Using BpyAla to generate copper artificial metalloenzymes: a catalytic and structural study.

Artificial metalloenzymes (ArMs) have emerged as a promising avenue in the field of biocatalysis, offering new reactivity. However, their design remains challenging due to the limited understanding of their protein dynamics and how the introduced cofactors alter the protein scaffold structure. Here we present the structures and catalytic activity of novel copper ArMs capable of (R)- or (S)-stereoselective control, utilizing a steroid carrier protein (SCP) scaffold. To incorporate 2,2'-bipyridine (Bpy) into SCP, two distinct strategies were employed: either Bpy was introduced as an unnatural amino acid (2,2'-bipyridin-5-yl)alanine (BpyAla) using amber stop codon expression or via bioconjugation of bromomethyl-Bpy to cysteine residues. The resulting ArMs proved to be effective at catalysing an enantioselective Friedel-Crafts reaction with SCP_Q111BpyAla achieving the best selectivity with an enantioselectivity of 72% ee (S). Interestingly, despite using the same protein scaffold, different attachment strategies for Bpy at the same residue (Q111) led to a switch in the enantiopreference of the ArM. X-ray crystal structures of SCP_Q111CBpy and SCP_Q111BpyAla ArMs with bound Cu(ii) ions unveiled crucial differences in the orientation of the catalytic centre. Combining structural information, alanine scanning studies, and computational analysis shed light on the distinct active sites of the ArMs, clarifying that these active sites stabilise the nucleophilic substrate on different sides of the electrophile leading to the observed switch in enantioselectivity. This work underscores the importance of integrating structural studies with catalytic screening to unravel the intricacies of ArM behaviour and facilitate their development for targeted applications in biocatalysis.

Gut microbiome profiling of a rural and urban South African cohort reveals biomarkers of a population in lifestyle transition.

BACKGROUND: Comparisons of traditional hunter-gatherers and pre-agricultural communities in Africa with urban and suburban Western North American and European cohorts have clearly shown that diet, lifestyle and environment are associated with gut microbiome composition. Yet, little is known about the gut microbiome composition of most communities in the very diverse African continent. South Africa comprises a richly diverse ethnolinguistic population that is experiencing an ongoing epidemiological transition and concurrent spike in the prevalence of obesity, largely attributed to a shift towards more Westernized diets and increasingly inactive lifestyle practices. To characterize the microbiome of African adults living in more mainstream lifestyle settings and investigate associations between the microbiome and obesity, we conducted a pilot study, designed collaboratively with community leaders, in two South African cohorts representative of urban and transitioning rural populations. As the rate of overweight and obesity is particularly high in women, we collected single time-point stool samples from 170 HIV-negative women (51 at Soweto; 119 at Bushbuckridge), performed 16S rRNA gene sequencing on these samples and compared the data to concurrently collected anthropometric data. RESULTS: We found the overall gut microbiome of our cohorts to be reflective of their ongoing epidemiological transition. Specifically, we find that geographical location was more important for sample clustering than lean/obese status and observed a relatively higher abundance of the Melainabacteria, Vampirovibrio, a predatory bacterium, in Bushbuckridge. Also, Prevotella, despite its generally high prevalence in the cohorts, showed an association with obesity. In comparisons with benchmarked datasets representative of non-Western populations, relatively higher abundance values were observed in our dataset for Barnesiella (log2fold change (FC) = 4.5), Alistipes (log2FC = 3.9), Bacteroides (log2FC = 4.2), Parabacteroides (log2FC = 3.1) and Treponema (log2FC = 1.6), with the exception of Prevotella (log2FC = - 4.7). CONCLUSIONS: Altogether, this work identifies putative microbial features associated with host health in a historically understudied community undergoing an epidemiological transition. Furthermore, we note the crucial role of community engagement to the success of a study in an African setting, the importance of more population-specific studies to inform targeted interventions as well as present a basic foundation for future research.

Long-range interaction between heterogeneously charged membranes.

Despite their neutrality, surfaces or membranes with equal amounts of positive and negative charge can exhibit long-range electrostatic interactions if the surface charge is heterogeneous; this can happen when the surface charges form finite-size domain structures. These domains can be formed in lipid membranes where the balance of the different ranges of strong but short-ranged hydrophobic interactions and longer-ranged electrostatic repulsion result in a finite, stable domain size. If the domain size is large enough, oppositely charged domains in two opposing surfaces or membranes can be strongly correlated by the electrostatic interactions; these correlations give rise to an attractive interaction of the two membranes or surfaces over separations on the order of the domain size. We use numerical simulations to demonstrate the existence of strong attractions at separations of tens of nanometers. Large line tensions result in larger domains but also increase the charge density within the domain. This promotes correlations and, as a result, increases the intermembrane attraction. On the other hand, increasing the salt concentration increases both the domain size and degree of domain anticorrelation, but the interactions are ultimately reduced due to increased screening. The result is a decrease in the net attraction as salt concentration is increased.

Hybrid lipids as a biological surface-active component.

Cell membranes contain small domains (on the order of nanometers in size, sometimes called rafts) of lipids whose hydrocarbon chains are more ordered than those of the surrounding bulk-phase lipids. Whether these domains are fluctuations, metastable, or thermodynamically stable, is still unclear. Here, we show theoretically how a lipid with one saturated hydrocarbon chain that prefers the ordered environment and one partially unsaturated chain that prefers the less ordered phase, can act as a line-active component. We present a unified model that treats the lipids in both the bulk and at the interface and show how they lower the line tension between domains, eventually driving it to zero at sufficiently large interaction strengths or at sufficiently low temperatures. In this limit, finite-sized domains stabilized by the packing of these hybrid lipids can form as equilibrium structures.

Self assembly modulated by interactions of two heterogeneously charged surfaces.

Recent experiments have measured attractive interactions between two surfaces that each bear two molecular species with opposite charge. Such surfaces form charged domains of finite size. We present a theoretical model that predicts the dependence of the domain size, phase behavior and the interlayer forces as a function of spacing and salt concentration for two such interacting surfaces. A strong correlation between two length scales, the screening length and the surface separation, at the spinodal is shown. Remarkably, the first-order phase transition to infinite sized domains depends logarithmically on the ratio of the domain size to the molecular size. Finally, we fit the predicted pressure with experiments.

Heterodimerization studies of calix[4]arene derivatives in polar solvents.

[reaction: see text] Several calix[4]arene derivatives propylated on the lower rim and substituted on the upper rim with amino or carboxyl groups have been synthesized. Examples include calixarenes substituted with alanino (C- and N-linked), amino, carboxy, carboxyphenyl, and amidino groups. The self-assembly of these derivatized calixarenes into heterodimers has been studied by NMR in DMSO-d(6) or CD(3)OD with 5% aqueous phosphate buffer.

Synthesis of a peptidocalix[4]arene library and identification of compounds with hydrolytic activity.

A 120 member library of peptidocalix[4]arenes was synthesized and screened for catalysis of the hydrolysis of p-nitrophenyl acetate. His-Ser-His-calix[4]arene was found to catalyze this reaction with v(0)=3.24 x 10(-8)M/s, an increase of 1520% above background and 30% above the tripeptide (His-Ser-His) alone.

Molecular recognition in methanol: the first example of hydrogen-bond-mediated self-association of a calix[4]arene in polar, protic solvent.

Tetraalaninecalixarene was prepared by coupling of tetraaminocalix[4]arene with alanine. It dimerizes in methanol, providing the first example of a substituted calixarene that undergoes self-association through hydrogen bonding in polar, protic solvent. The association constant in 24:1 MeOH:H2O was determined to be 29 000 M-1. Addition of arginine or lysine results in disruption of the dimer and formation of a 1:1 complex between the amino acid and the tetraalaninecalixarene. The preparation of a peptidocalixarene that associates in polar solvent opens new doors for the use of calixarenes for molecular recognition in biologically relevant environments.

Analyses of heat transfer in stationary and rotating ribbed blade cooling passages using computational fluid dynamics.

Computational fluid dynamics (CFD) predictions of the flow patterns and heat transfer in simplified ribbed-wall turbine blade cooling passages were performed for representative stationary and rotating conditions. Analyses have been performed with different mesh densities and using different turbulence models to assess the sensitivity of predictions to these variables. Computed local heat transfer results are compared to measurements available in the literature to assess their accuracy. The results generally agree well with experiment, although the peak values of the heat transfer coefficients were under-predicted in the first leg of the channel. Some sensitivity to mesh density was seen, while the choice of near-wall turbulence model appeared to have little effect.

The selector gene cut represses a neural cell fate that is specified independently of the Achaete-Scute-Complex and atonal.

The peripheral nervous system (PNS) of Drosophila offers a powerful system to precisely identify individual cells and dissect their genetic pathways of development. The mode of specification of a subset of larval PNS cells, the multiple dendritic (md) neurons (or type II neurons), is complex and still poorly understood. Within the dorsal thoracic and abdominal segments, two md neurons, dbd and dda1, apparently require the proneural gene amos but not atonal (ato) or Achaete-Scute-Complex (ASC) genes. ASC normally acts via the neural selector gene cut to specify appropriate sensory organ identities. Here, we show that dbd- and dda1-type differentiation is suppressed by cut in dorsal ASC-dependent md neurons. Thus, cut is not only required to promote an ASC-dependent mode of differentiation, but also represses an ASC- and ato-independent fate that leads to dbd and dda1 differentiation.

Hexokinase I is a Gli2-responsive gene expressed in the embryonic CNS.

Little is known about the downstream genes regulated by Gli zinc finger transcription factors, which are targets and mediators of Hedgehog signaling. Specifically, the identity and regulation of genes which mediate Gli2 function in neurogenesis are unclear. We describe here the cloning of frog Hexokinase I (HKI) as a Gli2-responsive gene. We show that HKI expression is induced by Gli2 and that it is detected in defined neuronal populations. Since the primary energy source of the brain is derived from glucose metabolism and hexokinase catalyses the first and rate limiting step in this process, the conversion of glucose into glucose-6-phosphate, these findings suggest a link between the regulation of neuronal induction and differentiation.

Gli2 functions in FGF signaling during antero-posterior patterning.

Patterning along the anteroposterior (A-P) axis involves the interplay of secreted and transcription factors that specify cell fates in the mesoderm and neuroectoderm. While FGF and homeodomain proteins have been shown to play different roles in posterior specification, the network coordinating their effects remains elusive. Here we have analyzed the function of Gli zinc-finger proteins in mesodermal A-P patterning. We find that Gli2 is sufficient to induce ventroposterior development, functioning in the FGF-brachyury regulatory loop. Gli2 directly induces brachyury, a gene required and sufficient for mesodermal development, and Gli2 is in turn induced by FGF signaling. Moreover, the homeobox gene Xhox3, a critical determinant of posterior development, is also directly regulated by Gli2. Gli3, but not Gli1, has an activity similar to that of Gli2 and is expressed in ventroposterior mesoderm after Gli2. These findings uncover a novel function of Gli proteins, previously only known to mediate hedgehog signals, in the maintenance and patterning of the embryonic mesoderm. More generally, our results suggest a molecular basis for an integration of FGF and hedgehog inputs in Gli-expressing cells that respond to these signals.

Getting a-head of the organizer: anterior-posterior patterning of the forebrain.

The molecular mechanisms that drive the development of embryonic tissues are being uncovered rapidly. One such fascinating example is the development of the forebrain, the most anterior part of the nervous system. In this review, we will discuss the mechanisms that induce the formation of the forebrain in multiple vertebrate systems, placing emphasis on a recent article published by Grinblat et al. ((1)) Using zebrafish as a model system, these authors combine elegant embryological manipulations with the use of early markers of the presumptive forebrain, to show that initial induction and patterning of this tissue occurs near the onset of gastrulation. In addition, their results confirm observations made in other systems that planar signals, those traveling in the plane of the ectoderm, are involved in forebrain induction and patterning.

The Drosophila sanpodo gene controls sibling cell fate and encodes a tropomodulin homolog, an actin/tropomyosin-associated protein.

Notch signaling is required in many invertebrate and vertebrate cells to promote proper cell fate determination. Mutations in sanpodo cause many different neuronal peripheral nervous system precursor cells to generate two identical daughter neurons, instead of a neuron and sibling cell. This phenotype is similar to that observed when Notch function is lost late in embryonic development and opposite to the numb loss-of-function phenotype. Genetic interaction studies show that sanpodo is epistatic to numb. sanpodo encodes a homolog of tropomodulin, an actin/tropomyosin-associated protein. Loss of sanpodo leads to an aberrant F-actin distribution and causes differentiation defects of actin-containing sensory structures. Our data suggest that an actin-based process is involved in Notch signaling.

Gli/Zic factors pattern the neural plate by defining domains of cell differentiation.

Three cell types differentiate in the early frog neural plate: neural crest at the lateral edges, floorplate at the midline and primary neurons in three bilateral stripes. Floorplate cells and ventral neurons are induced by Sonic hedgehog (Shh) and neural crest and dorsal neurons are induced by epidermal factors such as bone morphogenetic proteins (BMPs). Neurogenesis in a subset of cells within the stripes involves lateral inhibition. However, the process by which pools of precursors are defined in stereotypic domains in response to inductive signals is unknown. Here we show that frog Zic2 encodes a zinc-finger transcription factor of the Gli superfamily which is expressed in stripes that alternate with those in which primary neurons differentiate and overlap the domains of floorplate and neural crest progenitors. Zic2 inhibits neurogenesis and induces neural crest differentiation. Conversely, Gli proteins are widely expressed, induce neurogenesis and inhibit neural crest differentiation. Zic2 is therefore a vertebrate pre-pattern gene, encoding anti-neurogenic and crest-inducing functions that counteract the neurogenic but not the floorplate-inducing activity of Gli proteins. We propose that the combined function of Gli/Zic genes responds to inductive signals and induces patterned neural cell differentiation.

Cell lineage analysis of the Drosophila peripheral nervous system.

The peripheral nervous system (PNS) of Drosophila provides a very well-characterized model system for studying the genes involved in basic processes of neurogenesis. Because of its simplicity and stereotyped pattern, each cell of the PNS can be individually identified and the phenotypic consequences of mutations can be studied in detail. Thus, some of the genetic mechanisms leading to the formation of type I sensory organs, the external, bristle-type sensory organs (es), and the internal, stretch-receptive chordotonal organs (ch) have been elucidated. Each sensory organ seems to be generated by a stereotyped pattern of cell division of individual ectodermal precursor cells. Recent advances in cell lineage analysis of the PNS have provided a detailed picture of almost all the lineages in the PNS, including those giving rise to the type II sensory neurons, also known as multiple dendritic (md) neurons. This knowledge will be instrumental in the precise characterization of the phenotypes associated with mutations in known and new genes and their interactions which determine cell fate decisions during neurogenesis. Here, we describe and compare three recently developed methods by which cell lineages have been assessed: single cell transplantation, bromodeoxyuridine (BrdU) incorporation studies, and the flp/FRT recombinase system from yeast. In the light of a more complete knowledge of the PNS lineages, we will discuss the effects of known mutations that alter neuronal cell fates.

Origin and specification of type II sensory neurons in Drosophila.

The peripheral nervous system (PNS) of Drosophila is a preferred model for studying the genetic basis of neurogenesis because its simple and stereotyped pattern makes it ideal for mutant analysis. Type I sensory organs, the external (bristle-type) sensory organs (es) and the internal (stretch-receptive) chordotonal organs (ch), have been postulated to derive from individual ectodermal precursor cells that undergo a stereotyped pattern of cell division. Little is known about the origin and specification of type II sensory neurons, the multiple dendritic (md) neurons. Using the flp/FRT recombinase system from yeast, we have determined that a subset of md neurons derives from es organ lineages, another subset derives from ch organ lineages and a third subset is unrelated to sensory organs. We also provide evidence that the genes, numb and cut, are both required for the proper differentiation of md neurons.

Functional characterization of neurokinin-1 receptors on human U373MG astrocytoma cells.

The neurokinin-1 (NK-1, substance P) receptor belongs to the class of seven transmembrane domain (7-TM) receptors that interact with cellular effector systems via guanine nucleotide binding regulatory proteins (G-proteins). In this study, coupling mechanisms of functional NK-1 receptors endogenously expressed in a human astrocytoma cell line (U373MG) were analyzed. Stimulation with substance P (SP) resulted in 1) a rapid increase in inositol 1,4,5-trisphosphate (IP3) synthesis; 2) a rise in cytosolic free calcium concentration ([Ca2+]i); 3) induction of immediate early gene transcription as monitored by c-fos and c-jun expression; and 4) a significant increase in de novo DNA synthesis. Thus, the functional responses induced by stimulation of NK-1 receptors on U373MG strongly correlate with those observed after treatment of primary astrocytes with SP and make U373MG cells a useful in vitro model system for the analysis of NK-1 receptor function on astrocytes in vivo.

Recombinant bovine neurokinin-2 receptor stably expressed in Chinese hamster ovary cells couples to multiple signal transduction pathways.

Neurokinins are a family of neuropeptides with widespread distribution mediating a broad spectrum of physiological actions through three distinct receptor subtypes: NK-1, NK-2, and NK-3. We investigated some of the second messenger and cellular processes under control by the recombinant bovine NK-2 receptor stably expressed in Chinese hamster ovary cells. In this system the NK-2 receptor displays its expected pharmacological characteristics, and the physiological agonist neurokinin A stimulates several cellular responses. These include 1) transient inositol 1,4,5-trisphosphate (IP3) formation and Ca2+ mobilization, 2) increased out put of arachidonic acid and prostaglandin E2 (PGE2), 3) enhanced cyclic AMP (cAMP) generation, 4) increased de novo DNA synthesis, and 5) an induction of the "immediate early" genes c-fos and c-jun. Although NK-2 receptor-mediated IP3 formation involves activation of a pertussis toxin-insensitive G-protein, increased cAMP production is largely a secondary response and can be at least partially attributed to autocrine stimulation by endogenously generated eicosanoids, particularly PGE2. This is the first demonstration that a single recombinant neurokinin receptor subtype can regulate, either directly or indirectly, multiple signal transduction pathways and suggests several potential important mediators of neurokinin actions under physiological conditions.

Continuous warm blood cardioplegia: a new technique for myocardial protection.

Hypothermia is used to prolong the safe period of ischemic arrest by reducing the heart's oxygen demands. Due to this effect, hypothermia has been the fundamental component of most methods of myocardial protection during cardiac surgery. However, hypothermia has a number of unwanted side effects, such as detrimental effects on enzyme function, energy generation, and cell membranes. Since electromechanical arrest accounts for 90% of myocardial oxygen consumption, arresting the heart with chemical cardioplegia will reduce O2 consumption dramatically. Therefore, if the resting (arrested) heart is continuously perfused with oxygenated blood cardioplegia, one can easily provide the remaining 10% of O2 that it requires. Under these conditions, the need for hypothermia becomes questionable. In this paper, we describe the perfusionist's experience using the antegrade and retrograde technique of continuous warm blood cardioplegia.