Regulation of oxygen affinity by quaternary enhancement: Does hemoglobin ypsilanti represent an allosteric intermediate?

Recent crystallographic studies on the mutant human hemoglobin Ypsilanti (beta 99 Asp-->Tyr) have revealed a previously unknown quaternary structure called "quaternary Y" and suggested that the new structure may represent an important intermediate in the cooperative oxygenation pathway of normal hemoglobin. Here we measure the oxygenation and subunit assembly properties of hemoglobin Ypsilanti and five additional beta 99 mutants (Asp beta 99-->Val, Gly, Asn, Ala, His) to test for consistency between their energetics and those of the intermediate species of normal hemoglobin. Overall regulation of oxygen affinity in hemoglobin Ypsilanti is found to originate entirely from 2.6 kcal of quaternary enhancement, such that the tetramer oxygenation affinity is 85-fold higher than for binding to the dissociated dimers. Equal partitioning of this regulatory energy among the four tetrameric binding steps (0.65 kcal per oxygen) leads to a noncooperative isotherm with extremely high affinity (pmedian = .14 torr). Temperature and pH studies of dimer-tetramer assembly and sulfhydryl reaction kinetics suggest that oxygenation-dependent structural changes in hemoglobin Ypsilanti are small. These properties are quite different from the recently characterized allosteric intermediate, which has two ligands bound on the same side of the alpha 1 beta 2 interface (see ref. 1 for review). The combined results do, however, support the view that quaternary Y may represent the intermediate cooperativity state of normal hemoglobin that binds the last oxygen.     

A practical approach for quantitating specific mRNAs by solution hybridization

The preparation and use of a specific cDNA probe for quantitating mRNA by solution hybridization is described. Cloned DNA sequences are nick translated, denatured, hybridized to single-stranded M13 clones containing message strand (mDNA) sequences, and separated chromatographically on Bio-Gel A50 under first native and then denaturing conditions to yield a single-stranded cDNA probe. The details of a solution hybridization assay in which the single-stranded cDNA is used to quantitate mRNA in total nucleic acid samples are described. As little as 0.5 pg of mRNA can easily be detected within a day of sample isolation. Thus, the assay is both rapid and sensitive and can be used to measure RNAs complementary to any cloned DNA sequence. It is ideally suited to situations when accurate quantitation of multiple samples is anticipated.     

On the relationship of thermodynamic parameters with the buried surface area in protein-ligand complex formation

Prediction of thermodynamic parameters of protein-protein and antigen-antibody complex formation from high resolution structural parameters has recently received much attention, since an understanding of the contributions of different fundamental processes like hydrophobic interactions, hydrogen bonding, salt bridge formation, solvent reorganization etc. to the overall thermodynamic parameters and their relations with the structural parameters would lead to rational drug design. Using the results of the dissolution of hydrocarbons and other model compounds the changes in heat capacity (C_p), enthalpy (H) and entropy (S) have been empirically correlated with the polar and apolar surface areas buried during the process of protein folding/unfolding and protein-ligand complex formation. In this regard, the polar and apolar surfaces removed from the solvent in a protein-ligand complex have been calculated from the experimentally observed values of changes in heat capacity (C_p) and enthalpy (H) for protein-ligand complexes for which accurate thermodynamic and high resolution structural data are available, and the results have been compared with the x-ray crystallographic observations. Analyses of the available results show poor correlation between the thermodynamic and structural parameters. Probable reasons for this discrepancy are mostly related with the reorganization of water accompanying the reaction which is indeed proven by the analyses of the energetics of the binding of the wheat germ agglutinin to oligosaccharides.     

Study on the Adsorption of Cr3+ by Peanut Shell: Adsorption Kinetics,Thermodynamics, and Isotherm Properties

The pollution of heavy metals in soil to the environment is becoming more and more serious, resulting in the reduction of crop production and the occurrence of medical accidents. In order to remove heavy metal ions from soil and reduce the harm of heavy metals to the environment, modified peanut shell was used to adsorb Cr³⁺ in this article. The effects of different adsorption conditions on the adsorption rate and adsorption capacity of Cr³⁺ on ZnCl₂ modified peanut shell were studied, the best adsorption conditions were explored, and the relationship of kinetics, thermodynamics and adsorption isotherm properties of adsorption process were explored. The results showed that the optimum adsorption pH value, dosage, initial concentration, adsorption temperature and contact time of ZnCl₂ modified peanut shell were 2.5, 2.5 g/L, 75 μg/mL, 25 °C and 40 min, respectively. The prepared materials were characterized and analyzed by scanning electron microscope (SEM) and X-ray diffraction (XRD) analyzer. It was concluded that the modified peanut shell had a good adsorption capacity to Cr³⁺. The kinetic study showed that the adsorption process of Cr³⁺ on peanut shell modified by zinc chloride was in accordance with the quasi-second-order kinetic model. The adsorption process belonged to exothermic reaction and belonged to spontaneous reaction process. In summary, it is proved that zinc chloride modified peanut shell can efficiently adsorb Cr³⁺, which can be used for the treatment of heavy metal wastes in industry, which is beneficial to environmental protection and avoid heavy metal pollution.     

Non-equilibrium thermodynamics of Lotka-Volterra ecosystems: Stability and evolution

A non-equilibrium thermodynamic theory of generalized Lotka-Volterra ecosystem has been presented. The main results consist of the derivation of a generalized expression of entropy-production for the evolutionary ecosystem and the study of its role in the analysis of ecological stability, succession and also in the formulation of some extremum principles characterising the evolution of the ecosystem.     

Matric potential evaluations and measurements for gelled substrates

A new method for evaluating the matric potential of gelled media has been developed. The method allows the derivation of the matric potential as a limit of a series of measurements of water potential values from gelled media prepared without added components, from agar powders progressively cleaned of mineral impurities. Three commercial agar brands were tested, and for these the matric potential was found to contribute only between 1 and 2% of their total water potential. Thermodynamic features relating matric and osmotic potentials are described. New hypotheses for understanding the water flux mechanism from gel to tissue cultured explants are discussed. Movement of water along polymeric chains is postulated to be a facilitated step in comparison with bulk movement.     

An aminopeptidase from Agave americana thermodynamic studies

Purified Agave aminopeptidase was characterized with respect to the thermodynamic properties of the reaction catalysed by the enzyme. Kinetic studies were conducted at different temperatures ranging from 7.8 to 45°. The energy of activation, E_a, as well as the constants ΔH, ΔF and ΔS were calculated for both the formation of the enzyme-substrate complex, and the dissociation of the enzyme-product complex. Kinetic studies in buffers with varying dielectric constants enabled the determination of the electrostatic as well as the non-electrostatic components of ΔS. These results fit well into the overall kinetic picture of this enzyme-catalysed reaction as reported previously.     

A new thermodynamically based correlation of chemotrophic biomass yields

A new, generally applicable, thermodynamically based method is proposed to provide an estimation of the biomass yield on arbitrary organic and inorganic substrates. Aerobic, anaerobic, denitrifying growth systems with and without reversed electrontransport are covered. The biomass yield can be estimated with only 15% error in a very wide range of microbial growth systems and biomass yields (0.01–0.80 C-mol/(C)-mol). This method is based on the use of Gibbs energy dissipared per C-mol produced biomass (designated as D _infS ^sup01 /r_Ax) as the central parameter. Moreover the insufficiency of other methods based on Y_ATP, Y_Ave, ₀, Y_C and enthalpy or Gibbs energy efficiencies is shortly discussed. Also it appeared to be possible to understand the obtained correlation of D _infS ^sup01 /r_Ax in general biochemical terms.     

Organelle contacts: Sub‐organelle zones to facilitate rapid and accurate inter‐organelle trafficking of lipids

When one person wants to communicate securely with another, he/she should contact the other person directly. This rule applies not only to human society, but also to the intracellular micro‐society. In the past two decades, it has become increasingly clear that the sub‐organelle regions called membrane contact sites (MCSs) are pivotal for inter‐organelle transport of lipids in cells, as highlighted in the thematic review series “Interorganelle trafficking of lipids” held in Traffic in 2014–2015. In this commentary, we will describe how the currently prevailing model for lipid trafficking at MCSs was generated, and comment on three important issues that have not been explored: (a1) the principles guiding the generation of an asymmetrical inter‐organelle flow of lipids in cells, (b2) the advantages in lipid trafficking at organelle contacts, and (c3) the dynamic network of inter‐organelle lipid trafficking.     

The thermodynamics of thinking: connections between neural activity,energy metabolism and blood flow

Several current functional neuroimaging methods are sensitive to cerebral metabolism and cerebral blood flow (CBF) rather than the underlying neural activity itself. Empirically, the connections between metabolism, flow and neural activity are complex and somewhat counterintuitive: CBF and glycolysis increase more than seems to be needed to provide oxygen and pyruvate for oxidative metabolism, and the oxygen extraction fraction is relatively low in the brain and decreases when oxygen metabolism increases. This work lays a foundation for the idea that this unexpected pattern of physiological changes is consistent with basic thermodynamic considerations related to metabolism. In the context of this thermodynamic framework, the apparent mismatches in metabolic rates and CBF are related to preserving the entropy change of oxidative metabolism, specifically the O₂/CO₂ ratio in the mitochondria. However, the mechanism supporting this CBF response is likely not owing to feedback from a hypothetical O₂ sensor in tissue, but rather is consistent with feed-forward control by signals from both excitatory and inhibitory neural activity. Quantitative predictions of the thermodynamic framework, based on models of O₂ and CO₂ transport and possible neural drivers of CBF control, are in good agreement with a wide range of experimental data, including responses to neural activation, hypercapnia, hypoxia and high-altitude acclimatization.This article is part of the theme issue ‘Key relationships between non-invasive functional neuroimaging and the underlying neuronal activity’.