Structural changes and fluctuations of proteins: I. A statistical thermodynamic model

A general theory of the structural changes and fluctuations of proteins has been proposed based on statistical thermodynanic considerations at the chain level.The “structure” of protein was assumed to be characterized by the state of secondary bonds between unique pairs of specific sites on peptide chains. Every secondary bond changes between the bonded and unboned states by thermal agitation and the “structure” is continuously fluctuating. The free energy of the “structural state” that is defined by the fraction of secondary bonds in the bonded state has been expressed by the bond energy, the cooperative interaction between bonds, the mixing entropy of bonds, and the entropy of polypeptide chains. The most probable “structural state” can be simply determined by graphical analysis and the effect of temperature or solvent composition on it is discussed. The temperature dependence of the free energy, the probability distribution of structural states and the specific heat have been calculated for two examples of structural change.The theory predicts two different types of structural changes from the ordered to disordered state, a “structural transition” and a “gradual structural change” with rising temperature, In the “structural transition”, the probability distribution has two maxima in the temperature range of transition. In the “gradual structural change”, the probability distribution has only one maximum during the change.A considerable fraction of secondary bonds is in the unbonded state and is always fluctuating even in the ordered state at room temperature. Such structural fluctuations in a single protein molecule have been discussed quantitatively.The theory is extended to include small molecules which bind to the protein molecule and affect the structural state. The changes of structural state caused by specific and non-specific binding and allosteric effects are explained in a unified manner.     

Vestibular reactions of young ski jumpers

Autonomic responses to vestibular stimulation are predominately differently directed in groups of young athletes and children and adolescents who do not participate in sports, their expression being determined by the ontogenetic pattern and peaking at about 14 years of age. Ski jumping contributes to the physiologically adequate direction of autonomic reactions connected with the predominance of sympathetic activity. The somatic reactions of athletes to a rotational test are determined by the level level of their qualification and reach a considerably greater tolerance to the distracting effects of vestibular stimulation than those of subjects from control groups, and the intergroup differences in the levels of somatic reactions increase rather than decrease by 17 years of age, in contrast to the intergroup differences in autonomic reactions.     

The possibilities for partial rehabilitation of the integrative activity of the brain in patients in a vegetative state

An integrated neuroreconstructive approach to stimulating the pathogenetic mechanisms of a vegetative state developed due to a severe traumatic brain injury (TBI) is suggested. It has been shown that a faster and more pronounced therapeutic effect, compared with conventional therapies, could be achieved through the application of transtimpanal chemical vestibular dereception and transcranial micropolarization. The results of neurophysiological in-depth examination in dynamics have shown that over time interregional cortical interactions become more intense, “rigid,” and “tight” in patients with a vegetative state, while the temporal-parietal-occipital areas begin to dominate in the organization of these interactions in the cortex of both hemispheres. It is assumed that the vestibulothalamic tract, owing to its anatomical location, appears to be the least vulnerable under the conditions of brain stem dislocation due to a severe TBI. As a result, vestibular afferentation appears to become a predominant kind of afferentation for generating interregional cortical interactions. A pathological functional system develops on the basis of this afferentation, blocking other functional systems in the damaged brain. The suggested therapies significantly reduce the amount of vestibular afferent inputs and open a possibility for restoring more effective afferent interactions. This significantly facilitates the functioning of the brain as a multimodal analyzer.     

Role of social and individual experience in interaction of the meadow ant Formica pratensis (Hymenoptera: Formicidae) with ladybird imagines and hoverfly larvae

The ability to recognize aphidophages is one of the key points in the protection ants provide aphids against their natural enemies. Behavior of honeydew collectors from nature (“field,” control) and laboratory reared “naive” ants of Formica pratensis Retzius, which had never met either “mature” workers or aphids and aphidophages, was observed during their pairwise interactions with ladybird imagines and hoverfly larvae. The majority of the “naive” ants perceived ladybirds as an enemy at their first encounter attacking them immediately without any prior antennation. Ants seem to have a certain innate “enemy image” that lets them react very quickly to protect aphids. Hoverfly larvae were rarely attacked by both “field” and “naive” ants (>15%). During tests with ladybirds ants from nature attacked them and also demonstrated the most aggressive reactions (series of bites and “death grip”) less frequently than the “naive” ants. The percentage of ants avoiding aphidophages after a contact with their chemical defense (reflex bleeding and glue‐like saliva) was significantly higher in the control group. Whereas the “naive” ants did not learn to avoid danger, foragers from nature usually tried to avoid negative experience and used tactics of “short bites.” Overall, experience has been proved to be unimportant for displaying key behavioral reactions underlying ant–ladybird interaction. However, accumulation of experience has been assumed to play an important role in the formation of behavioral strategy that allows honeydew collectors to drive aphidophages away with lower energy costs and avoid or minimize negative consequences of aphidophages’ chemical defense.     

The Crystal Structure of Glutamine-binding Protein fromEscherichia coli

The crystal structure of the glutamine-binding protein (GlnBP) fromEscherichia coliin a ligand-free “open” conformational state has been determined by isomorphous replacement methods and refined to anR-value of 21.4% at 2.3 Å resolution. There are two molecules in the asymmetric unit, related by pseudo 4-fold screw symmetry. The refined model consists of 3587 non-hydrogen atoms from 440 residues (two monomers), and 159 water molecules. The structure has root-mean-square deviations of 0.013 Å from “deal” bond lengths and 1.5° from “ideal” bond angles.The GlnBP molecule has overall dimensions of approximately 60 Å × 40 Å × 35 Å and is made up of two domains (termed large and small), which exhibit a similar supersecondary structure, linked by two antiparallel β-strands. The small domain contains three α-helices and four parallel and one antiparallel β-strands. The large domain is similar to the small domain but contains two additional α-helices and three more short antiparallel β-strands. A comparison of the secondary structural motifs of GlnBP with those of other periplasmic binding proteins is discussed.A model of the “closed form” GlnBP-Gln complex has been proposed based on the crystal structures of the histidine-binding protein-His complex and “open form” GlnBP. This model has been successfully used as a search model in the crystal structure determination of the “closed form” GlnBP-Gln complex by molecular replacement methods. The model agrees remarkably well with the crystal structure of the Gln-GlnBP complex with root-mean-square deviation of 1.29 Å. Our study shows that, at least in our case, it is possible to predict one conformational state of a periplasmic binding protein from another conformational state of the protein. The glutamine-binding pockets of the model and the crystal structure are compared and the modeling technique is described.     

Modeling dynamical interactions between fast and slow movements: fast saccadic eye movement behavior in the presence of the slower VOR

An ongoing controversy has to do with the interactions between “fast” (saccadic, quick phase) and “slow” (all other) eye movements. By attacking such issues with both experimental and especially simulation studies using our nonlinear sixth order reciprocally innervated model of the eye mechanical system, insights can be gained into the nature of these nontrivial phenomena. In our present study we relied both (1) on simulation of saccades under a wide range of experimental conditions [vestibular ocular reflex (VOR) velocities from -100 to 100 deg/sec, VOR induced position ranges from -30 to 30 degrees, time-optimal saccades ranging from 2 to 40 degrees], and (2) on using a wide variety of computer simulation of eye movement models, ranging from nonlinear ones with first and especially second order multipulse step controller signal structures, to different controller signal interaction schemes, to simulation using linearized models. We have isolated two important nonlinear phenomena: a level I nonlinear mechanical interaction, dependent not only on the initial velocity but also on the “position effect,” a new finding; and a level II nonlinear neurological interaction, close to “squelching” of the VOR controller signals by the dominating saccadic signal. Furthermore, we have used our simulation findings to reinterpret others' experimental data on eye movement interactions, including saccadic-smooth pursuit, saccadic-vergence, and vestibular nystagmus.     

Room temperature crystal structure of the fast switching M159T mutant of the fluorescent protein dronpa

The fluorescent protein Dronpa undergoes reversible photoswitching reactions between the bright “on” and dark “off” states via photoisomerization and proton transfer reactions. We report the room temperature crystal structure of the fast switching Met159Thr mutant of Dronpa at 2.0‐Å resolution in the bright on state. Structural differences with the wild type include shifted backbone positions of strand β8 containing Thr159 as well as an altered A‐C dimer interface involving strands β7, β8, β10, and β11. The Met159Thr mutation increases the cavity volume for the p‐hydroxybenzylidene‐imidazolinone chromophore as a result of both the side chain difference and the backbone positional differences. Proteins 2015; 83:397–402. © 2014 Wiley Periodicals, Inc.     

Cardiac activity of freshwater crayfish at wakefulness, rest, and “animal hypnosis”

In laboratory experiments, simultaneous continuous recording of the circadian cycle of behavioral reactions and cardiac activity of freshwater crayfish Astacus astacus and Procambarus clarkii was carried out. A non-invasive fiber-optic method of recording of the heart rate (HR) was used. The obtained data were analyzed by the method of variational pulsometry (VP). It was revealed that certain values of HR and characteristics of VP corresponded to the physiological states of active wakefulness and rest. It was found that during long immobilization of crayfish it is possible to identify the states of operative rest and sleep by the animal behavioral reactions and parameters of cardiac activity. Crayfish were studied in the state of artificially evoked immobilization (“animal hypnosis”). During this state, a high HR level, an increase of indexes of tension and autonomic equilibrium, and changes of other VP characteristics were observed. It is suggested that the different level of cardiac activity in different physiological states of crayfish (active wakefulness, operative rest, sleep, and “animal hypnosis”) is regulated by nervous influences analogous to sympathetic and parasympathetic influences in vertebrates. It was concluded that freshwater crayfish as a representative of the highly organized invertebrates can serve an effective model for studying mechanisms of sleep-like states and “animal hypnosis” in animals.     

Adaptation to infectious disease. Australia antigen and hepatitis

Infectious diseases have probably acted as selective forces to generate polymorphisms in human populations. An example is given of a study related to this concept. There is evidence that “Australia antigen” is a hepatitis virus or closely associated with it. In some tropical populations there appears to be an inherited susceptibility to chronic infection with “Au(1) virus” controlled by a simple genetic mechanism. There are strikingly different frequencies of Australia antigen in different populations and these may have been determined by differences in the selective pressures in different environments.     

Kinetic and inhibitor studies with arylsulfhydrolases A and B from avian and mammalian sources

Arylsulfhydrolases A and B from chicken and from bovine liver have been isolated and their reactions with a range of synthetic arylsulfates examined using kinetic methods. Some differences of Michaelis-Menten parameters were observed in comparing the A with the B forms from the two sources at the level of individual substrates. At that level also, interspecies comparisons of A forms and B forms similarly showed differences. However, for none of the four enzymes examined was there consistent correlations of kinetic values with electronic, hydrophobicity, or steric properties of the substrates. The bovine A enzyme displayed the well-documented “anomalous” kinetic behavior at high substrate concentrations; at low concentrations conventional hydrolysis of p-nitrocatechol sulfate occurred, except that there was evidence with this substrate and others of product inhibition. The avian A enzyme reacted normally over all substrate concentrations examined, but again product inhibition occurred. The mammalian but not the avian B enzyme was also clearly subject to product inhibition.     

Experimental analysis of the migration and differentiation of neuroblasts of the autonomic nervous system and of neurectodermal mesenchymal derivatives, using a biological cell marking technique

By isotopic and isochronic transplantations of fragments of quail neural tube into chick, it has been previously shown that enteric ganglion cells arise from the “vagal” (somites 1–7) and the “lumbo-sacral” (behind somite 28) levels of the neural crest, while the trunk region (somites 8–28) gives rise to orthosympathetic ganglion chain and adrenomedullary cells. The latter originate precisely from the neural crest corresponding to somites 18–24 (i.e., “adrenomedullary” level of the crest). Heterotopic transplantations of fragments of quail neural tube into chick have been carried out in the present work. When the “adrenomedullary” level of the quail neural tube is grafted into the “vagal” region of a chick, the crest cells colonize the gut and differentiate into enteric ganglia of Auerbach's and Meissner's plexi. If quail cephalic neural crest is transplanted in the “adrenomedullary” level of a chick, quail cells migrate into the suprarenal glands and differentiate into adrenomedullary cells. Mesectodermal cells migrate laterally, and differentiate into cartilage, dermis and connective tissues. Thus it appears that preferential pathways located at precise levels of the embryo lead crest cells to their definitive sites. On the other hand the differentiation of the autonomic neuroblasts is controlled by the environment in which crest cells are localized at the end of their migration. On the contrary, mesenchymal derivatives of the cephalic neural crest appear to be early determined since they differentiate according to their presumptive fate when transplanted into the trunk.     

Synthesis and Structural Studies of a Pentapeptide Sequence of Elastin. Poly (Val-Gly-Gly-Leu-Gly)

Abstract

Poly (Val-Gly-Gly-Leu-Gly), a polypeptide mimicking the physico-chemical properties of the glycine-rich regions of elastin, has been synthesized and studied both in solution and in the aggregated state. By comparison, also the conformation of different “monomeric” units has been investigated. The polymer showed increased disorder with respect to the “monomers”, the molecular conformation being accounted for by a more or less random collection of isolated β-turns. Nevertheless, in the solid state the polymer is able to adopt supramolecular structures reminiscent of those found for elastin.     

Protein kinase‐mediated signalling in priming: Immune signal initiation,propagation, and establishment of long‐term pathogen resistance in plants

“Priming” in plant phytopathology describes a phenomenon where the “experience” of primary infection by microbial pathogens leads to enhanced and beneficial protection of the plant against secondary infection. The plant is able to establish an immune memory, a state of systemic acquired resistance (SAR), in which the information of “having been attacked” is integrated with the action of “being prepared to defend when it happens again.” Accordingly, primed plants are often characterized by faster and stronger activation of immune reactions that ultimately result in a reduction of pathogen spread and growth. Prerequisites for SAR are (a) the initiation of immune signalling subsequent to pathogen recognition, (b) a rapid defence signal propagation from a primary infected local site to uninfected distal parts of the plant, and (c) a switch into an immune signal‐dependent establishment and subsequent long‐lasting maintenance of phytohormone salicylic acid‐based systemic immunity. Here, we provide a summary on protein kinases that contribute to these three conceptual aspects of “priming” in plant phytopathology, complemented by data addressing the role of protein kinases crucial for immune signal initiation also for signal propagation and SAR.     

Preparation and conformational characterization of Cr(III) hemoglobin

Chromium(III) substituted hemoglobin has been prepared. Circular dichroism spectra in the UV region have been recorded in the presence and absence of the allosteric affector inositol hexaphosphate. The reactivity with bromthymol blue and p-mercuribenzoate has been measured. All data indicate a T state (or T state-like) structure, whereas an R structure would be expected from the chromium stereochemistry. Similarities to cobalt(III) hemoglobin suggest that the chromium derivative also exists as an internal hemichrome. Thus, despite major tertiary structure differences, “denatured” hemichromes may have a quaternary structure quite similar to deoxyhemoglobin.     

New field of insect science: Research on the use of insect properties

In recent years, research on “insect properties” has been attracting much attention for industrial applications of insect technology. This is a new field of research that attempts to analyze specific physiological properties of insects to develop technology for helping humankind. The term “insect properties” has been used to refer to “specific biological functions of insects” since around 1986, and it is now widely accepted in Japan. From 1996, the National Institute of Sericultural and Entomological Science (NISES) promoted “Research for utilization of insect properties” as a “Center of Excellence (COE)” project funded by the Science and Technology Agency. At this point, a new research field called “Research for utilization of insect properties” was initiated, and this led to the recognition of this field by the academic community. In the 21st century, remarkable results, including the development of transgenic silkworms and the full decoding of the silkworm genome, have been achieved. It is expected that this advanced technology will be a powerful tool for progress of research on the use of insect properties. This review presents an overview of the current state of research on use of insect properties as a new technology.     

Comparison of oxygen consumption rates in minimally transformed BALB/3T3 and virus-transformed 3T3B-SV40 cells

In the recent years, bioenergetics of tumor cells and particularly cell respiration have been attracting great attention because of the involvement of mitochondria in apoptosis and growing evidence of the possibility to diagnose and treat cancer by affecting the system of oxidative phosphorylation in mitochondria. In the present work, a comparative study of oxygen consumption in 3T3B-SV40 cells transformed with oncovirus SV40 and parental BALB/3T3 cells was conducted. Such fractions of oxygen consumption as “phosphorylating” respiration coupled to ATP synthesis, “free” respiration not coupled to ATP synthesis, and “reserve” or hidden respiration observed in the presence of protonophore were determined. Maximal respiration was shown to be only slightly decreased in 3T3B-SV40 cells as compared to BALB/3T3. However, in the case of certain fractions of cellular respiration, the changes were significant. “Phosphorylating” respiration was found to be reduced to 54% and “reserve” respiration, on the contrary, increased up to 160% in virus-transformed 3T3B-SV40 cells. The low rate of “phosphorylating” respiration and high “reserve” respiration indicate that under normal incubation conditions the larger part of mitochondrial respiratory chains of the virus-transformed cells is in the resting state (i.e. there is no electron transfer to oxygen). The high “reserve” respiration is suggested to play an important role in preventing apoptosis of 3T3B-SV40 cells.     

The cultural construction of gendered bodies: Biology and metaphors of production and destruction*

One way of conceiving of the anthropological task is that of countering the degradations and “dehumanizations” of the “other” to which the species is prone by promoting “transcendent humanization.” However efficiently and professionally anthropologists gather their materials and form them into their ethnographic and ethnologic analyses, may not this “ethical impulse” be postulated as the “final cause” of our efforts? But what could such a sonorous phrase mean ? And what is its relationship to the systematic study of the “differences that make or do not make a difference” in culture to which anthropology has long been devoted? I will argue that it involves a dynamic of categories and that this dynamic is itself an object of systematic study. Recently, for example, some anthropologists have been writing “against culture,” seeing the culture concept and associated theory more as barriers than as benefits to pan‐human understanding. I will argue that this is an instance of “transcendent humanization.” One cannot but be sympathetic to the thrust and merits of this argument. But at the same time one wants to ask what implications it holds for the systematic study and understanding of the other. This article, then, examines some elementary vectors in the “dynamic of the categorical” involved in these and related recent debates which also may be seen in terms of transcendence and humanization: the debate over relativism and the recently emergent debate over “enlightenment mythmaking” in anthropology.     

Biological systems of cellular organization and their computer models

The interactions of self-organizing systems possessing at least two hierarchical levels with the environment are dealt with. The dynamical deliberations taking place at the lower level Q of the organism are modelled by a finite state controlled Markov chain. The transitional probability matrix is parametrized on control variables which are related to the probabilities of “pay off” in an underlying two-agent “game” described in the paper.The environment is envisaged as another Markov chain with fixed transitional probabilities. The higher hierarchical level W plays the role of a controller which receives from the lower level Q collective properties which measure (a) the percentage of occupancy of a “homeostatic” state and (b) the cross-correlation between the dynamical processes at the level Q and the environment.The design of the controller is set up as a two-objective control problem having to do with the maximization of the long term average of an appropriately weighted sum of the conflicting terms: probability of the homeostatic state and cross-correlation with the environment.Optimal strategies are found through computing simulation which determine the efferent controls precipitated from the level W to the level Q. The relevance of the model to a number of problems related to the adaptability of hierarchical structures is discussed. Finally some extentions of the present work to do with the communication process between two multihierarchical systems are mentioned.     

Hypothesis test for causal explanations in human pathology: evaluation of pulmonary edema in 181 autopsied patients with leukemia

Symbolic logic, as used in the formal theory of scientific explanation proposed by Hempel and Oppenheim, has been suggested as the basis for automated medical diagnosis. In human autopsy pathology the determination of cause-and-effect relationships is a major area subject to logical analysis. We propose a modification of the Hempel-Oppenheim schema in which the logical relationships must only be satisfied “much” of the time, as determined by binomial significance tests. The analysis employs “certainty levels” logic with a more limited consistency requirement than classical logic. The analysis is applied to a series of 181 autopsied patients with leukemia in an attempt to determine a possible role of chemotherapeutic agents in the etiology of pulmonary edema. Among 51 patients who had received cytosine arabinoside (Ara-C) within 30 days of death, there was significantly more unexplained moderate or massive pulmonary edema than among patients with no or remote therapy (p<0.001). The results suggest that a symbolic logical analysis combined with a binomial significance test can elucidate cause-and-effect relationships observed at autopsy, especially when there are multiple possible explanations for the same effect.     

Differential effects of several “litter” types on the germination of dry grassland species

Question: Accumulation of litter can have serious implications on the recruitment of plant species, by modifying the physical, biological and chemical features of the microenvironment or acting as a mechanical barrier for seeds and seedlings. Isolating these different effects has rarely been achieved experimentally. Location: Transylvanian Lowland, Romania. Methods: We tested the effects of different “litter” types on the germination of dry grassland species using a controlled pot experiment with three natural litter types, differing in decay state and composition (Stipa pulcherrima fresh leaves, partly decomposed leaves and mixed and partly decomposed plant material) and an artificial plastic litter, with two levels of water addition. As a complementary field study, seed sowing was conducted in grassland plots with litter removal and plastic litter application. Results: Litter effects were mainly positive (intermittent watering) or neutral (frequent watering) under controlled experimental conditions, and mostly negative in the field. Seed size and environmental conditions were the major determinants of litter effects on germination. Significant differences were found in the effect of litter type on germination, much of which could be explained by chemical factors determined by the decay state, as we confirmed a higher concentration of allelopathic compounds in fresh S. pulcherrima litter than in the senescing leaf litter. Conclusions: The effects of litter on seed germination are strongly context dependent, and it is hard to define common rules that apply consistently under various environmental conditions. “Litter” identity and quality matter, i.e. the litter composition and decay state, and influence seed germination.