A correlation between respiration and synthesis of ATP in mitochondria at different degree of uncoupling of oxidative phosphorylation

It is known that mitochondrial respiration in state 3 is due to three simultaneous and independent processes: synthesis of ATP (1), endogenous passive proton leakage (2), and proton leakage by protonophoric uncoupler (3). The total rate of processes (2) and (3) is equal to the product of respiration rate in state 4 and coefficient KR, which is defined as the ratio of the deltamuH+ value in state 3 to that in state 4. It is shown that it is possible to calculate both the rates of processes (1), (2) and (3) separately and the protonophoric activity of uncoupler using the coefficient KR and other coefficients, which are determined as the ratio of deltamuH+ values in state 3 or in state 4 to its maximal value. Simple methods of determination of these coefficients were developed, which are based on the study of the dependence of respiration rate in states 3 and 4 on the concentration of protonophoric uncoupler. It was found that the uncoupling action of palmitate, a natural uncoupler of oxidative phosphorylation, unlike classic uncoupler-protonophores DNP and FCCP, depends not only on its protonophoric activity but also on the inhibition of the process (1).     

Effect of water on DNA structure in a model microemulsion system

The physical state of water in a system of reversed micelles at different molar rations of H2O and a nonionic surfactant (tetraethylene glycol monododecyl ether, Brij 30) was studied by NMR spectroscopy. In addition, the effect of water on the structure of the intramicellar DNA was investigated using the intercalator ethidium bromide. It was shown by NMR diffusometry that the state of water inside micelles can be considered as supercooled. It was found that the condensation of DNA inside micelles takes place only at definite ratios of water and Brij 30 (from 1.26 to 5). If free water is absent and if the percentage of free water inside in reversed micelles is more than 50%, the process of DNA condensation is disturbed. It is assumed that the molecular memory inherent in the supercooled state of water affects the formation and stabilization of the condensed state of DNA.     

Role of Sulfhydryl Groups in Functioning of Adenylyl Cyclase Signaling System

This review considers the literature data and author's own results on the role of SH-groups in functioning of the hormone-sensitive adenylyl cyclase system (ACS). It has been shown that the state of SH-groups affects crucially all main stages of the hormonal signal transudation: the ligand-binding properties of receptor and its coupling to G-proteins, interaction of G-proteins with adenylyl cyclase (AC) and its catalytic activity. It is noted that for the receptors, coupled to AC by a stimulating mode, the central aspect of the SH-dependent regulation of ACS is shifted to the receptor, while for the receptors coupled to AC by an inhibiting mode, it coincides with G-protein of the inhibiting type, which is sensitive to the SH-group state. Based on the performed comparative analysis of primary structures of signalling proteins—ACS components and of literature data, there are revealed the cysteine residues determining the functional activity of these proteins in the process of the hormonal signal transudation. The conclusion is made that the SH-group state (the ratio of free SH-groups and disulfide bonds) is the main factor determining the ACS reactivity to hormonal effects and selectivity of process of the signal transudation.     

Probing the wild-type HRas activation mechanism using steered molecular dynamics,understanding the energy barrier and role of water in the activation

Ras is one of the most common oncogenes in human cancers. It belongs to a family of GTPases that functions as binary conformational switches by timely switching of their conformations from GDP to GTP and vice versa. It attains the final active state structure via an intermediate GTP-bound state. The transition between these states is a millisecond-time-scale event. This makes studying this mechanism beyond the scope of classical molecular dynamics. In the present study, we describe the activation pathway of the HRas protein complex along the distance-based reaction coordinate using steered molecular dynamics. Approximately ~720 ns of MD simulations using CMD and SMD was performed. We demonstrated the change in orientation and arrangement of the two switch regions and the role of various hydrogen bonds during the activation process. The weighted histogram analysis method was also performed, and the potential of mean force was calculated between the inactive and active via the intermediate state (state 1) of HRas. The study indicates that water seems to play a crucial role in the activation process and to transfer the HRas protein from its intermediate state to the fully active state. The implications of our study hereby suggest that the HRas activation mechanism is a multistep process. It starts from the inactive state to an intermediate state 1 followed by trapping of water molecules and flipping of the Thr35 residue to form a fully active state (state 2). This state 2 also comprises Gly60, Thr35, GTP, Mg²⁺ and water-forming stable interactions.     

Exchangeability in multivariate Markov chain models.

Time-homogeneous Markov chain models with state space [0, 1]k are useful in analysis of binary follow-up data on k individuals that interact. The number of parameters increases exponentially with k so more restrictive models are imperative for statistical inference. The hypothesis that the matrix of transition probabilities is invariant under permutation of individuals is discussed. It is shown that if individuals are exchangeable, then the process counting the number of individuals occupying a given state is a Markov chain. This reduction of data is sufficient if either at most a single individual may change state between two consecutive time points or if a state is absorbing. Similar results are obtained for exchangeability within two subgroups. Inference in the multivariate process reduces to a univariate problem if individuals are independent given the group's previous response. It is shown how conditional independence could be tested assuming exchangeability. The different hypotheses re examined in an analysis of the occurrence of bacteria in milk samples of Danish dairy cattle.     

Neurontropy,an entropy-like measure of neural correlation,in binocular fusion and rivalry

Dynamic random dot stereograms were generated for which the left and right arrays were either identical (100% correlation), or uncorrelated (0% correlation), or the complements of each other (-100% correlation). Any two of these three states of correlation were presented in succession and duration thresholds for detecting the transitions were measured. These thresholds were much longer when the transition went from the uncorrelated state to the correlated state than vice versa. In order to explain the detection thresholds for the various transitions a model based on the notion of an entropy-like measure (to be called neurontropy) has been proposed. It was assumed that in binocular vision both a fusional and a rivalry process operate simultaneously, but in a dual fashion. Thus the correlated state would be regarded the same way by the fusional process as the complemented state by the rivalry process. Transitions from the uncorrelated to the complemented state (and vice versa) were the most difficult to detect, a task which only the rivalry process could accomplish. The long detection thresholds indicate that the rivalry process is less efficient than the fusional process.Address Fill Oct. 1, 1976: Prof. Dr. B. Julesz     

Thermal denaturation of porcine pepsin: a study by circular dichroism

Thermal denaturation of porcine pepsin in 10% ethanol was studied by circular dichroism (CD) spectroscopy. It was observed that the process is markedly irreversible. The denaturation unfolding process was strongly dependent on the heating rate, as is expected for an unfolding process kinetically controlled due to the presence of an irreversible reaction. Experimentally, we demonstrate the existence of an unfolded (U) state in equilibrium with the native (N) state. The U state is observed to exist at temperatures lower than 45 degrees C. The van't Hoff enthalpy, DeltaH(vH), was determined from direct estimation of the equilibrium constant at several temperatures (DeltaH(vH)=304.3 kJ/mol). To explain the observed behavior, we have considered a Lumry-Eyring model, which takes into account the presence of the U state in addition to N and denatured (D) states (i.e. N<-->U-->D).     

An Indicator to Evaluate the Thermodynamic Maturity of Industrial Process Units in Industrial Ecology

The article suggests a measure to evaluate the thermodynamic maturity of industrial systems at the level of single process units. The measure can be quantified with reasonable confidence on the basis of entropy production as defined by irreversible thermodynamics theory. It quantifies, for one process unit, the distance between its actual state of operation and its state with minimum entropy production or optimum exergy efficiency, when the two states are constrained with a fixed production capacity of the process unit. We suggest that the minimum entropy production state is a mature state, or that processes that operate at this state are mature. We propose to call the measure "the thermodynamic maturity indicator" (π), and we define it as the ratio between the minimum entropy production and the actual entropy production. We calculated π on the basis of literature data for some examples of industrial process units in the chemical and process industry (i.e., heat exchanger, chemical reactor, distillation column, and paper drying machine). The proposed thermodynamic measure should be of interest for industrial ecology because it emerges from the entropy production rate, a dynamic function that can be optimized and used to understand the thermodynamic limit to improving the exergy efficiency of industrial processes. Although not a tool for replacing one process with another or comparing one technology to another, π may be used to assess actual operation states of single process units in industrial ecology.     

Comparing internal models of the dynamics of the visual environment

It is well known that the human postural control system responds to motion of the visual scene, but the implicit assumptions it makes about the visual environment and what quantities, if any, it estimates about the visual environment are unknown. This study compares the behavior of four models of the human postural control system to experimental data. Three include internal models that estimate the state of the visual environment, implicitly assuming its dynamics to be that of a linear stochastic process (respectively, a random walk, a general first-order process, and a general second-order process). In each case, all of the coefficients that describe the process are estimated by an adaptive scheme based on maximum likelihood. The fourth model does not estimate the state of the visual environment. It adjusts sensory weights to minimize the mean square of the control signal without making any specific assumptions about the dynamic properties of the environmental motion.We find that both having an internal model of the visual environment and its type make a significant difference in how the postural system responds to motion of the visual scene. Notably, the second-order process model outperforms the human postural system in its response to sinusoidal stimulation. Specifically, the second-order process model can correctly identify the frequency of the stimulus and completely compensate so that the motion of the visual scene has no effect on sway. In this case the postural control system extracts the same information from the visual modality as it does when the visual scene is stationary. The fourth model that does not simulate the motion of the visual environment is the only one that reproduces the experimentally observed result that, across different frequencies of sinusoidal stimulation, the gain with respect to the stimulus drops as the amplitude of the stimulus increases but the phase remains roughly constant. Our results suggest that the human postural control system does not estimate the state of the visual environment to respond to sinusoidal stimuli.     

烫伤创面绿脓杆菌定植动态的实验研究

本文从细菌以多细胞生理活动观点出发,以认识定植稳定过程为目的。进行了实验大白鼠烫伤创面绿脓杆菌定植与抗定植动态观察。通过用铁浸染色法对细菌群体结构定量化研究,用糖包被负染法对群体结构内部结构观察,对粘附在组织表面细菌数量的测定,反映结构与粘附力的关系。进一步结合电镜观察及细菌生长状态的分析,证明了烫伤创面上绿脓杆菌群体结构的形成是细菌分裂繁殖所致。通过群体结构,糖包被,粘附力及生长状态的动态观察,表现出与定植的稳定程度呈平行关系,显示其重要性。联系抗定植力研究,表明定植与抗定植的一致性。最后分析了定植三个主要条件,和稳定性定植的三要素。     

Progress in monitoring, modeling and control of bioprocesses during the last 20 years

The paper gives a review on the recent development of bioprocess engineering. It includes monitoring of product formation processes by flow injection analysis, various types of chromatographic and spectroscopic methods as well as by biosensors. The evaluation of mycelial morphology and physiology by digital image analysis is discussed also. It deals with advanced control of indirectly evaluated process variables by means of state estimation/observer, with the use of structured and hybrid models, expert systems and pattern recognition for process optimization and gives a short report on the state of the art of metabolic flux analysis and metabolic engineering.     

Acid-base state of blood and accumulation of strontium in tissues of rats

It is shown that the increase of strontium content 1.5, 1.7, 2.0, 1.7, and 5.1 times, respectively, in the liver, kidneys, heart, muscles and bones of poisoned rats leads to the state of subcompensated metabolic acidosis in them. Experimental deepening of metabolic acidosis with per os introducing of chloride acid parallel with intramuscular injection of strontium chloride reduces the accumulation of strontium in the muscles and kidneys 1.6, in the liver - 1.5, in bones - 2.7 times. Introduction of rats into metabolic acidosis state after their poisoning with strontium causes acceleration of mentioned metal elimination process from the muscles and kidneys 1.5 times, from the liver 1.3 times, from the bones 1.4 times, on the 20th day of research. The issues concerning subcompensated metabolic alkaloses observed in rats' blood, poisoned by strontium after per os introducing of sodium hydrocarbon. It is proved that this phenomenon does not influence accumulation of strontium both in the heart and bones, and it does not essentially reduce the accumulation of this element in the muscles, liver and kidneys. Therefore, the experimental results performed evidence that in the case of changing the acid-base state indices of blood in the direction of metabolic acidosis, one could reach the reduction of strontium accumulation in poisoned animals' organism, and acceleration of mentioned metal elimination process. It should be mentioned that metabolic alkaloses does not influence the intensity of the mentioned metal elimination process.     

Folding of chymotrypsin inhibitor 2. 2. Influence of proline isomerization on the folding kinetics and thermodynamic characterization of the transition state of folding

The refolding of chymotrypsin inhibitor 2 (CI2) is, at least, a triphasic process. The rate constants are 53 s-1 for the major phase (77% of the total amplitude) and 0.43 and 0.024 s-1 for the slower phases (23% of the total amplitude) at 25 degrees C and pH 6.3. The multiphase nature of the refolding reaction results from heterogeneity in the denatured state because of proline isomerization. The fast phase corresponds to the refolding of the fraction of protein that has all its prolines in a native trans conformation in the denatured state. It is not catalyzed by peptidyl-prolyl isomerase. The rate-limiting step of folding for the slower phases, however, is proline isomerization, and they are both catalyzed by peptidyl-prolyl isomerase. The slowest phase has properties consistent with a process involving proline isomerization in a denatured state. In particular, the activation enthalpy is large, 16 kcal mol-1 K-1, and the rate is independent of guanidinium chloride concentration ([GdnHCl]). In comparison, the intermediate phase shows properties consistent with a process involving proline isomerization in a partially structured state. The activation enthalpy is small, 8 kcal mol-1 K-1, and the rate has a strong dependence on [GdnHCl]. Temperature dependences of the rate constants for unfolding and for the fast refolding phase, both in the absence and in the presence of GdnHCl, were used to characterize the thermodynamic nature of the transition state and its relative exposure to solvent. The Eyring plot for unfolding is linear, indicating that there is relatively little change in heat capacity between native state and transition state.(ABSTRACT TRUNCATED AT 250 WORDS)     

Evolutionarily Conserved Proline Residues Impede the Misfolding of the Mouse Prion Protein by Destabilizing an Aggregation-competent Partially Unfolded Form

The misfolding of the prion protein has been linked to several neurodegenerative diseases. Despite extensive studies, the mechanism of the misfolding process remains poorly understood. The present study structurally delineates the role of the conserved proline residues present in the structured C-terminal domain of the mouse prion protein (moPrP) in the misfolding process. It is shown that mutation of these Pro residues to Ala leads to destabilization of the native (N) state, and also to rapid misfolding. Using hydrogen–deuterium exchange (HDX) studies coupled with mass spectrometry (MS), it has been shown that the N state of moPrP is in rapid equilibrium with a partially unfolded form (PUF2*) at pH 4. It has been shown that the Pro to Ala mutations make PUF2* energetically more accessible from the N state by stabilizing it relative to the unfolded (U) state. The apparent rate constant of misfolding is found to be linearly proportional to the extent to which PUF2* is populated in equilibrium with the N state, strongly indicating that misfolding commences from PUF2*. It has also been shown that the Pro residues restrict the boundary of the structural core of the misfolded oligomers. Overall, this study highlights how the conserved proline residues control misfolding of the prion protein by modulating the stability of the partially unfolded form from which misfolding commences.     

The role of state 4 electron transport in the activation of state 3 respiration in potato mitochondria

The initial state 3 respiration rate of potato mitochondria is markedly depressed, or attenuated. With several consecutive state 3/state 4 cycles the state 3 rate rises to a maximum, while the state 4 rate remains essentially unchanged. The development of state 3 respiration has been termed conditioning. An analysis of the process has indicated that state 4 is a better conditioner than state3 per se. Conditioning is also attained by preincubation in state 2, or under conditions designated pseudostate 2, wherein ADP is present, with or without oligomycin, and inorganic phosphate is absent. ADP implements the conditioning process in the absence of oxidative phosphorylation. The action of ADP in its secondary or modulator role appears to be positively cooperative, the kinetics of ADP involvement being second-order. S_0.5 for ADP as a modulator of the conditioning process is approximately 62 M, a value in excess of the K _s for ADP in oxidative phosphorylation. Electron transport is indispensable for conditioning, and it is suggested that conditioning and ATP synthesis represent alternative uses of respiratory energy. It is further suggested that to some extent state 4 underlies state 3.     

Conserved Prosegment Residues Stabilize a Late-Stage Folding Transition State of Pepsin Independently of Ground States

The native folding of certain zymogen-derived enzymes is completely dependent upon a prosegment domain to stabilize the folding transition state, thereby catalyzing the folding reaction. Generally little is known about how the prosegment accomplishes this task. It was previously shown that the prosegment catalyzes a late-stage folding transition between a stable misfolded state and the native state of pepsin. In this study, the contributions of specific prosegment residues to catalyzing pepsin folding were investigated by introducing individual Ala substitutions and measuring the effects on the bimolecular folding reaction between the prosegment peptide and pepsin. The effects of mutations on the free energies of the individual misfolded and native ground states and the transition state were compared using measurements of prosegment-pepsin binding and folding kinetics. Five out of the seven prosegment residues examined yielded relatively large kinetic effects and minimal ground state perturbations upon mutation, findings which indicate that these residues form strengthened and/or non-native contacts in the transition state. These five residues are semi- to strictly conserved, while only a non-conserved residue had no kinetic effect. One conserved residue was shown to form native structure in the transition state. These results indicated that the prosegment, which is only 44 residues long, has evolved a high density of contacts that preferentially stabilize the folding transition state over the ground states. It is postulated that the prosegment forms extensive non-native contacts during the process of catalyzing correct inter- and intra-domain contacts during the final stages of folding. These results have implications for understanding the folding of multi-domain proteins and for the evolution of prosegment-catalyzed folding.     

An analysis of life history evolution in terms of the density-dependent Lefkovitch matrix model.

The evolution of demographic characteristics is considered in terms of the density-dependent Lefkovitch matrix model, which describes a species' population dynamics with a stage-specific pattern of reproduction and mortality. We obtain the invadability condition of a mutant-type into the wild-type population at the equilibrium state. The condition depends on the left and right eigenvectors at the equilibrium state. The condition depends on the left and right eigenvectors at the equilibrium state and the difference, between wild-type and mutant-type populations, of the values of elements in the Lefkovitch matrix at the equilibrium state. It is also shown that if elements of the density-dependent Lefkovitch matrix are decreasing functions of population density, then the equilibrium population density increases in the process of natural selection; that is, K-selection acts even on the stage-structured population. The evolution of life history in perennial plants is discussed through two models as an application of the above results. The evolution of perennial plants with no vegetative reproduction is analyzed in the first example. It is shown that whether monocarpic perennials (which reproduce once and die) or polycarpic perennial plants (which reproduce more than once) are favored depends on the cost of a produced seed. The second example concerns perennial plants that reproduce vegetatively. It is shown that whether monocarpic or polycarpic perennial plants are favored depends on the cost of a seed and that where vegetative reproduction is common, polycarpic perennials with no seed reproduction are favored.     

Interval observers for biochemical processes with uncertain kinetics and inputs

This paper concentrates on the state observation in bioprocesses when there is uncertainty on the process parameters and/or the process inputs. An interval observer is designed on the basis of the cooperativity properties of the model for a standard stirred tank bioreactor model with a single microbial growth and a kinetic model depending on the substrate concentration. Further assumptions are the (lower and upper) boundedness of the specific growth rate and the inlet substrate concentration. Mathematical analysis of the stability and convergence of the interval observer is performed both in absence and in presence of uncertainty on the measurements. It is shown in particular that when the process inputs are known, the static observation error on the unknown state is inversely proportional to one of the observer gains. The performance of the interval observer are also illustrated through numerical simulation.     

Effect of Substitutions in Surface Amino Acid on Energy Profile of Apomyoglobin

Studies on the process of spontaneous protein folding into a unique native state are an important issue of molecular biology. Apomyoglobin from the sperm whale is a convenient model for these studies in vitro. Here, we present the results of equilibrium and kinetic experiments carried out in a study on the folding and unfolding of eight mutant apomyoglobin forms of with hydrophobic amino acid substitutions on the protein surface. Calculated values of apparent constants of folding/unfolding rates, as well as the data on equilibrium conformational transitions in the urea concentration range of 0–6 M at 11°C are given. Based on the obtained information on the kinetic properties of the studied proteins, a Φ-value analysis of the transition state has been performed and values of urea concentrations corresponding to the midpoint of the transition from the native to intermediate state have been determined for the given forms of mutant apomyoglobin. It has been found that a significant increase in the stability of the native state can be achieved by a small number of amino acid substitutions on the protein surface. It has been shown that the substitution of only one amino acid residue exclusively affects the height of the energy barrier that separates different states of apomyoglobin.     

Relation between the conformational heterogeneity and reaction cycle of Ras: molecular simulation of Ras

Ras functions as a molecular switch by cycling between the active GTP-bound state and the inactive GDP-bound state. It is known experimentally that there is another GTP-bound state called state 1. We investigate the conformational changes and fluctuations arising from the difference in the coordinations between the switch regions and ligands in the GTP- and GDP-bound states using a total of 830 ns of molecular-dynamics simulations. Our results suggest that the large fluctuations among multiple conformations of switch I in state 1 owing to the absence of coordination between Thr-35 and Mg²⁺ inhibit the binding of Ras to effectors. Furthermore, we elucidate the conformational heterogeneity in Ras by using principal component analysis, and propose a two-step reaction path from the GDP-bound state to the active GTP-bound state via state 1. This study suggests that state 1 plays an important role in signal transduction as an intermediate state of the nucleotide exchange process, although state 1 itself is an inactive state for signal transduction.