Green butyryl-coenzyme A dehydrogenase. An enzyme–acyl-coenzyme A complex

1. Butyryl-CoA dehydrogenase from Peptostreptococcus elsdenii forms very tightly bound complexes with various acyl-CoA compounds. Spectra in some cases merely show resolution of the 450nm band, but those with acetoacetyl-, pent-2-enoyl- and 4-methylpent-2-enoyl-CoA show long-wavelength bands similar to the 710nm band of native enzyme. These complexes are formed instantaneously by the yellow form of the enzyme and much more slowly by the green form. 2. An acid extract of the green enzyme reconverts the yellow into the green form. 3. Hydroxylamine makes irreversible the otherwise reversible conversion of the green enzyme into the yellow form by phenylmercuric acetate. 4. Amino acid analysis for taurine and beta-alanine shows approx. 1mol of CoA/mol of flavin in green enzyme. Anaerobic dialysis of reduced enzyme removes the CoA. On acid precipitation of green enzyme the CoA is found only in the supernatant. 5. It is concluded that native green enzyme is probably complexed with unsaturated acyl-CoA. This is shown to be consistent with findings of other workers. Catalytic activity requires displacement of the acyl-CoA, which is therefore likely to be a potent inhibitor. 6. An explanation is offered for the irreversible conversion of green into yellow enzyme by sodium dithionite. 7. The enzyme displays a feeble, previously undetected, activity towards beta-hydroxybutyryl-CoA. 8. The product of oxidation of pent-4-enoyl-CoA forms a complex with reduced enzyme and strongly inhibits reoxidation of the FAD. This may contribute to inhibition of fatty acid oxidation by pent-4-enoic acid in mammals.     

A new polyaniline–catalase–glutaraldehyde-modified biosensor for hydrogen peroxide detection

A new biosensor based on catalase enzyme immobilized on electrochemically constructed polyaniline (PANI) film modified with glutaraldehyde has been developed for the determination of hydrogen peroxide (H₂O₂) in milk samples. Assembly processes of polyaniline and immobilization of the enzyme were monitored with the help of electrochemical impedance spectroscopy. Amperometric measurements have been performed at cathodic peak (?0.3?V vs. Ag/AgCI) which was attributed to reduction of PANI. Hydrogen peroxide was determined by using amperometric method at ?0.3?V. The biosensor responses were correlated linearly with the hydrogen peroxide concentrations between 5.0?×?10^?6 and 1.0?×?10^?4?M by amperometric method. Detection limit of the biosensor is 2.18?×?10^?6?M for H₂O₂. In the optimization studies of the biosensor, some parameters such as optimum pH, temperature, concentration of aniline, amount of enzyme, and number of scans during electropolymerization were investigated.     

Comparative properties of Aβ1–42, Aβ11–42, and [Pyr11]Aβ11–42 generated from O-acyl isopeptides

The use of water-soluble O-acyl isopeptides enabled us to investigate the biochemical properties of Aβ11–42 species, by preparing highly concentrated stock solutions after a pretreatment. Aβ11–42 and [Pyr¹¹]Aβ11–42 showed comparable aggregation capability and cytotoxicity, suggesting that the pyroglutamate modification at Glu¹¹ does not have a crucial role in these events. However, given that Aβ11–42 is converted to [Pyr¹¹]Aβ11–42 by a glutamyl cyclase in vivo, the potential aggregative and cytotoxic nature of [Pyr¹¹]Aβ11–42 that was observed in the present study provides valuable insights into the pathological functions of pyroglutamate-modified Aβ species in Alzheimer’s disease.     

Three-Dimensional Organization of Polyribosomes–A Modern Approach

Polyribosomes in cells usually have a certain structural organization whose significance has not yet been elucidated. The development of cryo electron tomography has provided a new approach to study polyribosome structure. New data confirm or correct observations made earlier by classical techniques of electron microscopy. The existence of circular and linear (zigzag) topology of polyribosomes was confirmed, and their relationship with the frequently observed tworow forms was clarified. Contacts between ribosomes have been identified in densely packed three-dimensional helical polyribosomes. At the same time, modern cell-free translation systems have opened the possibility of investigating polyribosomes on mRNA of a given structure to elucidate the mechanism of polyribosome structure formation, especially of circular polyribosomes. There is an increasing amount of data supporting the idea of interdependence between polyribosome structure and their translational activity. Moreover, participation of polyribosomes in mRNA transport and localization of protein synthesis in the cell has been shown. Improvement of the resolution and the development of the cryo electron tomography technique for the analysis of polyribosomes in situ will enable further progress in understanding the process of protein synthesis in cells.     

A cell–cell repulsion model on a hyperbolic Keller–Segel equation

Journal of Mathematical Biology - In this work, we discuss a cell–cell repulsion model based on a hyperbolic Keller–Segel equation with two populations, which aims at describing the...     

Molecular dynamics simulation of Axillaridine–A: A potent natural cholinesterase inhibitor

Molecular Dynamics (MD) simulations were carried out for human acetylcholinesterase (hAChE) and its complex with Axillaridine–A, in order to dynamically explore the active site of the protein and the behaviour of the ligand at the peripheral binding site. Simulation of the enzyme alone showed that the active site of AChE is located at the bottom of a deep and narrow cavity whose surface is lined with rings of aromatic residues while Tyr72 is almost perpendicular to the Trp286, which is responsible for stable π -π interactions. The complexation of AChE with Axillaridine-A, results in the reduction of gorge size due to interaction between the ligand and the active site residues. The gorge size was determined by the distance between the center of mass of Glu81 and Trp286. As far as the geometry of the active site is concerned, the presence of ligand in the active site alters its specific conformation, as revealed by stable hydrogen bondings established between amino acids. With the increasing interaction between ligand and the active amino acids, size of the active site of the complex decreases with respect to time. Axillaridine-A, forms stable π -π interactions with the aromatic ring of Tyr124 that results in inhibition of catalytic activity of the enzyme. This π -π interaction keeps the substrate stable at the edge of the catalytic gorge by inhibiting its catalytic activity. The MD results clearly provide an explanation for the binding pattern of bulky steroidal alkaloids at the active site of AChE.     

Enhanced Aβ1–40 Production in Endothelial Cells Stimulated with Fibrillar Aβ1–42

Amyloid accumulation in the brain of Alzheimer’s patients results from altered processing of the 39- to 43-amino acid amyloid β protein (Aβ). The mechanisms for the elevated amyloid (Aβ_1–42) are considered to be over-expression of the amyloid precursor protein (APP), enhanced cleavage of APP to Aβ, and decreased clearance of Aβ from the central nervous system (CNS). We report herein studies of Aβ stimulated effects on endothelial cells. We observe an interesting and as yet unprecedented feedback effect involving Aβ_1–42 fibril-induced synthesis of APP by Western blot analysis in the endothelial cell line Hep-1. We further observe an increase in the expression of Aβ_1–40 by flow cytometry and fluorescence microscopy. This phenomenon is reproducible for cultures grown both in the presence and absence of serum. In the former case, flow cytometry reveals that Aβ_1–40 accumulation is less pronounced than under serum-free conditions. Immunofluorescence staining further corroborates these observations. Cellular responses to fibrillar Aβ_1–42 treatment involving eNOS upregulation and increased autophagy are also reported.     

A NMR guided approach for CsrA–RNA crystallization

Structure determination of protein–nucleic acid complexes remains a challenging task. Here we present a simple method for generating crystals of a CsrA–nucleic acid complex, guided entirely by results from nuclear magnetic resonances spectroscopy (NMR) spectroscopy. Using a construct that lacks thirteen non-essential C-terminal residues, efficient binding to DNA could be demonstrated. One CsrA dimer interacts with two DNA oligonucleotides, similar to previous findings with RNA. Furthermore, the NMR study of the CsrA–DNA complex was the basis for successfully homing in on conditions that were suitable for obtaining crystals of the CsrA–DNA complex. Our results may be useful for those cases where RNA in protein–nucleic acid complexes may be replaced by DNA.     

A simple method for monitoring protein–DNA interactions

A simple, efficient and cheap method is reported for monitoring interactions between single stranded desoxyribonucleic acids and proteins, using fluorescence spectroscopy and complexes of 5′-dye–DNA conjugates with bovine serum albumin as probes. In the presence of a single stranded DNA-binding protein the complexes with bovine serum albumin are disrupted, which results in a reduction of fluorescence intensity.     

Regulating cell–cell junctions from A to Z

Epithelial sheets often present a “cobblestone” appearance, but the mechanisms underlying the dynamics of this arrangement are unclear. In this issue, Choi et al. (2016. J. Cell Biol. http://dx.doi.org/10.1083/jcb.201506115) show that afadin and ZO-1 regulate tension and maintain zonula adherens architecture in response to changes in contractility.The textbook view of epithelial cells is that once such cells adopt a close, hexagonal packing, their “honeycomb” or “cobblestone” arrangement is static. This fixed appearance is misleading, as these cells are more like players in a rugby scrum, locked in a tussle in which the forces exerted by each of the players on the others maintains their seemingly static arrangement, but by a very dynamic force balance. How such balance is maintained in epithelia is a subject of substantial interest. A crucial role is played by F-actin and nonmuscle myosin II isoforms, which are deployed in contractile networks that transiently attach to cell–cell junctions to generate tensile forces along cell–cell boundaries (Lecuit and Yap, 2015). Contractile arrays of actomyosin are regulated by the monomeric G protein Rho, its upstream regulators, including Rho guanine nucleotide exchange factors (Quiros and Nusrat, 2014), and its effectors ROCK/Rho kinase and Shroom3 (Nishimura and Takeichi, 2008), but also by tension-mediated feedback between the myosin network and the junction (Lecuit and Yap, 2015). Cell–cell adhesion, including cadherin-dependent adhesion, also plays a crucial role in this process. As cells engage with one another via interactions of the extracellular domains of their cadherin complexes, they transduce forces to the actomyosin cytoskeleton through catenins. β-Catenin binds to the cytoplasmic domain of classical cadherins and recruits α-catenin, which binds F-actin.Given the dynamic nature of epithelia, the attachment of contractile actomyosin networks to junctions are also subject to regulation. One aspect of epithelial architecture that has received relatively little attention is that a typical epithelial monolayer (Fig. 1 A) displays two main types of cell–cell interfaces: bilateral junctions (BCJs), in which two cells establish a relatively long stretch of contact, and cellular vertices, which represent a confluence of three or more cell edges to form tricellular junctions (TCJs) or multicellular junctions. TCJs are not well understood, but are known to contain unique molecular components (Furuse et al., 2014; Flores-Benitez and Knust, 2015). In this issue, Choi et al. show that the multivalent scaffolding proteins afadin and ZO-1/2 regulate the spacing of and tension along lateral contacts in cultured cells, thereby shedding light on how contractile arrays containing bilateral and tri- or multicellular contact points are regulated in epithelia.Open in a separate windowFigure 1.ZO proteins and afadin regulate junctional tension and organization in cultured cells. (A) Untreated MDCK cells have sinuous cell boundaries, whereas ZO KD cells show extremely straight boundaries. When ZO proteins and afadin are knocked down, cells adopt contact zones of irregular length with other cells, sometimes clustering into foci (asterisks). Images courtesy of Mark Peifer (Choi et al., 2016). (B) A model for actomyosin organization at adherens junctions (adapted from Choi et al., 2016). Contractile actomyosin arrays run parallel to bicellular junctions and are anchored by side-on attachments (pink circles). At TCJs, end-on binding of actin, likely stabilized by afadin, anchors actomyosin filaments. In ZO KD cells, contractile elements and cadherin complexes collapse toward TCJs, and myosin minifilaments adopt a regularly spaced arrangement.Afadin and ZO-1/2 are far from new players at junctions. Afadin binds α-catenin, actin, and other cytoskeletal and junctional proteins and associates with the transmembrane protein nectin, which appears to form an alternative adhesion system at adherens junctions (Mandai et al., 2013). The zonula occludens proteins ZO-1 and ZO-2 are tight junction proteins that bind claudins and are required for tight junction formation (Itoh et al., 1999; Balda and Matter, 2008). In addition, ZO proteins also bind to α-catenin (Itoh et al., 1997), are involved in establishing the zonula adherens (ZA; Ikenouchi et al., 2007), and potentiate cadherin-dependent adhesion in Caenorhabditis elegans (Lockwood et al., 2008) and Drosophila melanogaster (Choi et al., 2011). Knockdown of ZO-1 and ZO-2 (ZO KD) in MDCK cells has previously been shown (Fanning et al., 2012) to lead to dramatic alterations of the ZA: F-actin and myosin IIs assemble into striking apical arrays at the ZA, spaced at regular intervals. In addition, the normally sinuous boundaries between cells give way to very straight borders (Fig. 1 A).Using superresolution microscopy, diffraction-limited junctional laser ablation, cell morphometry, kinetic analysis, and a whole-monolayer approach to contractility, Choi et al. (2016) now extend this story. To test whether contractility is increased after ZO KD, the authors first measured the recoil after laser ablation of ZO KD cells; an increase in recoil velocity indicated that the straight junctional boundaries between ZO-depleted cells are under tension. Imaging analysis of BCJs showed that the increase in contractility in ZO KD cells is associated with a strikingly dynamic behavior of the BCJs. Individual BCJs were found to undergo periods of shortening and elongation, whereas neighboring BCJs underwent compensatory, opposite changes in length. These changes in contractility have effects on the entire tissue sheet as well: whereas control cell sheets remained flat when detached from the substratum, ZO KD cells contracted into a cup-like shape. This constriction was blocked by the myosin inhibitor blebbistatin. Overall, these experiments indicated that ZO proteins regulate myosin assembly and contractility across the cellular sheet.To dissect the protein network mediating increased contractility in ZO KD cells, Choi et al. (2016) examined the role of ROCK and found that ROCK inhibitors abolished the straight BCJs, which became curvilinear. Additionally, Shroom3, which is known to recruit ROCK (Nishimura and Takeichi, 2008), was cytoplasmic in control cells but junctional in ZO KD cells. Transient Shroom3 overexpression led to ROCK recruitment to the ZA and drove formation of an actomyosin network similar to that in ZO KD cells. Conversely, Shroom3 knockdown resulted in loss of the actomyosin arrays in ZO KD cells. Collectively, these data indicated that Shroom3 is an effector of increased apical contractility in ZO KD cells.The researchers used ZO KD cells to test how tissue integrity is maintained despite elevated contractibility and how junctions are remodeled to maintain integrity when increased tension is present. Afadin is a good candidate: the Drosophila homologue of afadin, Canoe, plays roles in convergent extension and collective cell migration; in its absence, actomyosin networks at the apex of constricting epithelial cells in the embryo contract in a catastrophic, uncontrolled fashion (Sawyer et al., 2009), suggesting a potential role for afadin in the maintenance of tissue integrity during morphogenetic movements. Choi et al. (2016) therefore turned their attention to afadin. ZO KD cells have significantly more afadin at their adherens junctions and TCJs, a pattern reminiscent of the normal distribution of Canoe in Drosophila (Sawyer et al., 2009). Knocking down afadin by shRNA in ZO KD cells led to further defects in cell–cell boundary maintenance. In addition to the taut appearance of bicellular borders, cell boundary length became much more irregular, with occasional foci of highly contracted cells (Fig. 1 A). Velocimetry analysis and live-cell imaging indicated that loss of both ZO proteins and afadin led to large-scale cell movements within the monolayer not seen after ZO KD alone.New imaging techniques used by Choi et al. (2016) revealed further details about the changes in actomyosin arrays in ZO KD cells. Superresolution imaging of myosin light chain kinase staining via structured illumination showed that myosin II assembles into arrays of myosin minifilaments spaced ∼415 nm apart along bicellular contacts. Superresolution and transmission electron microscopy also revealed reorganization of F-actin and E-cadherin at TCJs in ZO KD cells. Lateral F-actin bundles appeared to terminate end-on at TCJs at sites where E-cadherin was present. ZO KD therefore induces assembly of a remarkably ordered actomyosin array along BCJs, and these arrays appear to be separate contractile units that anchor end-on at the ZA. Moreover, based on staining for vinculin and a specific epitope in αE-catenin that serve as markers for regions under high tension (Yonemura et al., 2010), the end-on attachments of actin cables to the ZA at TCJs experience significant tensile stress. Strikingly, although vinculin and αE-catenin accumulation at TCJs was relatively uniform after ZO KD, their distribution was more heterogeneous after ZO/afadin KD. Differences in staining paralleled differences in cell border length and correlated with the level of tension measured at BCJs after laser cutting, suggesting that afadin contributes to the ability of cells to distribute forces at TCJ/multicellular junctions throughout the monolayer. Lastly, the researchers investigated whether internal cues downstream of ZO KD are sufficient for myosin recruitment or whether such recruitment depends on mechanical cues exerted by neighboring cells. They designed an assay mixing small islands of wild-type cells surrounded by ZO KD cells (or vice versa) and found that the development of the contractile array at the ZA depends on the contractility of neighboring cells; however, afadin recruitment to the ZA was less dependent on the sustained contractility of neighboring cells. Taking these data together, Choi et al. (2016) propose that cells respond to elevated contractility by increasing junctional afadin; because combined ZO/afadin knockdown dramatically alters cell shape and barrier function in response to elevated contractility, afadin acts as a robust scaffold that maintains ZA architecture most crucially at TCJs.Although many aspects of the model proposed by Choi et al. (2016) remain to be tested, their data suggest new features regarding the detailed assembly of actomyosin contractile arrays in confluent cells (Fig. 1 B). In control cells, actomyosin arrays presumably extend parallel to individual BCJs. Choi et al. (2016) propose that these actomyosin bundles act as separate contractile units that terminate near TCJs, allowing the generation of tension along BCJs. In ZO KD cells, excessive assembly of actomyosin filaments, perhaps exacerbated by the tendency of F-actin/myosin minifilament arrays to self-assemble, somehow leads to regularly spaced actomyosin arrays, and perhaps collapse of cadherin complexes and other components toward TCJs. There is a precedent for such lateral collapse of cadherin-dependent attachments: it is a prominent feature of cadherin complexes at sites of high tension in the epidermis of the C. elegans embryo (Choi et al., 2015). If the new model of Choi et al. (2016) is correct, then the foci seen in ZO KD/afadin KD cells may be similar to what happens in a game of tug of war when one team stops pulling. If some end-on attachments (assisted by afadin) fail, filaments might be expected to collapse along BCJs as the other, still tethered end of a set of filaments contracts toward the remaining attachment at the opposite cell vertex.Several other interesting questions remain. First, what is the relationship of the striking, regularly spaced bipolar myosin II minifilaments that form in ZO KD cells to myosin arrays in normal cells? It is clear that untreated cells have junctional actomyosin networks, but not with this strict periodicity. One possibility is that this spacing is simply an epiphenomenon; when not appropriately anchored along junctions, actomyosin networks may self-organize as they are known to do in other systems, such as in the contractile ring and in migrating cells (Srivastava et al., 2015; Fenix et al., 2016). More optimistically, the spacing may represent an intensified version of processes that operate in normal cells at bicellular and multicellular contact sites. If so, components of the model of Choi et al. (2016) will require further investigation. For example, the organization of F-actin along BCJs remains unclear, as are the proteins that mediate the side-on binding envisioned in this model. It is also uncertain whether proteins assist bundling of filaments and what role dynamic growth and shrinkage of actin filaments plays in end-on binding. In some contexts, junctions are capable of seeding polymerization of F-actin (Brieher and Yap, 2013), and it may be that actin dynamics are important in the processes studied here.A second question has to do with the community events within monolayers that Choi et al. (2016) describe. The neighbor effects on ZA morphology that they document are intriguing, as are the long-range accelerated movements of cells lacking both ZO proteins and afadin. Collective properties of monolayers are only beginning to be explored; connecting these properties with subcellullar events is an exciting future challenge. Whatever the answers to these new questions, the work of Choi et al. (2016) refines our understanding of the roles of key scaffolding proteins in organizing and anchoring junctions in epithelia.     

A Model of the Hippocampal–cortical Memory System

Based on physiological evidence, we propose a theoretical model of the hippocampal–cortical memory system. The model consists of the following components: the sensory system, the hippocampus (short-term memory), and the association cortex (long-term memory). A series of key codes (local information) is supplied from the sensory system, while context (global information) is inputted from the hippocampus. The two inputs interact dynamically in the association cortex. The interactive neurons work as a detector of coincidence. The cortical network learns the memory information through the coincidence window and, finally, stores it in the form of attractors. This local–global information works as an addressor to designate the stored location of the memory in the association cortex and accelerates the process of storing and retrieving memory information.     

A Lotka–Volterra competition model with seasonal succession

A complete classification for the global dynamics of a Lotka–Volterra two species competition model with seasonal succession is obtained via the stability analysis of equilibria and the theory of monotone dynamical systems. The effects of two death rates in the bad season and the proportion of the good season on the competition outcomes are also discussed.     

A Fuzzy Reed–Frost Model for Epidemic Spreading

In this paper, we present a fuzzy approach to the Reed–Frost model for epidemic spreading taking into account uncertainties in the diagnostic of the infection. The heterogeneities in the infected group is based on the clinical signals of the individuals (symptoms, laboratorial exams, medical findings, etc.), which are incorporated into the dynamic of the epidemic. The infectivity level is time-varying and the classification of the individuals is performed through fuzzy relations. Simulations considering a real problem with data of the viral epidemic in a children daycare are performed and the results are compared with a stochastic Reed–Frost generalization.     

A nonlocal kinetic model for predator–prey interactions

We extend the aggregation model from Fetecau (2011) by adding a field of vision to individuals and by including a second species. The two species, assumed to have a predator–prey relationship, have dynamics governed by nonlocal kinetic equations that include advection and turning. The latter is the main mechanism for aggregation and orientation, which results from interactions among individuals of the same species as well as predator–prey relationships. We illustrate numerically a diverse set of predator–prey behaviors that can be captured by this model. We show that a prey’s escape outcome depends on the social interactions between its group members, the prey’s field of vision and the sophistication of the predator’s hunting strategies.     

A DOTA–peptide conjugate by copper-free click chemistry

Attachment of DOTA to a novel monofluoro-cyclooctyne facilitates bioconjugation to an azide-modified peptide via Cu-free click chemistry. The resulting conjugate was radiolabeled with ¹¹¹In to afford a potential targeted molecular imaging agent with high specific activity and an excellent radiochemical purity.