Turbidimetric method for determination of glycogen phosphorylase activity and its use for estimation of equilibrium position of enzymic reaction

A turbidimetric method has been developed for the continous monitoring of the enzyme reaction catalyzed by glycogen phosphorylase. This method is based on the registration of the turbidity of glycogen solution at wavelengths above 300 nm. It has been shown that increase in the turbidity is strictly proportional to the quantity of glucose 1-phosphate formed during the enzyme reaction. The method has the advantage of continuity, and it is suitable for determining the initial rate of catalytic synthesis or degradation of glycogen in a relatively simple and fast way. The kinetic experiments may be carried out under various conditions. The method of calculation of the overall equilibrium constant of the enzyme reaction catalyzed by glycogen phosphorylase has been elaborated. This method is based on the analysis of the dependence of the initial rate of the enzyme reaction on the proportiona of the substrate of the forward reaction: [P_i]/([P_i]+[G-1-P]).     

Bargaining in biology?

This paper surveys the economic theory of bargaining with a view to applications in biology, using Roughgarden’s recent Genial Gene as a case study in mistakes to be avoided.     

Monte Carlo Simulation of the β-Sheet–Random Coil Transition of a Homopolypeptide. I. Equilibrium Study

Abstract

Monte Carlo simulation of the β-sheet – random coil conversion of a homopolypeptide chain was carried out on the basis of a model where successive two amino acid residues were assumed to change their states simultaneously and hence constituted a basic unit. Only three states were considered for each unit: extended, turn and coil. The conversion exhibited a transition between two states, random coil (C) and the β-sheet (B). In the transition region, two population maxima were always found, each corresponded to the local minimum of the free energy and there was an energy barrier between them. This behavior is characteristic of the all-or-none type transition. We have found that the nature of the first-order transition is retained in the case of a small system consisting of 100 units. The size of the cooperative unit was evaluated. According to the analytical theory of Kanô, a transition curve was obtained which was very close to the present one. This consistent result has suggested that equilibrium properties of the β-sheet-random coil transition are well evaluated with the mean field approximation. The matrix method of Mattice is also discussed.     

The pyruvate kinase model system, a cautionary tale for the use of osmolyte perturbations to support conformational equilibria in allostery

In the study of rabbit muscle pyruvate kinase (M₁‐PYK), proline has previously been used as an osmolyte in an attempt to determine a role for preexisting conformational equilibria in allosteric regulation. In this context, osmolytes are small molecules assumed to have no direct interaction with the protein. In contrast to proline's proposed role as an osmolyte, the structure of M₁PYK‐Mn‐pyruvate‐proline complex reported herein demonstrates that proline binds specifically to the allosteric site of M₁‐PYK. Therefore, this amino acid is an allosteric effector rather than a benign osmolyte. Other compounds often used as osmolytes (polyethyleneglycol and glycerol) are also present in the structure, suggesting an interaction with the protein that would, in turn, prevent the usefulness of these compounds in the study of this and most likely other proteins. These findings highlight the need to verify that compounds used as osmolytes to perturb preexisting conformational equilibrium do not directly interact with the protein, a consideration not commonly addressed in the past.     

Carbon Monoxide (CO) Is a Novel Inhibitor of Connexin Hemichannels

Hemichannels (HCs) are hexamers of connexins that can form gap-junction channels at points of cell contacts or “free HCs” at non-contacting regions. HCs are involved in paracrine and autocrine cell signaling, and under pathological conditions may induce and/or accelerate cell death. Therefore, studies of HC regulation are of great significance. Nitric oxide affects the activity of Cx43 and Cx46 HCs, whereas carbon monoxide (CO), another gaseous transmitter, modulates the activity of several ion channels, but its effect on HCs has not been explored. We studied the effect of CO donors (CORMs) on Cx46 HCs expressed in Xenopus laevis oocytes using two-electrode voltage clamp and on Cx43 and Cx46 expressed in HeLa cells using a dye-uptake technique. CORM-2 inhibited Cx46 HC currents in a concentration-dependent manner. The C-terminal domain and intracellular Cys were not necessary for the inhibition. The effect of CORM-2 was not prevented by guanylyl-cyclase, protein kinase G, or thioredoxin inhibitors, and was not due to endocytosis of HCs. However, the effect of CORM-2 was reversed by reducing agents that act extracellularly. Additionally, CO inhibited dye uptake of HeLa cells expressing Cx43 or Cx46, and MCF-7 cells, which endogenously express Cx43 and Cx46. Because CORM-2 carbonylates Cx46 in vitro and induces conformational changes, a direct effect of that CO on Cx46 is possible. The inhibition of HCs could help to understand some of the biological actions of CO in physiological and pathological conditions.     

Novel complex hydrogels based on N-carboxyethyl chitosan and quaternized chitosan and their controlled in vitro protein release property

A novel pH-responsive hydrogel (CHC) composed of N-carboxyethyl chitosan (CEC) and N-[(2-hydroxy-3-trimethylammonium) propyl] chitosan chloride (HTCC) was synthesized by the redox polymerization technique. Turbidimetric titrations were used to determine the stoichiometric ratio of these two chitosan derivatives. The hydrogel was characterized by FT-IR, thermal gravimetric analysis (TGA), X-ray diffractometry (XRD), and scanning electron microscopy (SEM). The dynamic transport of water showed that the hydrogel reached equilibrium within 48 h. The swelling ratio of CHC hydrogel depended significantly on the pH of the buffer solution. The performance of the CHC as a matrix for the controlled release of BSA was investigated. It was found that the release behavior was determined by pH value of the medium as well as the intermolecular interaction between BSA and the hydrogels.     

Dynamically probing ATP‐dependent RNA helicase A‐assisted RNA structure conversion using single molecule fluorescence resonance energy transfer

RNA helicase A (RHA) as a member of DExH‐box subgroup of helicase superfamily II, participates in diverse biological processes involved in RNA metabolism in organisms, and these RNA‐mediated biological processes rely on RNA structure conversion. However, how RHA regulate the RNA structure conversion was still unknown. In order to unveil the mechanism of RNA structure conversion mediated by RHA, single molecule fluorescence resonance energy transfer was adopted to in our assay, and substrates RNA were from internal ribosome entry site of foot‐and‐mouth disease virus genome. We first found that the RNA structure conversion by RHA against thermodynamic equilibrium in vitro, and the process of dsRNA YZ converted to dsRNA XY through a tripartite intermediate state. In addition, the rate of the RNA structure conversion and the distribution of dsRNA YZ and XY were affected by ATP concentrations. Our study provides real‐time insight into ATP‐dependent RHA‐assisted RNA structure conversion at the single molecule level, the mechanism displayed by RHA may help in understand how RHA contributes to many biological functions, and the basic mechanistic features illustrated in our work also underlay more complex protein‐assisted RNA structure conversions.     

Equilibrium and kinetic measurements of the redox potentials of cytochromes c2 in vitro and in vivo

The equilibrium oxidation-reduction mipoint potential (E_m) of isolated Rhodopseudomonas sphaeroides cytochrome c₂ exhibits a pH-dependent behavior which can be ascribed to a pK on the oxidized form at pH 8.0 (Pettigrew et al. (1975) Biochim. Biophys. Acta 430, 197–208). However, as with mammalian cytochrome c (Brandt, K.G., Parks, P.C., Czerlinski, G.H. and Hess, G.P. (1966) J. Biol. Chem. 241, 4180–4185) this pK can more properly be attributed to the combination of a pK beyond pH 11, and a slow conformational change of the ferricytochrome. This has been demonstrated by resolving the E_m of cytochrome c₂ before and after the conformational change. The E_m of the unaltered form is essentially pH independent between pH 7 and 11.5, and the lower equilibrium E_m is due solely to the conformational change. In vivo the conformational change is prevented by the binding of the cytochrome c₂ to the photochemical reaction center, and the cytochrome exhibits an essentially pH-independent E_m from pH 5 to 11. The alkaline transition thus has little physiological significance, and it is unlikely that the redox reactions of cytochrome c₂ in vivo involve protons.     

Disequilibrial island turnover dynamics: a 17‐year record of Bahamian ants

Aim To document long‐term rates of immigration, extinction and turnover in insular ant faunas and evaluate the relative impacts of recent hurricane activity and climate change. Location Small islands in the Exuma Cays, Andros and Abaco archipelagos of the Bahamas. Methods I surveyed the ant faunas of > 140 small islands in three archipelagos of the Bahamas over several multi‐year periods, spanning up to 17 years, by recording species attracted to baits. Immigrations, extinctions and species turnover were documented, as were the relative abundances of species. Four major hurricanes affected the study archipelagos in the second decade of this study. Results Rates of ant turnover were generally low among archipelagos and time periods. Immigrations outnumbered extinctions in the first decade of this study, although this pattern was reversed in the second decade. General physical characteristics of the islands were not significant predictors of the occurrence of extinctions. The relative abundance (based on proportion of baits occupied) of persistent populations of the two most common species both declined in the second decade, indicating, along with higher extinction rates, a generalized decline in these insular ant faunas. Main conclusions The available evidence suggests that hurricanes were not directly responsible for the observed declines in the ant faunas. Regional changes in insular ant species richness, however, are correlated with generalized North Atlantic hurricane activity over the last half century. Indirect effects of hurricanes on the vegetation of these islands, such as increased herbivory and possible decreased nutrient availability, along with a long‐term (quarter century) increase in temperature and decline in rainfall, are possible contributing factors to the changing ant turnover dynamics.