Coarse-graining and renormalisation group methods for the elucidation of the kinetics of complex nucleation and growth processes

We review our work on generalisations of the Becker-Doring model of cluster-formation as applied to nucleation theory, polymer growth kinetics, and the formation of upramolecular structures in colloidal chemistry. One valuable tool in analysing mathematical models of these systems has been the coarse-graining approximation which enables macroscopic models for observable quantities to be derived from microscopic ones. This permits assumptions about the detailed molecular mechanisms to be tested, and their influence on the large-scale kinetics of surfactant self-assembly to be elucidated. We also summarise our more recent results on Becker-Doring systems, notably demonstrating that cross-inhibition and autocatalysis can destabilise a uniform solution and lead to a competitive environment in which some species flourish at the expense of others, phenomena relevant in models of the origins of life.

Theoretical and experimental study on the role of benzoquinone in the Guerbet reaction catalyzed by a ruthenium complex

The benzoquinone was found as an effective co-catalyst in the ruthenium/NaOEt-catalyzed Guerbet reaction. The co-catalyst behavior has therefore been investigated through experimental and computational methods. The reaction products distribution shows that the reaction speed is improved by the benzoquinone supplement since the beginning of the process, having a minimal effect on the selectivity toward alcoholic species. DFT calculations were performed to investigate two hypotheses for the kinetic effects: i) a hydrogen storage mechanism or ii) a basic co-catalysis of 4-hydroxiphenolate. The most promising results were found for the latter hypothesis, where a new mixed mechanism for the aldol condensation step of the Guerbet process involves the hydroquinone (i.e. the reduced form of benzoquinone) as proton source instead of ethanol. This mechanism was found to be energetically more favorable than an aldol condensation in absence of additive, suggesting that the hydroquinone derived from benzoquinone could be the key species affecting the kinetics of the overall process. To verify this theoretical hypothesis, new phenol derivatives were tested as additives in the Guerbet reaction. The outcomes confirmed that an aromatic acid (stronger than ethanol) could improve the reaction kinetics. Lastly, theoretical products distributions were simulated and compared to the experimental one, using the DFT computations to build the kinetic models.

Nitric oxide photorelease from hydrogels and from skin containing a nitro-ruthenium complex

Nitric oxide (NO) is a gaseous molecule that has specific functions dictated by its localization and its kinetics of release. As NO-donors have a range of potential uses in the skin, much attention has been paid to the development of topical NO delivery systems. The aim of this work was to study the release rate and the skin penetration of the NO-donor cis[Ru(NO(2))(bpy)(2)(4-pic)](+) from different gel formulations and their potential as topical NO delivery systems under light stimuli. Among the formulations developed, the anionic gel retarded the nitro-ruthenium complex diffusion and also obstructed NO release after light irradiation. On the other hand, NO release before light irradiation was observed when the complex was dispersed in the cationic chitosan gel, possibly due to oxi-redox reactions between the amino groups of the polymer and the drug molecule. Finally, the non-ionic gel released the NO after light irradiation to the same extent as a drug aqueous solution at the same pH. The drug dispersed in this gel also penetrated into the stratum corneum skin layer, and the nitro-ruthenium complex present in the skin was able to release the NO after light stimuli, suggesting the potential use of this formulation as a topical NO delivery system. (C) 2010 Elsevier B.V. All rights reserved.

Photoinduced Nitric Oxide and Singlet Oxygen Release from ZnPC Liposome Vehicle Associated with the Nitrosyl Ruthenium Complex: Synergistic Effects in Photodynamic Therapy Application

Under continuous photolysis at 675 nm, liposomal zinc phthalocyanine associated with nitrosyl ruthenium complex [Ru(NH.NHq)(tpy)NO](3+) showed the detection and quantification of nitric oxide (NO) and singlet oxygen ((1)O(2)) release. Photophysical and photochemical results demonstrated that the interaction between the nitrosyl ruthenium complex and the photosensitizer can enable an electron transfer process from the photosensitizer to the nitrosyl ruthenium complex which leads to NO release. Synergistic action of both photosensitizers and the nitrosyl ruthenium complex results in the production of reactive oxygen species and reactive nitrogen species, which is a potent oxidizing agent to many biological tissues, in particular neoplastic cells.

The Ruthenium Complex cis-(Dichloro)tetraammineruthenium(III) Chloride Presents Selective Cytotoxicity Against Murine B Cell Lymphoma (A-20), Murine Ascitic Sarcoma 180 (S-180), Human Breast Adenocarcinoma (SK-BR-3), and Human T Cell Leukemia (Jurkat) Tumor Cell Lines

The aim of present study was to verify the in vitro antitumor activity of a ruthenium complex, cis-(dichloro)tetraammineruthenium(III) chloride (cis-[RuCl(2)(NH(3))(4)]Cl) toward different tumor cell lines. The antitumor studies showed that ruthenium(III) complex presents a relevant cytotoxic activity against murine B cell lymphoma (A-20), murine ascitic sarcoma 180 (S-180), human breast adenocarcinoma (SK-BR-3), and human T cell leukemia (Jurkat) cell lines and a very low cytotoxicity toward human peripheral blood mononuclear cells. The ruthenium(III) complex decreased the fraction of tumor cells in G0/G1 and/or G2-M phases, indicating that this compound may act on resting/early entering G0/G1 cells and/or precycling G2-M cells. The cytotoxic activity of a high concentration (2 mg mL(-1)) of cis-[RuCl(2)(NH(3))(4)]Cl toward Jurkat cells correlated with an increased number of annexin V-positive cells and also the presence of DNA fragmentation, suggesting that this compound induces apoptosis in tumor cells. The development of new antineoplastic medications demands adequate knowledge in order to avoid inefficient or toxic treatments. Thus, a mechanistic understanding of how metal complexes achieve their activities is crucial to their clinical success and to the rational design of new compounds with improved potency.

The Ruthenium Complex cis-(Dichloro) Tetraammineruthenium(III) Chloride Presents Immune Stimulatory Activity on Human Peripheral Blood Mononuclear Cells

Ruthenium compounds in general are well suited for medicinal applications. They have been investigated as immunosuppressants, nitric oxide scavengers, antimicrobial agents, and antimalarials. The aim of this study is to evaluate the immunomodulatory activity of cis-(dichloro) tetraammineruthenium(III) chloride (cis-[RuCl(2)(NH(3))(4)]Cl) on human peripheral blood mononuclear cells (PBMC). The cytotoxic studies performed here revealed that the ruthenium( III) complex presents a cytotoxic activity towards normal human PBMC, only at very high concentration. Results also showed that cis-[ RuCl(2)(NH(3))(4)] Cl presents a dual role on PBMC stimulating proliferation and interleukin-2 (IL-2) production at low concentration and inducing cytotoxicity, inability to proliferate, and inhibiting IL-2 production at high concentration. The noncytotoxic activity of cis-[RuCl(2)(NH(3))(4)] Cl at low concentration towards PBMC, which correlates with the small number of annexin V positive cells and also the absence of DNA fragmentation, suggest that this compound does not induce apoptosis on PBMC. For the first time, we show that, at low concentration (10-100 mu g L(-1)), the cis-[ RuCl(2)(NH(3))(4)] Cl compound induces peripheral blood lymphocytes proliferation and also stimulates them to IL-2 production. These results open a new potential applicability of ruthenium(III) complexes as a possible immune regulatory compound acting as immune suppressor at high concentration and as immune stimulator at low concentration.

Tissue-specific expression of head-to-tail cyclized miniproteins in Violaceae and structure determination of the root cyclotide Viola hederacea root cyclotide1

The plant cyclotides are a family of 28 to 37 amino acid miniproteins characterized by their head-to-tail cyclized peptide backbone and six absolutely conserved Cys residues arranged in a cystine knot motif: two disulfide bonds and the connecting backbone segments form a loop that is penetrated by the third disulfide bond. This knotted disulfide arrangement, together with the cyclic peptide backbone, renders the cyclotides extremely stable against enzymatic digest as well as thermal degradation, making them interesting targets for both pharmaceutical and agrochemical applications. We have examined the expression patterns of these fascinating peptides in various Viola species (Violaceae). All tissue types examined contained complex mixtures of cyclotides, with individual profiles differing significantly. We provide evidence for at least 57 novel cyclotides present in a single Viola species (Viola hederacea). Furthermore, we have isolated one cyclotide expressed only in underground parts of V, hederacea and characterized its primary and three-dimensional structure. We propose that cyclotides constitute a new family of plant defense peptides, which might constitute an even larger and, in their biological function, more diverse family than the well-known plant defensins.

Antileishmanial activity of ruthenium(II)tetraammine nitrosyl complexes

The complexes trans-[Ru(NO)(NH(3))(4)L](X)(3) (X = BF(4)(-), PF(6)(-) or Cl(-) and L = N-heterocyclic ligands, P (OEt)(3), SO(3)(-2)), and [Ru(NO)Hedta)] were shown to exhibit IC(50pro) in the range of 36 (L = imN) to 5000 mu M (L = imC). The inhibitory effects of trans-[Ru(NO)(NH(3))(4)imN](BF(4))(3) and of the Angeli`s salt on the growth of the intramacrophage amastigote form studied were found to be similar while the trans-[Ru(NH(3))(4)imN(H(2)O)](2+) complex was found not to exhibit any substantial antiamastigote effect. The trans-[Ru(NO)(NH(3))(4)imN](BF(4))(3) compound, administered (500 nmol kg(-1) day(-1)) in BALB/c mice infected with Leishmania major, was found to exhibit a 98% inhibition on the parasite growth. Furthermore, this complex proved to be at least 66 times more efficient than glucantime in in vivo experiments. (C) 2010 Elsevier Masson SAS. All rights reserved.

Studies of the Antiproliferative Activity of Ruthenium (II) Cyclopentadienyl-Derived Complexes with Nitrogen Coordinated Ligands

Four cationic ruthenium(II) complexes with the formula [Ru(eta(5)-C5H5)(PPh3)(2)](+), with L = 5-phenyl-1H-tetrazole (TzH) 1, imidazole (ImH) 2, benzo[1,2-b; 4,3-b'] dithio-phen-2-carbonitrile (Bzt) 3, and [5-(2-thiophen-2-yl)-vinyl]-thiophene-2-carbonitrile] (Tvt) 4 were prepared and characterized in view to evaluate their potentialities as antitumor agents. Studies by Circular Dichroism indicated changes in the secondary structure of ct-DNA. Changes in the tertiary structure of pBR322 plasmid DNA were also observed in gel electrophoresis experiment and the images obtained by atomic force microscopy (AFM) suggest strong interaction with pBR322 plasmid DNA; the observed decreasing of the viscosity with time indicates that the complexes do not intercalate between DNA base pairs. Compounds 1, 2, and 3 showed much higher cytotoxicity than the cisplatin against human leukaemia cancer cells (HL-60 cells).

Biosynthesis-Assisted Structural Elucidation of the Bartolosides, Chlorinated Aromatic Glycolipids from Cyanobacteria

The isolation of the bartolosides, unprecedented cyanobacterial glycolipids featuring aliphatic chains with chlorine substituents and C-glycosyl moieties, is reported. Their chlorinated dialkylresorcinol (DAR) core presented a major structural-elucidation challenge. To overcome this, we discovered the bartoloside (brt) biosynthetic gene cluster and linked it to the natural products through in vitro characterization of the DAR-forming ketosynthase and aromatase. Bioinformatic analysis also revealed a novel potential halogenase. Knowledge of the bartoloside biosynthesis constrained the DAR core structure by defining key pathway intermediates, ultimately allowing us to determine the full structures of the bartolosides. This work illustrates the power of genomics to enable the use of biosynthetic information for structure elucidation.

HCF-1 self-association via an interdigitated Fn3 structure facilitates transcriptional regulatory complex formation.

Host-cell factor 1 (HCF-1) is an unusual transcriptional regulator that undergoes a process of proteolytic maturation to generate N- (HCF-1(N)) and C- (HCF-1(C)) terminal subunits noncovalently associated via self-association sequence elements. Here, we present the crystal structure of the self-association sequence 1 (SAS1) including the adjacent C-terminal HCF-1 nuclear localization signal (NLS). SAS1 elements from each of the HCF-1(N) and HCF-1(C) subunits form an interdigitated fibronectin type 3 (Fn3) tandem repeat structure. We show that the C-terminal NLS recruited by the interdigitated SAS1 structure is required for effective formation of a transcriptional regulatory complex: the herpes simplex virus VP16-induced complex. Thus, HCF-1(N)-HCF-1(C) association via an integrated Fn3 structure permits an NLS to facilitate formation of a transcriptional regulatory complex.

ASIC1a oligomerization structure-function of its extracellular vestibule and functional characterization of αS243Pβɣ ENaC

Quatre cristaux du canal ASIC1a ont été publiés et soutiennent une stoechiométrie trimérique. Cependant, ces données contredisant de précédentes analyses fonctionnelles effectuées sur des canaux de la même famille, notre intérêt fut porté sur l'oligomérisation d'ASIC1a. Dans ce sens, un nouvel essai couplant la méthode d'analyse par substitution de cystéines (SCAM) avec l'utilisation de réactifs sulfhydryls bifonctionnels (crosslinkers) a été mis en place. Le but étant de stabiliser, puis sélectionner les canaux fonctionnels, pour ensuite les séparer selon leur taille par SDS-PAGE. Grâce à cette technique, nous avons démontré que le complexe stabilisé a une taille coïncidant avec une organisation tétramérique. En plus de son oligomérisation, le chemin emprunté par les ions pour traverser le canal n'est pas clairement défini dans ces structures. De ce fait, utilisant une approche électrophysiologique, nous avons étudié le lien entre la structure et la fonction du vestibule extracellulaire d'ASIC1a. Dans ce but, nous nous sommes intéressés l'accessibilité de cystéines spécifiques localisées dans ce vestibule pour des réactifs méthanethiosulfonates (MTS). Ainsi, nous avons pu corréler les cinétiques de modification de ces cystéines par les MTS avec les effets sur le courant sodique, et donc avoir des informations supplémentaires sur la voie empruntée par les ions. De plus, la simulation informatique de liaison de ces réactifs illustre le remplissage total de ce vestibule. Fonctionnellement, cette interaction ne perturbe pas le passage de ions, c'est pourquoi il nous apparaît probable que le vestibule présente une taille plus large que celle illustrée par les cristaux. Dans un deuxième temps, notre intérêt fut porté sur ENaC. Ce canal est composé des trois sous-unités (a, ß et y) et est exprimé dans divers épithéliums, dont les tubules des reins. Il participe à l'homéostasie sodique et est essentiellement régulé par voie hormonale via l'aldostérone et la Vasopressine, mais également par des sérines protéases ou le Na+. Nous avons étudié la répercussion fonctionnelle de la mutation aS243P, découverte chez un nouveau-né prématuré atteint de pseudohypoaldostéronisme de type 1. Cette maladie autosomale récessive se caractérise, généralement, par une hyponatrémie liée à d'importantes pertes de sel dans les urines, une hyperkaliémie, ainsi qu'un niveau élevé d'aldostérone. Tout d'abord aucune des expériences biochimiques et électrophysiologiques n'a pu démontrer un défaut d'expression ou une forte diminution de l'activité soutenant les données cliniques. Cependant, en challengeant aS243PßyENaC avec une forte concentration de Na+ externe, une hypersensibilité de canal fut observée. En effet, ni les phénomènes régulateurs de « feedback inhibition » ou de « Na+ self-inhibition » n'étaient semblables au canal sauvage. De ce fait, ils apparaissaient exacerbés en présence de la mutation, amenant ainsi à une diminution de la réabsorption de Na+. Ceci corrobore entièrement l'hyponatrémie diagnostiquée. Le rein d'un prématuré étant immature, la quantité de Na+ atteignant la partie distale du néphron est plus élevée, du fait que les autres mécanismes de réabsorption en amont ne sont probablement pas encore en place. Cette hypothèse est renforcée par l'existence d'un frère présentant la même mutation, mais qui, né à terme, ne présentait aucun signe d'hyponatrémie. - The main topic of my thesis is the structure-function relationship of the ENaC/Deg family of ion channels, namely the Acid-Sensing Ion Channel ASIC1a and the Epithelial Na Channel ENaC. The primary part of this research is dedicated to the structure of ASIC1a. Four channel crystals have been published, which support a trimeric stoichiometry, although these data contradict previous functional experiments on other ENaC/Deg members. We are therefore interested in ASIC1a oligomerization and have set up a new assay combining the Substituted- Cysteine Accessibility Method (SCAM) with Afunctional sulfhydryl reagents (crosslinkers) allowing its study. The aim was to first stabilize the channels, then select those that are functional and then resolve them according to their size on SDS-PAGE. We demonstrated that the stabilized complex has a molecular weight corresponding to a tetrameric stoichiometry. In addition to our interest in the oligomerization of the ENaC/Deg family of ion channels, we also wanted to investigate the thus far undefined way of permeation for these channels. Therefore, taking the advantage of a more electrophysiological approach, we studied the accessibility of specific cysteines for methanethiosulfonate reagents (MTS) and were able to correlate the MTS association kinetics on cysteine residues with Na+ currents. These results have given us an insight into ion permeation and our functional evidence indicates that the extracellular is larger than that depicted by the crystal structures. As a side project, we focused on ENaC, which is made up of three subunits (a, ß and y) and is expressed in various epithelia, especially in the distal nephron of the kidneys. It plays a role in Na+ homeostasis and is essentially regulated by hormones via aldosterone and vasopressin, but also by serine proteases or Na+. We have studied the functional impact of the aS243P mutation, discovered in a premature baby suffering from pseudohypoaldosteronism of type 1. This autosomal recessive disease is characterized by hyponatremia, hyperkalemia and high aldosterone levels. Firstly, neither biochemical nor electrophysiological experiments indicated an expression defect or a strong decrease in activity. However, challenging aS243PßyENaC with increased external Na+ concentration showed channel hypersensitivity. Indeed, both the "feedback inhibition" and the "Na+ self-inhibition" regulatory mechanisms are impaired, leading to a decrease in Na+ reabsorption, entirely supports the diagnosis. The kidneys in preterm infants are immature and Na+ levels reaching the distal nephron are higher than normally observed. We hypothesize that the upstream reabsorption machinery is unlikely to be sufficiently matured and this assumption is supported by an asymptomatic sibling carrying the same mutation, but born at term. - La cellule, unité fonctionnelle du corps humain, est délimitée par une membrane plasmique servant de barrière biologique entre les milieux intra et extracellulaires. Une communication entre cellules est indispensable pour un fonctionnement adéquat. Sa survie dépend, entre autres, du maintien de la teneur en ions dans chacun des milieux qui doivent pouvoir être réabsorbés, ou sécrétés, selon les besoins. Les protéines insérées dans la membrane forment un canal et sont un moyen de communication permettant spécifiquement à des ions tel que le sodium (Na+) de traverser. Le Na+ se trouve dans la plupart des aliments et le sel, et est spécifiquement réabsorbé au niveau des reins grâce au canal sodique épithélial ENaC. Cette réabsorption se fait de l'urine primaire vers l'intérieur de la cellule, puis est transporté vers le sang. Pour maintenir un équilibre, une régulation de ce canal est nécessaire. En effet, des dysfonctionnements impliquant la régulation ou l'activité d'ENaC lui-même sont à l'origine de maladies telles que la mucoviscidose, l'hypertension ou encore, le pseudohypoaldostéronisme (PHA). Cette maladie est caractérisée, notamment, par d'importantes pertes de sel dans les urines. Des pédiatres ont diagnostiqué un PHA chez un nouveau-né, ce dernier présentant une modification du canal ENaC, nous avons recréé cette protéine afin d'étudier l'impact de ce changement sur son activité. Nous avons démontré que la régulation d'ENaC était effectivement perturbée, conduisant ainsi à une forte réduction de la réabsorption sodique. Afin de développer des molécules capables de moduler l'activité de protéines. Il est nécessaire d'en connaître la structure. Celle du canal sodique sensible à l'acidification ASIC1, un canal cousin d'ENaC, est connue. Ces données structurales contredisant cependant les analyses fonctionnelles, nous nous sommes penchés une nouvelle fois sur ASIC1. Une protéine est une macromolécule biologique composée d'une chaîne d'acides aminés (aa). De l'enchaînement d'aa à la protéine fonctionnelle, quatre niveaux de structuration existent. Chaque aa donne une indication quant au repliement et plus particulièrement la cystéine. Arborant un groupe sulfhydryle (SH) capable de former une liaison spécifique et stable avec un autre SH, celle-ci est souvent impliquée dans la structure tridimensionnelle de la protéine. Ce type de liaison intervient également dans la stabilisation de la structure quaternaire, qui est l'association de plusieurs protéines identiques (homomère), ou pas (hétéromère). Dans cette partie, nous avons remplacé des aa par des cystéines à des endroits spécifiques. Le but était de stabiliser plusieurs homomères d'ASICl ensemble avec des réactifs créant des ponts entre deux SH. Ainsi, nous avons pu déterminer le nombre de protéines ASIC1 participant à la formation d'un canal fonctionnel. Nos résultats corroborent les données fonctionnelles soutenant un canal tétramérique. Nous avons également étudié l'accessibilité de ces nouvelles cystéines afin d'obtenir des informations supplémentaires sur la structure du chemin emprunté par le Na+ à travers ASIC1 et plus particulièrement du vestibule extracellulaire.

Error and attack tolerance of layered complex networks.

Many complex systems may be described by not one but a number of complex networks mapped on each other in a multi-layer structure. Because of the interactions and dependencies between these layers, the state of a single layer does not necessarily reflect well the state of the entire system. In this paper we study the robustness of five examples of two-layer complex systems: three real-life data sets in the fields of communication (the Internet), transportation (the European railway system), and biology (the human brain), and two models based on random graphs. In order to cover the whole range of features specific to these systems, we focus on two extreme policies of system's response to failures, no rerouting and full rerouting. Our main finding is that multi-layer systems are much more vulnerable to errors and intentional attacks than they appear from a single layer perspective.

Fast atom bombardment mass spectrometry studies of ruthenium (II) polypyridy coordination complexes and of group V Triptycenes and related complexes

In order to investigate the use of Fast Atom Bombardment Mass Spectrometry (FAB-MS) as a tool for structural characterization, two groups of complexes are analyzed. The first group is a set of ruthenium(II) coordination complexes containing bidentate polypyridyl ligands. The positive and negative ion FAB-MS spectra are found to be sufficient to allow for an almost complete characterization of the central metal atom, the ligands and the counter anions contained in the intact complex. An unusual observation of mUltiply charged ions in the positive ion FAB-MS spectra (i.e. [RUL 3 ]2+) is explained to be as a result of the oxidative quenching of the excited state of the doubly charged ion by the matrix, 3-nitrobenzyl alcohol. An analysis of a mixture shows that the technique is a good one for identifying components therein. A group of triptycene and related complexes containing Group V elements is also analyzed by FAB-MS and the results. in terms of relative abundances of fragment ions, are found to be consistent with known metal-carbon bond strengths.

Elucidation of the components involved in the antioxidant activity of honey

Canadian honeys were analyzed for sugar concentration, honey colour, total phenolic content, the level of brown pigments, and antioxidant activity in order to elucidate the main components involved in the antioxidant activity of honey. By employing size-exclusion chromatography in combination with activity-guided fractionation, it was demonstrated that the antioxidant components are of high molecular weight (HMW), brown in colour and absorb at both 280nm and 450nm. The presence of brown HMW antioxidant components prompted an investigation on the influence of heattreatment on the Maillard reaction and the formation of melanoid ins. Heat-treatment of honey resulted in an increase in the level of phenolics in the melanoidin fractions which correlated with an increase in antioxidant activity. The preliminary results of this study suggest for the first time that honey melanoidins underlie the antioxidant activity of unheated and heat-treated honey, and that phenolic constituents are involved in the melanoidin structure and are likely incorporated by covalent or non-covalent interaction.