The Q-cycle reviewed: How well does a monomeric mechanism of the bc1 complex account for the function of a dimeric complex?

Recent progress in understanding the Q-cycle mechanism of the bc₁ complex is reviewed. The data strongly support a mechanism in which the Q_o-site operates through a reaction in which the first electron transfer from ubiquinol to the oxidized iron–sulfur protein is the rate-determining step for the overall process. The reaction involves a proton-coupled electron transfer down a hydrogen bond between the ubiquinol and a histidine ligand of the [2Fe–2S] cluster, in which the unfavorable protonic configuration contributes a substantial part of the activation barrier. The reaction is endergonic, and the products are an unstable ubisemiquinone at the Q_o-site, and the reduced iron–sulfur protein, the extrinsic mobile domain of which is now free to dissociate and move away from the site to deliver an electron to cyt c₁ and liberate the H⁺. When oxidation of the semiquinone is prevented, it participates in bypass reactions, including superoxide generation if O₂ is available. When the b-heme chain is available as an acceptor, the semiquinone is oxidized in a process in which the proton is passed to the glutamate of the conserved -PEWY- sequence, and the semiquinone anion passes its electron to heme b_L to form the product ubiquinone. The rate is rapid compared to the limiting reaction, and would require movement of the semiquinone closer to heme b_L to enhance the rate constant. The acceptor reactions at the Q_i-site are still controversial, but likely involve a “two-electron gate” in which a stable semiquinone stores an electron. Possible mechanisms to explain the cyt b₁₅₀ phenomenon are discussed, and the information from pulsed-EPR studies about the structure of the intermediate state is reviewed.The mechanism discussed is applicable to a monomeric bc₁ complex. We discuss evidence in the literature that has been interpreted as shown that the dimeric structure participates in a more complicated mechanism involving electron transfer across the dimer interface. We show from myxothiazol titrations and mutational analysis of Tyr-199, which is at the interface between monomers, that no such inter-monomer electron transfer is detected at the level of the b_L hemes. We show from analysis of strains with mutations at Asn-221 that there are coulombic interactions between the b-hemes in a monomer. The data can also be interpreted as showing similar coulombic interaction across the dimer interface, and we discuss mechanistic implications.     

The Q-cycle reviewed: How well does a monomeric mechanism of the bc(1) complex account for the function of a dimeric complex?

Recent progress in understanding the Q-cycle mechanism of the bc(1) complex is reviewed. The data strongly support a mechanism in which the Q(o)-site operates through a reaction in which the first electron transfer from ubiquinol to the oxidized iron-sulfur protein is the rate-determining step for the overall process. The reaction involves a proton-coupled electron transfer down a hydrogen bond between the ubiquinol and a histidine ligand of the [2Fe-2S] cluster, in which the unfavorable protonic configuration contributes a substantial part of the activation barrier. The reaction is endergonic, and the products are an unstable ubisemiquinone at the Q(o)-site, and the reduced iron-sulfur protein, the extrinsic mobile domain of which is now free to dissociate and move away from the site to deliver an electron to cyt c(1) and liberate the H(+). When oxidation of the semiquinone is prevented, it participates in bypass reactions, including superoxide generation if O(2) is available. When the b-heme chain is available as an acceptor, the semiquinone is oxidized in a process in which the proton is passed to the glutamate of the conserved -PEWY- sequence, and the semiquinone anion passes its electron to heme b(L) to form the product ubiquinone. The rate is rapid compared to the limiting reaction, and would require movement of the semiquinone closer to heme b(L) to enhance the rate constant. The acceptor reactions at the Q(i)-site are still controversial, but likely involve a "two-electron gate" in which a stable semiquinone stores an electron. Possible mechanisms to explain the cyt b(150) phenomenon are discussed, and the information from pulsed-EPR studies about the structure of the intermediate state is reviewed. The mechanism discussed is applicable to a monomeric bc(1) complex. We discuss evidence in the literature that has been interpreted as shown that the dimeric structure participates in a more complicated mechanism involving electron transfer across the dimer interface. We show from myxothiazol titrations and mutational analysis of Tyr-199, which is at the interface between monomers, that no such inter-monomer electron transfer is detected at the level of the b(L) hemes. We show from analysis of strains with mutations at Asn-221 that there are coulombic interactions between the b-hemes in a monomer. The data can also be interpreted as showing similar coulombic interaction across the dimer interface, and we discuss mechanistic implications.     

How well does cholesteryl hemisuccinate mimic cholesterol in saturated phospholipid bilayers?

Journal of Molecular Modeling - We studied the doping effects on the electronic and structural properties of graphene upon interaction with phenol. Calculations were performed within the periodic...     

How well does Turing's theory of morphogenesis work?

In 1952 Turing published a paper which showed how under restricted conditions a class of chemical reactions could give biological patterns in diffusion-coupled cells. Although this theory has been much discussed, little has been learnt about the range and type of pattern it can generate. In order to do this and to see how stable the patterns are, we have examined the system in detail and written a computer program to simulate Turing's kinetics for two morphogens over various assemblies of cells. We find that on one-dimensional lines of cells, patterns can indeed be produced and that the chemical wavelengths follow all of Turing's predictions. The results show that stable repeating peaks of chemical concentration of periodicity 2–20 cells can be obtained in embryos in periods of time of less than an hour. We do find however that these patterns are not reliable: small variations in initial conditions give small but significant changes in the number and positions of observed peaks. Similar results are observed in two-dimensional assemblies of cells. On rectangles, random blotches are observed whose position cannot be reliably predicted. On cylinders whose circumference is less than the chemical wavelength, annular stripes are produced. For larger cylinders, blotches that lie very approximately on helices are generated; again sharp prediction of the detailed pattern is impossible.The significance of these results for the developing embryo is discussed. We conclude that Turing kinetics, at least in the simple cases that we have studied, are too unreliable to serve as the generating mechanism for features such as digits which are characterized by a consistent number of units. The theory is however more than adequate by these criteria to specify less well-defined developing patterns such as those of hair follicles or leaf organization. It is emphasized however that the Turing theory is quite unable to generate regulative systems, only mosaicpatterns can be produced.     

How to account for habitat suitability in weed management programmes?

Designing efficient management strategies for already established invasive alien species is challenging. Here, we ask whether environmental suitability, as predicted by species distribution models, is a useful basis of cost-effective spatial prioritization in large-scale surveillance and eradication programmes. We do so by means of spatially and temporarily explicit simulations of the spread of a case study species (Ambrosia artemisiifolia L.) in Austria and southern Germany under different management regimes. We ran these simulations on a contiguous grid of the study area with each grid cell (~35 km²) characterized by a habitat suitability value derived from the predictions of a species distribution model. The management regimes differed in terms of (a) a minimum habitat suitability rank p (suitability threshold) used to separate cells for surveillance from those which are not controlled; and (b) the strategy for selecting cells for annual campaigns from the pool defined by p. According to the results (i.e., number of cells infested in 2050 as well as infested on average per year) the most efficient way to base surveillance on suitability is to define the temporal sequence of management according to the grid cells’ suitability ranks. Management success declines sharply when the suitability threshold is set too high, but only moderately when it is set too low. We conclude that accounting for environmental suitability is important for large-scale management programmes of invasive alien species and that species distribution models are hence useful tools for designing such programmes.     

How does a hypha grow? The biophysics of pressurized growth in fungi

The mechanisms underlying the growth of fungal hyphae are rooted in the physical property of cell pressure. Internal hydrostatic pressure (turgor) is one of the major forces driving the localized expansion at the hyphal tip which causes the characteristic filamentous shape of the hypha. Calcium gradients regulate tip growth, and secretory vesicles that contribute to this process are actively transported to the growing tip by molecular motors that move along cytoskeletal structures. Turgor is controlled by an osmotic mitogen-activated protein kinase cascade that causes de novo synthesis of osmolytes and uptake of ions from the external medium. However, as discussed in this Review, turgor and pressure have additional roles in hyphal growth, such as causing the mass flow of cytoplasm from the basal mycelial network towards the expanding hyphal tips at the colony edge.     

How does visual thinking work in the mind of a person with autism? A personal account

My mind is similar to an Internet search engine that searches for photographs. I use language to narrate the photo-realistic pictures that pop up in my imagination. When I design equipment for the cattle industry, I can test run it in my imagination similar to a virtual reality computer program. All my thinking is associative and not linear. To form concepts, I sort pictures into categories similar to computer files. To form the concept of orange, I see many different orange objects, such as oranges, pumpkins, orange juice and marmalade. I have observed that there are three different specialized autistic/Asperger cognitive types. They are: (i) visual thinkers such as I who are often poor at algebra, (ii) pattern thinkers such as Daniel Tammet who excel in math and music but may have problems with reading or writing composition, and (iii) verbal specialists who are good at talking and writing but they lack visual skills.     

Evaluation of binding and antagonism/downregulation of brilanestrant molecule in estrogen receptor-α via quantum mechanics/molecular mechanics,molecular dynamics and binding free energy calculations

Abstract

The resistance to the endocrine therapy of breast cancer leads to the emergence of new class of drugs that downregulates the estrogen receptor action known as selective estrogen receptor downregulators (SERDs). The first approved SERD is fluvestrant; after this, there are several downregulators evolved and are in clinical trials, in which the brilanestrant (BRI) molecule shows nM range of binding affinity and efficacy. In the present study, to understand the binding nature of BRI molecule in the active site of ERα, the molecular docking analysis has been performed. Further, the QM/MM calculations were performed for the BRI–ERα complex to analyze the charge density distribution of intermolecular interactions. The molecular dynamics (MD) simulation was employed to understand the stability and binding mechanism of BRI molecule through root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF) and binding free energy calculations. From the MD simulation trajectory analysis, the alterations of Helix12 conformation and the key residue (Lys529), which is responsible for the ERα downregulation, have been identified. Further, the interaction between the H3 and H12 regions was identified for the antagonism of BRI molecule. The current study led us to understand the binding mechanism, antagonism and downregulation of BRI molecule, and this knowledge is essential to design novel SERDs for the treatment of endocrine-resistant positive breast cancer.

Communicated by Ramaswamy H. Sarma     

How well does a commercially available wearable device measure sleep in young athletes?

ABSTRACT

The validity of a commercially available wearable device for measuring total sleep time was examined in a sample of well-trained young athletes during night-time sleep periods and daytime naps. Participants wore a FitBit HR Charge on their non-dominant wrist and had electrodes attached to their face and scalp to enable polysomnographic recordings of sleep in the laboratory. The FitBit automatically detected 24/30 night-time sleep periods but only 6/20 daytime naps. Compared with polysomnography, the FitBit overestimated total sleep time by an average of 52 ± 152 min for night-time sleep periods, and by 4 ± 8 min for daytime naps. It is important for athletes and practitioners to be aware of the limitations of wearable devices that automatically detect sleep duration.     

How does endothelial cell injury start? The role of endothelin in systemic sclerosis

A considerable amount of research time has been invested in studies aimed at elucidating pathogenic processes in systemic sclerosis (SSc). Despite this, major challenges for biomedical science remain, such as identification of the key factors that determine susceptibility to SSc, and elucidation of the precise nature of the initiating event that causes endothelial cell injury and ultimately brings about the biological cascade(s) that lead to the pathologic vascular changes. Involved factors are likely to include genetic perturbations, environmental cues, tissue injury, infection and hypoxia/oxidative stress. As important as determining the initiating events are the identification and characterization of key factors that are functionally important in driving vascular disease progression, because these factors are potential targets for therapeutic intervention. This article reviews the role of endothelin as an example of a pleiotropic mediator with effects on various aspects of SSc pathogenesis, such as inflammation, vasculopathy and tissue remodelling.     

Integration of omics data: how well does it work for bacteria?

In the current omics era, innovative high-throughput technologies allow measuring temporal and conditional changes at various cellular levels. Although individual analysis of each of these omics data undoubtedly results into interesting findings, it is only by integrating them that gaining a global insight into cellular behaviour can be aimed at. A systems approach thus is predicated on data integration. However, because of the complexity of biological systems and the specificities of the data-generating technologies (noisiness, heterogeneity, etc.), integrating omics data in an attempt to reconstruct signalling networks is not trivial. Developing its methodologies constitutes a major research challenge. Besides for their intrinsic value towards health care, environment and industry, prokaryotes are ideal model systems to further develop these methods because of their lower regulatory complexity compared with eukaryotes, and the ease with which they can be manipulated. Several successful examples outlined in this review already show the potential of the systems approach for both fundamental and industrial applications, which would be time-consuming or impossible to develop solely through traditional reductionist approaches.     

The myosin filament superlattice in the flight muscles of flies: A-band lattice optimisation for stretch-activation?

Low-angle X-ray diffraction patterns from relaxed fruitfly (Drosophila) flight muscle recorded on the BioCat beamline at the Argonne Advanced Photon Source (APS) show many features similar to such patterns from the "classic" insect flight muscle in Lethocerus, the giant water bug, but there is a characteristically different pattern of sampling of the myosin filament layer-lines, which indicates the presence of a superlattice of myosin filaments in the Drosophila A-band. We show from analysis of the structure factor for this lattice that the sampling pattern is exactly as expected if adjacent four-stranded myosin filaments, of repeat 116 nm, are axially shifted in the hexagonal A-band lattice by one-third of the 14.5 nm axial spacing between crowns of myosin heads. In addition, electron micrographs of Drosophila and other flies (e.g. the house fly (Musca) and the flesh fly (Sarcophaga)) combined with image processing confirm that the same A-band superlattice occurs in all of these flies; it may be a general property of the Diptera. The different A-band organisation in flies compared with Lethocerus, which operates at a much lower wing beat frequency (approximately 30 Hz) and requires a warm-up period, may be a way of optimising the myosin and actin filament geometry needed both for stretch activation at the higher wing beat frequencies (50 Hz to 1000 Hz) of flies and their need for a rapid escape response.     

The molecular and cellular basis of pathogenesis in melioidosis: how does Burkholderia pseudomallei cause disease?

Melioidosis, a febrile illness with disease states ranging from acute pneumonia or septicaemia to chronic abscesses, was first documented by Whitmore & Krishnaswami (1912) . The causative agent, Burkholderia pseudomallei , was subsequently identified as a motile, gram-negative bacillus, which is principally an environmental saprophyte. Melioidosis has become an increasingly important disease in endemic areas such as northern Thailand and Australia ( Currie et al. , 2000 ). This health burden, plus the classification of B. pseudomallei as a category B biological agent ( Rotz et al. , 2002 ), has resulted in an escalation of research interest. This review focuses on the molecular and cellular basis of pathogenesis in melioidosis, with a comprehensive overview of the current knowledge on how B. pseudomallei can cause disease. The process of B. pseudomallei movement from the environmental reservoir to attachment and invasion of epithelial and macrophage cells and the subsequent intracellular survival and spread is outlined. Furthermore, the diverse assortment of virulence factors that allow B. pseudomallei to become an effective opportunistic pathogen, as well as to avoid or subvert the host immune response, is discussed. With the recent increase in genomic and molecular studies, the current understanding of the infection process of melioidosis has increased substantially, yet, much still remains to be elucidated.     

How does small-scale fragmentation affect litter-dwelling ants? The role of isolation

Remnant isolation following fragmentation is considered to be one of the main drivers of ecological decline in modified landscapes. Thereby, connecting remnants using ecological corridors has been increasingly suggested as being important for conservation. Our objectives were to test isolation effects on extinction, colonization and turnover rates of a litter-dwelling ant assemblage, and to evaluate effectiveness of ecological corridors to mitigate habitat fragmentation consequences. We used a mesocosm manipulative design, with three different isolation treatments: far, near and near connected by a corridor, sampled fortnightly for 60?days. Fragmentation caused an ongoing decrease in ant species richness, probably due to a negative balance between extinction and colonization. Extinction was steady with time, while colonization decreased over the same period. This outcome highlights the key role that colonization plays in the persistence of populations of litter-dwelling ants. Turnover rates increased with time in the treatment with a corridor, but remained steady in the other treatments. We conclude that corridors are important for not only immigration to remnants, but also emigration, acting as a two way traffic route. Thus, it may be an important “leakage” point for threatened species, with implications for their conservation status.     

Sperm storage in the vertebrate female reproductive tract: How does it work so well?

The capacity for sperm storage within the female reproductive tract occurs widely across all groups of vertebrate species and is exceptionally well developed in some reptiles (maximum duration, 7 yr) and fish (maximum duration, >1 yr). Amphibians (most salamanders and one species of frog; duration approximately 5 mo), all birds examined to date and some bats, have also evolved the ability to store spermatozoa in the female reproductive tract. Although there are many reports on both the occurrence of female sperm storage and its adaptive benefits, few studies have been directed toward explaining the mechanisms involved. Phylogenetic evidence suggests that the capacity for sperm storage has evolved independently within different taxonomic groups, and it is by no means clear whether these groups have established similar or different mechanisms or whether simple and common principles have been exploited during evolution. If the process has indeed developed by the invention of numerous different and species-specific mechanisms, it is surprising that none have yet been elucidated by technologists wishing to improve the long-term storage of fresh semen. On the other hand, if there is a simple and common solution to the problem, readily accessed by diverse groups of species, it is equally logical to suppose that the mechanism should be easily discovered in the laboratory. While recognizing that studies on wild species are usually neither practically or ethically easy to undertake, it is clear that there is a huge and largely unexplored field to be investigated.     

How does vestibule surface charge affect ion conduction and toxin binding in a sodium channel?

We describe various models for the dielectric geometry and pore mouth charge distribution of a Na channel. The electric potential due to the vestibule charges is then computed on the basis of the nonlinear Possion-Boltzmann equation. The results are used to account for the effect of permeant ion concentration and ionic strength on channel conductance and on toxin association rate constants for Na channels. We find that a single negatively charged group near the entrance to the channel constriction is adequate to account for deviations from Michaelis-Menten conductance kinetics and for the concentration dependence of toxin-binding coefficients. We find further that only a limited range of vestibule geometries and pore mouth charge distributions are consistent with experiment.     

The mitochondrial permeability transition pore (PTP) - an example of multiple molecular exaptation?

The mitochondrial permeability transition (PT) is a well-recognized phenomenon that allows mitochondria to undergo a sudden increase of permeability to solutes with molecular mass ≤ 1500Da, leading to organelle swelling and structural modifications. The relevance of PT relies on its master role in the manifestation of programmed cell death (PCD). This function is performed by a mega-channel (in some cases inhibited by cyclosporin A) named permeability transition pore (PTP), whose function could derive from the assembly of different mitochondrial proteins. In this paper we examine the distribution and characteristics of PTP in mitochondria of eukaryotic organisms so far investigated in order to draw a hypothesis on the mechanism of its evolution. As a result, we suggest that PTP may have arisen as a new function linked to a multiple molecular exaptation of different mitochondrial proteins, even though they could nevertheless still play their original role. Furthermore, we suggest that the early appearance of PTP could have had a crucial role in the establishment of endosymbiosis in eukaryotic cells, by the coordinated balancing of ATP production by glycolysis (performed by the primary phagocyte) and oxidative phosphorylation (accomplished by the endosymbiont). Indeed, we argue on the possibility that this new energetic equilibrium could have opened the way to the subsequent evolution toward metazoans.     

The mitochondrial permeability transition pore (PTP) — An example of multiple molecular exaptation?

The mitochondrial permeability transition (PT) is a well-recognized phenomenon that allows mitochondria to undergo a sudden increase of permeability to solutes with molecular mass ≤ 1500 Da, leading to organelle swelling and structural modifications. The relevance of PT relies on its master role in the manifestation of programmed cell death (PCD). This function is performed by a mega-channel (in some cases inhibited by cyclosporin A) named permeability transition pore (PTP), whose function could derive from the assembly of different mitochondrial proteins.In this paper we examine the distribution and characteristics of PTP in mitochondria of eukaryotic organisms so far investigated in order to draw a hypothesis on the mechanism of its evolution. As a result, we suggest that PTP may have arisen as a new function linked to a multiple molecular exaptation of different mitochondrial proteins, even though they could nevertheless still play their original role.Furthermore, we suggest that the early appearance of PTP could have had a crucial role in the establishment of endosymbiosis in eukaryotic cells, by the coordinated balancing of ATP production by glycolysis (performed by the primary phagocyte) and oxidative phosphorylation (accomplished by the endosymbiont). Indeed, we argue on the possibility that this new energetic equilibrium could have opened the way to the subsequent evolution toward metazoans.