A crystallographic study of bright far-red fluorescent protein mKate reveals pH-induced cis-trans isomerization of the chromophore

The far-red fluorescent protein mKate (lambda(ex), 588 nm; lambda(em), 635 nm; chromophore-forming triad Met(63)-Tyr(64)-Gly(65)), originating from wild-type red fluorescent progenitor eqFP578 (sea anemone Entacmaea quadricolor), is monomeric and characterized by the pronounced pH dependence of fluorescence, relatively high brightness, and high photostability. The protein has been crystallized at a pH ranging from 2 to 9 in three space groups, and four structures have been determined by x-ray crystallography at the resolution of 1.75-2.6 A. The pH-dependent fluorescence of mKate has been shown to be due to reversible cis-trans isomerization of the chromophore phenolic ring. In the non-fluorescent state at pH 2.0, the chromophore of mKate is in the trans-isomeric form. The weakly fluorescent state of the protein at pH 4.2 is characterized by a mixture of trans and cis isomers. The chromophore in a highly fluorescent state at pH 7.0/9.0 adopts the cis form. Three key residues, Ser(143), Leu(174), and Arg(197) residing in the vicinity of the chromophore, have been identified as being primarily responsible for the far-red shift in the spectra. A group of residues consisting of Val(93), Arg(122), Glu(155), Arg(157), Asp(159), His(169), Ile(171), Asn(173), Val(192), Tyr(194), and Val(216), are most likely responsible for the observed monomeric state of the protein in solution.     

Stopped-flow cryoenzymological investigation of the pre-steady-state kinetics of hydrolysis of Leu-Gly-NHNH-Dns by leucine aminopeptidase

Stopped-flow fluorescence experiments have been carried out to study the steady-state kinetics of hydrolysis of Leu-Gly-NHNH-Dns [Dns = 5-(dimethylamino)naphthalene-1-sulfonyl] by porcine kidney cytosol leucine aminopeptidase (LAP) in 50% v/v methanol/buffer solution at ambient temperature and the pre-steady-state kinetics of this reaction in the -35 to 0 degrees C temperature range. Experiments have been carried out on LAP species containing Mg(II), Mn(II), Cu(II), Ni(II), Zn(II), and no metal ion at the regulatory metal binding site. At ambient temperatures, the stopped-flow fluorescence changes observed on hydrolysis of the substrate have been used to measure the steady-state kinetic parameters kcat and KM. The results show that 50% v/v methanol lowers the values of kcat from 2- to 12-fold compared to the reactions in the absence of methanol for all of the metallo-LAP, but that the values of KM are essentially unaffected. The pre-steady-state reactions carried out under nonturnover conditions at -35 degrees C reveal a new relaxation for LAP species with Ni(II), Cu(II), and Zn(II) in the regulatory site. The value of kobsd for this relaxation reaches a plateau at high substrate concentrations, and the magnitude of its fluorescence change at a fixed concentration of substrate is proportional to the enzyme concentration. Thus, this relaxation corresponds to the production and decay of a new enzyme-substrate intermediate not observed at higher temperatures whose fluorescence differs from that of the succeeding intermediate that is normally seen above -26 degrees C.     

Steady-state kinetics of hydrolysis of dansyl-peptide substrates by leucine aminopeptidase

Stopped-flow fluorescence experiments have been carried out at 23 degrees C to study the hydrolysis of Leu-Gly-NHNH-Dns [Dns = 5-(dimethylamino)naphthalene-1-sulfonyl] and Leu-Gly-NH(CH2)2NH-Dns by porcine kidney cytosol leucine aminopeptidase (LAP). Experiments have been performed with LAP species containing Mg(II), Mn(II), Ni(II), Cu(II), Zn(II), and no metal ion at the regulatory metal binding site. The fluorescence changes observed on hydrolysis of these dansyl substrates by LAP arise from changes in the concentration of substrate. Several kinetic relationships have been developed that allow the steady-state kinetic parameters for these reactions to be determined from the stopped-flow fluorescence traces. When any of the five metal ions are bound at the regulatory site, kcat and KM are both raised to approximately the same extent with the result that the maximum increase observed for kcat/KM is only approximately twofold. The effects of these metal ions on kcat, KM, and kcat/KM observed for these substrates differ markedly from those for less physiologically relevant substrates, such as Leu-p-nitroanilide, that do not have amino acids on both sides of the scissile bond. This suggests that earlier conclusions regarding the effect of the regulatory metal ion on the activity of LAP may have been misleading and casts doubt as to whether the term "regulatory site" has validity in the context of LAP-catalyzed reactions under physiological conditions.     

Variability of milk fat globule membrane protein gene between cattle and riverine buffalo.

A study on butyrophilin (BTN) gene was conducted to detect variability at nucleotide level between cattle and buffalo. Hae III PCR-RFLP was carried out in crossbred cattle and it revealed polymorphism at this locus. Three genotypes namely, AA, BB and AB and two alleles were observed with frequencies 0.78, 0.17, 0.04 and 0.87, 0.13, respectively. The sequences of different cattle, buffalo and sheep breeds have been reported in the EMBL gene bank with accession numbers: AY491468 to AY491475. The nucleotides, which have been substituted from allele A to B, were found to be C to G (71st nucleotide), C to T (86th nucleotide), A to T (217th nucleotide), G to A (258th nucleotide), A to C (371st nucleotide) and C to T (377th nucleotide). The nucleotide substitution at 71st, 86th and 377th position of the fragment were expected to be a silent mutation where as nucleotide changes at 217th, 258th and 371st positions were expected to be substituted by lysine with arginine, valine with isoleucine and leucine with proline in allele B. The differences of nucleotides and amino acids between cattle, buffalo and sheep breeds have been revealed and on the basis of nucleotide as well as protein variability the phylogenetic diagram have been developed indicating closeness between cattle and buffalo.     

State of the system of antioxidant defense in tissues of the black sea turbot during the spawning

The system of antioxidant (AO) defense and processes of lipid peroxidation (LP) of the Black Sea turbot Psetta (Scophtalmus) maxima maeotica (L., 1758) have been investigated during the spawning season. The activity of glutathione peroxidase (GP), glutathione reductase (GR), catalase and content of reduced glutathione (GSH) and TBA-reactive products have been determined in gonads, gills, liver, red and white muscles of males and females at different stages of gonad's maturity (V and VI stages). The peculiarities of AO complex and LP depended on tissue specificity and sexual distinctions of the turbot have been found. The turbot females at VI stage were found to have the most significant changes. In gonads and liver the level of TBA-reactive products decreased. In gonads the activities of GP and GR decreased, but the level of GSH increased. In gills of these females the activity of GP and the level of GSH increased, while in the red muscles the activity of catalase raised. In white muscles the activity of GR dropped. In the males' tissues of the turbot at VI stage the growth of the activity of GP in gills and GSH content in white muscles have been found. In all tissues of males the decrease of the TBA-reactive products content has been observed.     

Thermodynamics of the conversion of aqueous L-aspartic acid to fumaric acid and ammonia

The thermodynamics of the conversion of aqueous L-aspartic acid to fumaric acid and ammonia have been investigated using both heat conduction microcalorimetry and high-pressure liquid chromatography. The reaction was carried out in aqueous phosphate buffer over the pH range 7.25-7.43, the temperature range 13-43 degrees C, and at ionic strengths varying from 0.066 to 0.366 mol kg(-1). The following values have been found for the conversion of aqueous L-aspartateH- to fumarate2- and NH4+ at 25 degrees C and at zero ionic strength: K = (1.48 +/- 0.10) x 10(-3), DeltaG degrees = 16.15 +/- 0.16 kJ mol(-1), DeltaH degrees = 24.5 +/- 1.0 kJ mol(-1), and DeltaC(p) degrees = -147 +/- 100 J mol(-1) K(-1). Calculations have also been performed which give values of the apparent equilibrium constant for the conversion of L-aspartic acid to fumaric acid and ammonia as a function of temperature, pH and ionic strength.     

The utilization of recombinant prostanoid receptors to determine the affinities and selectivities of prostaglandins and related analogs

Stable cell lines that individually express the eight known human prostanoid receptors (EP(1), EP(2), EP(3), EP(4), DP, FP, IP and TP) have been established using human embryonic kidney (HEK) 293(EBNA) cells. These recombinant cell lines have been employed in radioligand binding assays to determine the equilibrium inhibitor constants of known prostanoid receptor ligands at these eight receptors. This has allowed, for the first time, an assessment of the affinity and selectivity of several novel compounds at the individual human prostanoid receptors. This information should facilitate interpretation of pharmacological studies that employ these ligands as tools to study human tissues and cell lines and should, therefore, result in a greater understanding of prostanoid receptor biology.     

Rotational correlation time of spin-labeled alpha-chymotrypsin

α-Chymotrypsin has been spin labeled with (I), 3-carboxy 2,2,5,5-tetramethyl pyrrolidine-N-oxyl-p-nitrophenyl ester, and (II), the N-oxyl-4′,4′-dimethyl oxazolidine of 5-α-androstan-3-one-17-β-methyl phosphono-fluoridate. The positions of the high field hyperfine components in the paramagnetic resonance spectra of the spin-labeled enzymes have been measured as a function of solvent viscosity and have been used to determine a rotational correlation time of 12 nanoseconds for α-chymotrypsin in water at 20° C.     

Synthesis and physicochemical studies of polymeric coordination complexes of some lanthanides with 1,4-dihydroxyanthraquinone

Coordination polymers of lanthanum(III), praseodymium(III), neodymium(III), samarium(III), dysprosium(III) and holmium(III) with 1,4-dihydroxyanthraquinone have been synthesized and characterised. Their magnetic moments, infrared spectra and electronic spectra have been studied to establish their structure. All the polychelates are amorphous, dark coloured powders, insoluble in common organic solvents and sparingly soluble in dimethylformamide. Nephelauxetic ratio (β), covalency factor (b^1/2), etc. have been evaluated wherever possible. Thermogravimetric studies (TGA) indicate a higher decomposition temperature of polychelates than the parent ligand. A.c.-conductivity, dielectric constant (ϵ′), dielectric loss (ϵ″), all at various frequencies, as well as d.c.-conductivity of the prepared polychelates, are reported. The analytical data are suggestive of a 2:3 metal-ligand stoichiometry in the polychelates.     

Investigation of the thermal stability of nucleic acids and their structural components

The thermal stability of homopolynucleotides (poly(A), poly(G), poly(C), poly(U)) and natural DNA, as well as their structural components: nucleoside (uridine), nucleotides (uridine-5′-monaphosphate, uridine-5′-diphosphate, and uridine-5′-triphosphate) and sugar (D-ribose) have been studied by the method of differential scanning microcalorimetry. The dependences of the heat flow on temperature have been obtained for the compounds having individual features in the temperature range from 20 to 400°C. All samples showed exothermic peaks at temperatures higher than 200°C (for DNA, this peak was found at a temperature of ∼160°C), which are related to processes of irreversible thermal destruction. The temperatures of thermal destruction and the effective energy of activation of this process for all compounds studied have been determined. The values of the effective heat of exothermal processes have been calculated for the polynucleotides. The experimental results indicate that there is a significant difference in the thermal stability between these homopolynucleotides and DNA, poly(G) being the most stable and DNA, the least stable. Based on the analysis of D-ribose, nucleoside, and nucleotides, it was concluded that the sugar ring is the most probable region of the destruction.     

Isentropic and isothermal compressibilities of the backbone glycyl group of proteins in aqueous solution

The partial molar isentropic compressibilities at infinite dilution, K(S,2)(o), have been determined for the peptides serylglycine, serylglycylglycine and serylglycylglycylglycine in aqueous solution at 25 degrees C. The partial molar volumes at infinite dilution, V(2)(o), have also been determined for these peptides in aqueous solution at the temperatures 15, 30 and 40 degrees C. These results, along with those obtained previously at 25 degrees C, were used to derive the partial molar exansibilities, E(2)(o), of the peptides at 25 degrees C, which in turn were used to convert the isentropic compressibilities into the partial molar isothermal compressibilities at infinite dilution, K(T,2)(o). These K(S,2)(o) and K(T,2)(o) results were used to obtain the partial molar compressibilities of the glycyl group CH(2)CONH at 25 degrees C. The results are compared with those obtained using data for other series of peptides of sequence ala(gly)(n), n=1-4, and (gly)(n), n=2-5.     

Effect of cholesterol on the bond ordering in hydrated unsaturated lipid bilayers

Molecular dynamics computer simulations of hydrated bilayers of unsaturated phosphatidylcholines in which double bonds are in the states: 18:0/18:1(n-9)cis (PC), 18:0/18:2(n-6)cis (PC), 18:0/18:3(n-3)cis (PC), 18:0/20:4(n-6)cis (PC), and 18:0/22:6(n-3)cis in the presence of cholesterol (40 mol%) and its absence have been performed. The simulation have been performed at 303 K and 1 atm, under the conditions corresponding to the experimentally observed liquid-crystalline state of the bilayer from phosphatidylcholine. The C-C and C-H bond order parameter profiles with respect to the bilayer normal and the C-C bond orientation distribution functions have been calculated. The widths of the functions and positions of their maxima have been determined. The dependence of these characteristics on the type of the bond, the degree of unsaturation of the chain, the presence of cholesterol in the bilayer, and the bond order parameters have been analyzed.     

小麦新品种(系)Glu-1位点等位基因变异研究

应用SDS-PAGE技术分析了40份小麦新品种(系)的高分子量麦谷蛋白亚基等位基因变异。在Glu-1位点共检测到10种变异类型,其中Glu-Al位点有3种类型：Null、1、26 ,Glu-B1位点有5种类型：7 8、7 9、14 15、7、17 18,Glu-D1位点有2种类型：2 12、5 10;Null(54．3％)、7 8(51．4％)和2 12(62．9％)分别是Glu-Al、Glu-B1和Glu-D1位点上的主要亚基变异类型。另外,在2份材料的Glu-B1和Glu-D1位点各检测到1个新的亚基,分别命名为1By8．1和1Dx5^ 。Glu-1位点的Nei‘s遗传变异指数平均为0,5648,Glu-B1的遗传多样性最高,Glu-D1最低。供试小麦材料Glu-1位点的HMW-GS组合共有17种类型,以(Null,7 8,2 12)组合为主要类型,占31．4％;有9种亚基组合类型分别只在1份材料中出现,占26.1％。结果表明,这些小麦新品种(系)存在着丰富的亚基组合类型。     

Triplet state characteristics and singlet oxygen generation properties of anthracyclines

The triplet states of adriamycin (Ad), daunomycin (D) and two daunomycin analogues, daunomycinone (Dc) and daunomycin N-trifluoroacetamide (DAc), have been studied using laser flash photolysis and pulse radiolysis techniques. Triplet lifetimes, molar absorption coefficients, energy levels and quantum yields have been obtained for Dc and DAc, and estimated for D and Ad. Time-resolved near-infrared singlet oxygen luminescence measurements have been carried out on D, Ad and 5-iminodaunomycin (5-ID) in 2H2O solution and Dc in benzene solution at room temperature. Singlet oxygen quenching by the water-soluble anthracyclines was observed and a second-order rate constant of approx. 10(8) M-1.s-1 obtained. Electron spin resonance experiments have demonstrated that D photoexcited at lambda less than or 365 nm gives rise to singlet oxygen as shown by its reaction with 2,2,6,6-tetramethyl-4-piperidone to give the corresponding nitroxyl radical. Although all the anthracyclines studied have the ability to photosensitize the formation of singlet oxygen, the quantum yields are very low (phi delta approximately 0.02-0.03), suggesting that these anthracyclines would be poor photodynamic sensitisers.     

The use of Pseudomonas sp. M plasmid pM3 for the transposon mutagenesis of Erwinia

The transposon containing derivatives pMTF9 (Tn9), pMTF10 (Tn10) and pMTF59 (Tn5, Tn9) of the Pseudomonas sp. M conjugative plasmid pM3 demonstrating temperature-dependent instability in Erwinia cells incubated at 37 degrees C have been isolated. The obtained plasmids have been shown to be usable for transposon-mediated mutability in the bacterial cells of Erwinia generum incubated at 37 degrees C.     

pH-dependent local structure of ferricytochrome c studied by x-ray absorption spectroscopy

We have studied, using x-ray absorption spectroscopy by synchrotron radiation, the native state of the horse heart cytochrome c (N), the HCl denatured state (U(1) at pH 2), the NaOH denatured state (U(2) at pH 12), the intermediate HCl induced state (A(1) at pH 0.5), and the intermediate NaCl induced state (A(2) at pH 2). Although many results concerning the native and denatured states of this protein have been published, a site-specific structure analysis of the denatured and intermediate solvent induced states has never been attempted before. Model systems and myoglobin in different states of coordination are compared with cytochrome c spectra to have insight into the protein site structure in our experimental conditions. New features are evidenced by our results: 1) x-ray absorption near edge structure (XANES) of the HCl intermediate state (A(1)) presents typical structures of a pentacoordinate Fe(III) system, and 2) local site structures of the two intermediate states (A(1) and A(2)) are different.     

Synthetic and pharmacological studies on some transition metal chelates involving N-pyrimidino benzamide-2-carboxylic acid as ligand

N-pyrimidino benzamide-2-carboxylic acid (NPBCA) and its Cu(II), Ni(II), Co(II), Zn(II), and Mn(II) chelates have been synthesized and characterized by using elemental analyses, molar conductance, molecular weight determination, magnetic moment, infrared, and electronic spectra. Antifungal activity of the synthesized compounds has been screened on common fungi, viz., Aspergillus niger, Aspergillus nidulense, and Candida albicans at 28 degrees C and antibacterial activity has been observed on gram-positive (Staphylococcus aureus) and gram-negative (Escherichia coli) bacteria at 37 degrees C. Anti-inflammatory and ulcerogenic potential of the synthesized compounds have been discussed.     

Antiviral activities of hybrids of two major human leukocyte interferons.

Four hybrid human leukocyte interferon (LeIF or IFN-alpha) genes have been constructed by in vitro recombination of LeIF-A (IFN-alpha 2) and LeIF-D (IFN-alpha 1) genes at common restriction endonuclease sites located within their coding regions. These hybrid genes have been expressed in E. coli under trp promoter control. The interferons produced [LeIF-AD (BglII), -AD (PvuII), -DA (BglII), -DA (PvuII)] have antiviral properties distinct from the parental molecules LeIF-A and -D, varying considerably in their abilities to inhibit plaque formation by different viruses in a range of mammalian cells. All six of the cloned LeIFs exhibit the heat stability, pH 2 stability and antigenic specificity of natural leukocyte interferons.     

Properties of adenyl cyclase and cyclic adenosine 3'',5''-monophosphate receptor protein-deficient mutants of Escherichia coli.

Several spontaneous cya and crp mutants of Escherichia coli have been selected as clones simultaneously resistant to phage lambda and nalidixic acid and characterized. Both cya and crp mutants have been found to grow as cocci with increased doubling times. They have increased resistance to some mutagens (methylmethanesulfonate, ultraviolet light, gamma rays), antibiotics (nalidixic acid, ampicillin), phages (lambda, T6), sublethal heat and hypotonic shock, and decreased resistance to neutral detergents (sodium dodecyl sulfate, sodium deoxycholate), a protein synthesis inhibitor (streptomycin), and a respiratory inhibitor (sodium azide). The nature of changes in cell parameters indicate fundamental alterations in the envelope structure of the cya and crp mutant cells. The new cya and crp mutants have been found to be multiply carbohydrate negative and nonmotile in conformity with similar previously isolated mutants. Studies of revertants and phi80 cya+ and phi80 cya transductants indicated that the pleiotropic phenotype is related to a single mutational event at the cya or the crp locus in the mutants.     

Structural and microbial studies of some transition metal complexes

N-pyridinobenzamide-2-carboxylic acid has been synthesized. Its binary and ternary (using 8-hydroxy-quinoline as the other ligand) Cu(II), Ni(II), Co(II), and Zn(II) complexes have been synthesized and characterized by their elemental analysis, molecular weight determination, molar conductance, infrared and electronic spectral data, and magnetic measurements. Antibacterial activity of these ligands and their metal complexes has been determined on gram-positive (Staphylococcus aureus) and gram-negative (Escherichia coli) bacteria at 37 degrees C, and antifungal activity has been determined on common fungi viz. Aspergillus niger, Aspergillus nidulense, and Candida albicans at 28 degrees C. A considerable increase in the biocidal activity of these ligands on being coordinated with metal ions has been reported.