Improvement of heme oxygenase-1-based heme sensor for quantifying free heme in biological samples

We recently reported a novel heme sensor using fluorescently labeled heme oxygenase-1; however, its inherent enzyme activity would be a potential obstacle in quantifying heme in biological samples. Here, we found that mutation of the catalytically important residue, Asp140, with histidine in the sensor not only diminished the heme degradation activity but also increased heme binding affinity. The sensor with a visible fluorophore was also found to be beneficial to avoid background emission from endogenous substance in biological samples. By using the improved heme sensor, we succeeded in quantifying free heme in rat hepatic samples for the first time.     

On the physico-chemical basis of voltage-dependent molecular gating mechanisms in biological membranes

Summary The possible nature and theoretical treatment of electric field-induced molecular processes in a membrane are examined. Special attention is given to fairly fast switching phenomena as reflected by asymmetry currents as well as ionic gating in squid axon and similar systems. The apparent charge displacement associated with the underlying mechanisms is argued to be brought about by conformational transitions of integral macromolecular structures. Under these circumstances, voltage changes can actually control the functional state of membranes by direct interference with conformational equilibria. A basic model is quantitatively discussed and shown to account for certain observed asymmetry currents. Effects due to temperature, pressure, or chemical interactions can be readily described. It is indicated how more complicated voltage-dependent membrane processes may be approached along these lines.     

Recent advances in the microgravity crystallization of biological macromolecules

The status of microgravity research in the crystallization of biological macromolecules is presented. Currently, two paths of investigation are being undertaken. The first is the production of high-quality crystals in space for biotechnology and research applications. The second is the study of the mechanisms by which these superior crystals are formed in microgravity. Emphasis is also placed on macromolecules and the exploration of the flash-frozen-samples-Dewar approach for multiple crystallizations. Future space flight opportunities to continue this research are discussed.     

Arbuscular mycorrhizas and biological control of soil-borne plant pathogens – an overview of the mechanisms involved

 Biological control of plant pathogens is currently accepted as a key practice in sustainable agriculture because it is based on the management of a natural resource, i.e. certain rhizosphere organisms, common components of ecosystems, known to develop antagonistic activities against harmful organisms (bacteria, fungi, nematodes etc.). Arbuscular mycorrhizal (AM) associations have been shown to reduce damage caused by soil-borne plant pathogens. Although few AM isolates have been tested in this regard, some appear to be more effective than others. Furthermore, the degree of protection varies with the pathogen involved and can be modified by soil and other environmental conditions. This prophylactic ability of AM fungi could be exploited in cooperation with other rhizospheric microbial angatonists to improve plant growth and health. Despite past achievements on the application of AM in plant protection, further research is needed for a better understanding of both the ecophysiological parameters contributing to effectiveness and of the mechanisms involved. Although the improvement of plant nutrition, compensation for pathogen damage, and competition for photosynthates or colonization/infection sites have been claimed to play a protective role in the AM symbiosis, information is scarce, fragmentary or even controversial, particularly concerning other mechanisms. Such mechanisms include (a) anatomical or morphological AM-induced changes in the root system, (b) microbial changes in rhizosphere populations of AM plants, and (c) local elicitation of plant defence mechanisms by AM fungi. Although compounds typically involved in plant defence reactions are elicited by AM only in low amounts, they could act locally or transiently by making the root more prone to react against pathogens. Current research based on molecular, immunological and histochemical techniques is providing new insights into these mechanisms. Accepted: 29 October 1996     

Characterization of heme ligation properties of Rv0203, a secreted heme binding protein involved in Mycobacterium tuberculosis heme uptake

The secreted Mycobacterium tuberculosis (Mtb) heme binding protein Rv0203 has been shown to play a role in Mtb heme uptake. In this work, we use spectroscopic (absorption, electron paramagnetic resonance, and magnetic circular dichrosim) methods to further characterize the heme coordination environments of His-tagged and native protein forms, Rv0203-His and Rv0203-notag, respectively. Rv0203-His binds the heme molecule through bis-His coordination and is low-spin in both ferric and ferrous oxidation states. Rv0203-notag is high-spin in both oxidation states and shares spectroscopic similarity with pentacoordinate oxygen-ligated heme proteins. Mutagenesis experiments determined that residues Tyr59, His63, and His89 are required for Rv0203-notag to efficiently bind heme, reinforcing the hypothesis based on our previous structural and mutagenesis studies of Rv0203-His. While Tyr59, His63, and His89 are required for the binding of heme to Rv0203-notag, comparison of the absorption spectra of the Rv0203-notag mutants suggests the heme ligand may be the hydroxyl group of Tyr59, although an exogenous hydroxide cannot be ruled out. Additionally, we measured the heme affinities of Rv0203-His and Rv0203-notag using stopped flow techniques. The rates for binding of heme to Rv0203-His and Rv0203-notag are similar, 115 and 133 μM(-1) s(-1), respectively. However, the heme off rates differ quite dramatically, whereby Rv0203-His gives biphasic dissociation kinetics with fast and slow rates of 0.0019 and 0.0002 s(-1), respectively, and Rv0203-notag has a single off rate of 0.082 s(-1). The spectral and heme binding affinity differences between Rv0203-His and Rv0203-notag suggest that the His tag interferes with heme binding. Furthermore, these results imply that the His tag has the ability to stabilize heme binding as well as alter heme ligand coordination of Rv0203 by providing an unnatural histidine ligand. Moreover, the heme affinity of Rv0203-notag is comparable to that of other heme transport proteins, implying that Rv0203 may act as an extracellular heme transporter.     

Eclectic mechanisms of heme regulation of hematopoiesis

Regulatory features of heme (ferroprotoporphyrin IX) on hematopoietic growth/differentiation and related processes are reviewed. It is emphasized that expressions of specific erythroid and nonerythroid heme biosynthetic and degradatory enzymes are required, and the regulatory processes whereby this occurs is considered. The specificity of heme, relationship to cellular events such as differentiation, response to growth factors, oncogene and receptor expression, and how heme counteracts toxic effects such as viral growth are all discussed. The significance of heme in the hemopoietic bone marrow microenvironment and growth factor network are considered. Finally, the third pathway for arachidonic acid metabolism via the heme-cytochrome P450 monooxygenase system, in addition to cyclooxygenase and lipoxygenase, by bone marrow adherent cells and its role in cellular differentiation is briefly reviewed.     

Lysine-specific gingipain K and heme/hemoglobin receptor HmuR are involved in heme utilization in Porphyromonas gingivalis

We have previously reported on the identification and characterization of the Porphyromonas gingivalis A7436 strain outer membrane receptor HmuR, which is involved in the acquisition of hemin and hemoglobin. We demonstrated that HmuR interacts with the lysine- (Kgp) and arginine- (HRgpA) specific proteases (gingipains) and that Kgp and HRgpA can bind and degrade hemoglobin. Here, we report on the physiological significance of the HmuR-Kgp complex in heme utilization in P. gingivalis through the construction and characterization of a defined kgp mutant and a hmuR kgp double mutant in P. gingivalis A7436. The P. gingivalis kgp mutant exhibited a decreased ability to bind both hemin and hemoglobin. Growth of this strain with hemoglobin was delayed and its ability to utilize hemin as a sole iron source was diminished as compared to the wild type strain. Inactivation of both the hmuR and kgp genes resulted in further decreased ability of P. gingivalis to bind hemoglobin and hemin, as well as diminished ability to utilize either hemin or hemoglobin as a sole iron source. Collectively, these in vivo results further confirmed that both HmuR and Kgp are involved in the utilization of hemin and hemoglobin in P. gingivalis A7436.     

Vestibular mechanisms involved in idiopathic scoliosis

Patients affected by idiopathic scoliosis (IS) show not only a spinal deformity, but also postural and oculomotor deficits suggesting that such syndrome can be related to a vestibular disfunction. It appears, however, that, in children, a slight unbalance in the activity of vestibular complex of both sides escapes the neuronal mechanisms responsible for vestibular compensation and leads to the spinal curvature which characterises IS. Such process could be reinforced by a disrupted integration of vestibular and visual signals at cortical level, leading to an altered perception of the vertical and to abnormal motor commands. In addition to the classical ascending and descending pathways arising from the vestibular nuclei, which utilize glutamate or GABA as neurotransmitters, labyrinthine afferents may also affect spinal, cerebellar and cerebrocortical structures, through the noradrenergic and serotoninergic systems, which originate from the locus coeruleus and the raphe nuclei, respectively. Due to the role of these neuromodulators in brain plasticity, a disruption in the activity of monoaminergic neurons could favour the development of postural and oculomotor deficits. An impaired release of monoamine at cerebrocortical level could also explain the cognitive deficits which may occur in IS patients.     

The DOMON domains are involved in heme and sugar recognition

We expand the functionally uncharacterized DOMON domain superfamily to identify several novel families, including the first prokaryotic representatives. Using several computational tools we show that it is involved in ligand binding--either as heme- or sugar-binding domains. We present evidence that the DOMON domain along with the DM13 domain comprises a novel electron-transfer system potentially involved in oxidative modification of animal cell-surface proteins. Other novel versions might function as sugar sensors of histidine kinases of bacterial two component systems. Supplementary information: Supplementary data are available at Bioinformatics online and also at ftp://ftp.ncbi.nih.gov/pub/aravind/domon/.     

Neural mechanisms involved in pituitary control

The final common pathway of hypothalamo-hypophyseal regulation is composed of neurosecretory neurons elaborating over 20 different neurotransmitters or neuropeptides. Cell bodies of these neurons are located in four major hypothalamic structures (supraoptic and paraventricular nuclei, the preoptic hypothalamic area, and the arcuate-ventromedial region). Their axons build up the tuberoinfundibular bundle, which innervates the median eminence and the posterior pituitary. In those structures, neurosecretory nerve terminals release their secretion product into a microcirculation across neurovascular junctions. Each of the five adenohypophyseal cell types, as well as secretory cells of the intermediate lobe, express specific receptors for several neurotransmitters, many of which are colocalised in the same neuron. In addition, most pituitary neuropeptide receptors are located on more than one cell type. Consequently, pituitary secretion is controlled by multiple neural signals.

Integration of these signals by the cell is achieved by reciprocal interactions between receptor coupling mechanisms. Those involve protein complexes which activate or inhibit adenylate cyclase, as well as mediation by phospholipases. Depending upon its particular mode of coupling, each transmitter-receptor complex can determine activation of phospholipase A or C, phosphoinositide-induced opening of Ca²⁺ channels, or formation of arachidonic acid, a precursor of prostaglandins and leukotrienes. The present chapter reviews the cellular distribution and the coupling pathways of major neural signals driving pituitary functions, and discusses the functional consequences of reciprocal interactions between adenylate cyclase and phospholipase modulation.     

Roles of water in heme peroxidase and catalase mechanisms

A water molecule is coproduced with the Compound I intermediate in the reactions of native heme peroxidases and catalases with hydrogen peroxide. As a result of water release/rebinding from/to the coproduct formation site the Compound I intermediate may exist in two forms: a "wet" form, Compound I(H(2)O), in which a water molecule is present at or near the site of coproduct water formation, and Compound I, in which the coproduct water formation site is "dry." It is postulated that the absence or presence of a water molecule at this site provides the structural basis for a redox pathway switching mechanism, such that the transition states for 2-electron equivalent reduction of Compound I intermediates are accessible in the dry form, but that in the wet form only 1-electron equivalent processes are possible, unless release of water can be stimulated. This concept provides the basis of a general mechanism in which the classical functional distinction between catalases and peroxidases, as well as the more complex behavior observed in halide oxidation and halogenation reactions, appear as particular cases in which variations in the degree of retention of water at the coproduct formation site influence Compound I reactivity.     

On the stationary state analysis of reaction-diffusion mechanisms for biological pattern formation

We present a biologically plausible two-variable reaction-diffusion model for the developing vertebrate limb, for which we postulate the existence of a stationary solution. A consequence of this assumption is that the stationary state depends on only a single concentration-variable. Under these circumstances, features of potential biological significance, such as the dependence of the steady-state concentration profile of this variable on parameters such as tissue size and shape, can be studied without detailed information about the rate functions. As the existence and stability of stationary solutions, which must be assumed for any biochemical system governing morphogenesis, cannot be investigated without such information, an analysis is made of the minimal requirements for stable, stationary non-uniform solutions in a general class of reaction-diffusion systems. We discuss the strategy of studying stationary-state properties of systems that are incompletely specified. Where abrupt transitions between successive compartment-sizes occur, as in the developing limb, we argue that it is reasonable to model pattern reorganization as a sequence of independent stationary states.     

Decarboxylation mechanisms in biological system

This review examines the mechanisms propelling cofactor-independent, organic cofactor-dependent and metal-dependent decarboxylase chemistry. Decarboxylation, the removal of carbon dioxide from organic acids, is a fundamentally important reaction in biology. Numerous decarboxylase enzymes serve as key components of aerobic and anaerobic carbohydrate metabolism and amino acid conversion. In the past decade, our knowledge of the mechanisms enabling these crucial decarboxylase reactions has continued to expand and inspire. This review focuses on the organic cofactors biotin, flavin, NAD, pyridoxal 5′-phosphate, pyruvoyl, and thiamin pyrophosphate as catalytic centers. Significant attention is also placed on the metal-dependent decarboxylase mechanisms.     

On the crystallization of proteins

We report on theoretical and experimental work aimed at a systematic approach to the crystallization of proteins. Successful crystallization depends on the competition between the growth rates for compact three-dimensional structures and long-chain structures leading to an amorphous precipitate. Quasi-elastic light scattering was used to monitor the size and shape distribution of small aggregates in a model system (lysozyme) during the pre-nucleation stage. With the aid of a simple model, the line-width of the scattered light was used to predict whether crystals or an amorphous precipitate would result. Once visible crystals appeared, the lysozyme concentration near the crystal surface was monitored and the kinetic parameters for growth obtained. A peculiar self-limiting phenomenon causes crystals to stop growing after a certain size has been reached. When these terminal size crystals were cleaved, growth occurred at the surface until the original size was approximately restored.     

Zinc protoporphyrin IX binds heme crystals to inhibit the process of crystallization in Plasmodium falciparum

The intraerythrocytic Plasmodium falciparum parasite converts most of host hemoglobin heme into a nontoxic heme crystal. Erythrocyte zinc protoporphyrin IX, normally present at 0.5 microM, which is a ratio of 1:40,000 hemes, can elevate 10-fold in some of the anemias associated with malaria disease protection. This work examines a binding mechanism for zinc protoporphyrin IX inhibition of heme crystallization similar to the antimalarial quinolines. Zinc protoporphyrin IX neither forms crystals alone nor extends on preformed heme crystals. Inhibition of both seed heme crystal formation and crystal extension occurs with an inhibitory concentration (IC)50 of 5 microM. Field emission in-lens scanning electron microscopy depicts the transition and inhibition of heme monomer aggregates to heme crystals with and without seeding of preformed hemozoin templates. In vitro zinc protoporphyrin IX, like the quinolines, binds to heme crystals in a saturable, specific, pH, and time-dependent manner. The ratio at saturation is approximately 1 zinc protoporphyrin IX per 250 hemes of the crystal. Unlike the quinolines, zinc protoporphyrin IX binds measurably in the absence of heme. Isolated ring and trophozoite stage parasites have an elevated zinc protoporphyrin IX to heme ratio 6 to 10 times that in the erythrocyte cytosol, which also corresponds to elevated ratios found in heme crystals purified from Plasmodium parasites. This work implicates protection from malaria by a mechanism where elevated zinc protoporphyrin IX in anemic erythrocytes binds to heme crystals to inhibit further crystallization. In endemic malaria areas, severe iron deficiency anemia should be treated with antimalarials along with iron replenishment.