Statistical analysis of data pertaining to complex state systems by stepwise regression with reformulated parameters; Application to spectroscopically monitored hemoglobin oxygen binding data

A method is described for the statistical analysis of data pertaining to complex state systems, based on the concept of reformulating the parameters describing the system as a hierarchy of interactions, and this method demonstrated on the analysis of spectroscopically monitored hemoglobin oxygen binding data [K. Imai, Biophys. Chem. 37 (1990) 197-210]. The concept of reformulation was first extended to state parameters other than ΔG°s, such as the extinction coefficients (εs) associated with different ligation states during hemoglobin oxygen binding. The reformulated parameters are incrementally allowed to vary in the data fitting procedure, and the statistical significance of the added parameters tested by F and Kolmogorov-Smirnov tests. The result of this method is the minimal set of statistically significant parameters required to describe the data. The hierarchical nature of reformulated parameters allows the physical significance of the subset of statistically significant parameters to be discussed even when all reformulated terms may not be statistically significant. Applying this method to hemoglobin oxygen binding data with the reformulated Adair model demonstrated that at least two, and at most three, of the four reformulated Adair constants are statistically significant. A reformulated square model was found to give a statistically indistinguishable fit from the Adair model, with the statistically significant thermodynamic terms essentially those proposed by Linus Pauling in 1935. A change in Δ ε with subsequent oxygen binding events was found to be significant in both models. These results are consistent with a model for hemoglobin oxygen binding where a subunit changes its conformation upon oxygen binding, and affects the conformation of adjacent subunits.     

Functional properties of hemoglobin in the goldfish <Emphasis Type="Italic">Carassius auratus</Emphasis> before death

The effect of the prelethal state on functional properties of hemoglobin has been studied in the goldfish Carassius auratus. A considerable decrease in hemoglobin affinity for oxygen and the Bohr effect values and the change in the shape of the curve of oxygen equilibrium have been detected. Such state may be compared to the effect of strong short-term stress.     

Folding and stability of helical bundle proteins from coarse‐grained models

We develop a coarse‐grained model where solvent is considered implicitly, electrostatics are included as short‐range interactions, and side‐chains are coarse‐grained to a single bead. The model depends on three main parameters: hydrophobic, electrostatic, and side‐chain hydrogen bond strength. The parameters are determined by considering three level of approximations and characterizing the folding for three selected proteins (training set). Nine additional proteins (containing up to 126 residues) as well as mutated versions (test set) are folded with the given parameters. In all folding simulations, the initial state is a random coil configuration. Besides the native state, some proteins fold into an additional state differing in the topology (structure of the helical bundle). We discuss the stability of the native states, and compare the dynamics of our model to all atom molecular dynamics simulations as well as some general properties on the interactions governing folding dynamics. Proteins 2013; 81:1200–1211. © 2013 Wiley Periodicals, Inc.     

Effect of nitrite-induced methemoglobinemia on the kinetics of blood deoxygenation

Kinetics of blood deoxygenation was studied during acute hypoxia induced by subcutaneous administration of sodium nitrite using polarographic method. Plasma oxygen tension remained unaltered as the dose of sodium nitrite increased, while the dynamics of oxygen release was dose-dependent. The constant of oxyhemoglobin deoxygenation rate proved to vary with blood deoxygenation. The nitrite-induced deceleration of oxyhemoglobin deoxygenation was due to the inactivation of a fraction of hemoglobin as well as to the increased hemoglobin oxygen affinity and possible changes in the oxygen permeability of erythrocyte membranes during acute methemoglobinemia.     

Hematological and immunological properties of herring gull (<Emphasis Type="Italic">Larus argentatus</Emphasis>) nestlings experimentally infected with <Emphasis Type="Italic">Diphyllobothrium dendriticum</Emphasis> (Cestoda: Pseudophyllidae)

The morphological structure of the blood in herring gull nestlings and their immune system response to experimental infection with tapeworm Diphyllobothrium dendriticum have been studied. The leukocyte reaction pattern and the dynamics of immunoglobulin synthesis and populations of immunocompetent cells in the blood of nestlings during early invasion indicated a short duration of the cellular immune response and an insignificant humoral response. A pronounced trend to decrease in the hemoglobin level in the blood of infected nestlings has been revealed and this reduction was in part compensated by intensified erythropoiesis. It is shown, that the changes in hematologic and immune responses of the obligate definitive host provide for the mutual host-parasite adaptation.     

Cooperative cyanide dissociation from ferrous hemoglobin.

Rapid reduction of cyano-met hemoglobin (Hb+CN-) leads to the formation of an intermediate species, the cyanide derivative of ferrous hemoglobin, which dissociates to unliganded hemoglobin because of the extremely low affinity of the ligand for the ferrous heme iron. The properties of the intermediate were studied by transient spectroscopy in human hemoglobin and its isolated alpha and beta chains, in the presence and absence of CO. When mixing with dithionite, the time courses of reduction of the heme iron and dissociation of cyanide overlap considerably; addition to the reaction mixture of the redox indicator methyl viologen considerably increases the rate of reduction and allows unequivocal determination of the spectroscopic and kinetic properties of the intermediate. The results show that (i) the dissociation of cyanide from the isolated alpha and beta chains (as well as the (alpha CO)2(beta + CN-)2 hybrid) is a simple process; (ii) the two chains display similar rate parameters, but show spectroscopic inequivalence, both in the Soret and the visible regions; (iii) cooperative effects are shown to control the rate of dissociation of cyanide from hemoglobin, similarly to what happens for oxygen; and (iv) allosteric effectors (typically inositol hexaphosphate) increase the overall rate of dissociation by stabilization of the T state. We have, therefore, shown for the first time that the dissociation of cyanide from ferrous hemoglobin is controlled by the quaternary state, thereby adding one more ligand to the analysis of the structure-function relationships in hemoglobin.     

Cellular Responses of Congenital Immunity in the Starfish <Emphasis Type="Italic">Asterias rubens</Emphasis>

The work deals with analysis of changes of cellular defense factors in the starfish Asterias rubens in response to injection of human erythrocytes (HE). The number of circulating coelomocytes, dynamics of their production of active oxygen forms, activity of peroxidase, and dynamics of elimination of human hemoglobin from coelomic fluid were estimated before immunization with HE as well as at 6–144 h. The number of coelomocytes was counted in Goryaev chamber, production of active oxygen forms was determined in the test of spontaneous and zymosan-induced reduction of Tetrazolium Nitro Blue, peroxidase activity—in a color enzymatic reaction. Time of human hemoglobin elimination from the coelomic fluid was determined by spectrophotometric method by hemoglobin binding with acetone cyanohydrin with formation of a colored product. It is revealed that injection of human erythrocytes into the starfish Asterias rubens leads to a decrease of the number of coelomocytes in 24–96 h and to an increase of their specific production of active oxygen forms in 96–120 h after the HE injection. In coelomic fluid of Asterias rubens the presence of peroxidase activity is established. The circulation time of human hemoglobin released from erythrocytes in coelomic fluid of these animals does not exceed 24 h. It is suggested that the cellular defense reactions are the major factor of the starfish congenital immunity.__________Translated from Zhurnal Evolyutsionnoi Biokhimii i Fiziologii, Vol. 41, No. 2, 2005, pp. 107–113.Original Russian Text Copyright © 2005 by Kudryavtsev, D’yachkov, Kazakov, Kanaikin, Kharazova, Polevshchikov.     

High temperature unfolding of a truncated hemoglobin by molecular dynamics simulation

Heme containing proteins are associated with peroxidase activity. The proteins like hemoglobin, myoglobins, cytochrome c and micro-peroxidase other than peroxidases have been shown to exhibit weak peroxidase-like activity. This weak peroxidase–like activity in hemoglobin-like molecules is due to heme moiety. We conducted molecular dynamics (MD) studies to decipher the unfolding path of Ba-Glb (a truncated hemoglobin from Bacillus anthracis) and the role of heme moiety to its unfolding path. The similar unfolding path is also observed in vitro by UV/VIS spectroscopy. The data confirmed that the unfolding of Ba-Glb follows a three state process with a meta-stable (intermediate) state between the native and unfolded conformations. The present study is supported by several unfolding parameters like root-mean-square-deviation (RMSD), dictionary of protein secondary structure (DSSP), and free energy landscape. Understanding the structure of hemoglobin like proteins in unicellular dreaded pathogens like B. anthracis will pave way for newer drug discovery targets and in the disease management of anthrax.     

Adaptation of cultured salmon <Emphasis Type="Italic">Salmo salar</Emphasis> (Salmonidae) yearlings to natural environments

The process of adaptation of the yearling Atlantic salmon Salmo salar cultured under the farming conditions in the Umba fish hatchery to the natural environments has been studied during a 1-year period after releasing them into the river. The significant differences in a range of the morphophysiological parameters between the hatchery-reared juveniles and their wild-origin peers, which were revealed immediately before the release into the river and 1 month later, are gradually reduced. The index of body condition, the liver index, and the body cavity fat content are normalized 4 months later; 13 months later, the other analyzed parameters (the hemoglobin concentration and the indices of heart, gills, and pectoral fins) are brought back into the normal ranges. The behavioral patterns of the hatchery-reared and wild-origin juveniles remain different during the whole observation period, since the behavioral habits acquired under the farming conditions, when compared to the developmental abnormalities, more commonly affect the juvenile fish survival in the natural environments.     

Molecular dynamics simulations indicate that deoxyhemoglobin,oxyhemoglobin, carboxyhemoglobin,and glycated hemoglobin under compression and shear exhibit an anisotropic mechanical behavior

We developed a new mechanical model for determining the compression and shear mechanical behavior of four different hemoglobin structures. Previous studies on hemoglobin structures have focused primarily on overall mechanical behavior; however, this study investigates the mechanical behavior of hemoglobin, a major constituent of red blood cells, using steered molecular dynamics (SMD) simulations to obtain anisotropic mechanical behavior under compression and shear loading conditions. Four different configurations of hemoglobin molecules were considered: deoxyhemoglobin (deoxyHb), oxyhemoglobin (HbO₂), carboxyhemoglobin (HbCO), and glycated hemoglobin (HbA_1C). The SMD simulations were performed on the hemoglobin variants to estimate their unidirectional stiffness and shear stiffness. Although hemoglobin is structurally denoted as a globular protein due to its spherical shape and secondary structure, our simulation results show a significant variation in the mechanical strength in different directions (anisotropy) and also a strength variation among the four different hemoglobin configurations studied. The glycated hemoglobin molecule possesses an overall higher compressive mechanical stiffness and shear stiffness when compared to deoxyhemoglobin, oxyhemoglobin, and carboxyhemoglobin molecules. Further results from the models indicate that the hemoglobin structures studied possess a soft outer shell and a stiff core based on stiffness.     

Binding of human hemoglobin and its polypeptide chains with haptoglobin coupled to an agarose matrix.

The interactions of human haptoglobin covalently linked to agarose with human hemoglobin and with p-chloromercuribenzoic-acid-treated alpha and beta chains (alpha* and beta* chains) were studied by flow chromatography and equilibrium binding. The results indicate that in solid state, haptoglobin maintains the same binding characteristics as in solution, the order of binding affinities being: hemoglobin greater than alpha* chain greater than beta* chain. The study of the binding parameters of the alpha* chain shows an heterogeneity of binding sites on the haptoglobin and an average affinity constant Ka of 3.6 X 10(4)l/mol.     

Changes in hematological parameters in free-living pigeons (Columba livia f. urbana) during the breeding cycle

The blood parameters—red blood cell (RBC) count, hematocrit (Ht), hemoglobin concentration (Hb), mean corpuscular volume (MCV), mean corpuscular hemoglobin (MCH), and mean corpuscular hemoglobin concentration (MCHC)—were studied for the first time in free ranging pigeons Columba livia f. urbana. The aim of the study was to establish a set of reference values for this ubiquitous urban species and to examine a potential influence of the factors such as sex and phase of the breeding cycle on the hematological parameters. Blood was sampled from the adult individuals of both sexes during the breeding cycle. Significant variations in Ht and Hb were observed, while RBC count remained unchanged. The lower hematocrit value and hemoglobin concentration found in both males and females during molt probably resulted from the increase of plasma volume not accompanied by an increase in RBC. On the other hand, a significant physiological stress of nutritional deficiency during this energy-consuming stage may manifest itself in the decreased Ht and Hb values. The higher values of Ht and Hb during the laying phase could be related to the dehydration status. There were no overall differences in MCV, MCH, and MCHC values in either of the breeding stage. A lack of sex dimorphism in the measured and calculated blood parameters was apparent. Data collected herein contribute to the better understanding of general physiology of the ubiquitous urban species. The knowledge of variation in the blood indexes with respect to sex and breeding stage is crucial before blood parameters can provide an useful information on physical condition of the bird.     

On the kinetics of erythroid cell differentiation in fetal mice. II. DNA and hemoglobin measurements of individual erythroblasts during gestation

Microspectrophotometric absorption measurements were used to determine the hemoglobin content of erythroid cells derived from the yolk sac during gestation of fetal C3H mice, from day 9 to day 15. Using the DNA content as a marker for the mitotic state between 2C and 4C phase, five successive cell generations and their mean hemoglobin contents were distinguished: 12 pg (pg, picogram = 10^?12 gm). 22.2 pg, 37 pg, 50 pg and 56 pg. In the final state, nucleated erythrocytes contained 98 ± 22 pg hemoglobin. Erythroid cells derived from the liver were measured on day 15 of fetal gestation. The hemoglobin content of proerythroblasts was below 0.3 pg. The two cell generations in the basophilic state had 0.6 pg and 1.7 pg respectively. Polychromatic erythroblasts yielded a hemoglobin content of 5.1 pg in the first cell generation and 7.5 pg in the second one. Orthochromatic erythroblasts contained 8 pg, reticulocytes 12 pg and mature erythrocytes 28 ± 7 pg hemoglobin. Calculations based on these data suggest that the rate of total hemoglobin synthesis is similar in both yolk sac and liver erythropoiesis. The difference between the final hemoglobin content in nucleated erythrocytes of yolk sac origin and that in hepatic erythrocytes can be explained by the different cell generation times.     

Seasonal dynamics of activity of oxidative modification of proteins and oxidation-inhibiting enzymes in the blood of goby Neogobius melanostomus inhabiting the Black Sea and the Sea of Azov

Seasonal dynamics of activity of oxidative modification of proteins and oxidation-inhibiting enzymes was studied in the blood of round goby Neogobius melanostomus that inhabits the coastal areas of the Black Sea and the Sea of Azov. The activity of oxidative modification of proteins and oxidation-inhibiting processes depend on the physiological state of a peculiar specimen, on the hydrochemical parameters of the environment, and on the anthropogenic load in the studied areas during different seasons.     

Beam discharge excited by distributed virtual cathode

A new type of beam discharge, i.e., beam discharge with a distributed virtual cathode (VC) is proposed and considered by numerical simulation. The discharge is established during counter motion of high-current electron beams in a gas-filled equipotential cavity and is characterized by a state of hot dense electron plasma of primary electrons. The discharge temporal dynamics is studied. It is shown that the VC lifetime depends linearly from this sum in a wide range of the sum of beam currents, from the boundary current of two-beam instability to the critical current of Pierce instability. Generation of nonlinear electrostatic structures shaped as phase bubbles in the discharge is detected, and their dynamics is studied. The parameters are determined, at which the multiple coexistence of phase bubbles and their coalescence during collisions is observed.     

Linked functions in allosteric proteins: Extension of the concerted (MWC) model for ligand-linked subunit assembly and its application to human hemoglobins

The allosteric model of Monod et al. (1965) (MWC) has been extended to take into account the effects of subunit dissociation. The problem is formulated theoretically in terms of a general model for two allosteric species (dimers and tetramers) linked by a polymerization reaction. Relationships are presented for interpreting the dimer-tetramer association constants in terms of allosteric model parameters.Sub-cases of the general model were tested against recent experimental data on the oxygenation-linked dimer-tetramer equilibria in normal human hemoglobin and in the variant hemoglobin Kansas (β₁₀₂, Asp → Thr). The objectives of these analyses were: (1) to find the simplest models capable of describing the linked dimer-tetramer equilibria in the two hemoglobin systems, and (2) to evaluate the corresponding model parameters so that allosteric properties of the two hemoglobins may be compared.In the simplest version of the model, the dimer is half of an R-state tetramer. This model was found to be excluded unequivocally by the data for both normal hemoglobin and hemoglobin Kansas when the α and β chains have equal binding affinities. When this two-state model was modified to permit non-equivalent affinities for the chains, the model could be fitted to hemoglobin Kansas, but not to hemoglobin A. A model, in which the dimers are allowed to exist in a state different from the tetramer R state, was found to be consistent with the data for hemoglobin A, with equivalent binding by the α and β chains. For hemoglobin A, the unliganded R-state tetramers have a different subunit dissociation energy from that of fully liganded R-state tetramers. The simplest model capable of describing both hemoglobin A and hemoglobin Kansas was obtained by extending this three-state model to permit (but not require) functional non-equivalence of the α and β chains. For these MWC models, unique estimates were obtained for the model parameters.The allosteric constants for tetrameric hemoglobins A and Kansas are approximately equal. The value obtained from hemoglobin A is similar to previous estimates, whereas the value for hemoglobin Kansas is lower than previously estimated (Edelstein, 1971) by approximately two orders of magnitude. The low affinity of hemoglobin Kansas tetramer does not arise from an unusually high allosteric constant favoring the T-state species. It is largely the consequence of a greatly reduced oxygen affinity of β chains in the T state, and reduced values for the ratio between affinities in the R and T states.     

Malnutrition in rats during pregnancy and lactation period: a study on body, spleen and thymus weights and hematologic parameters in dams and their offspring

Physiological changes in the rat dams and their offspring as sequelae of malnutrition during pregnancy and lactation and their capacity for recuperation from early malnutrition is studied. The dams were killed during the lactation period (15th and 30th days of postpartum) and the absolute and relative weights of the thymus and spleen were recorded. The following hematologic parameters were examined: red blood cell count, hemoglobin, hematocrit, mean cell volume, mean cell homoglobin, mean cell hemoglobin concentration, white blood cell count, lymphocytes, monocytes, eosinophils, polimorphonuclear neutrophil, basophils. The offspring were sacrificed at 15, 30 and 90 days of age. Their body weight and the same hematic parameters and organ weights as their mothers were determined. Results indicate a highly significant decrease in body weight and organ weights in experimental dams and an important alteration in their hematic parameters, which may be an important determinant of retardation of growth in pups, whose body and organ weights were significantly smaller than those of the controls. In addition, the hematologic parameters of the malnourished offspring were modified in relation to those of the controls at all times (15, 30 and 90 days old) studied.     

Direct Determination of Protonation States of Histidine Residues in a 2 Å Neutron Structure of Deoxy-Human Normal Adult Hemoglobin and Implications for the Bohr Effect

We have investigated the protonation states of histidine residues (potential Bohr groups) in the deoxy form (T state) of human hemoglobin by direct determination of hydrogen (deuterium) positions with the neutron protein crystallography technique. The reversible binding of protons is key to the allosteric regulation of human hemoglobin. The protonation states of 35 of the 38 His residues were directly determined from neutron scattering omit maps, with 3 of the remaining residues being disordered. Protonation states of 5 equivalent His residues—αHis20, αHis50, αHis89, βHis143, and βHis146—differ between the symmetry-related globin subunits. The distal His residues, αHis58 and βHis63, are protonated in the α1β1 heterodimer and are neutral in α2β2. Buried residue αHis103 is found to be protonated in both subunits. These distal and buried residues have the potential to act as Bohr groups. The observed protonation states of His residues are compared to changes in their pK_a values during the transition from the T to the R state and the results provide some new insights into our understanding of the molecular mechanism of the Bohr effect.     

Diurnal and seasonal changes in blood composition of the free-living Egyptian fruit bat (Rousettus aegyptiacus)

We studied the blood profile of the free-living fruit bat (Rousettus aegyptiacus) during the beginning of the activity period (around various feeding trees) and upon return to the day roost during 1994–1995. Results of the present study suggest that during winter and early spring bats are characterized by a poor physical and physiological state as reflected in the blood profile, revealing elevated urea and uric acid concentrations. It was found that at the end of the resting phase, R. aegyptiacus was in a mild state of dehydration (increased hematocrit and hemoglobin levels). At the end of activity, upon return to the day roost, both hematocrit and hemoglobin levels decreased but bats still maintained a high plasma osmolality. Several components in the blood are effected by the feeding time and show a cyclic change in concentration. The reverse relationship between glucose and triglyceride levels may indicate that glucose is the energy source during the active phase and that fat is the energy source during the resting period. The low cholesterol level in the blood reflects its absence in the fruit diet. Accepted: 5 February 1999