Modelling peptide adsorption energies on gold surfaces with an effective implicit solvent and surface model.

The interaction of proteins and peptides with inorganic surfaces is relevant in a wide array of technological applications. A rational approach to design peptides for specific surfaces would build on amino-acid and surface specific interaction models, which are difficult to characterize experimentally or by modeling. Even with such a model at hand, the large number of possible sequences and the large conformation space of peptides make comparative simulations challenging. Here we present a computational protocol, the effective implicit surface model (EISM), for efficient in silico evaluation of the binding affinity trends of peptides on parameterized surface, with a specific application to the widely studied gold surface. In EISM the peptide surface interactions are modeled with an amino-acid and surface specific implicit solvent model, which permits rapid exploration of the peptide conformational degrees of freedom. We demonstrate the parametrization of the model and compare the results with all-atom simulations and experimental results for specific peptides.

Rational Design of Iron Oxide Binding Peptide Tags.

Owing to their extraordinary magnetic properties and low-cost production, iron oxide nanoparticles (IONs) are in the focus of research. In order to better understand interactions of IONs with biomolecules, a tool for the prediction of the propensity of different peptides to interact with IONs is of great value. We present an effective implicit surface model (EISM), which includes several interaction models. Electrostatic interactions, van der Waals interactions, and entropic effects are considered for the theoretical calculations. However, the most important parameter, a surface accessible area force field contribution term, derives directly from experimental results on the interactions of IONs and peptides. Data from binding experiments of ION agglomerates to different peptides immobilized on cellulose membranes have been used to parameterize the model. The work was carried out under defined environmental conditions; hence, effects because of changes, for example structure or solubility by changing the surroundings, are not included. EISM enables researchers to predict the binding of peptides to IONs, which we then verify with further peptide array experiments in an iterative optimization process also presented here. Negatively charged peptides were identified as best binders for IONs in Tris buffer. Furthermore, we investigated the constitution of peptides and how the amount and position of several amino acid side chains affect peptide-binding. The incorporation of glycine leads to higher binding scores compared to the incorporation of cysteine in negatively charged peptides.

Gas-Phase Ion Chemistry of Metalloporphyrin Anions with Molecular Oxygen: Probing the Influence of the Oxidation and Spin State of the Central Transition Metal by Experiment and Theory.

We performed a comprehensive gas-phase experimental and quantum-chemical study of the binding properties of molecular oxygen to iron and manganese porphyrin anions. Temperature-dependent ion-molecule reaction kinetics as probed in a Fourier-transform ion-cyclotron resonance mass spectrometer reveal that molecular oxygen is bound by, respectively, 40.8 ± 1.4 and 67.4 ± 2.2 kJ mol-1 to the FeII or MnII centers of isolated tetra(4-sulfonatophenyl)metalloporphyrin tetraanions. In contrast, FeIII and MnIII trianion homologues were found to be much less reactive-indicating an upper bound to their dioxygen binding energies of 34 kJ mol-1. We modeled the corresponding O2 adsorbates at the density functional theory and CASPT2 levels. These quantum-chemical calculations verified the stronger O2 binding on the FeII or MnII centers and suggested that O2 binds as a superoxide anion.

Divergent Coordination Chemistry: Parallel Synthesis of [2×2] Iron(II) Grid-Complex Tauto-Conformers.

The coordination of iron(II) ions by a homoditopic ligand L with two tridentate chelates leads to the tautomerism-driven emergence of complexity, with isomeric tetramers and trimers as the coordination products. The structures of the two dominant [Fe(II) 4 L4 ](8+) complexes were determined by X-ray diffraction, and the distinctness of the products was confirmed by ion-mobility mass spectrometry. Moreover, these two isomers display contrasting magnetic properties (Fe(II) spin crossover vs. a blocked Fe(II) high-spin state). These results demonstrate how the coordination of a metal ion to a ligand that can undergo tautomerization can increase, at a higher hierarchical level, complexity, here expressed by the formation of isomeric molecular assemblies with distinct physical properties. Such results are of importance for improving our understanding of the emergence of complexity in chemistry and biology.

Lung epithelial NOX/DUOX and respiratory virus infections.

Determining the role of NADPH oxidases in the context of virus infection is an emerging area of research and our knowledge is still sparse. The expression of various isoforms of NOX/DUOX (NADPH oxidase/dual oxidase) in the epithelial cells (ECs) lining the respiratory tract renders them primary sites from which to orchestrate the host defence against respiratory viruses. Accumulating evidence reveals distinct facets of the involvement of NOX/DUOX in host antiviral and pro-inflammatory responses and in the control of the epithelial barrier integrity, with individual isoforms mediating co-operative, but surprisingly also opposing, functions. Although in vivo studies in mice are in line with some of these observations, a complete understanding of the specific functions of epithelial NOX/DUOX awaits lung epithelial-specific conditional knockout mice. The goal of the present review is to summarize our current knowledge of the role of individual NOX/DUOX isoforms expressed in the lung epithelium in the context of respiratory virus infections so as to highlight potential opportunities for therapeutic intervention.

Sustained activation of interferon regulatory factor 3 during infection by paramyxoviruses requires MDA5.

Retinoic acid-inducible gene I (RIG-I) and melanoma differentiation-associated gene 5 (MDA5) are the main cytosolic sensors of single-stranded RNA viruses, including paramyxoviruses, and are required to initiate a quick and robust innate antiviral response. Despite different ligand-binding properties, the consensus view is that RIG-I and MDA5 trigger common signal(s) to activate interferon regulatory factor 3 (IRF-3) and NF-κB, and downstream antiviral and proinflammatory cytokine expression. Here, we performed a thorough analysis of the temporal involvement of RIG-I and MDA5 in the regulation of IRF-3 during respiratory syncytial virus (RSV) infection. Based on specific RNA interference-mediated knockdown of RIG-I and MDA5 in A549 cells, we confirmed that RIG-I is critical for the initiation of IRF-3 phosphorylation, dimerization and downstream gene expression. On the other hand, our experiments yielded the first evidence that knockdown of MDA5 leads to early ubiquitination and proteasomal degradation of active IRF-3. Conversely, ectopic expression of MDA5 prolonged RIG-I-induced IRF-3 activation. Altogether, we provide novel mechanistic insight into the temporal involvement of RIG-I and MDA5 in the innate antiviral response. While RIG-I is essential for initial IRF-3 activation, engagement of induced MDA5 is essential to prevent early degradation of IRF-3, thereby sustaining IRF-3-dependent antiviral gene expression. MDA5 plays a similar role during Sendai virus infection suggesting that this model is not restricted to RSV amongst paramyxoviruses.

Genome-wide RNAi screen reveals a new role of a WNT/CTNNB1 signaling pathway as negative regulator of virus-induced innate immune responses.

To identify new regulators of antiviral innate immunity, we completed the first genome-wide gene silencing screen assessing the transcriptional response at the interferon-ß (IFNB1) promoter following Sendai virus (SeV) infection. We now report a novel link between WNT signaling pathway and the modulation of retinoic acid-inducible gene I (RIG-I)-like receptor (RLR)-dependent innate immune responses. Here we show that secretion of WNT2B and WNT9B and stabilization of ß-catenin (CTNNB1) upon virus infection negatively regulate expression of representative inducible genes IFNB1, IFIT1 and TNF in a CTNNB1-dependent effector mechanism. The antiviral response is drastically reduced by glycogen synthase kinase 3 (GSK3) inhibitors but restored in CTNNB1 knockdown cells. The findings confirm a novel regulation of antiviral innate immunity by a canonical-like WNT/CTNNB1 signaling pathway. The study identifies novel avenues for broad-spectrum antiviral targets and preventing immune-mediated diseases upon viral infection.

IFNß/TNFα synergism induces a non-canonical STAT2/IRF9-dependent pathway triggering a novel DUOX2 NADPH oxidase-mediated airway antiviral response.

Airway epithelial cells are key initial innate immune responders in the fight against respiratory viruses, primarily via the secretion of antiviral and proinflammatory cytokines that act in an autocrine/paracrine fashion to trigger the establishment of an antiviral state. It is currently thought that the early antiviral state in airway epithelial cells primarily relies on IFNß secretion and the subsequent activation of the interferon-stimulated gene factor 3 (ISGF3) transcription factor complex, composed of STAT1, STAT2 and IRF9, which regulates the expression of a panoply of interferon-stimulated genes encoding proteins with antiviral activities. However, the specific pathways engaged by the synergistic action of different cytokines during viral infections, and the resulting physiological outcomes are still ill-defined. Here, we unveil a novel delayed antiviral response in the airways, which is initiated by the synergistic autocrine/paracrine action of IFNß and TNFα, and signals through a non-canonical STAT2- and IRF9-dependent, but STAT1-independent cascade. This pathway ultimately leads to the late induction of the DUOX2 NADPH oxidase expression. Importantly, our study uncovers that the development of the antiviral state relies on DUOX2-dependent H2O2 production. Key antiviral pathways are often targeted by evasion strategies evolved by various pathogenic viruses. In this regard, the importance of the novel DUOX2-dependent antiviral pathway is further underlined by the observation that the human respiratory syncytial virus is able to subvert DUOX2 induction.

Homoleptic 1-D iron selenolate complexes-synthesis, structure, magnetic and thermal behaviour of (1)(∞)[Fe(SeR)2] (R=Ph, Mes).

The first examples of polymeric homoleptic iron chalcogenolato complexes (1)(∞)[Fe(SePh)(2)] and (1)(∞)[Fe(SeMes)(2)] (Ph = phenyl = C(6)H(5), Mes = mesityl = C(6)H(2)-2,4,6-(CH(3))(3)) have been both prepared by reaction of [Fe(N(SiMe(3))(2))(2)] with two equivalents of HSeR (R = Ph, Mes) while (1)(∞)[Fe(SePh)(2)] was found to be also easily accessible through reactions of either FeCl(2), Fe(OOCCH(3))(2) or FeCl(3) with PhSeSiMe(3) in THF. In the crystal, the two compounds form one-dimensional chains with bridging selenolate ligands comprising distinctly different Fe-Se-Fe bridging angles, namely 71.15-72.57° in (1)(∞)[Fe(SePh)(2)] and 91.80° in (1)(∞)[Fe(SeMes)(2)]. Magnetic measurements supported by DFT calculations reveal that this geometrical change has a pronounced influence on the antiferromagnetic exchange interactions of the unpaired electrons along the chains in the two different compounds with a calculated magnetic exchange coupling constant of J = -137 cm(-1) in (1)(∞)[Fe(SePh)(2)] and J = -20 cm(-1) in (1)(∞)[Fe(SeMes)(2)]. In addition we were able to show that the ring molecule [Fe(SePh)(2)](12) which is a structural isomer of (1)(∞)[Fe(SePh)(2)] behaves magnetically similar to the latter one. Investigations by powder XRD reveal that the ring molecule is only a metastable intermediate which converts in THF completely to form (1)(∞)[Fe(SePh)(2)]. Thermal gravimetric analysis of (1)(∞)[Fe(SePh)(2)] under vacuum conditions shows that the compound is thermally labile and already starts to decompose above 30 °C in a two step process under cleavage of SePh(2) to finally form at 250 °C tetragonal PbO-type FeSe. The reaction of (1)(∞)[Fe(SePh)(2)] with the Lewis base 1,10-phenanthroline yielded, depending on the conditions, the octahedral monomeric complexes [Fe(SePh)(2)(1,10-phen)(2)] and [Fe(1,10-phen)(3)][Fe(SePh)(4)].

Requirement of NOX2 and reactive oxygen species for efficient RIG-I-mediated antiviral response through regulation of MAVS expression.

The innate immune response is essential to the host defense against viruses, through restriction of virus replication and coordination of the adaptive immune response. Induction of antiviral genes is a tightly regulated process initiated mainly through sensing of invading virus nucleic acids in the cytoplasm by RIG-I like helicases, RIG-I or Mda5, which transmit the signal through a common mitochondria-associated adaptor, MAVS. Although major breakthroughs have recently been made, much remains unknown about the mechanisms that translate virus recognition into antiviral genes expression. Beside the reputed detrimental role, reactive oxygen species (ROS) act as modulators of cellular signaling and gene regulation. NADPH oxidase (NOX) enzymes are a main source of deliberate cellular ROS production. Here, we found that NOX2 and ROS are required for the host cell to trigger an efficient RIG-I-mediated IRF-3 activation and downstream antiviral IFNbeta and IFIT1 gene expression. Additionally, we provide evidence that NOX2 is critical for the expression of the central mitochondria-associated adaptor MAVS. Taken together these data reveal a new facet to the regulation of the innate host defense against viruses through the identification of an unrecognized role of NOX2 and ROS.

Synthesis and structure of an "iron-doped" copper selenide cluster molecule: [Cu30Fe2Se6(SePh)24(dppm)4].

CuCl and bis(diphenylphosphanyl)methane (dppm) react in the presence of small amounts of FeCl(3) with PhSeSiMe(3) and Se(SiMe(3))(2) to yield [Cu(30)Fe(2)Se(6)(SePh)(24)(dppm)(4)]. The crystal structure of the compound was determined by single-crystal X-ray analysis to give a mixed copper selenide/selenolate cluster molecule of a new structural type incorporating two central iron atoms. The formal oxidation state of the iron atoms was determined by Mössbauer spectroscopy to be +3, in agreement with quantum chemical calculations and modeling of the magnetic data. In addition, Mössbauer studies show no magnetic hyperfine structure in zero field, and the magnetically perturbed spectrum displays a pattern typical for a diamagnetic species in a transverse field, suggesting a singlet ground state. However, the inclusion of the iron atoms has a distinct influence on the optical properties of the compound compared to similar clusters containing only copper and selenium atoms.

Expanding the coordination cage: a ruthenium(II)-polypyridine complex exhibiting high quantum yields under ambient conditions.

A mononuclear ruthenium(II) polypyridyl complex with an enlarged terpyridyl coordination cage was synthesized by the formal introduction of a carbon bridge between the coordinating pyridine rings. Structurally, the ruthenium(II) complex shows an almost perfect octahedral N6 coordination around the central Ru(II) metal ion. The investigation of the photophysical properties reveals a triplet metal-to-ligand charge transfer emission with an unprecedented quantum yield of 13% and a lifetime of 1.36 mus at room temperature and in the presence of air oxygen. An exceptional small energy gap between light absorption and light emission, or Stokes shift, was detected. Additionally, time-dependent density functional theory calculations were carried out in order to characterize the ground state and both the singlet and triplet excited states. The exceptional properties of the new compound open the perspective of exploiting terpyridyl-like ruthenium complexes in photochemical devices under ambient conditions.

Dual role of NOX2 in respiratory syncytial virus- and sendai virus-induced activation of NF-kappaB in airway epithelial cells.

Human respiratory syncytial virus (RSV), a member of the Paramyxoviridae family, is the most important viral agent of pediatric respiratory tract disease worldwide. Human airway epithelial cells (AEC) are the primary targets of RSV. AEC are responsible for the secretion of a wide spectrum of cytokines and chemokines that are important mediators of the exacerbated airway inflammation triggered by the host in response to RSV infection. NF-kappaB is a key transcription factor responsible for the regulation of cytokine and chemokine gene expression and thus represents a potential therapeutic target. In the present study, we sought to delineate the role of RSV-induced reactive oxygen species in the regulation of the signaling pathways leading to NF-kappaB activation. First, we demonstrate that besides the well-characterized IkappaBalpha-dependent pathway, phosphorylation of p65 at Ser(536) is an essential event regulating NF-kappaB activation in response to RSV in A549. Using antioxidant and RNA-interference strategies, we show that a NADPH oxidase 2 (NOX2)-containing NADPH oxidase is an essential regulator of RSV-induced NF-kappaB activation. Molecular analyses revealed that NOX2 acts upstream of both the phosphorylation of IkappaBalpha at Ser(32) and of p65 at Ser(536) in A549 and normal human bronchial epithelial cells. Similar results were obtained in the context of infection by Sendai virus, thus demonstrating that the newly identified NOX2-dependent NF-kappaB activation pathway is not restricted to RSV among the Paramyxoviridae. These results illustrate a previously unrecognized dual role of NOX2 in the regulation of NF-kappaB in response to RSV and Sendai virus in human AEC.