Impact of cysteine variants on the structure,activity, and stability of recombinant human α-galactosidase A

Recombinant human α-galactosidase A (rhαGal) is a homodimeric glycoprotein deficient in Fabry disease, a lysosomal storage disorder. In this study, each cysteine residue in rhαGal was replaced with serine to understand the role each cysteine plays in the enzyme structure, function, and stability. Conditioned media from transfected HEK293 cells were assayed for rhαGal expression and enzymatic activity. Activity was only detected in the wild type control and in mutants substituting the free cysteine residues (C90S, C174S, and the C90S/C174S). Cysteine-to-serine substitutions at the other sites lead to the loss of expression and/or activity, consistent with their involvement in the disulfide bonds found in the crystal structure. Purification and further characterization confirmed that the C90S, C174S, and the C90S/C174S mutants are enzymatically active, structurally intact and thermodynamically stable as measured by circular dichroism and thermal denaturation. The purified inactive C142S mutant appeared to have lost part of its alpha-helix secondary structure and had a lower apparent melting temperature. Saturation mutagenesis study on Cys90 and Cys174 resulted in partial loss of activity for Cys174 mutants but multiple mutants at Cys90 with up to 87% higher enzymatic activity (C90T) compared to wild type, suggesting that the two free cysteines play differential roles and that the activity of the enzyme can be modulated by side chain interactions of the free Cys residues. These results enhanced our understanding of rhαGal structure and function, particularly the critical roles that cysteines play in structure, stability, and enzymatic activity.     

Dose-, time-, and tissue-dependent effects of 5-bromo-2′ -deoxyuridine on the in-vitro organogenesis of Arabidopsis thaliana

Vigorous organogenesis can be induced from hypocotyl and root explants of Arabidopsis thaliana using a two-step culture procedure consisting of preculture on callus-inducing medium (CIM) and subsequent culture on shoot-inducing medium (SIM) or root-inducing medium (RIM). With this culture system, we examined the influence of 5-bromo-2′-deoxyuridine (BrdU), a thymidine (dT) analogue, on plant organogenesis in vitro. Treatment with BrdU during SIM or RIM culture had negative effects on shoot and root redifferentiation over a broad range of concentrations. When explants were exposed to low concentrations of BrdU during preculture and then transferred onto BrdU-free SIM, shoot redifferentiation was accelerated significantly. At higher doses, BrdU treatment during the pre-culture inhibited shoot redifferentiation strongly in hypocotyl explants, but not in root explants. This suggests that a target of the BrdU action lies within the process of acquisition of cell proliferation competence specifically involved in hypocotyl dedifferentiation. These effects of BrdU were counteracted by the simultaneous addition of excess dT. BrdU-pretreated and untreated explants did not differ significantly in the phytohormone dependency of shoot redifferentiation. Our results provide a basis for future studies on plant organogenesis combining pharmacological analysis with BrdU as a probe and molecular genetics with Arabidopsis mutants.     

How long is too long? Effects of loop size on G-quadruplex stability

We compared here 80 different sequences containing four tracts of three guanines with loops of variable length (between 1 and 15 bases for unmodified sequences, up to 30 for fluorescently labeled oligonucleotides). All sequences were capable of forming stable quadruplexes, with T_m above physiological temperature in most cases. Unsurprisingly, the melting temperature was systematically lower in sodium than in potassium but the difference between both ionic conditions varied between 1 and >39°C (average difference: 18.3°C). Depending on the sequence context, and especially for G4 sequences involving two very short loops, the third one may be very long without compromising the stability of the quadruplex. A strong inverse correlation between total loop length and T_m was found in K⁺: each added base leads to a 2°C drop in T_m or ∼0.3 kcal/mol loss in ΔG°. The trend was less clear in Na⁺, with a longer than expected optimal loop length (up to 5 nt). This study will therefore extend the sequence repertoire of quadruplex-prone sequences, arguing for a modification of the widely used consensus (maximal loop size of 7 bases).     

5-Ethyl-2′-deoxyuridine: Absence of effects on the chromosomes of human lymphocytes and fibroblasts in culture

Summary In vitro studies have been performed with 5-ethyl-2-deoxyuridine (EDU) concerning its incorporation into the cell nuclear material and its effects on the chromosome morphology of cultivated human lyphocytes and skin fibroblasts. This compound is presumably incorporated in the DNA without visible chromosome aberrations as is seen with many other pyrimidine analogues. A slight inhibition of the cell growth was noted at high concentration (120g/ml) of EDU. A similar degree of cell growth inhibition was found with corresponding doses of deoxythymidine.

---

Zusammenfassung Es wurden in vitro-Untersuchungen hinsichtlich des Äthyldeoxyuridineinbaus (ÄDU) und dessen Einfluß auf menschliche Lymphocyten- und Fibroblastenchromosomen durchgeführt. Diese Substanz wird in die DNS eingebaut und führt nicht zu sichtbaren Chromosomenaberrationen wie bei einigen anderen Pyrimidinanaloga. Eine leichte Hemmung des Zellwachstums wurde mit 120 g/ml ÄDU festgestellt. Eine ähnliche Hemmung des Zellwachstums ließ sich auch mit gleicher Deoxythymidinkonzentration nachweisen.

---

---

Supported by the Deutsche Forschungsgemeinschaft.     

Spectroscopic investigation of nickel cation binding with adenine mononucleotides: stability and structure of the 1:2 complex with adenosine 5′-monophosphate

 The interaction of Ni(II) ions with adenine mononucleotides (5′-AMP, 3′-AMP, 2′-AMP, 2′,3′-cAMP, 3′,5′-cAMP) was studied in aqueous solution using Raman spectroscopy and ¹³C and ³¹P NMR paramagnetic relaxation measurements. Macrochelate structures were observed to form for all non-cyclic AMPs, with increasing stability in the series: 3′-AMP < 2′-AMP < 5′-AMP. N7 of adenine was found to be the key site of the Ni(II)-adenine interaction for all non-cyclic AMPs. For 2′-AMP, an alternative binding to the pyrimidine ring may also exist. The dependence of Raman spectra on AMP and Ni(II) concentration confirmed the existence of a stable 1 : 2 Ni(II)-(5′-AMP) complex, besides the 1 : 1 complexes. In this complex, the adenine moieties of both 5′-AMP molecules are situated close to Ni(II), and their relative orientations with respect to the cation are very similar. The paramagnetic relaxation enhancements of the carbons indicate that the nickel ion is not located in the plane of the adenine units, but that the line connecting Ni(II) and N7 deviates strongly from the adenine planes. Phosphates are outer-sphere coordinated by the cation. Findings from both methods have led us to propose possible global architectures of the complex. Received: 26 June 1998 / Accepted: 22 July 1998     

Effects of congenital cataract mutation R116H on αA-crystallin structure,function and stability

α-crystallin is a molecular chaperone that maintains the optical properties of the lens and delays the onset scattering caused by aging-related protein aggregation. In this research, we found that the missense mutation R116H resulted in an altered size distribution, impaired packing of the secondary structures and modified quaternary structure with great hydrophobic exposure. The mutant exhibited a substrate-dependent chaperone (aggregation–inhibition) or anti-chaperone (aggregation–promotion) effect. Equilibrium unfolding experiments indicated that the mutation stabilized an aggregation-prone intermediate which was not populated during the unfolding of the wild-type protein. The accumulation of this intermediate greatly promoted the formation of non-native large oligomers or aggregates during unfolding. These results suggested that both the aggregation of the mutant upon stress and co-deposition with the target proteins were likely to be responsible for the onset of cataract.     

The comparative effects of 5′-methylthioadenosine and some of its analogs on cells containing,and deficient in, 5′-methylthioadenosine phosphorylase

The antiproliferative effects of 5′-methylthioadenosine and the 5′-methylthioadenosine analogs, 5′-isobutylthioadenosine, 5′-deoxyadenosine and 5′-methylthiotubercidin were examined using two mouse cell lines, one 5′-methylthioadenosine phosphorylase-deficient the other containing 5′-methylthioadenosine phosphorylase. All of the compounds were found to be growth inhibitory to both cell lines, demonstrating that these compounds need not be degraded to exert their inhibitory effects. A correlation was observed between the potency of the growth inhibitory effect and the ability of the cells to degrade these compounds. 5′-Methylthioadenosine, 5′-deoxyadenosine and 5′-isobutylthioadenosine, all of which are substrates for the 5′-methylthioadenosine phosphorylase in vitro, were more growth inhibitory to the 5′-methylthioadenosine phosphorylase-deficient cells than to the 5′-methylthioadenosine phosphorylase-containing cells, whereas, the 7-deaza analog, 5′-methylthiotubercidin, a nondegradable inhibitor of the 5′-methylthioadenosine phosphorylase, was a more potent inhibitor of the 5′-methylthioadenosine phosphorylase-containing cell line. Due to the inhibition by 5′-methylthiotubercidin on 5′-methylthioadenosine phosphorylase in vitro the disposition of cellularly-synthesized 5′-methylthioadenosine was explored using both cell types. 5′-Methylthiotubercidin inhibited the accumulation of exogenous 5′-methylthioadenosine from 5′-methylthioadenosine phosphorylase-deficient cells with no effect on intracellular 5′-methylthioadenosine. In contrast, 5′-methylthiotubercidin caused a large accumulation of extracellular 5′-methylthioadenosine with a concomitant smaller increase intracellularly in 5′-methylthioadenosine phosphorylase-containing cells. That cellularly-synthesized 5′-methylthioadenosine as well as the cellular excretion of this nucleoside are altered in response to treatment with 5′-methylthiotubercidin suggests two possible sites at which 5′-methylthiotubercidin may exert its effect.     

Acetylation of αA-crystallin in the human lens: effects on structure and chaperone function

α-Crystallin is a major protein in the human lens that is perceived to help to maintain the transparency of the lens through its chaperone function. In this study, we demonstrate that many lens proteins including αA-crystallin are acetylated in vivo. We found that K70 and K99 in αA-crystallin and, K92 and K166 in αB-crystallin are acetylated in the human lens. To determine the effect of acetylation on the chaperone function and structural changes, αA-crystallin was acetylated using acetic anhydride. The resulting protein showed strong immunoreactivity against a N(ε)-acetyllysine antibody, which was directly related to the degree of acetylation. When compared to the unmodified protein, the chaperone function of the in vitro acetylated αA-crystallin was higher against three of the four different client proteins tested. Because a lysine (residue 70; K70) in αA-crystallin is acetylated in vivo, we generated a protein with an acetylation mimic, replacing Lys70 with glutamine (K70Q). The K70Q mutant protein showed increased chaperone function against three client proteins compared to the Wt protein but decreased chaperone function against γ-crystallin. The acetylated protein displayed higher surface hydrophobicity and tryptophan fluorescence, had altered secondary and tertiary structures and displayed decreased thermodynamic stability. Together, our data suggest that acetylation of αA-crystallin occurs in the human lens and that it affects the chaperone function of the protein.     

The effects of cholesterol and β-sitosterol on the structure of saturated diacylphosphatidylcholine bilayers

The structures of DMPC and DPPC bilayers in unilamellar liposomes, in the presence of 33.3 mol% cholesterol or the plant sterol β-sitosterol, have been studied by small-angle neutron scattering. The bilayer thickness d _L increases in a similar way for both sterols. The repeat distance in multilamellar liposomes, as determined by small-angle X-ray diffraction, is larger in the presence of β-sitosterol than in the presence of cholesterol. We observe that each sterol modifies the interlamellar water layer differently, cholesterol reducing its thickness more efficiently than β-sitosterol, and conclude that cholesterol suppresses bilayer undulations more effectively than β-sitosterol.     

The effect of counterion,water concentration,and stirring on the stability of subtilisin BPN′ in organic solvents

The stability of subtilisin BPN′ in organic solvents or cosolvent/water mixtures was studied as a function of the type and concentration of counterion at the time of freeze-drying, water concentration, and stirring speed/method. It was found that the enzyme is stabilized by high concentrations of counterion, at least at very high cosolvent concentrations. The type of counterion also has a remarkable impact on the enzyme stability; at high concentrations of DMF (dimethylformamide), multivalent counterions with low solubility in organic solvents are far superior to monovalent, soluble ones. Sodium citrate is the best salt tested in terms of enzyme stability, increasing the half life of the enzyme better than a millionfold over Tris in 99% DMF. The stability of the enzyme was found to have a complex dependence on the amount of water in the DMF. Enzyme lyophilized from the sodium phosphate displays a stability minimum at about 90% DMF, while enzyme lyophilized from Tris becomes increasingly unstable from 30% to 99% DMF, without inflection. Vigorous stirring with a magnetic stir bar, which broke apart the enzyme particles, was found to be extremely deleterious to enzyme stability, while swirling the enzyme with a wrist-action stirrer, which did not grind the enzyme particles, had no effect. Explanations for this are discussed.     

Isolation,structure determination and biological activity of A-16686 factors A′ 1, A′ 2 and A′ 3 glycolipodepsipeptide antibiotics

Summary WhenActinoplanes strain ATCC 33076, the producer of A-16686 A1, A2 and A3 complex, is fermented in a suitable medium three additional factors, designated A1, A2 and A3 are produced. These were isolated and characterized, and were shown to differ from the parent components of the original complex by lacking one mannose unit. Bioconversion of A factors into A factors was achieved by incubation with the mycelium ofActinoplanes ATCC 33076. Factor A2 has better antibacterial activity than A2 against some bacteria.     

γ-Glutamyl transpeptidase architecture: Effect of extra sequence deletion on autoprocessing,structure and stability of the protein from Bacillus licheniformis

γ-Glutamyl transpeptidases (γ-GTs, EC 2.3.2.2) are a class of ubiquitous enzymes which initiate the cleavage of extracellular glutathione (γ-Glu-Cys-Gly, GSH) into its constituent glutamate, cysteine, and glycine and catalyze the transfer of its γ-glutamyl group to water (hydrolysis), amino acids or small peptides (transpeptidation). These proteins utilize a conserved Thr residue to process their chains into a large and a small subunit that then form the catalytically competent enzyme. Multiple sequence alignments have shown that some bacterial γ-GTs, including that from Bacillus licheniformis (BlGT), possess an extra sequence at the C-terminal tail of the large subunit, whose role is unknown. Here, autoprocessing, structure, catalytic activity and stability against both temperature and the chemical denaturant guanidinium hydrochloride of six BlGT extra-sequence deletion mutants have been characterized by SDS-PAGE, circular dichroism, intrinsic fluorescence and homology modeling. Data suggest that the extra sequence has a crucial role in enzyme activation and structural stability. Our results assist in the development of a structure-based interpretation of the autoprocessing reaction of γ-GTs and are helpful to unveil the molecular bases of their structural stability.     

The effects of fishing on the diversity,biomass and trophic structure of Seychelles’ reef fish communities

A fishery independent underwater visual census technique was used to assess the effects of fishing on the diversity, biomass and trophic structure of the diurnally active non-cryptic reef-associated fish communities of the Seychelles. One hundred and thirty four species associated with three significantly different types of reef habitat were censused at one unfished ground and in six fishing grounds subject to different fishing intensity and the biomass of several species targeted by the fishery. The diversity of families containing target species (lutjanidae, lethrinidae) was significantly higher at unfished and lightly fished sites as was the total biomass of the fish community and the biomass of piscivorous, piscivorous/invertebrate feeding and herbivorous trophic groups. However, there was no indication that the biomass of non-target species increased in response to the removal of their predators by fishing. The findings of this study are significant for fishery managers because they suggest that the intensive differential cropping of top predators will not necessarily lead to increases in the biomass and productivity of their prey.     

Anesthetic effects on the structure and dynamics of the second transmembrane domains of nAChR α4β2

Channel functions of the neuronal α4β2 nicotinic acetylcholine receptor (nAChR), one of the most widely expressed subtypes in the brain, can be inhibited by volatile anesthetics. Our Na⁺ flux experiments confirmed that the second transmembrane domains (TM2) of α4 and β2 in 2:3 stoichiometry, (α4)₂(β2)₃, could form pentameric channels, whereas the α4 TM2 alone could not. The structure, topology, and dynamics of the α4 TM2 and (α4)₂(β2)₃ TM2 in magnetically aligned phospholipid bicelles were investigated using solid-state NMR spectroscopy in the absence and presence of halothane and isoflurane, two clinically used volatile anesthetics. ²H NMR demonstrated that anesthetics increased lipid conformational heterogeneity. Such anesthetic effects on lipids became more profound in the presence of transmembrane proteins. PISEMA experiments on the selectively ¹⁵N-labeled α4 TM2 showed that the TM2 formed transmembrane helices with tilt angles of 12° ± 1° and 16° ± 1° relative to the bicelle normal for the α4 and (α4)₂(β2)₃ samples, respectively. Anesthetics changed the tilt angle of the α4 TM2 from 12° ± 1° to 14° ± 1°, but had only a subtle effect on the tilt angle of the (α4)₂(β2)₃ TM2. A small degree of wobbling motion of the helix axis occurred in the (α4)₂(β2)₃ TM2. In addition, a subset of the (α4)₂(β2)₃ TM2 exhibited counterclockwise rotational motion around the helix axis on a time scale slower than 10^- 4 s in the presence of anesthetics. Both helical tilting and rotational motions have been identified computationally as critical elements for ion channel functions. This study suggested that anesthetics could alter these motions to modulate channel functions.     

Influence of 4′-6-diamidino-2-phenylindole on the secondary structure and template activities of DNA and polydeoxynucleotides

Summary The interaction between 4-6-Diamidino-2-Phenylindole-hydrochloride (DAPI) and a variety of DNAs and synthetic polydeoxynucleotides was investigated in order to delineate the nucleic acid structural features necessary for binding. The spectra of DAPI-DNA complexes, measured at various DAPI-DNA molar ratios (r), are hypochromic relative to DNA in the region of its maximum absorption. All the curves pass through an isosbestic point at 268 nm. A new maxima appears in the region of 380–392 nm for DAPI-DNA complexes. The magnitude of the peaks in the region are directly proportional to the amount of drug present in the complex.Studies with various DNA types and synthetic polydeoxynucleotides indicate that the drug preferentially binds to dAT-rich regions of DNA. This was also confirmed by enzymatic studies. The inhibition of template action by DAPI in a purified DNA-polymerase reaction was dependent on the dAT-content of the template. The implication of these data to explain a selective binding of DAPI to mitochondrial DNA have been discussed.     

Characterization of the effects of phosphorylation by CK2 on the structure and binding properties of human HP1β

Proteins of the Heterochromatin Protein 1 (HP1) family are regulators of chromatin structure and genome function in eukaryotes. Post-translational modifications expand the repertoire of the chemical diversity of HP1 proteins and regulate their activity. Here, we investigated the effect of phosphorylation by Casein kinase 2 (CK2) on the structure, dynamics and binding activity of human HP1β. We show that Ser89 in the hinge region is the most effective substrate, followed by Ser175 at the C-terminal tail. Phosphorylation at these sites results in localized conformational changes in HP1β that do not compromise the ability of the protein to bind chromatin.     

Interaction of γ-conglutin from Lupinus albus with model phospholipid membranes: Investigations on structure,thermal stability and oligomerization status

Interaction with model phospholipid membranes of lupin seed γ-conglutin, a glycaemia-lowering protein from Lupinus albus seeds, has been studied by means of Fourier-Transform infrared spectroscopy at p²H 7.0 and at p²H 4.5. The protein maintains the same secondary structure both at p²H 7.0 and at p²H 4.5, but at p²H 7.0 a higher ¹H/²H exchange was observed, indicating a greater solvent accessibility. The difference in T_m and T_D1/2 of the protein at the abovementioned p²H's has been calculated around 20 °C. Infrared measurements have been then performed in the presence of DMPG and DOPA at p²H 4.5. DMPG showed a little destabilizing effect while DOPA exerted a great stabilizing effect, increasing the T_m of γ-conglutin at p²H 4.5 of more than 20 °C. Since γ-conglutin at p²H 4.5 is in the monomeric form, the interaction with DOPA likely promotes the oligomerization even at p²H 4.5. Interaction between DMPG or DOPA and γ-conglutin has been confirmed by turbidity experiments with DMPC:DMPG or DOPC:DOPA SUVs. Turbidity data also showed high-affinity binding of γ-conglutin to anionic SUVs made up with DOPA. The molecular features outlined in this study are relevant to address the applicative exploitation and to delineate a deeper comprehension of the natural functional role of γ-conglutin.     

Benzimidazole 2′-Isonucleosides: Design,Synthesis, and Antiviral Activity of 2-Substituted-5,6-Dichlorobenzimidazole 2′-Isonucleosides

Abstract

2,5,6-Trihalogenated benzimidazole-β-D-ribofuranosyl nucleosides and 2-substituted amino-5,6-dichlorobenzimidazole-β-L-ribofuranosyl nucleosides are potent and selective inhibitors of human cytomegalovirus (HCMV). The D-ribofuranosyl analogs are metabolized rapidly in vivo rendering them unsuitable as drug candidates. The primary source of instability is thought to be the anomeric bond. The synthesis of a series of chemically stable benzimidazole-2′-isonucleosides is presented. The synthetic schemes employed are based on nucleophilic displacements of a 2′-tosylate from carbohydrate intermediates with 2-bromo-5,6-dichlorobenzidazole. 2-Bromo and 2-isopropyl amino analogs with 3′- and 5′-oxo and deoxy substitutions were prepared. The benzimidazole-2′-isonucleosides presented here demonstrated reduced activity against HCMV when compared to other D-ribofuranosyl benzimidazole analogs. In addition, they were not found to be inhibitors of HIV.