Resonance assignments of the 56 kDa chimeric avidin in the biotin-bound and free forms

Avidin is a homotetrameric ~56 kDa protein found in chicken egg white. Avidin’s ability to bind biotin with a very high affinity has widely been exploited in biotechnological applications. Protein engineering has further diversified avidin’s feasibility. ChiAVD(I117Y) is a product of rational protein engineering. It is a hyperthermostable synthetic hybrid of avidin and avidin-related protein 4 (AVR4). In this chimeric protein a 23-residue segment in avidin has been replaced with the corresponding sequence found in AVR4, and a point mutation at subunit interface 1–3 (and 2–4) has been introduced. Here we report the backbone and sidechain resonance assignments of the biotin-bound form of ChiAVD(I117Y) as well as the backbone resonance assignments of the free form.     

Mechanistic study of the structure–activity relationship for the free radical scavenging activity of baicalein

Density functional theory calculations were performed to evaluate the antioxidant activity of baicalein. The conformational behaviors of both the isolated and the aqueous-solvated species (simulated with the conductor-like polarizable continuum solvation model) were analyzed at the M052X/6-311 + G(d,p) level. The most stable tautomers of various forms of baicalein displayed three IHBs between O4 and OH5, O5 and OH6, and O6 and OH7. The most stable tautomer of the baicalein radical was obtained by dehydrogenating the hydroxyl at C6, while the most stable anion tautomer was obtained by deprotonating the C7 hydroxyl in gaseous and aqueous phases. The expected antioxidant activity of baicalein was explained by its ionization potentials (IPs) and homolytic O–H bond dissociation enthalpies (BDEs), which were obtained via the UM052X optimization level of the corresponding radical species. Heterolytic O–H bond cleavages (proton dissociation enthalpies, PDEs) were also computed. The calculated IP, BDE, and PDE values suggested that one-step H-atom transfer, rather than sequential proton loss–electron transfer or electron transfer–proton transfer, would be the most favorable mechanism for explaining the antioxidant activity of baicalein in the gas phase and in nonpolar solvents. In aqueous solution, the SPLET mechanism was more important.     

Do we know the absolute values of intracellular free calcium concentration?

More than 20 years ago, it was shown that the addition of EGTA increases the affinity of the plasma membrane Ca2+ pump for Ca2+ by an order of magnitude. The left-hand shift of Ca2+-dependencies in the presence of EGTA has been also documented in studies of the sarcoplasmic reticulum Ca2+ pump, mitochondrial Ca2+-transporter as well as Ca2+-binding by calmodulin and troponin C. These data allow us to hypothesise that this effect is caused by an admixture of di- and trivalent cations possessing high affinity for EGTA and interacting with Ca2+-transporting and binding proteins. Here, we propose that polyvalent cations affect the estimation of absolute values of free intracellular Ca2+ concentration. Indeed, EGTA sharply increases the apparent affinity of the fluorescent Ca2+ indicators quin-2 and fluo-3 for Ca2+. The impact of polyvalent cations on Ca2+ measurement was further confirmed by the study showing the high sensitivity of Ca2+-induced fluo-3 fluorescence to Mn2+, Fe2+, Cu2+, and Co2+ seen in the absence of EGTA.     

Is the genotoxic effect of arsenic mediated by oxygen free radicals?

Previous investigations have shown that trivalent arsenic is inducing chromosomal aberrations and sister chromatid exchanges (SCEs). In a search for the genotoxic mechanism we have studied the effects of the oxygen-radical-scavenging enzymes superoxide dismutase (SOD) and catalase (CAT) on arsenic-induced SCEs in cultured human lymphocytes. The results indicate that SOD and possibly also CAT have a protective effect against arsenic-induced DNA damage. Arsenic, which is emitted in environmental pollutions e.g. from smelters and coal-fired power plants, appears to be underestimated as environmental mutagen and potential synergist to ionizing radiation.     

E. coli DNA replication in the absence of free β clamps

During DNA replication, repetitive synthesis of discrete Okazaki fragments requires mechanisms that guarantee DNA polymerase, clamp, and primase proteins are present for every cycle. In Escherichia coli, this process proceeds through transfer of the lagging-strand polymerase from the β sliding clamp left at a completed Okazaki fragment to a clamp assembled on a new RNA primer. These lagging-strand clamps are thought to be bound by the replisome from solution and loaded a new for every fragment. Here, we discuss a surprising, alternative lagging-strand synthesis mechanism: efficient replication in the absence of any clamps other than those assembled with the replisome. Using single-molecule experiments, we show that replication complexes pre-assembled on DNA support synthesis of multiple Okazaki fragments in the absence of excess β clamps. The processivity of these replisomes, but not the number of synthesized Okazaki fragments, is dependent on the frequency of RNA-primer synthesis. These results broaden our understanding of lagging-strand synthesis and emphasize the stability of the replisome to continue synthesis without new clamps.     

The osteocutaneous free fibula flap: is the skin paddle reliable?

This clinical and anatomic study was undertaken to see if the skin paddle of the osteocutaneous fibula flap could be made more reliable. Eighty cadaver limbs were dissected to evaluate the type, number, and location of the cutaneous perforators supplying the lateral leg. Three types of perforators were identified: septocutaneous, musculocutaneous, and a type we termed septomuscular, which does not actually run within the muscle substance but is adherent to the muscle. Although not a true musculocutaneous perforator, it should be treated as such clinically. Musculocutaneous perforators were found to be more numerous and more proximal than the septocutaneous perforators. Eighteen clinical cases demonstrate a 33 percent skin paddle survival when dissected as a septocutaneous flap and a 93 percent skin paddle survival when dissected as a septomusculocutaneous flap. In using the osteocutaneous fibula flap, it is recommended that a cuff of soleus and flexor hallucis longus be incorporated into the flap to help ensure flap viability.     

Non-pegylated doxorubicin (Myocet®) as the less cardiotoxic alternative of free doxorubicin

Anthracyclines have probably been considered to be the most active agents for the treatment of breast cancer and some other solid tumors and hematological malignancies. However, they are associated with dose-related cardiotoxicity, which can lead to progressive myocardial damage and limits the maximal cumulative dose that can be given. This review focuses on the non-pegylated liposome-encapsulated doxorubicin (Myocet?), which has been developed to increase the therapeutic index of free doxorubicin. The encapsulation of doxorubicin within a macromolecular vector, such as a liposome ("nanoparticle based drug delivery system") reduces its distribution volume, diminishing its toxicity for healthy tissues while increasing the concentration within the neoplastic tissue. The most common adverse event is neutropenia, which is consistent with previous experience with free doxorubicin. Available evidence suggests that the incidence of hematological toxicity is lower than with conventional doxorubicin. Myocet? both as a single agent and in combination is effective and safe with an associated reduction in incidence and severity of cardiac events. Nagykálnai T. Non-pegylated doxorubicin (Myocet?) as the less cardiotoxic alternative of free doxorubicin.     

What is the source of free radicals causing hemolysis in stored blood?

The quality of stored blood can be deteriorated by hemolysis caused by free radicals. The purpose of this study was to elucidate whether neutrophile leukocytes are the source of free radicals in stored blood as in hemodialyzed patients. Resuspensions with low (LL) or high (HL) leukocyte concentrations were prepared from samples of twenty healthy volunteers. The samples were incubated for 10 days at 4 degrees C and then for one day at 37 degrees C. Markers of hemolysis and free radical metabolism were examined before and after incubation in LL and HL samples. In spite of the difference of leukocytes counts in LL and HL resuspensions (p<0.0001), the pre-incubation values of all laboratory parameters were practically identical. In post-storage samples, superoxide dismutase and glutathione peroxidase activities did not differ in either group. Reduced glutathione in erythrocytes and extracellular antioxidant capacity were insignificantly lower in HL resuspensions, but the increase of malondialdehyde was much more pronounced in the HL samples (p<0.0001). The degree of hemolysis, expressed as the extracellular increase of potassium (p<0.001), hemoglobin (p<0.05) and lactate dehydrogenase (p<0.05), was higher in the HL samples. Our results support the hypothesis that leukocytes participate in free radical production in stored blood.     

The free energy method and the Wright–Fisher model with 2 alleles

We systematically investigate the Wright–Fisher model of population genetics with the free energy functional formalism of statistical mechanics and in the light of recent mathematical work on the connection between Fokker–Planck equations and free energy functionals. In statistical physics, entropy increases, or equivalently, free energy decreases, and the asymptotic state is given by a Gibbs-type distribution. This also works for the Wright–Fisher model when rewritten in divergence to identify the correct free energy functional. We not only recover the known results about the stationary distribution, that is, the asymptotic equilibrium state of the model, in the presence of positive mutation rates and possibly also selection, but can also provide detailed formulae for the rate of convergence towards that stationary distribution. In the present paper, the method is illustrated for the simplest case only, that of two alleles.     

Stop the bullying in the corridors: Can including shrubs make your revegetation more Noisy Miner free?

Summary   Noisy Miners ( Manorina melanocephala ) are aggressive Australian honeyeaters that dominate many areas of remnant vegetation and forest edges from which they competitively exclude small birds. A similar domination can also occur in planted wildlife corridors. The aim of this study was to determine which corridor plantings encouraged the presence of small native birds in regions where Noisy Miners dominate. Six vegetation mixes were investigated in the main study: eucalypts with and without shrubby understorey; acacia with and without shrubby understorey; exotic conifer; and exotic deciduous trees. A supplementary study then examined sites with a mixture of eucalypt and acacia trees with a shrubby understorey. The findings showed that Noisy Miners dominated corridors of eucalypts, virtually excluding small birds, whereas native acacias, exotic conifer and exotic deciduous corridors had small birds and no resident Noisy Miners. The greatest abundance and richness of small birds occurred in plantings combining eucalypts with at least 15% acacias, in this case bipinnate species. Given these results, it is recommended that eucalypt plantings should be supplemented with both acacias (preferably bipinnate) and a shrubby understorey.     

Does exogenous melatonin influence the free radicals metabolism and pain sensation in rat?

Melatonin has been shown to play a role in antioxidative defence. We therefore studied its effect on oxidative damage to the rat cerebral cortex evoked by painful stimulation and immobilization-induced stress. Moreover, the effect of melatonin on chronic pain perception was examined. Rats were injected with either a high dose of melatonin (100 mg/kg i.p.) or a vehicle for five days and were subjected to painful stimulation or immobilization stress 30 min after the treatment. To determine the degree of oxidative stress, the levels of free radicals, thiobarbituric acid reactive substances (TBARS) as indicators of lipid peroxidation and glutathione peroxidase (GSHPx) were estimated in somatosensory cortex. Pain perception was measured by the tail-flick and plantar test. Melatonin reduced the level of TBARS previously increased by painful stimulation. Melatonin also exhibited a slight analgesic effect in those animals exposed to painful stimulation but its role in free radical scavenging did not contribute to this effect.     

Properties and participation of “free” endotoxin in the toxic activity ofMorganella morganii

"Free" and "bound" Morganella morganii endotoxin was characterized by chemical (determination of proteins, saccharides and 3-deoxy-2-octulosonic acid) and immunochemical (double-diffusion test, immunoelectrophoresis, tandem crossed immunoelectrophoresis) methods. Chemical analysis showed that "free" endotoxin contains more protein and phosphorus and less saccharides than bound endotoxin. Immunochemical tests revealed differences in the structure of polysaccharide portions of both endotoxins, and, on the other hand, identity of certain antigenic determinants. Free endotoxin possessed a higher biological activity.     

Trade-offs in the vertical distribution of zooplankton: ideal free distribution with costs?

Zooplankton vertical migratory patterns are a classic example of optimal habitat choice. We hypothesize that zooplankton distribute themselves vertically in the water column according to an ideal free distribution (IFD) with costs such as to optimize their fitness. In lakes with a deep-water chlorophyll maximum, zooplankton are faced with a trade-off, either experiencing high food (high reproductive potential) but low temperature (slow development) in the hypolimnion or high temperature and low food in the epilimnion. Thus, in the absence of fish predation (e.g. at night) they should allocate the time spent in the different habitats according to fitness gain dependent on the temperature gradient and distribution of food. We tested this hypothesis with a Daphnia hyalina x galeata clone in large indoor columns (Plön Plankton Towers) and with a dynamic energy budget model. In the tower experiments, we simulated a deep-water algal maximum below the thermocline with epilimnetic/hypolimnetic temperature differences of 2, 5 and 10 degrees C. Experimental data supported the model. We found a significantly larger proportion of daphniids in the hypolimnion when the temperature difference was smaller. Our results are consistent with the concept of IFD with costs originally developed for stream fishes. This concept can be applied to predict the vertical distribution of zooplankton in habitats where fish predation is of minor importance.     

A comparison of the kinetic properties of free and immobilized Aspergillus oryzae β-galactosidase

The objective of this work was to compare the properties of free and immobilized β-galactosidase (Aspergillus oryzae), entrapped in alginate–gelatin beads and cross-linked with glutaraldehyde. The free and immobilized forms of the enzyme showed no decrease in enzyme activity when incubated in buffer solutions in pH ranges of 4.5–7.0. The kinetics of lactose hydrolysis by the free and immobilized enzymes were studied at maximum substrate concentrations of 90 g/L and 140 g/L, respectively, a temperature of 35 °C and a pH of 4.5. The Michaelis–Menten model with competitive inhibition by galactose fit the experimental results for both forms. The K_m and V_m values of the free enzyme were 52.13 ± 2.8 mM and 2.56 ± 0.3 g_glucose/L min mg_enzyme, respectively, and were 60.30 ± 3.3 mM and 1032.07 ± 51.6 g_lactose/min m³_catalyst, respectively, for the immobilized form. The maximum enzymatic activity of the soluble form of β-galactosidase was obtained at pH 4.5 and 55 °C. Alternatively, the immobilized form was most active at pH 5.0 at 60 °C. The free and immobilized enzymes presented activation energies of 6.90 ± 0.5 kcal/mol and 7.7 ± 0.7 kcal/mol, respectively, which suggested that the immobilized enzyme possessed a lower resistance to substrate transfer.     

Are planktonic naked amoebae predominately floc associated or free in the water column?

The spatial distribution of planktonic naked amoebae in thewaters of a mangrove and estuarine habitat was investigated.Amoebae were grouped either as ‘attached’ (whenon suspended flocs) or ‘free’ (when floating inthe open water). Consistent with previous studies, amoebae werenumerically important in the water column. For example, in mangrovewater from south Florida, they averaged 94 640 cells l^-1. Inthe mangrove, 91.6% of planktonic amoebae were attached to suspendedflocs. Likewise, the majority of amoebae in Hudson waters werefloc associated (86.7%). The results using a novel capture protocol,employing suspended capillary tubes to catch floating amoebae,suggested that free amoebae readily colonized available surfaces.Transmission electron microscopy demonstrated that amoebae werecapable of penetrating deep into the cracks and crevices offloc particles. The implications of these results are far reaching.For example, in the mangrove waters where the floc fractionin a liter of water accounted for 0.5 ml volume, the absolutedensity of amoebae at these loci was 173 380 amoebae per milliliterof floc material. Such high local abundance may have importanttrophic implications, particularly if amoebae, because of theirclose association with surfaces, graze attached bacteria unavailableto other micrograzers. The results presented here clearly showthat future studies on the microecology of flocs need to includeamoebae as well as the more widely investigated ciliates andheterotrophic flagellates.     

On the free energy “cost of transition” in intermediary Metabolic processes and the evolution of cellular infrastructure

Certain questions are discussed regarding the evolution of spatial order in cellular metabolism. The treatment focuses on the significance of the transient phase (in steady-state transitions). For the purpose of simple, semi-quantitative analysis, an arbitrary metabolic process (multi-enzyme system) is modeled as a linear sequence of monomolecular reactions, governed by an initial “master reaction”. For such designs, explicit definition of the transient time τ may be obtained from previous studies; it is just a function of the K_m's and V_max's of the individual enzyme reactions. As indicated herein, the free energy “cost of transition” (ΔG)_τ, is related straightforwardly to the individual transient times of the multienzyme system. Using representations for K_m and V_max from a recent molecular enzyme-kinetic model (Somogyi & Damjanovich, 1971, 1975), the present report yields a novel expression for transient time, which depends explicitly on medium viscosity, enzyme concentration, and Boltzmann energy factor. It is seen that τ [and (ΔG)_τ] might be exceedingly large if a given metabolic process be pictured in complete communication with a bulk reaction-diffusion milieu in vivo. In general, excessive time delay and undue energy expenditures might arise from any of the following: (i) metabolic interferences due to pathway competition for common substrates; (ii) bulk motion; (iii) diffusional (viscosity) interference, e.g. that due to generalized Fickian diffusion. The situation would be acute particularly for cases where metabolites must be maintained at low intracellular concentration. It is recognized that living protoplasm may have obviated some of these difficulties and, concomitantly, economized on free energy by compartmentalizing much (if not all) of intermediary metabolism via multi-enzyme complexes and/or membrane-associated schemes. Experimental evidence lends support to such claim. The progression toward increased spatial organization is viewed here from the perspective of the following thermodynamic correlates of biological evolution: (a) increasing free energy dissipation and (b) increasing energetic efficiency. It is suggested that the evolution toward structuralization may be regarded simply as a trend toward increased “energetic profitableness” in cellular metabolism. In this context, a correspondence is proposed between real time and “thermodynamic time”. In conclusion, the basis of the thermodynamic approach to evolution is discussed.