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See detailMolecular dynamic simulations of a beta amphiphilic peptide
Crowet, Jean-Marc ULg; Deschamps, Antoine; Soumillion, Patrice et al

Conference (2013, October 03)

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See detailEliciteurs dérivés de rhamnolipides : synthèses, modélisations et activités biologiques
Mayon, Patrick; Ait Barka, Essaid; Baillieul, Fabienne et al

Poster (2013, July 04)

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See detailAn interaction map for HTLV-1 Tax and PDZ-containing proteins.
Blibek, Karim ULg; Rambout, Xavier ULg; beaufays, Jérôme et al

Poster (2013, June 29)

Human T-cell leukemia virus type 1 (HTLV-1) retrovirus encodes for the Tax protein, which has a transforming capacity in vitro. Tax contains at its C-terminus a binding motif for PDZ domain-containing ... [more ▼]

Human T-cell leukemia virus type 1 (HTLV-1) retrovirus encodes for the Tax protein, which has a transforming capacity in vitro. Tax contains at its C-terminus a binding motif for PDZ domain-containing proteins (PSD95-DLG1-ZO1). It has been shown that the C-terminal motif of Tax is involved in Tax oncogenic capacity. Ten different PDZ domain-containing proteins have been reported to interact with Tax, but the specificity of Tax-human PDZome interactions has not been investigated. The objective of this study is to obtain a comprehensive interactome map for Tax and the human PDZome and to determine a global role of Tax-PDZ interactions in HTLV-1 biology. [less ▲]

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See detailGaining speed in molecular dynamics simulations by implicit representation of water and membrane molecules
Steinhauer, Sven ULg; Crowet, Jean-Marc ULg; Brasseur, Robert ULg et al

Poster (2013, June 19)

Molecular dynamics (MD) is an appropriate method for investigation of peptide-membrane systems and helps in analyzing results from experiments. In many cases, the ability of viral fusion proteins and ... [more ▼]

Molecular dynamics (MD) is an appropriate method for investigation of peptide-membrane systems and helps in analyzing results from experiments. In many cases, the ability of viral fusion proteins and toxins for destabilizing the membrane is due to their hydrophobic profile, leading to particular membrane insertion. By now, many relevant processes for drug design, toxicological studies and other fields of application, are not feasible by MD simulations, when each atom is represented over time. Processes such as protein folding, often take place above the time scales reachable by MD simulations, which are of the order of micro seconds. The necessary time effort for carrying out such simulations stays considerable and depends mainly on (1) the complexity of the simulated system (2) the simulated time scale (3) the simulation method (4) the efficiency of used hardware and software algorithms. Nowadays, MD simulations can still take weeks of calculation on high end computers. Impala is an implicit water and lipids forcefield, initially developed by our laboratory. Implicit forcefields replace water and/or lipid molecules by a couple of simple and partially precalculable equations. Using this method, thousands of water and lipid molecules can be replaced in MD simulations using Gromacs software. This leads to a considerable reduction of system complexity. The original Impala algorithm based on the assumption of rigid peptides and used a Monte Carlo algorithm with the aim of finding the insertion characteristics of these molecules in membranes. Our current work is the integration of the Impala forcefield into Gromacs, a freely accessible MD software. Replacing the aqueous and lipid phase atomic description in Gromacs MD by an implicit forcefield is supposed to lead to a gain of speed compared to full atomistic simulations. A gain of precision compared to Impala is expected, too. This will be achieved by turning molecules flexible, when implementing Impala into Gromacs. [less ▲]

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See detailAnalysis of the interactions of xylose-based bolaforms with model membranes
Nasir, Mehmet Nail ULg; Monhonval, Pierre; Legrand, Vincent et al

Poster (2013, June)

Sugar-based surfactants are natural and biocompatible compounds. Among sugar-based surfactants, there is an increase of interest for the xylose-based bolaforms because of their potential applications in ... [more ▼]

Sugar-based surfactants are natural and biocompatible compounds. Among sugar-based surfactants, there is an increase of interest for the xylose-based bolaforms because of their potential applications in pharmaceutical and cosmetic fields and of their original physicochemical properties. Xylose-based bolaforms have interfacial and membrane-interacting properties making them potential molecules for drug delivery systems. For this work, we chemically synthetized by metathesis in the presence of Grubbs I catalyzer, a novel symmetric bolaform composed of two xylose polar heads connected by an ether link to a hydrocarbon chain having 18 carbon atoms with an unsaturation (BolaX). We were able to obtain two bolaforms differing only at the level of the anomeric configuration of the xylose moieties, or orBolaX). The surface activities of both compounds were analyzed. The anomeric configuration  gives interfacial properties at the air-water interface contrary to the  one. The interactions of the BolaX with model membranes were then analyzed in order to determine if it can be used for drug delivery systems. Our results show that BolaX were able to interact and insert within lipid monolayers containing phospholipids and sterols. In order to have informations at the molecular level of these interactions, another model membrane, called multilamellar vesicles (MLVs), containing phospholipids and sterols with or without  BolaX were prepared. Both MLVs were analyzed by the means of the FTIR spectroscopy. In parallel, we have calculated the interaction energy of the  BolaX with different lipid molecules by the means of the Hypermatrix method developed at our laboratory. Moreover, the insertion of the  BolaX within the lipid bilayers was simulated using our IMPALA method. Taking together, our findings indicate that BolaX would be a potential candidate for drug delivery systems because of its surface active properties and its ability to insert within membranes. [less ▲]

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See detailNovel phenolic glycolipids: antioxidant activity and effect on membrane models
Sainvitu, Pauline ULg; Nasir, Mehmet Nail ULg; Draguet, Florian et al

Poster (2013, May 30)

Aromatic glycolipids are of both medical as well as pharmaceutical interest. Antimicrobial, antiviraland antiinflammatory activities have been reported (Otto, 2000, Journal of Molecular Catalysis B ... [more ▼]

Aromatic glycolipids are of both medical as well as pharmaceutical interest. Antimicrobial, antiviraland antiinflammatory activities have been reported (Otto, 2000, Journal of Molecular Catalysis B: Enzymatic). Moreover, they are expected to have interesting antioxidant properties when they contain phenolic groups. The alkyl chain should enhance their ability to penetrate into the cellular membrane (Nicolosi, 2002, Journal of Molecular Catalysis B: Enzymatic). The presence of a sugar unit could also be useful to target specific cells. In this study, novel aromatic glycolipids were synthesized as useful models for studying the structure–activity relationship, in particular as regards to their aromatic group.Theireffect on cell viability when an oxidative stress is induced was tested. In parallel, their interaction with cell models (liposomes) was studied through membrane fusion and permeability experiments. [less ▲]

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See detailBiophysical characterization of the interaction of novel aromatic glycolipid surfactants with membrane models.
Sainvitu, Pauline ULg; Nasir, Mehmet Nail ULg; Draguet, Florian et al

Poster (2013, May 15)

Aromatic glycolipids are of both medical and pharmaceutical interest. Antimicrobial, antiviral and anti-inflammatory activities have been reported (Otto, 2000, Journal of Molecular Catalysis B: Enzymatic ... [more ▼]

Aromatic glycolipids are of both medical and pharmaceutical interest. Antimicrobial, antiviral and anti-inflammatory activities have been reported (Otto, 2000, Journal of Molecular Catalysis B: Enzymatic). Moreover, they are expected to have interesting antioxidant properties when they contain phenolic groups. The alkyl chain should enhance their ability to penetrate into the cellular membrane (Nicolosi, 2002, Journal of Molecular Catalysis B: Enzymatic). The presence of a sugar unit could also be useful to target specific cells. In this study, novel aromatic glycolipids were synthesized as useful models for studying the structure–activity relationship, in particular as a function of their aromatic group. Their interaction with membranes was studied with monolayer models and was predicted by a computational approach. The relationships between these data and their cytotoxicity and antioxidant properties evaluated on cell cultures are discussed. [less ▲]

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See detailBiophysical characterization of the interaction of novel aromatic glycolipid surfactants with membrane models.
Sainvitu, Pauline ULg; Nasir, Mehmet Nail ULg; Nott, Katherine ULg et al

in World Academy of Science, Engineering and Technology (2013, May), 77

Aromatic glycolipids are of both medical and pharmaceutical interest. Antimicrobial, antiviral and anti-inflammatory activities have been reported (Otto, 2000, Journal of Molecular Catalysis B: Enzymatic ... [more ▼]

Aromatic glycolipids are of both medical and pharmaceutical interest. Antimicrobial, antiviral and anti-inflammatory activities have been reported (Otto, 2000, Journal of Molecular Catalysis B: Enzymatic). Moreover, they are expected to have interesting antioxidant properties when they contain phenolic groups. The alkyl chain should enhance their ability to penetrate into the cellular membrane (Nicolosi, 2002, Journal of Molecular Catalysis B: Enzymatic). The presence of a sugar unit could also be useful to target specific cells. In this study, novel aromatic glycolipids were synthesized as useful models for studying the structure–activity relationship, in particular as a function of their aromatic group. Their interaction with membranes was studied with monolayer models and was predicted by a computational approach. The relationships between these data and their cytotoxicity and antioxidant properties evaluated on cell cultures are discussed. [less ▲]

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See detailBiophysical characterization of the interaction of novel aromatic glycolipid surfactants with membrane models.
Sainvitu, Pauline ULg; Nasir, Mehmet Nail ULg; Nott, Katherine ULg et al

in World Academy of Science, Engineering and Technology (2013, May), 77

Aromatic glycolipids are of both medical and pharmaceutical interest. Antimicrobial, antiviral and anti-inflammatory activities have been reported (Otto, 2000, Journal of Molecular Catalysis B: Enzymatic ... [more ▼]

Aromatic glycolipids are of both medical and pharmaceutical interest. Antimicrobial, antiviral and anti-inflammatory activities have been reported (Otto, 2000, Journal of Molecular Catalysis B: Enzymatic). Moreover, they are expected to have interesting antioxidant properties when they contain phenolic groups. The alkyl chain should enhance their ability to penetrate into the cellular membrane (Nicolosi, 2002, Journal of Molecular Catalysis B: Enzymatic). The presence of a sugar unit could also be useful to target specific cells. In this study, novel aromatic glycolipids were synthesized as useful models for studying the structure–activity relationship, in particular as a function of their aromatic group. Their interaction with membranes was studied with monolayer models and was predicted by a computational approach. The relationships between these data and their cytotoxicity and antioxidant properties evaluated on cell cultures are discussed. [less ▲]

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See detailSAHBNET, an Accessible Surface-Based Elastic Network: An Application to Membrane Protein
Dony, Nicolas ULg; Crowet, Jean-Marc ULg; Joris, Bernard ULg et al

in International Journal of Molecular Sciences (2013), 14(6), 11510-26

Molecular Dynamics is a method of choice for membrane simulations and the rising of coarse-grained forcefields has opened the way to longer simulations with reduced calculations times. Here, we present an ... [more ▼]

Molecular Dynamics is a method of choice for membrane simulations and the rising of coarse-grained forcefields has opened the way to longer simulations with reduced calculations times. Here, we present an elastic network, SAHBNET (Surface Accessibility Hydrogen-Bonds elastic NETwork), that will maintain the structure of soluble or membrane proteins based on the hydrogen bonds present in the atomistic structure and the proximity between buried residues. This network is applied on the coarse-grained beads defined by the MARTINI model, and was designed to be more physics-based than a simple elastic network. The SAHBNET model is evaluated against atomistic simulations, and compared with ELNEDYN models. The SAHBNET is then used to simulate two membrane proteins inserted in complex lipid bilayers. These bilayers are formed by self-assembly and the use of a modified version of the GROMACS tool genbox (which is accessible through the gcgs.gembloux.ulg.ac.be website). The results show that SAHBNET keeps the structure close to the atomistic one and is successfully used for the simulation of membrane proteins. [less ▲]

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See detailModeling simple lipid phase separation and effects of amphiphilic molecules on lipid domains
Lins, Laurence ULg; Deleu, Magali ULg; Mingeot-Leclercq, Marie-Paule et al

Poster (2013, April 28)

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See detailPrediction of membrane protein structures and TM interactions Rosetta and molecular dynamic studies
Crowet, Jean-Marc ULg; Dony, Nicolas ULg; Joris, Bernard ULg et al

Poster (2013, February 26)

The structures of membrane domains of the Divisome proteins and BlaR are not known and there is no homolog proteins of known structure to build homolgy models. Although the structure prediction of ... [more ▼]

The structures of membrane domains of the Divisome proteins and BlaR are not known and there is no homolog proteins of known structure to build homolgy models. Although the structure prediction of membrane proteins seems easier than for globular proteins, their ab initio prediction remains a difficult task. Only few methods have been used and validated on experimental pdb structures. By using the MARTINI or Bond coarse grain representation, the multimerization of transmembrane helices has been carried out by molecular dynamics, and the structure of several membrane proteins has been predicted by a tool of the Rosetta package. These methods are used here to predict the structure of the membrane embedded part of the politopic proteins from the divisome (FtsW, FtsK, FtsX and MraY) and BlaR. In a following part the MARTINI force field can be used to predict the TM helices interactions between the Divisome protein members. [less ▲]

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See detailIn silico study of antimicrobial cyclic peptides Sequence analysis, molecular modelling and multi-scale molecular dynamics
Crowet, Jean-Marc ULg; Soumillion, Patrice; Brasseur, Robert ULg et al

Poster (2013, February 26)

The selection and use of antimicrobial cyclic peptides is an active way of research. These peptides are naturally produced by several microorganisms et libraries of biosynthetic peptides are actually ... [more ▼]

The selection and use of antimicrobial cyclic peptides is an active way of research. These peptides are naturally produced by several microorganisms et libraries of biosynthetic peptides are actually build to find new antibiotics candidats. However, the mecanism of action of these peptides is not well known and it exists several hypothesis for their interactions with membrane. These peptides are causing broad perturbations to lipidic membranes and it has been shown that they can form disordered toroidal pores or self assemble as amphipathic nanotubes leading to lipid extrusion. Through the analysis of several peptides from the libraries of Pr Soumillion with increasing activity it will be possible to study the relation between the sequence/structure and the membrane activity of these peptides. This will help to decipher between preferential modes of action and the parameters important for the activity. [less ▲]

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See detailSAHBEN, an accessible surface-based elastic network to insert a protein in a complex lipid membrane
Dony, Nicolas ULg; Crowet, Jean-Marc ULg; Joris, Bernard ULg et al

Poster (2013, February 26)

Study of membrane proteins have become one of the most challenging fields in biology. Solving their structure is one important step toward the understanding of their physiological activity but despite the ... [more ▼]

Study of membrane proteins have become one of the most challenging fields in biology. Solving their structure is one important step toward the understanding of their physiological activity but despite the recent advances in membrane protein crystallization, it represents less than 1 % of the entries in the Protein Data Bank. Therefore, calculation methods to study membrane proteins are helpful to complement experimental studies and fill the gap between the information obtained from the sequence and/or structure, the experimental results and the biological activity. Molecular Dynamics (MD) is a method of choice for membrane simulations and the rising of coarse-grained forcefields has opened the way to longer simulations with reduced calculations times. However, these approaches have two main drawbacks, the preparation of the membrane system and the preservation of the 3D protein structure, which is not trivial in CG approach. To circumvent these problems, we propose to use a modified version of the Gromacs tool genbox to easily insert lipids and a network based on hydrogen bonds and accessible surface to maintain the protein 3D structure. This protocol is available through a website (gcgs.gembloux.ulg.ac.be). [less ▲]

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See detailPhysico-chemical and membrane-interacting properties of D-xylose-based bolaforms. Influence of the anomeric configuration
Nasir, Mehmet Nail ULg; Legrand, Vincent; Gatard, Sylvain et al

in MATEC Web of Conferences (2013), 4

Sugar-based biosurfactants such as xylose-derived bolaforms have interesting properties, for example high biocompatibility and biodegradability which make them potential useful molecules in the ... [more ▼]

Sugar-based biosurfactants such as xylose-derived bolaforms have interesting properties, for example high biocompatibility and biodegradability which make them potential useful molecules in the pharmaceutical and cosmetic fields. Until now, no detailed analyses of the physico-chemical properties of these compounds have been undertaken. Two symmetrical D-xylose-based bolaforms were chemically synthesized where the two xylose heads are linked via an acetal link to a hydrocarbon chain containing 18 carbon atoms and an unsaturation. The two bolaforms differ only by their anomeric configuration: or The bolaform exhibits interfacial properties at the air-water interface which is not the case for the . FTIR spectroscopy showed that the interactions between the bolaform and POPC, a model phospholipid, involve the carbonyl groups of the phospholipid [less ▲]

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See detailModeling of non-covalent complexes of the cell-penetrating peptide CADY and its siRNA cargo
Crowet, Jean-Marc ULg; Lins, Laurence ULg; Deshayes, Sébastien et al

in European Biophysics Journal [=EBJ] (2013), 42(S1), 63

CADY is a cell-penetrating peptide spontaneously making non-covalent complexes with short interfering RNAs (siRNAs) in water. Neither the structure of CADY nor that of the complexes is resolved. We have ... [more ▼]

CADY is a cell-penetrating peptide spontaneously making non-covalent complexes with short interfering RNAs (siRNAs) in water. Neither the structure of CADY nor that of the complexes is resolved. We have calculated and analyzed 3D models of CADY and of the non-covalent CADY–siRNA complexes in order to understand their formation and stabilization. Data from the ab initio calculations and molecular dynamics support that, in agreement with the experimental data, CADY is a polymorphic peptide partly helical. We calculated and compared several complexes with peptide/siRNA ratios of up to 40. The initial binding of CADYs is essentially due to the electrostatic interactions of the arginines with siRNA phosphates. Due to a repetitive arginine motif (XLWR(K)), CADYs can adopt multiple positions at the siRNA surface. Nevertheless, several complex properties are common: an average of 14 ± 1 CADYs is required to saturate a siRNA. The 40 CADYs/siRNA that is the optimal ratio for vector stability always corresponds to two layers of CADYs per siRNA and the peptide cage is stabilized by hydrophobic CADY–CADY contacts. The analysis demonstrates that the hydrophobicity, the positive charges and the polymorphism of CADY are mandatory to make stable the CADY–siRNA complexes. [less ▲]

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See detailMechanism of Trypanosoma brucei gambiense resistance to human serum.
Uzureau, Pierrick; Uzureau, Sophie; Lecordier, Laurence et al

in Nature (2013), 501(7467), 430-4

The African parasite Trypanosoma brucei gambiense accounts for 97% of human sleeping sickness cases. T. b. gambiense resists the specific human innate immunity acting against several other tsetse-fly ... [more ▼]

The African parasite Trypanosoma brucei gambiense accounts for 97% of human sleeping sickness cases. T. b. gambiense resists the specific human innate immunity acting against several other tsetse-fly-transmitted trypanosome species such as T. b. brucei, the causative agent of nagana disease in cattle. Human immunity to some African trypanosomes is due to two serum complexes designated trypanolytic factors (TLF-1 and -2), which both contain haptoglobin-related protein (HPR) and apolipoprotein LI (APOL1). Whereas HPR association with haemoglobin (Hb) allows TLF-1 binding and uptake via the trypanosome receptor TbHpHbR (ref. 5), TLF-2 enters trypanosomes independently of TbHpHbR (refs 4, 5). APOL1 kills trypanosomes after insertion into endosomal/lysosomal membranes. Here we report that T. b. gambiense resists TLFs via a hydrophobic beta-sheet of the T. b. gambiense-specific glycoprotein (TgsGP), which prevents APOL1 toxicity and induces stiffening of membranes upon interaction with lipids. Two additional features contribute to resistance to TLFs: reduction of sensitivity to APOL1 requiring cysteine protease activity, and TbHpHbR inactivation due to a L210S substitution. According to such a multifactorial defence mechanism, transgenic expression of T. b. brucei TbHpHbR in T. b. gambiense did not cause parasite lysis in normal human serum. However, these transgenic parasites were killed in hypohaptoglobinaemic serum, after high TLF-1 uptake in the absence of haptoglobin (Hp) that competes for Hb and receptor binding. TbHpHbR inactivation preventing high APOL1 loading in hypohaptoglobinaemic serum may have evolved because of the overlapping endemic area of T. b. gambiense infection and malaria, the main cause of haemolysis-induced hypohaptoglobinaemia in western and central Africa. [less ▲]

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See detailSurface and lipid interaction properties of novel rhamnolipids to explain their eliciting activity
Nasir, Mehmet Nail ULg; Monhonval, Pierre; Nott, Katherine ULg et al

in European Biophysics Journal [=EBJ] (2013), 42(S1), 168

Detailed reference viewed: 33 (9 ULg)