Mechanism of thioredoxin-catalyzed disulfide reduction. Activation of the buried thiol and role of the variable active-site residues

Thioredoxins (Trx) are enzymes with a characteristic CXYC active-site motif that catalyze the reduction of disulfide bonds in other proteins. We have theoretically explored this reaction mechanism, both in the gas phase and in water, using density functional theory. The mechanism of disulfide reduction involves two consecutive thiol-disulfide exchange reactions, that is, nucleophilic substitutions at sulfur (S(N)2@S): first, by one Trx cysteine-thiolate group (Cys-32) at a sulfur atom of the disulfide substrate and, second, by the other Trx cysteine-thiolate group (the buried thiol of Cys-35) at the sulfur atom of the first Trx cysteine. We have investigated the intrinsic nature of such S(N)2@S substitution using the simple CH3S(-) + CH3SSCH3 model and how it is affected by solvation in aqueous solution. Next, we have examined how the behavior of the elementary S(N)2@S steps changes in the more realistic enzyme-substrate model CGPC + CH3SSCH3, which contains the active-site of Trx. In all model reactions, solvation turns the hypervalent trisulfide anion (i.e., the S(N)2@S transition species) from a stable complex into a transition state. Importantly, our analyses suggest that the deprotonation of the buried thiol (which is required before the latter can enter into the second S(N)2@S step) is done by the leaving group evolving from the first S(N)2@S step. Finally, molecular dynamics (MD) simulations, in the gas phase and in water, of CGPC, CGGC, and the corresponding wild-type Trx and P34G Trx show that the activity of the thioredoxin active-site motif (CXYC) is determined not only by the structural rigidity associated with the particular variable residues (XY) but also by the number of amide N-H groups. The latter are involved in the stabilization of the Cys-32 thiolate and thus affect the acidity and nucleophilicity of this residue.     

Electron transfer between guanosine radicals and amino acids in aqueous solution. II. Reduction of guanosine radicals by tryptophan

The efficiency of the chemical pathway of DNA repair is studied by time-resolved chemically induced dynamic nuclear polarization (CIDNP) using the model system containing guanosyl base radicals, and tryptophan as the electron donor. Radicals were generated photochemically by pulsed laser irradiation of a solution containing the photosensitizer 2,2'-dipyridyl, guanosine-5'-monophosphate, and N-acetyl tryptophan. Depending on the pH of the aqueous solution, four protonation states of the guanosyl radical are formed via electron or hydrogen atom transfer to the triplet excited dye. The rate constants of electron transfer from the amino acid to the guanosyl radical were determined by quantitative analysis of the CIDNP kinetics, which is very sensitive to the efficiency of radical reactions in the bulk, and rate constants vary from (1.0 +/- 0.3) x 10(9) M(-1) s(-1) for the cation and dication radicals of the nucleotide to (1.2 +/- 0.3) x 10(7) M(-1) s(-1) for the radical in its anionic form. They were found to be higher than the corresponding values for electron transfer in the case of N-acetyl tyrosine as the reducing agent.     

Aminium cation radical of glycylglycine and its deprotonation to aminyl radical in aqueous solution

The photochemical reaction between glycylglycine and triplet 4-carboxybenzophenone has been investigated using time-resolved chemically induced dynamic nuclear polarization (CIDNP). It is shown that the mechanism of the peptide reaction with triplet excited carboxybenzophenone is electron transfer from the amino group of the peptide, leading to the formation of an aminium cation radical that deprotonates to a neutral aminyl radical. Simulation of the CIDNP kinetics leads to an estimation of the paramagnetic relaxation time for the alpha-protons at the N-terminus at 20 to 40 mus with the best-fit value of 25 mus.     

Photopolymerization of water-soluble acrylic monomers induced by colloidal CdS and Cd x Zn1 − x S nanoparticles

Photocatalytic activity of CdS and Cd _x Zn_1−x S nanoparticles in the polymerization of acrylamide and acrylic acid in aqueous solutions has been found. It has been shown that the most probable way of the photogeneration of primary radicals is the reduction of an adsorbed monomer by the conduction band electrons of the semiconductor nanoparticles, a monomer oxidation by the valence band holes and atomic hydrogen addition to a monomer being complementary photoinitiation routes. A correlation between the composition of Cd_xZn_1-xS nanoparticles and their photocatalytic activity in the acrylamide polymerization has been established. It has been shown that an increase in the quantum yield of the photopolymerization in a sequence СdS < Cd_0.75Zn_0.25S < CdS_0.5Zn_0.5S < Cd_0.3Zn_0.7S originates from a concurrent increase of the conduction band potential of the semiconductor nanoparticles. A kinetic equation of the photocatalytic acrylamide polymerization has been derived. Quantum yields of the photoinitiation have been found to be as small as 10⁻⁴ to 10⁻³.     

Preparation and modification of collagen-based porous scaffold for tissue engineering

In the effort to generate cartilage tissues using mesenchymal stem cells, porous scaffolds with prescribed biomechanical properties were prepared. Scaffolds with interconnected pores were prepared via lyophilisation of frozen hydrogels made from collagen modified with chitosan nanofibres, hyaluronic acid, copolymers based on poly(ethylene glycol) (PEG), poly(lactic-co-glycolic acid) (PLGA), and itaconic acid (ITA), and hydroxyapatite nanoparticles. The modified collagen compositions were cross-linked using N-(3-dimethylamino propyl)-N′-ethylcarbodiimide hydrochloride (EDC) combined with N-hydroxysuccinimide (NHS) in water solution. Basic physicochemical and mechanical properties were measured and an attempt to relate these properties to the molecular and supermolecular structure of the modified collagen compositions was carried out. Scaffolds containing hydrophilic chitosan nanofibres showed the highest swelling ratio (SR = 20–25) of all the materials investigated, while collagen modified with an amphiphilic PLGA-PEG-PLGA copolymer or functionalised with ITA exhibited the lowest swelling ratio (SR = 5–8). The best resistance to hydrolytic degradation was obtained for hydroxyapatite containing scaffolds. On the other hand, the fastest degradation rate was observed for synthetic copolymer-containing scaffolds. The results showed that the addition of hydroxyapatite or hyaluronic acid to the collagen matrix increases the rigidity in comparison to the collagen-chitosan scaffold. Collagen scaffold modified with hyaluronic acid presented reduced deformation at break while the presence of hydroxypatatite enhanced the scaffold deformation under tensile loading. The tensile elastic modulus of chitosan nanofibre collagen scaffold was the lowest but closest to the articular cartilage; however, the strength and deformation to failure increased up to 200 %. Presented at the 1st Bratislava Young Polymer Scientists Workshop, Bratislava, 20–23 August 2007.     

Directed self-assembly in laponite/CdSe/polyaniline nanocomposites

Laponite films provide versatile inorganic scaffolds with materials architectures that direct the self-assembly of CdSe quantum dots (QDs or EviTags) and catalytic surfaces that promote the in situ polymerization of polyaniline (PANI) to yield novel nanocomposites for light emitting diodes (LEDs) and solar cell applications. Water-soluble CdSe EviTags with varying, overlapping emission wavelengths in the visible spectrum were incorporated using soft chemistry routes within Na-Laponite host film platforms to achieve broadband emission in the visible spectrum. QD concentrations, composition and synthesis approach were varied to optimize photophysical properties of the films and to mediate self-assembly, optical cascading and energy transfer. In addition, aniline tetramers coupled to CdSe (QD-AT) surfaces using a dithioate linker were embedded within Cu-Laponite nanoscaffolds and electronically coupled to PANI via vapor phase exposure. Nanotethering and specific host-guest and guest-guest interactions that mediate nanocomposite photophysical behavior were probed using electronic absorption and fluorescence spectroscopies, optical microscopy, AFM, SEM, powder XRD, NMR and ATR-FTIR. Morphology studies indicated that Lap/QD-AT films synthesized using mixed solvent, layer by layer (LbL) methods exhibited anisotropic supramolecular structures with unique mesoscopic ordering that affords bifunctional networks to optimize charge transport.     

The effect of Me<Subscript>4</Subscript>NBr,Et<Subscript>4</Subscript>NBr,Bu<Subscript>4</Subscript>NBr,and (EtOH)<Subscript>3</Subscript>EtNBr on the Temperature of Maximum Density of Water

The densities of aqueous solutions of Me₄NBr, Et₄NBr, Bu₄NBr, and Et(OH)₃EtNBr were measured in the concentration range 0.002 to 0.05 mol⋅kg⁻¹. The temperature of the determinations ranged from 275.15 to 279.15 K in 0.5 K steps, and the uncertainty of the densities was around ±1×10⁻⁶ g⋅cm⁻³. Eleven concentrations were used for each of the salts. It was found that all the solutes follow Despretz’ law. The absolute value of the Despretz’s constants increases with increasing number of carbon atoms in the cation, except for Et(OH)₃EtNBr which has the highest value. The ionic contributions to the Despretz’s constants were calculated. The volumetric data obtained allows the calculation proposed by Kalgud and Pokale. The effective ionic radii were calculated using a semi-empirical equation, as proposed previously by several workers. The nonlinearity of the plot of the ionic Despretz constants versus effective ionic radius is confirmed.     

Concentration polarization and nonequilibrium electroosmotic slip in hierarchical monolithic structures

This article illustrates the appearance and electrohydrodynamic consequences of concentration polarization (CP) in hierarchically structured monolithic fixed beds used as stationary phases in CEC and related electrical-field-assisted separation techniques. Subject of the investigation are silica-based monoliths in capillary format with a bimodal pore size distribution. Ion-permselectivity in the intraskeleton pore space together with diffusive and electrokinetic transport induces depleted and enriched CP zones at the anodic and cathodic interfaces, respectively, of the cation-selective mesoporous skeleton. The extent of electrical-field-induced CP is shown to be governed by the fluid phase ionic strength, which tunes the ion-permselectivity of the mesoporous monolith skeleton via local electrical double layer overlap, and by the applied electrical field strength, which determines local transport. The analysis of quantitative confocal laser scanning microscopy data, resolving CP on the local skeleton scale, indicates that at sufficiently high field strength a transition from intraskeleton to interskeleton boundary-layer-dominated transport of charged species occurs. This transition is correlated to the onset of macroscopically measured, nonlinear EOF velocities, whose occurrence is explained in the framework of a nonequilibrium electroosmotic slip. It is shown that the onset of nonlinear electrokinetics in the system can be tuned by properties of the BGE, particularly buffer pH, which modulates the pH-dependent surface charge density and consequently the ion-permselective skeleton's charge selectivity. Finally, the CP dynamics of monolithic and particulate fixed beds are compared, and the observed differences are related to the specific morphologies of the two hierarchical fixed bed structures.     

Mononuclear dioxomolybdenum(VI) complexes with the quinolones enrofloxacin and sparfloxacin: Synthesis,structure, antibacterial activity and interaction with DNA

The neutral mononuclear dioxomolybdenum(VI) complexes of the quinolone antibacterial agents enrofloxacin and sparfloxacin have been prepared and characterized with physicochemical and spectroscopic techniques. In these complexes, enrofloxacin and sparfloxacin act as bidentate deprotonated ligands bound to the metal through the pyridone oxygen and one carboxylate oxygen. The central molybdenum atoms are six-coordinate with slightly distorted octahedral geometry. The lowest energy model structure of each complex has been proposed with molecular modeling calculations. The antimicrobial activity of the complexes has been tested on three different microorganisms. The investigation of the interaction of the complexes with calf-thymus DNA has been performed with diverse spectroscopic techniques.     

Isolation of Novel Alkaliphilic <Emphasis Type="Italic">Bacillus</Emphasis> Strains for Cyclodextrin Glucanotransferase Production

New alkaliphilic Bacillus producers of cyclodextrin glucanotransferase (CGTase, EC 2.4.1.19) were isolated from 17 Bulgarian alkaline and normal habitats (springs and soils) by three steps of a selection. None of the isolates obtained, producing CGTase, appeared to be thermophilic in character. One hundred and thirty-seven strains were estimated for CGTase activity by batch cultivation in a liquid alkaline medium. Twenty-seven of them had a detectable CGTase activity in their culture supernatants under the enzyme assay conditions, despite of the significant growth of all isolates. The phenotypic properties of three selected strains (20RF, 8SB and 24WE) were determined. They were aerobic endospore-forming Bacillus strains: two of them were obligated alkaliphiles (20RF and 8SB) and one, alkalitolerant (24WE). Both obligated alkaliphiles were further characterised by 16S rRNA analysis. According to the full 16S rRNA gene sequences obtained and deposited to the NCBI GenBank database, both isolated obligated alkaliphiles 20RF and 8SB were clustered into the group of alkaliphilic Bacillus species. The exhibited CGTase production by them (230–250 U ml⁻¹ for 20RF and 130–160 U ml⁻¹ for 8SB) defined these new isolates as promising producers of the enzyme, especially Bacillus sp. 8SB synthesising thermostable alkaline β-CGTase. Both new enzymes from 20RF and 8SB Bacillus strains formed only two types of cyclodextrins, beta and gamma, which could be of interest for their easy separation and industrial production.