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See detailMolecular dynamic simulation of the cyclic lipodepsipeptide Pseudodesmin A self-assembly
Crowet, Jean-Marc ULg; Sinnaeve, Davy; Fehér, Krisztina et al

Conference (2014, February 10)

Pseudodesmine A is a cyclic lipodepsipeptide of nine residues which presents a moderate antibacterial activity and whose structure has been resolved by X-ray and NMR1,2. In acetonitrile, Pseudodesmine A ... [more ▼]

Pseudodesmine A is a cyclic lipodepsipeptide of nine residues which presents a moderate antibacterial activity and whose structure has been resolved by X-ray and NMR1,2. In acetonitrile, Pseudodesmine A is monomeric while in chloroform it has the same structure but assemble in a supramolecular complex. This structure could associate with membranes and be responsible of the biological activity of this peptide. Comparison of the NMR data between the two solvents has given indications on the intermolecular contacts that arise in chloroform and a model for the self association was proposed2,3. To study in more details this assembly, molecular dynamics have been carried on. In acetonitrile, the peptide show transient interactions while in chlorofom interactions between monomers was always observed. As stated in Sinnaeve et al. in 2009, these interactions arise mainly between the backbone protons of the LEU1 and the GLN2, the GLN2 sidechain and the loop located on the opposite end of the monomer structure. From 10 simulations of dimerization, hydrogen bonds were followed and specific interaction patterns were identified regarding the hydrogen bonds formed. The peptide interactions are mainly described by 13 interaction patterns; 8 with the peptides in a linear configuration, 1 perpendicular and 4 with peptides side by side. The patterns are characterized by 2 to 4 hydrogen bonds. From the linear dimer, it is possible to reconstruct filaments and, by combining a linear and a lateral dimer, it is possible to build fibrils with multi filaments, as expected in the NMR derived model. Besides, the perpendicular dimer can gives peptide rings that can also explain the potential ability of this peptide to form ion pores in membranes. 1. Sinnaeve, D., Michaux, C., Van hemel, J., Vandenkerckhove, J., Peys, E., Borremans, F. a. M., Sas, B., Wouters, J. and Martins, J. C. Tetrahedron 2009, 65, 4173–4181. 2. Sinnaeve, D., Hendrickx, P. M. S., Van Hemel, J., Peys, E., Kieffer, B. and Martins, J. C. Chemistry (Weinheim an der Bergstrasse, Germany) 2009, 15, 12653–62. 3. Sinnaeve, D., Delsuc, M.-A., Martins, J. C. and Kieffer, B. Chemical Science 2012, 3, 1284. [less ▲]

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See detailInteractions between new phenolic glycolipids and model membrane
Sainvitu, Pauline ULg; Nasir, Mehmet Nail ULg; Crowet, Jean-Marc ULg et al

Poster (2014, February 07)

Model membrane based on phospholipids (PL) layers are useful to mimic properties of plasma membranes. The interactions between new synthesized phenolic glycolipids (PGL) and biological membrane are ... [more ▼]

Model membrane based on phospholipids (PL) layers are useful to mimic properties of plasma membranes. The interactions between new synthesized phenolic glycolipids (PGL) and biological membrane are crucial to determine their potential as drug candidates and their cytotoxicity . [less ▲]

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See detailSimulations of a beta amphiphilic peptide as potential surfactant of membrane proteins
Crowet, Jean-Marc ULg; Dony, Nicolas ULg; Deschamps, Antoine et al

Poster (2014, February 07)

The peptide studied here was designed to form beta amphiphilic films with the aim to stabilize purified membrane proteins. This interaction has notably been followed by FRET. Hydrophobic and hydrophilic ... [more ▼]

The peptide studied here was designed to form beta amphiphilic films with the aim to stabilize purified membrane proteins. This interaction has notably been followed by FRET. Hydrophobic and hydrophilic residues are alternate and positively and negatively charged residues place respectively at the start end the end of the peptide. The peptide has been studied by atomistic and coarse grained molecular dynamics in water, chloroform and mixed solutions. The peptide was observed to spontaniously form beta films at the chloroform water interface. Moreover, when we simulate the interaction of this peptide with a membrane protein and with a membrane protein in a micelle of dodecylphosphocholine. The peptide was observed to form beta films at the membrane protein surface and even remove surfactants from the membrane protein surface. The simulations confirms the behaviour of this peptide observed in vitro and shows that it could be used instead of detergents. [less ▲]

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See detailInteractions of a potential plant elicitor mannolipid with plant model membranes
Polo Lozano, Damien ULg; Lins, Laurence ULg; Ongena, Marc ULg et al

Poster (2014, February 07)

The use of chemical pesticides causes problems for human health and environment. In this context, there is an increasing interest for alternative products such as biopesticides. Among them, elicitors act ... [more ▼]

The use of chemical pesticides causes problems for human health and environment. In this context, there is an increasing interest for alternative products such as biopesticides. Among them, elicitors act on the plants by inducing systemic resistance against diseases caused by fungal, viral, bacterial agents and insects. The target of the elicitors is supposed to be the plant plasma membranes (PPM). The main mechanisms of interaction of many elicitors involve proteic receptors but lipid-based elicitors (LBE) may preferably interact with the lipidic fractions of PPM. However there is no detailed information at the molecular level on the PPM-LBE interactions. Our work is focused on a original synthetic LBE composed of a mannoside linked to a myristic acid. It has potential elicitor activities as shown by the assays on tobacco root cells. These activities could be related to its interaction with the lipidic phase of PPM. Since PPM are complex entities, the analyses of the PPM- molecule interactions are quite difficult. In this context, these interactions were carried out using biomimetic membranes of PPM such as Langmuir monolayers and multilayers. The effects of our molecule on these membranar systems were investigated by biophysical and in silico approaches. [less ▲]

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See detailNew alternatives to chemical pesticides: deciphering the action mechanisms of lipid based plant elicitors via complementary biophysical and biological approaches.
Nasir, Mehmet Nail ULg; Polo Lozano, Damien ULg; Luzuriaga Loaiza, Walter ULg et al

Poster (2014, February)

Nowadays, many health and environmental problems are caused by the use of chemical pesticides. In this context, an increasing demand for alternative products such as biopesticides has been observed. Among ... [more ▼]

Nowadays, many health and environmental problems are caused by the use of chemical pesticides. In this context, an increasing demand for alternative products such as biopesticides has been observed. Among biopesticides, elicitor molecules which are able to trigger immune defense responses in plants are one of the most promising options. Although numerous elicitors have been discovered, the mechanisms involved in the perception, by plants, of only a few molecules have been identified. These elicitors usually interact with proteic receptors but we have recently shown that they may also act on the lipid phase of the plasma membrane. This project first aims to improve our understanding of the molecular mechanisms involved in the recognition of specific lipid based elicitors (LBE). On that basis, the FIELD project will contribute to the design and the development of innovative compounds derived natural LBE. A multi-disciplinary approach, based on chemistry, bio-physics, bio-chemistry, and phytopathology will be followed by a consortium of different research groups from Gembloux Agro-Bio Tech in close collaboration with teams from foreign institutions. [less ▲]

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See detailExploration on structure activity relation of natural, self-assembling cyclic lipodepsipeptides
Geudens, Niels; Feher, Kristina; De Vleeschouwer, Matthias et al

Poster (2014, February)

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See detailSpectroscopic analysis of the remorin-lipid interactions at the moleculaer level
Nasir, Mehmet Nail ULg; Perraki, Artemis; Mongrand, Sébastien et al

Poster (2014)

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Peer Reviewed
See detailSAHBNET, 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

Conference (2013, November 11)

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 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 complex systems and the preservation of the 3D protein structure, which is not trivial in coarse grained 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 detailLIPID INTERACTION PROPERTIES OF NOVEL RHAMNOLIPIDS
Nasir, Mehmet Nail ULg; Crowet, Jean-Marc ULg; Lins, Laurence ULg et al

Conference (2013, November)

Biosurfactants which are surface active molecules produced by micro-organisms present a wide structural diversity (glycolipids, lipoaminoacids, lipopeptides, polymers,...) and numerous advantages compared ... [more ▼]

Biosurfactants which are surface active molecules produced by micro-organisms present a wide structural diversity (glycolipids, lipoaminoacids, lipopeptides, polymers,...) and numerous advantages compared to their chemically synthesized counterparts. Among glycolipids, rhamnolipids which are secondary metabolites produced mainly by strains of Pseudomonas aeruginosa, have drawn particular attention as they have several interesting biological properties such as antimicrobial, antiphytoviral, zoosporicidal and plant defense elicitor activities [1-3]. It is generally recognized that these activities must be linked to the interaction of these molecules with constituents of biological membranes [4] but the detailed mechanism is far from being fully understood. In our laboratory, new rhamnolipids with various chain lengths and with or without a terminal carboxylic acid function were obtained via the development of a synthesis procedure consisting of two biocatalyzed steps involving naringinase and lipase [5]. The objective of this work was to investigate their interaction with model membranes in relation with their structure in order to give insight about the mechanism of their biological action. A range of complementary experimental and modelling methods was used to analyze their interaction with membrane models. Results reveal differential interaction with lipids according to the structure of the rhamnolipid. The nature of the lipid is also a key parameter for the ınteractions. [less ▲]

Detailed reference viewed: 44 (18 ULg)
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See detailINFLUENCE OF THE NATURE OF SUGAR RESIDUES ON THE INTERACTIONS OF SYMETRIC SUGAR- BASED BOLAFORMS WITH MODEL MEMBRANES
Nasir, Mehmet Nail ULg; Crowet, Jean-Marc ULg; Lins, Laurence ULg et al

Poster (2013, November)

Glycolipid surfactants constitute a class of natural compound having interest in biological field such as antifungal, antiviral and plant-elicitor and for pharmaceutical formulation as well as for food ... [more ▼]

Glycolipid surfactants constitute a class of natural compound having interest in biological field such as antifungal, antiviral and plant-elicitor and for pharmaceutical formulation as well as for food and cosmetic field. Their action may be modulated through their interactions with plasma membranes of target cells and more particularly by their interactions with membrane lipid molecules. Among glycolipid surfactants, bolaforms constitute an important class; they are composed of two hydrophilic heads connected by a hydrophobic carbon segment.Their interest lies mainly in the development of the efficient and low cost lipid-based drug delivery systems. In this context, our work was focused on two sugar-based bolaforms. They are composed by two identical hydrophilic head constituted by xylose ( BolaX) or rhamnose ( BolaR), connected by an ether link to a hydrocarbon segment with an insaturation. The interactions of  BolaX and BolaR with model phopsholipid and phospholipid/sterol model membranes (Langmuir monolayers at the air-water interface and multilamellar vesicles) were investigated with biophysical and in silico approaches. Our results indicate that both bolaforms interact with model membranes at the level of hydrocarbon chain and, at the phosphate and the carbonyl group of phospholipids. The presence of sterol in the system has an influence on insertion of bolaforms and change slightly the nature of the interactions. The insertion of BolaR within a phospholipid bilayer was deeper than that of  BolaX and its interactions with phospholipids were energetically more favorable, suggesting an important role of the nature of sugar residue. [less ▲]

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Peer Reviewed
See detailSimulations of a beta amphiphilic peptide as potential surfactant of membrane proteins
Crowet, Jean-Marc ULg; Dony, Nicolas ULg; Deschamps, Antoine et al

Conference (2013, October 25)

The peptide studied here was designed to form beta amphiphilic films with the aim to stabilize purified membrane proteins. This interaction has notably been followed by FRET. Hydrophobic and hydrophilic ... [more ▼]

The peptide studied here was designed to form beta amphiphilic films with the aim to stabilize purified membrane proteins. This interaction has notably been followed by FRET. Hydrophobic and hydrophilic residues are alternate and positively and negatively charged residues place respectively at the start end the end of the peptide. The peptide has been studied by atomistic and coarse grained molecular dynamics in water, chloroform and mixed solutions. The peptide was observed to spontaniously form beta films at the chloroform water interface. Moreover, when we simulate the interaction of this peptide with a membrane protein and with a membrane protein in a micelle of dodecylphosphocholine. The peptide was observed to form beta films at the membrane protein surface and even remove surfactants from the membrane protein surface. The simulations confirms the behaviour of this peptide observed in vitro and shows that it could be used instead of detergents. [less ▲]

Detailed reference viewed: 22 (4 ULg)
See detailMolecular dynamic simulations of a beta amphiphilic peptide
Crowet, Jean-Marc ULg; Deschamps, Antoine; Soumillion, Patrice et al

Conference (2013, October 03)

Detailed reference viewed: 26 (7 ULg)
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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)

Detailed reference viewed: 40 (6 ULg)
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Peer Reviewed
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 ▲]

Detailed reference viewed: 59 (6 ULg)