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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

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See detailAnalysis of calcium-induced effects on the conformation of fengycin
Nasir, Mehmet Nail ULg; Laurent, Pascal ULg; Flore, Christelle ULg et al

in Spectrochimica Acta Part A : Molecular and Biomolecular Spectroscopy (2013), 110

A combination of CD, FT-IR, NMR and fluorescence spectroscopic techniques was applied to elucidate the conformation of fengycin, a natural lipopeptide with antifungal and eliciting activities, in a ... [more ▼]

A combination of CD, FT-IR, NMR and fluorescence spectroscopic techniques was applied to elucidate the conformation of fengycin, a natural lipopeptide with antifungal and eliciting activities, in a membrane-mimicking environment and to investigate the effect of calcium ions on the conformation. We mainly observed that fengycin adopts a turn conformation and that the side chain of glutamate residues plays a key role on the stabilization of the peptide ring backbone conformation. More particularly, the binding of calcium ions by the carboxylic moieties has a consequence on the environment of the tyrosine residues. Our data suggest also an arrangement of fengycin molecules into “-sheet like micelles” in a membrane-mimicking environment and the enhancement of this aggregating effect in presence of calcium ions. The modulation of the fengycin conformation by the environmental conditions may influence its biological properties. [less ▲]

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See detailEffects of surfactin on membrane models displaying lipid phase separation.
Deleu, Magali ULg; Lorent, Joseph; Lins, Laurence ULg et al

in Biochimica et Biophysica Acta (2013), 1828(2), 801-815

Surfactin, a bacterial amphiphilic lipopeptide is attracting more and more attention in view of its bioactive properties which are in relation with its ability to interact with lipids of biological ... [more ▼]

Surfactin, a bacterial amphiphilic lipopeptide is attracting more and more attention in view of its bioactive properties which are in relation with its ability to interact with lipids of biological membranes. In this work, we investigated the effect of surfactin on membrane structure using model of membranes, vesicles as well as supported bilayers, presenting coexistence of fluid-disordered (DOPC) and gel (DPPC) phases. A range of complementary methods was used including AFM, ellipsometry, dynamic light scattering, fluorescence measurements of Laurdan, DPH, calcein release, and octadecylrhodamine B dequenching. Our findings demonstrated that surfactin concentration is critical for its effect on the membrane. The results suggest that the presence of rigid domains can play an essential role in the first step of surfactin insertion and that surfactin interacts both with the membrane polar heads and the acyl chain region. A mechanism for the surfactin lipid membrane interaction, consisting of three sequential structural and morphological changes, is proposed. At concentrations below the CMC, surfactin inserted at the boundary between gel and fluid lipid domains, inhibited phase separation and stiffened the bilayer without global morphological change of liposomes. At concentrations close to CMC, surfactin solubilized the fluid phospholipid phase and increased order in the remainder of the lipid bilayer. At higher surfactin concentrations, both the fluid and the rigid bilayer structures were dissolved into mixed micelles and other structures presenting a wide size distribution. [less ▲]

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See detailSynthesis and physico-chemical characterization of fatty esters
Sainvitu, Pauline ULg; Nott, Katherine ULg; Nicks, Francois ULg et al

Poster (2012, November 16)

Specific antioxidant molecules (e.g. phenolics) help to prevent oxidation reaction of the cell membrane. A fatty chain grafted on these compounds should enhance their capacity to interact with the ... [more ▼]

Specific antioxidant molecules (e.g. phenolics) help to prevent oxidation reaction of the cell membrane. A fatty chain grafted on these compounds should enhance their capacity to interact with the membrane lipids. In our study, three fatty esters comprising an aromatic part were synthesized. They differentiate the aromatic substituent and the number of carbons between the aromatic ring and the ester function. A structure-function relationships study was performed to identify the structural pattern affecting the interfacial properties and the membrane interaction properties. The behavior of their monolayer film at an air-water interface was studied. The interactions with membrane were assessed on living cells and were predicted by a computational approach. In the future, we will investigate the effect of the presence of a sugar unit on these molecules. [less ▲]

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See detailMolecular analysis of the interfacial and membrane-interacting properties of D-xylose-based bolaforms
Nasir, Mehmet Nail ULg; Legrand, Vincent; Gatard, Sylvain et al

Poster (2012, October)

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See detailReplacing explicit water and lipids by implicit representation in molecular dynamics simulations
Steinhauer, Sven ULg; Crowet, Jean-Marc ULg; Lins, Laurence ULg et al

Poster (2012, September 11)

Molecular dynamics (MD) is an appropriate method for investigation of biomolecular systems and helps in explaining results from wet lab experiments or in getting further insight into details, which are ... [more ▼]

Molecular dynamics (MD) is an appropriate method for investigation of biomolecular systems and helps in explaining results from wet lab experiments or in getting further insight into details, which are not accessible by experimental methods(Lindahl, 2008). By now, many biologically relevant processes for drug design, toxicological studies and other fields of application, can not be performed by atomistic MD simulations (Lindahl, 2008). <br />In MD, the necessary time effort for carrying out a simulation is 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. Carried out MD simulations nowadays may still take weeks of calculation on high end computers. <br /> <br />In practice, biologically relevant processes, as e.g. protein folding, take usually place above the time scale of milli seconds. They can take up to the order of some thousands of seconds (in case of the folding of membrane proteins). Molecular dynamics computer simulations have reached the scale of micro seconds for simulations of systems where each atom was described and simulated over time.(Lindahl, 2008) <br /> <br />Nevertheless, MD has risen to an important promoter methodology for many different fields of application. By replacing bunches of atoms by artificial particles, complexity of the systems can be reduced. This method is called the coarse grain method (CG). Biggin and Bond (2008) found an acceleration of their simulation processes for self assembling membrane / protein systems in water by factor 100. They estimated one to two days of calculation for a simulated time scale of 0.1 to 0.2 micro seconds for their systems. <br /> <br />Implicit force fields like "IMPALA", aim to describe water and/or membrane molecules in simulations by a couple of simple and partially precalculable equations. “IMPALA” is a force field initially developed by our laboratory. Using this method, thousands of water and lipid molecules can be replaced, leading to a reduced complexity of the system to be simulated. <br />"IMPALA"(Ducarme et al., 1998) based on the assumption of rigid peptides and aimed to find the insertion characteristics of such in membranes. Elimination of the necessity for simulating the aqueous and lipid phase atom by atom in the software package "Gromacs"(Berendsen et al., 1995) will permit both: a gain of speed, as it was already the case for the introduction of the coarse grain method, and a gain of precision by turning rigid molecules flexible through "Gromacs". Our current work is the integration of the "IMPALA" implicit force field into "Gromacs". <br /> <br />Biggin, P.C. & Bond, P.J. Molecular dynamics simulations of membrane proteins. Methods Mol. Biol. 443, 147-60(2008). <br />Berendsen, et al. (1995) Comp. Phys. Comm. 91: 43-56. <br />Ducarme, P., Rahman, M. & Brasseur, R. IMPALA: a simple restraint field to simulate the biological membrane in molecular structure studies. Proteins 30, 357-71(1998). <br />Lindahl, E.R. (2008). Molecular dynamics simulations. Methods Mol. Biol. 443, 3-23. [less ▲]

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See detailCharacterizing of protein dataset with GO ontology
Dmitrieva, Joelia Borisnova; Florea, B; Li, N et al

Poster (2012, September 09)

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See detailPlasma membrane localization of StREM1.3 Remorin is mediated by conformational changes in a novel C-terminal anchor and required for the restriction of PVX movement.
Perraki, Artemis; Cacas, Jean-Luc; Crowet, Jean-Marc ULg et al

in Plant Physiology (2012), 160(1),

The formation of plasma membrane (PM) micro-domains plays a crucial role in the regulation of membrane signalling and trafficking. Remorins are a plant-specific family of proteins organized in six ... [more ▼]

The formation of plasma membrane (PM) micro-domains plays a crucial role in the regulation of membrane signalling and trafficking. Remorins are a plant-specific family of proteins organized in six phylogenetic groups, and Remorins of the group 1 are among the few plant proteins known to specifically associate with membrane rafts. As such, they are valuable to understand the molecular bases for PM lateral organization in plants. However, little is known about the structural determinants underlying group 1 Remorins specific association with membrane rafts. We used a structure-function approach to identify a short C-terminal anchor (RemCA) indispensable and sufficient for tight direct binding of Solanum tuberosum REMORIN 1.3 (StREM1.3) to the PM. RemCA switches from unordered to an alpha-helical structure in a non-polar environment. Protein structure modelling indicates that RemCA folds into a tight hairpin of amphipathic helices. Consistently, mutations reducing RemCA amphipathy abolished StREM1.3 PM localization. Furthermore, RemCA directly binds to biological membranes in vitro, shows higher affinity for Detergent-Insoluble Membranes (DIM) lipids, and targets YFP to DIMs in vivo. Mutations in RemCA resulting in cytoplasmic StREM1.3 localization abolish StREM1.3 function in restricting potato virus X movement. The mechanisms described here provide new insights on the control and function of lateral segregation of plant PM. [less ▲]

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See detailCharacterization of the interaction of xylose-based bolaamphiphiles with biomimetic membrane systems
Nasir, Mehmet Nail ULg; Legrand, Vincent; Gatard, Sylvain et al

Conference (2012, July)

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