References of "Crowet, Jean-Marc"
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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 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 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 ▲]

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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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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 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 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 ▲]

Detailed reference viewed: 26 (6 ULg)