2), and G_o (o genes) groups form another cluster. During mammalian evolution, the rates of synonymous substitutions for these genes were estimated to be between 1.77 × 10^–9/site/year and 5.63 × 10^–9/site/year, whereas those of nonsynonymous substitutions were between 0.008 × 10^–9/site/year and 0.067 × 10^–9/site/year. These evolutionary rates are similar to those for histone genes, suggesting equally important biological functions of the G protein a subunits. Offprint requests to: S. Yokoyama     

Hypo-osmotic stimulation of active Na+ transport in frog muscle: Apparent upregulation of Na+ pumps

Summary The purpose of this work was to determine if hypotonicity, in addition to the stimulation of active Na⁺ transport (Venosa, R.A., 1978,Biochim. Biophys. Acta 510:378–383), promoted changes in (i) active K⁺ influx, (ii) passive Na^– and K⁺ fluxes, and (iii) the number of³H-ouabain binding sites.The results indicate that a reduction of external osmotic pressure () to one-half of its normal value (=0.5) produced the following effects: (i) an increase in active K⁺ influx on the order of 160%, (ii) a 20% reduction in Na⁺ influx and K⁺ permeability (P _K), and (iii) a 40% increase in the apparent density of ouabain binding sites. These data suggest that the hypotonic stimulation of the Na⁺ pump is not caused by an increased leak of either Na⁺ (inward) or K⁺ (outward). It is unlikely that the stimulation of active Na⁺ extrusion and the rise in the apparent number of pump sites produced by hypotonicity were due to a reduction of the intracellular ionic strength. It appears that, at least in part, the stimulation of active Na⁺ transport takes place whenever muscles are transferred from one medium to another of lower tonicity even if neither one was hypotonic (for instance =2 to =1 transfer). Comparison of the present results with those previously reported indicate that in addition to the number of pump sites, the cycling rate of the pump is increased by hypotonicity. Active Na⁺ and K⁺ fluxes were not significantly altered by hypertonicity (=2).     

Tandem mass spectrometry for characterization of unsaturated disaccharides from chondroitin sulfate,dermatan sulfate and hyaluronan

Fast atom bombardment tandem mass spectrometry has been used in the characterization of non-, mono-, di- and trisulfated disaccharides from chondriotin sulfate, dermatan sulfate and hyaluronan. The positional isomers of the sulfate group of mono- and disulfated disaccharides were distinguished from each other by both positive- and negative-ion fast atom bombardment tandem mass spectra, which gave sufficient information characteristic of the isomers. The anomeric isomers of nonsulfated disaccharides were characterized by the technique in the positive-ion mode. This fast atom bombardment collision induced dissociation mass spectrometry/mass spectrometry technique was also applied successfully to the characterization of trisulfated disaccharide.Abbreviations FABMS fast atom bombardment mass spectrometry - MI metastable ion - CID collision induced dissociation - MIKE mass analysed ion kinetic energy - SIMS secondary ion mass spectrometry - MS/MS mass spectrometry/mass spectrometry - HPLC high performance liquid chromatography - GlcA d-gluco-4-enepyranosyluronic acid - CS chondroitin sulfate - DS dermatan sulfate - HA hyaluronan - UA-GalNAc 2-acetamido-2-deoxy-3-O-(-d-gluco-4-enepyranosyluronic acid)-d-galactose - UA-GalNAc4S 2-acetamido-2-deoxy-3-O-(-d-gluco-4-enepyranosyluronic acid)-4-O-sulfo-d-galactose - UA-GalNAc6S 2-acetamido-2-deoxy-3-O-(-d-gluco-4-enepyranosyluronic acid)-6-O-sulfo-d-galactose - UA2S-GalNAc 2-acetamido-2-deoxy-3-O-(2-O-sulfo--d-gluco-4-enepyranosyluronic acid)-d-galactose - UA2S-GalNAc4S 2-acetamido-2-deoxy-3-O-(2-O-sulfo--d-gluco-4-enepyranosyluronic acid)-4-O-sulfo-d-galactose - UA2S-GalNAc6S 2-acetamido-2-deoxy-3-O-(2-O-sulfo--d-gluco-4-enepyranosyluronic acid)-6-O-sulfo-d-galactose - UA-GalNAcDiS 2-acetamido-2-deoxy-3-O-(-d-gluco-4-enepyranosyluronic acid)-4,6-di-O-sulfo-d-galactose - UA2S-GalNAcDiS 2-acetamido-2-deoxy-3-O-(2-O-sulfo--d-gluco-4-enepyranosyluronic acid)-4,6-di-O-sulfo-d-galactose - UA-GlcNAc 2-acetamido-2-deoxy-3-O-(-d-gluco-4-enepyranosyluronic acid)-d-glucose