Ultrafast excited-state deactivation of flavins bound to dodecin

Dodecins, a group of flavin-binding proteins with a dodecameric quaternary structure, are able to incorporate two flavins within each of their six identical binding pockets building an aromatic tetrade with two tryptophan residues. Dodecin from the archaeal Halobacterium salinarum is a riboflavin storage device. We demonstrate that unwanted side reactions induced by reactive riboflavin species and degradation of riboflavin are avoided by ultrafast depopulation of the reactive excited state of riboflavin. Intriguingly, in this process, the staggered riboflavin dimers do not interact in ground and photoexcited states. Rather, within the tetrade assembly, each riboflavin is kept under the control of the respective adjacent tryptophan, which suggests that the stacked arrangement is a matter of optimizing the flavin load. We further identify an electron transfer in combination with a proton transfer as a central element of the effective excited state depopulation mechanism. Structural and functional comparisons of the archaeal dodecin with bacterial homologs reveal diverging evolution. Bacterial dodecins bind the flavin FMN instead of riboflavin and exhibit a clearly different binding pocket design with inverse incorporations of flavin dimers. The different adoption of flavin changes photochemical properties, making bacterial dodecin a comparably less efficient quencher of flavins. This supports a functional role different for bacterial and archaeal dodecins.     

Modelling foraging ants in a dynamic and confined environment

In social insects, the superposition of simple individual behavioral rules leads to the emergence of complex collective patterns and helps solve difficult problems inherent to surviving in hostile habitats. Modelling ant colony foraging reveals strategies arising from the insects’ self-organization and helps develop of new computational strategies in order to solve complex problems. This paper presents advances in modelling ants’ behavior when foraging in a confined and dynamic environment, based on experiments with the Argentine ant Linepithema humile in a relatively complex artificial network. We propose a model which overcomes the problem of stagnation observed in earlier models by taking into account additional biological aspects, by using non-linear functions for the deposit, perception and evaporation of pheromone, and by introducing new mechanisms to represent randomness and the exploratory behavior of the ants.     

Fluorescence properties of reduced flavins and flavoproteins

Fluorescence lifetimes and polarized emission properties of reduced flavin were measured using several model compounds and flavoproteins. Depending on the conditions of solvent and temperature or reduction method the lifetimes vary between 1 and 15 ns. The longer lifetime values are found in several forms of reduced lactate oxidase, in which a good correlation exists between fluorescence intensity and lifetime. In practically all flavoproteins the fluorescence is heterogeneous. Several mechanisms are proposed to explain the observed heterogeneity in lifetimes. The reduced models in glycerol at subzero temperature exhibit high degrees of polarization of the fluorescence, whereas distinct depolarization is encountered in several reduced flavoproteins suggesting a certain mobility of the flavin chromophor.     

Self-assembly of surfactant aqueous solution confined in a Janus amphiphilic nanotube

Abstract

In recent years, Janus amphiphilic nanotubes with complex surfaces have been synthesized. However, the self-assembly behaviour of surfactant solutions confined in a Janus amphiphilic nanotube has not been investigated so far. We performed molecular simulations to investigate the morphologies and phase diagrams of a surfactant confined in Janus amphiphilic nanotube consisting of both hydrophobic and hydrophilic surfaces. We derived a phase diagram of the representative snapshots of equilibrium morphologies. Morphologies that were not observed in the bulk eventuated in confined systems. Moreover, the self-assembled structures were found to be dependent on the spatial confinement. Furthermore, the self-assembled structures confined in hydroneutral and Janus amphiphilic nanotubes were compared. The results suggested that the self-assembled structures confined in the Janus amphiphilic nanotube resembled that confined in the hydroneutral nanotube owing to a strong confinement effect. Further developments in controlling the morphologies and self-assemblies will greatly advance their applications of these materials in nanofluidic devices, or for nanopatterning.     

Experimental study of the excited-state properties and photostability of the mycosporine-like amino acid palythine in aqueous solution.

Characterization of the excited states of the mycosporine-like amino acid palythine (lambda(max) = 320 nm) in aqueous solutions was achieved experimentally. The low value for the photodegradation quantum yield, (1.2 +/- 0.2) x 10(-5), confirms that palythine is highly photostable in air saturated-aqueous solutions. Laser flash photolysis of acetone in the presence of palythine allowed for the observation of a transient spectrum which is consistent with the triplet-triplet absorption of palythine. Kinetic treatment of the transient signals yields a lifetime of the triplet state of ca. 9 micros and a triplet energy around 330 kJ mol(-1). The photoacoustic calorimetry results are consistent with non-radiative decay as the major fate of excited palythine. A comparison of the photodegradation quantum yields and photophysical properties of palythine with those previously determined for the other mycosporine-like amino acids, shinorine and porphyra-334, suggests that geometrical isomerization around the C=N bond may contribute to the rapid deactivation of this group of molecules.     

A microstructural model of elastostatic properties of articular cartilage in confined compression

A microstructural model of cartilage was developed to investigate the relative contribution of tissue matrix components to its elastostatic properties. Cartilage was depicted as a tensed collagen lattice pressurized by the Donnan osmotic swelling pressure of proteoglycans. As a first step in modeling the collagen lattice, two-dimensional networks of tensed, elastic, interconnected cables were studied as conceptual models. The models were subjected to the boundary conditions of confined compression and stress-strain curves and elastic moduli were obtained as a function of a two-dimensional equivalent of swelling pressure. Model predictions were compared to equilibrium confined compression moduli of calf cartilage obtained at different bath concentrations ranging from 0.01 to 0.50 M NaCl. It was found that a triangular cable network provided the most consistent correspondence to the experimental data. The model showed that the cartilage collagen network remained tensed under large confined compression strains and could therefore support shear stress. The model also predicted that the elastic moduli increased with increasing swelling pressure in a manner qualitatively similar to experimental observations. Although the model did not preclude potential contributions of other tissue components and mechanisms, the consistency of model predictions with experimental observations suggests that the cartilage collagen network, prestressed by proteoglycan swelling pressure, plays an important role in supporting compression.     

Conformation and dynamic properties of a saturated hydrocarbon chain confined in a model membrane: a Brownian dynamics simulation

A Brownian dynamics simulation of a saturated hydrocarbon chain with simple mean-field potentials, namely anchorage, orientation and enclosing, reproducing a biological membrane environment is presented. The simulation was performed for a time equivalent to 1.4 micros thanks to the simplicity of our model. The results are compared with those obtained for a hydrocarbon chain simulated in the absence of the membrane potentials but with confinement. With the appropriate choice of parameters, equilibrium properties, such as deuterium order parameter, chain length, tilt angle and geometry, and dynamic properties, such as dihedral angle transition rate, rotational and translational diffusion, recovered from our simulations, correctly reproduced, are consistent with hydrocarbon-derived molecule experimental results and simulation results obtained from other more complex studies.     

Chemical synthesis and some properties of 6-substituted flavins

A number of derivatives of riboflavin and of 3-methyllumiflavin substituted in the 6 position have been synthesized starting with 6-nitro flavins, reduction to the 6-amino flavin, and diazotization, followed by reaction with the appropriate nucleophile. The absorption spectra, oxidation-reduction potentials, and the electron spin resonance spectra of the radical cationic forms of several of these synthetic compounds have been determined, including 6-S-cysteinyl-3-methyllumiflavin and 6-S-cysteinylriboflavin. The latter has been shown to be identical with the dephosphorylated form of the aminoacyl flavin isolated from trimethylamine dehydrogenase [Steenkamp, D. J., Kenney, W. C. & Singer, T. P. (1978) J. Biol. Chem. 253, 2812-2817; Steenkamp, D. J., McIntire, W., & Kenney, W. C. (1978) J. Biol. Chem. 253, 2818-2824] in regard to absorption specturm, photochemical properties, and mobility in high-voltage electrophoresis and in thin-layer chromatography. An unusually pronounced interaction between the amino group and the isoalloxazine ring system was deduced from the absorption spectra of 6-amino-3-methyllumiflavin and 6-aminoriboflavin.     

Catalytic properties of streptococcal NADH oxidase containing artificial flavins.

The flavoprotein NADH oxidase from Streptococcus faecalis 10C1, which catalyzes the tetravalent reduction of O2-->2H2O, has been purified as the apoenzyme to allow reconstitution studies with both native and artificial flavins. Turnover numbers for the enzyme containing 1-deaza-, 2-thio-, and 4-thio-FAD range from 51 to 4% of that of the native FAD enzyme; these reconstituted oxidases also catalyze the four-electron reduction of oxygen. Dithionite and NADH titrations of the native FAD oxidase require 1.7 eq of reductant/FAD and follow spectral courses very similar to those previously reported for the purified holoenzyme. Azide is a linear mixed-type inhibitor with respect to NADH, and dithionite titrations in the presence of azide yield significant stabilization of the neutral blue semiquinone. Redox stoichiometries for the oxidase containing modified flavins range from 1.1 to 1.4 eq of reductant/FAD. Spectrally distinct reduced enzyme.NAD+ complexes result with all but the 2-thio-FAD enzyme on titration with NADH. The reduced 4-thio-FAD oxidase shows little or no evidence of desulfurization to native FAD on reduction and reoxidation. Both the 8-mercapto- (E'o = -290 mV) and 8-hydroxy-FAD (E'o = -335 mV) oxidase are readily reduced by excess NADH. These results offer a further basis for analysis of the active-site structure and oxygen reactivity of this unique flavoprotein oxidase.     

Transabiotic factors in an aqueous environment (a review)

Excretion of metabolites is a characteristic feature of any alive organism. A big group of these products--second metabolites--because of their variability, quantity and physico-biological activity have a special importance in aquatic environment. Exometabolites of some organisms become an important part of environment for the others. The authors discussed the origin and evolution of exometabolites from simple waste products to biologically active substances. Quantitative and qualitative aspects of metabolic excretion by organisms in water conditions are analysed. The data on composition, origin and biological function of some second metabolites of different groups of aquatic organisms are presented. The authors propose a classification of second metabolites according to their functional significance. The role of metabolites and decay products in the development of chemical information streams in hydrobiocoenosis is analysed. Metabolites (soluble organic substances) form a field of chemical information for biotic community. The most important functions of this field are communication and conditioning. The authors emphasize the importance of investigations of chemical bioinformation field in aquatic ecosystems.     

On the stability properties of a stochastic model for phage-bacteria interaction in open marine environment

In this paper we extend the deterministic model for the epidemics induced by virulent phages on bacteria in marine environment introduced by Beretta and Kuang [Math. Biosci. 149 (1998) 57], allowing random fluctuations around the positive equilibrium. The stochastic stability properties of the model are investigated both analytically and numerically suggesting that the deterministic model is robust with respect to stochastic perturbations.     

A study of solvent effects on the phosphorescence properties of flavins.

A combination of zero field triplet state techniques are used to study the excited electronic states of a series of flavin and flavin related molecules both in single crystals and glass matrices. Particular attention is given to the effects of solvent interaction on the triplet state properties of the flavin molecules. The total phosphorescence decay rate constants at 1.4 degrees K are reported for the flavin molecules in polar and nonpolar solvents. The rate constants are then correlated to the degree of solvent interaction. Results indicate possible complex formation between the isoalloxazine and adenine groups in FAD. Finally, the results and possible interpretation on the study of a flavoenzyme, L-amino acid oxidase are presented.     

Relating reflex gain modulation in posture control to underlying neural network properties using a neuromusculoskeletal model

During posture control, reflexive feedback allows humans to efficiently compensate for unpredictable mechanical disturbances. Although reflexes are involuntary, humans can adapt their reflexive settings to the characteristics of the disturbances. Reflex modulation is commonly studied by determining reflex gains: a set of parameters that quantify the contributions of Ia, Ib and II afferents to mechanical joint behavior. Many mechanisms, like presynaptic inhibition and fusimotor drive, can account for reflex gain modulations. The goal of this study was to investigate the effects of underlying neural and sensory mechanisms on mechanical joint behavior. A neuromusculoskeletal model was built, in which a pair of muscles actuated a limb, while being controlled by a model of 2,298 spiking neurons in six pairs of spinal populations. Identical to experiments, the endpoint of the limb was disturbed with force perturbations. System identification was used to quantify the control behavior with reflex gains. A sensitivity analysis was then performed on the neuromusculoskeletal model, determining the influence of the neural, sensory and synaptic parameters on the joint dynamics. The results showed that the lumped reflex gains positively correlate to their most direct neural substrates: the velocity gain with Ia afferent velocity feedback, the positional gain with muscle stretch over II afferents and the force feedback gain with Ib afferent feedback. However, position feedback and force feedback gains show strong interactions with other neural and sensory properties. These results give important insights in the effects of neural properties on joint dynamics and in the identifiability of reflex gains in experiments.     

An epidemic model in a patchy environment

An epidemic model is proposed to describe the dynamics of disease spread among patches due to population dispersal. We establish a threshold above which the disease is uniformly persistent and below which disease-free equilibrium is locally attractive, and globally attractive when both susceptible and infective individuals in each patch have the same dispersal rate. Two examples are given to illustrate that the population dispersal plays an important role for the disease spread. The first one shows that the population dispersal can intensify the disease spread if the reproduction number for one patch is large, and can reduce the disease spread if the reproduction numbers for all patches are suitable and the population dispersal rate is strong. The second example indicates that a population dispersal results in the spread of the disease in all patches, even though the disease can not spread in each isolated patch.     

Oscillations in a patchy environment disease model

For a single patch SIRS model with a period of immunity of fixed length, recruitment-death demographics, disease related deaths and mass action incidence, the basic reproduction number R(0) is identified. It is shown that the disease-free equilibrium is globally asymptotically stable if R(0)<1. For R(0)>1, local stability of the endemic equilibrium and Hopf bifurcation analysis about this equilibrium are carried out. Moreover, a practical numerical approach to locate the bifurcation values for a characteristic equation with delay-dependent coefficients is provided. For a two patch SIRS model with travel, it is shown that there are several threshold quantities determining its dynamic behavior and that travel can reduce oscillations in both patches; travel may enhance oscillations in both patches; or travel can switch oscillations from one patch to another.     

Detection of surface charge-related properties in model membrane systems by aqueous two-phase partition

Unilamellar vesicles composed of phosphatidylcholine (PC) and either phosphatidic acid (PA) or phosphatidylglycerol (PG) partition to the upper poly(ethylene glycol) (PEG)-rich phase of a charge-sensitive 5%:5% (w/w) PEG 8000/Dextran T-500 phase system containing 10 mM sodium phosphate at pH 7, consistent with the vesicles bearing a net negative charge. When prepared in the presence of a pH gradient (interior acidic), PC/PA vesicles exhibit an increased partition to the top PEG-rich phase, consistent with a redistribution of the PA from the inner to the outer monolayer of the vesicle bilayer. Conversely, when prepared in the presence of a pH gradient (interior basic), PC/PG vesicles exhibit a decreased top-phase partition, consistent with a redistribution of the PG from the outer to the inner monolayer of the vesicle bilayer. Unilamellar vesicles composed of PC and stearylamine partition to the lower dextran-rich phase of a 5%:5% (w/w) PEG 8000/Dextran T-500 phase system containing 10 mM sodium phosphate at pH 8.5, consistent with the vesicles bearing a net positive charge. When prepared in the presence of a pH gradient (interior acidic), conditions under which the stearylamine is trapped on the inner monolayer of the bilayer, the vesicles now partition predominantly to the interface in a manner similar to vesicles composed of PC alone. These results demonstrate that partitioning in aqueous two-phase polymer systems is a sensitive method for monitoring the asymmetry of charged lipids in model membrane systems and also suggests that partitioning in charge-sensitive systems depends only on the physical nature of the exterior surface of the membrane.