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Peer Reviewed
See detailAnalysis of the interactions of natural elicitor rhamnolipids with plant plasma membranes by in silico methods
Polo Lozano, Damien ULg; Nasir, Mehmet Nail ULg; Deleu, Magali ULg et al

Poster (2014, October 20)

Rhamnolipids are surface active molecules produced mainly by various strains of the bacterium Pseudomonas aeruginosa. These secondary metabolites are composed of one to three fatty acids with various ... [more ▼]

Rhamnolipids are surface active molecules produced mainly by various strains of the bacterium Pseudomonas aeruginosa. These secondary metabolites are composed of one to three fatty acids with various chain lengths linked through a glycosidic bond to one or two rhamnose moieties. The fatty acids are linked together through an ester bond. These molecules have shown several biological activities including plant defense stimulation. It has be suggested that this elicitor activity could be related to an interaction of rhamnolipids with the lipid bilayer of the plant plasma membrane (PPM) and lead to its destabilization, which can activate the plant defense signaling pathways. In this context, interactions of two rhamnolipids (Rha-C10-C10 and Rha-Rha-C10-C10) with membrane models and lipidic constituents of the PPM were investigated using in silico approaches. Most probable chemical structures of the rhamnolipids were determined using the STRUCTURE TREE procedure according to the molecule potential energy. The ability of these rhamnolipid structures to insert within the PPM was assessed using IMPALA simulations. IMPALA uses a membrane model in which phospholipids molecules are implicitly modeled by an empirical function and the membrane properties are modeled by energetic restraints. The ability of each rhamnolipid structure to form an assembly with several PPM constituents (phospholipid (PLPC), sterols (Sitosterol, Stigmasterol, Campesterol) and sphingolipids (GIPC, Glucosylceramide)) was calculated using the HYPERMATRIX procedure, which calculate and minimize the energies of interaction between all molecules of the complex until the lowest energy structure is reached. [less ▲]

Detailed reference viewed: 26 (1 ULg)
Peer Reviewed
See detailModeling of the cyclic lipodepsipeptide Pseudodesmin A self-assembly through molecular dynamic simulations
Crowet, Jean-Marc ULg; Sinnaeve, Davy; Fehér, Krisztina et al

Conference (2014, September 30)

The self-assembly of short peptides into supramolecular structures represents an active field of research with potential applications, ranging from material sciences to medicine. Pseudodesmine A is a ... [more ▼]

The self-assembly of short peptides into supramolecular structures represents an active field of research with potential applications, ranging from material sciences to medicine. 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 NMR. In acetonitrile, Pseudodesmine A is monomeric while in chloroform, it has the same structure but assembles in a supramolecular complex. This structure could associate with membranes and be responsible for the biological activity of the peptide. Comparison of NMR data in the two solvents has given indications on the intermolecular contacts that arise in chloroform and a model for the self-association was proposed. To study in more details this assembly, molecular dynamics simulations have been carried on. The resultswere compared with detailed information given by NMR, regarding the dimensions of the assembly and the orientation of the individual peptide building blocks inside the supramolecular assembly. In acetonitrile, the simulations show that the peptide has transient interactions while in chloroform, interactions between monomers are always observed. In agreement with NMR, 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. Peptide interactions are mainly described by 13 interaction patterns characterized by 2 to 4 hydrogen bonds. In dimers, the peptides can have a linear, a perpendicular or a side by side configuration. 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 multifilaments, as found in the NMR-derived model. Two self-consistent supramolecular models can be built from dimers and they present a very good correlation with NMR data regarding the supramolecular organization. Besides, the perpendicular dimer can gives peptide rings that can also explain the potential ability of this peptide to form ion pores in membranes. [less ▲]

Detailed reference viewed: 18 (4 ULg)
Peer Reviewed
See detailModeling of the cyclic lipodepsipeptide Pseudodesmin A self-assembly through molecular dynamic simulations
Crowet, Jean-Marc ULg; Sinnaeve, Davy; Fehér, Krisztina et al

Poster (2014, August 21)

The self-assembly of short peptides into supramolecular structures represents an active field of research with potential applications, ranging from material sciences to medicine. Pseudodesmine A is a ... [more ▼]

The self-assembly of short peptides into supramolecular structures represents an active field of research with potential applications, ranging from material sciences to medicine. 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 NMR. In acetonitrile, Pseudodesmine A is monomeric while in chloroform, it has the same structure but assembles in a supramolecular complex. This structure could associate with membranes and be responsible for the biological activity of the peptide. Comparison of NMR data in the two solvents has given indications on the intermolecular contacts that arise in chloroform and a model for the self-association was proposed. To study in more details this assembly, molecular dynamics simulations have been carried on. The resultswere compared with detailed information given by NMR, regarding the dimensions of the assembly and the orientation of the individual peptide building blocks inside the supramolecular assembly. In acetonitrile, the simulations show that the peptide has transient interactions while in chloroform, interactions between monomers are always observed. In agreement with NMR, 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. Peptide interactions are mainly described by 13 interaction patterns characterized by 2 to 4 hydrogen bonds. In dimers, the peptides can have a linear, a perpendicular or a side by side configuration. 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 multifilaments, as found in the NMR-derived model. Two self-consistent supramolecular models can be built from dimers and they present a very good correlation with NMR data regarding the supramolecular organization. Besides, the perpendicular dimer can gives peptide rings that can also explain the potential ability of this peptide to form ion pores in membranes. [less ▲]

Detailed reference viewed: 4 (1 ULg)
Peer Reviewed
See detailModeling of the cyclic lipodepsipeptide Pseudodesmin A self-assembly through molecular dynamic simulations
Crowet, Jean-Marc ULg; Sinnaeve, Davy; Fehér, Krisztina et al

Conference (2014, August 20)

The self-assembly of short peptides into supramolecular structures represents an active field of research with potential applications, ranging from material sciences to medicine. Pseudodesmine A is a ... [more ▼]

The self-assembly of short peptides into supramolecular structures represents an active field of research with potential applications, ranging from material sciences to medicine. 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 NMR. In acetonitrile, Pseudodesmine A is monomeric while in chloroform, it has the same structure but assembles in a supramolecular complex. This structure could associate with membranes and be responsible for the biological activity of the peptide. Comparison of NMR data in the two solvents has given indications on the intermolecular contacts that arise in chloroform and a model for the self-association was proposed. To study in more details this assembly, molecular dynamics simulations have been carried on. The resultswere compared with detailed information given by NMR, regarding the dimensions of the assembly and the orientation of the individual peptide building blocks inside the supramolecular assembly. In acetonitrile, the simulations show that the peptide has transient interactions while in chloroform, interactions between monomers are always observed. In agreement with NMR, 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. Peptide interactions are mainly described by 13 interaction patterns characterized by 2 to 4 hydrogen bonds. In dimers, the peptides can have a linear, a perpendicular or a side by side configuration. 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 multifilaments, as found in the NMR-derived model. Two self-consistent supramolecular models can be built from dimers and they present a very good correlation with NMR data regarding the supramolecular organization. Besides, the perpendicular dimer can gives peptide rings that can also explain the potential ability of this peptide to form ion pores in membranes. [less ▲]

Detailed reference viewed: 8 (2 ULg)
Peer Reviewed
See detailMembrane interactions of cyclic lipodepsipeptides from the viscosin group
Geudens, Niels; Feher, Krisztina; De Vleeschouwer et al

Poster (2014, June)

Detailed reference viewed: 12 (4 ULg)
Peer Reviewed
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 ▲]

Detailed reference viewed: 28 (4 ULg)
Full Text
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 ▲]

Detailed reference viewed: 40 (4 ULg)
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 ▲]

Detailed reference viewed: 27 (0 ULg)
Peer Reviewed
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 ▲]

Detailed reference viewed: 89 (15 ULg)
Peer Reviewed
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 ▲]

Detailed reference viewed: 73 (14 ULg)
Peer Reviewed
See detailExploration on structure activity relation of natural, self-assembling cyclic lipodepsipeptides
Geudens, Niels; Feher, Kristina; De Vleeschouwer, Matthias et al

Poster (2014, February)

Detailed reference viewed: 17 (4 ULg)