Calculation of the energy difference between the quaternary structures of deoxy- and oxyhemoglobin.

The energy difference between the quaternary structures of deoxy- and oxyhemoglobin is evaluated on the basis of the atomic coordinates determined by X-ray diffraction analysis. Calculation of the van der Waals interaction between subunits shows that in a hemoglobin molecule as a whole, the interaction is more attractive in the oxy form than in the deoxy form by about 8 kcal/mol, and that in each pair of two subunits except the pair alpha1alpha2, the interaction energy varies by about 15 kcal/mol. The electrostatic interactions originating in the partial charges on all constituent atoms of hemoglobin and in the polar residues on the surface of hemoglobin make only a small contribution to the energy difference between the quaternary structures of deoxy- and oxyhemoglobin. Thus, the contribution of the clusters of the polar residues in the internal cavity between like subunits and also of the freedom of rotation of the C-terminal of each subunit in oxyhemoglobin may be important energetically in the transition from deoxy to oxy quaternary structure. In this point, the present calculation supports Perutz' model, but suggests necessity of further investigations on the transitional characteristics of the quaternary structure in the intermediate steps of oxygenation. The discussion on the transitional characteristics is given in the last section.     

The origin of eukaryotes: the difference between prokaryotic and eukaryotic cells.

Eukaryotes have long been thought to have arisen by evolving a nucleus, endomembrane, and cytoskeleton. In contrast, it was recently proposed that the first complex cells, which were actually proto-eukaryotes, arose simultaneously with the acquisition of mitochondria. This so-called symbiotic association hypothesis states that eukaryotes emerged when some ancient anaerobic archaebacteria (hosts) engulfed respiring alpha-proteobacteria (symbionts), which evolved into the first energy-producing organelles. Therefore, the intracellular compartmentalization of the energy-converting metabolism that was bound originally to the plasma membrane appears to be the key innovation towards eukaryotic genome and cellular organization. The novel energy metabolism made it possible for the nucleotide synthetic apparatus of cells to be no longer limited by subsaturation with substrates and catalytic components. As a consequence, a considerable increase has occurred in the size and complexity of eukaryotic genomes, providing the genetic basis for most of the further evolutionary changes in cellular complexity. On the other hand, the active uptake of exogenous DNA, which is general in bacteria, was no longer essential in the genome organization of eukaryotes. The mitochondrion-driven scenario for the first eukaryotes explains the chimera-like composition of eukaryotic genomes as well as the metabolic and cellular organization of eukaryotes.     

The pH dependence of the binding of D-glycerate 2,3-bisphosphate to deoxyhemoglobin and oxyhemoglobin. Determination of the number of binding sites in oxyhemoglobin.

The number of Bohr protons released upon oxygenation has been measured over a large range of human hemoglobin concentrations (0.02 to 4.5 mM) in the presence of equimolar amounts of D-glycerate 2,3-bisphosphate. From these data the association constants for the binding of this organic phosphate to deoxyhemoglobin and oxyhemoglobin were calculated at different pH values. The maximum number of protons absorbed upon binding to oxyhemoglobin was determined as well. The maximum number of protons bound to deoxyhemoglobin upon binding of D-glycerate 2,3-bisphosphate was measured independently. From the pH dependence of the association constants and the maximum number of protons absorbed it could be concluded that only one D-glycerate 2,3-bisphosphate can be bound to both deoxyhemoglobin and oxyhemoglobin.     

The effect of diphenols upon the autoxiation of oxyhemoglobin and oxymyoglobin.

P-Hydroquinone and catechol catalytically promote the oxidation of oxyhemoglobin and Oxymyoglobin to the ferriform. Kinetic data for oxyhemoglobin oxidation indicates a first-order dependence upon the hemeprotein concentration and half-order dependence upon diphenol; however at high catalyst concentration, saturation is observed with similar V values for both diphenols despite the difference in reactivity.It is proposed that initially formed quinone oxidizes the hemeprotein with oxygen release; in turn, the semiquinone oxidizes a second molecule of hemeprotein and regenerates the quinone, with the bound oxygen acquiring two electrons. Except for the more reactive oxymyoglobin, the reduced form of the catalyst must be present to oppose semiquinone disappearance by dismutation.Since the expected release of O₂ for water formation is observed, the system may be considered a model for terminal oxidase, the couple $\text{Q}\text{S}$ replacing a $\text{Fe}{}^{\mathrm{2+}}\text{Fe}{}^{\mathrm{2+}}$ or a $\text{Cu}{}^{\mathrm{+}}\text{Cu}{}^{\mathrm{2+}}$ system.It is tentatively inferred that oxyhemoglobin has the structure HbFe²⁺---O₂ and that the rate of the catalyzed oxidation is limited by the rate of generation of the true reacting form, the superoxide ferri structure, HbFe³⁺---O₂^?.     

Scanning molecular sieve chromatography of interacting protein systems. IV. The difference profile method as applied to the Gibbs-Duhem expression in the analysis of the dimer-tetramer equilibria of oxyhemoglobin A.

The recently-developed large zone difference profile method in scanning molecular sieve chromatography is applied to the analysis of the Gibbs-Duhem expression in the tetramer-dimer equilibrium of human oxyhemoglobin A. The preferential binding term and solvation parameters of the Hofmeister anion phosphate are examined. Results indicate that as the concentration of phosphate ions increase, a hydrated phosphate is formed which enhances the association by perturbing the solvation layer of the hemoglobin molecules. The standard free energy change at a given Hofmeister anion activity of ln Ax = -3.2476 is 9.4 +/- 0.2 kcal/mole. delta G0 at ln Ax = -1.2711 is 10.90 +/- 0.05 kcal/mole, suggesting that approximately 11 kcal are required to dissociate one mole of tetramer into dimer.     

Stoichiometry of the reaction of oxyhemoglobin with nitrite.

During the reaction of oxyhemoglobin (HbO2) with nitrite, the concentration of residual nitrite, nitrate, oxygen, and methemoglobin (Hb+) was determined successively. The results obtained at various pH values indicate the following stoichiometry for the overall reaction: 4HbO2 + 4NO2- 4H+ leads to 4Hb+ + 4NO3- + O2 + 2H2 O (Hb denotes hemoglobin monomer). NO2- binds with methemoglobin noncooperatively with a binding constant of 340 M-1 at pH 7.4 and 25 degrees C. Thus, the major part of Hb+ produced is aquomethemoglobin, not methemoglobin nitrite, when less than 2 equivalents of nitrite is used for the oxidation.     

Scanning molecular sieve chromatography of interacting protein systems. IV. The difference profile method as applied to the Gibbs-Duhem expression in the analysis of the dimer-tetramer equilibria of oxyhemoglobin A

The recently-developed large zone difference profile method in scanning molecular sieve chromatography is applied to the analysis of the Gibbs-Duhem expression in the tetramer-dimer equilibrium of human oxyhemoglobin A. The preferential binding term and solvation parameters of the Hofmeister anion phosphate are examined. Results indicate that as the concentration of phosphate ions increase, a hydrated phosphate is formed which enhances the association by perturbing the solvation layer of the hemoglobin molecules. The standard free energy change at a given Hofmeister anion activity of InA(x) = -3.2476 is 9.4 +/- 0.2 kcal mole . DeltaG degrees at InA(x) = -1.2711 is 10.90 +/- 0.05 kcal mole , suggesting that approximately 11 kcal are required to dissociate one mole of tetramer into dimer.     

The filtered Fourier difference spectrum predicts psychophysical letter discrimination in the peripheral retina

We wished to devise a measure of dissimilarity (D) which could predict psychophysical discrimination performance for Snellen letter pairs in peripheral vision. Threshold size for discriminating 33 pairs of Snellen letters was measured at 30 degrees eccentricity in the nasal retina for two subjects. D was computed for each pair by performing an overlap subtraction in the spatial domain, followed by a Fast Fourier Transform on this difference image, and dividing the total power in the resultant 'difference spectrum' by the sum of the powers of the individual letter spectra. A plot of D vs. psychophysical threshold letter size gave a mean correlation of R = -0.81. When D was calculated for letters that were low-pass filtered at different cut-off frequencies, the correlation with psychophysical performance was greatest when cut-off was between 1.25-1.9 cycles/letter (R = -0.85). Conversely, when the difference spectrum was high-pass filtered at different cut-off frequencies, the correlation decreased continuously as the cut-off increased. These results imply that the band of frequencies between zero and 1.25 cycles/letter are most important for letter discrimination in peripheral vision.     

Venation networks and the origin of the leaf economics spectrum

The leaf economics spectrum describes biome-invariant scaling functions for leaf functional traits that relate to global primary productivity and nutrient cycling. Here, we develop a comprehensive framework for the origin of this leaf economics spectrum based on venation-mediated economic strategies. We define a standardized set of traits - density, distance and loopiness - that provides a common language for the study of venation. We develop a novel quantitative model that uses these venation traits to model leaf-level physiology, and show that selection to optimize the venation network predicts the mean global trait-trait scaling relationships across 2548 species. Furthermore, using empirical venation data for 25 plant species, we test our model by predicting four key leaf functional traits related to leaf economics: net carbon assimilation rate, life span, leaf mass per area ratio and nitrogen content. Together, these results indicate that selection on venation geometry is a fundamental basis for understanding the diversity of leaf form and function, and the carbon balance of leaves. The model and associated predictions have broad implications for integrating venation network geometry with pattern and process in ecophysiology, ecology and palaeobotany.     

Band 3-hemoglobin associations. The band 3 tetramer is the oxyhemoglobin binding site

The associations between the band 3 protein of the human erythrocyte membrane and oxyhemoglobin, in solutions of a nonionic detergent, were studied by sedimentation equilibrium experiments in the analytical ultracentrifuge. The following results were obtained: (i) hemoglobin is bound virtually exclusively to the band 3 tetramer, but not to the monomer or dimer; (ii) the band 3 tetramer can bind up to four hemoglobin tetramers; (iii) unlike the unstable dimers of unmodified band 3, stable dimers crosslinked via S-S-bridges also represent hemoglobin binding sites.     

The origin of the eukaryotic cell. IV. The general hypothesis of the autogenous origin of eukaryotes

The general hypothesis of autogenous (non-symbiotic) origin of the eukaryotic cell summarises some hypotheses explaining possible ways of the origin of main components and organelles of such a cell (the primary unicellular protist). Six hypothesises are suggested. Arising of the eukaryotic surface membrane of protist (cell) as a result of modification of its lipidoacidic composition, when most of synblocks and ensembles of eukaryotic enzymes sink into the cytoplasm (due to membrane vesiculation). Establishment of eukaryotic cytoplasm on the basis of successive formation of two locomotory-supporting apparates: the primary one (microtrabecular system), and the second one (cytoskeleton). Arising of the nucleus from a polyheteronomous nucleoid of proeukaryotes. A combinatorical hypothesis of mitosis formation. Polyheteronucleoid hypothesis of the origin of the mitochondria and chloroplasts. Arising of the flagellum from the contractile tentacle-like organelle, whose axoneme is made of single microtubules. A close interrelation and interaction in the process of evolution is noted between surface membranes, the cytoplasm and the nucleus. In accord a principles of block-construction and heterochrony (see: Seravin, 1986r), the author explains the preservation of prokaryotic signs of organization in some components (and organelles) of eukaryotic cell (and protists).     

The origin of the genetic code.

A new approach to the origin of the genetic code is proposed based on some regularities in the nucleotide distribution pattern of the code. The relative amounts of various amino acids in primitive proteins were possibly different from those in organisms living today. The primordial ratio was supposed to shift to the modern one guided by the action of primitive nucleotides. Each primitive tRNA had a discriminator site and, distinguished from it, an anticodon site. It also postulated that primordially each amino acid could correspond to a wide variety of codons. During the course of the evolutionary change, a selective mechanism worked among the protobionts so that less frequent nucleotides became associated with more abundant amino acids in the primordial conditions,thus finally leading to the present codon catalogue.     

The origin of the planetesimal theory.

T. C. Chamberlin suggested in 1897, on the basis of geological and climatological arguments, that the planets were formed by accretion of cold solid partices. With F. R. Moulton he developed convincing arguments against the Laplace nebular hypothesis and published a comprehensive 'planetesimal theory' of the origin of the solar system in 1905. The Chamberlin-Moulton theory has current as well as historical interest.     

Reaction intermediates of H-meromyosin-ATPase and ultraviolet difference spectrum of H-meromyosin induced by ATP.

UV Difference spectra of H-meromyosin (HMM) during the steady state of the myosin-ATPase reaction [EC 3.6.1.3] were measured in 1.5 and 0.05M KC1 in the presence of 5mM MgC1(2) and 20mM Tris-HC1 at pH 8.0 and 24 degrees, using pyruvate kinase [EC 2.7.1.40] and phosphoenolpyruvate to regenerate ATP. It was found that the difference spectrum and its dependence on ATP concentration were the same in 1.5M KC1 as in 0.05M KC1. On the bases of these and other results, the nature of the intermediates of HMM ATPase in the steady-state reaction of HMM ATPase was discussed.     

A novel antioxidant role for hemoglobin. The comproportionation of ferrylhemoglobin with oxyhemoglobin

Ferrylhemoglobin (X-FeIV-OH, where X denotes an amino acid residue in the globin moiety) has long been suspected as a cytotoxic agent produced by the interaction of oxyhemoglobin (X-FeIIO2) or methemoglobin (X-FeIII) with H2O2 in red blood cells. To date, however, technical difficulties have prevented the identification and quantification of X-FeIV-OH. Oxyhemoglobin exposed to a continuous flux of H2O2 (generated at a rate of 120 microM/min during the glucose oxidase-catalyzed oxidation of glucose) was oxidized to (a) X-FeIV-OH when [X-FeIIO2] less than 75 microM and (b) X-FeIII when [X-FeIIO2] greater than 75 microM (the production of X-FeIII proceeded with intermediate formation of X-FeIV-OH). The reduction of the X-FeIV-OH to X-FeIII could be explained by either of two alternative mechanisms: a O2(-)-mediated X-FeIV-OH---X-FeIII transition or a comproportionation of X-FeIV-OH and X-FeIIO2 to yield X-FeIII (a process mediated by a tyrosine moiety in the hemoprotein). The low rate of X-FeIIO2 autoxidation plus the negligible decrease in the rate of X-FeIII formation in the presence of either native or heat-denatured superoxide dismutase or apoenzyme (1 microM) suggested that O2- does not contribute to the reduction of X-FeIV-OH. Moreover, the dependence of X-FeIII formation on X-FeIIO2 concentration, together with the results of O2 uptake and H2O2 consumption measurements, provide experimental evidence to support the comproportionation reaction. Comproportionation is apparently catalyzed by intermolecular electron transfer between tyrosine residues, since the reaction did not occur when tyrosine residues were blocked by acetylation. Intact red blood cells exposed to the same flow rate of H2O2 presented a spectral profile which could be explained as a transition from X-FeIIO2 to X-FeIII. The intermediate production of X-FeIV-OH was detected by adding Na2S (2 mM), which revealed a spectral profile identical with that obtained with purified X-FeIV-OH. Measurements of concentrations and relative rate constants for the reaction of various intracellular reductants (glutathione, NAD(P)H, uric acid, ascorbic acid) with X-FeIV-OH revealed that comproportionation of X-FeIV-OH with X-FeIIO2 is the favored reaction. Our results provide (to our knowledge) the first definitive evidence for X-FeIV-OH in intact red blood cells. The rapid comproportionation reaction between X-FeIV-OH and X-FeIIO2 (to produce X-FeIII) explains why X-FeIV-OH has been elusive to date.(ABSTRACT TRUNCATED AT 400 WORDS)