References of "Dony, Nicolas"
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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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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 ▲]

Detailed reference viewed: 16 (5 ULg)
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: 23 (4 ULg)
Full Text
Peer Reviewed
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)
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 ▲]

Detailed reference viewed: 22 (1 ULg)
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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 ▲]

Detailed reference viewed: 8 (2 ULg)
See detailLa biosynthèse des lipopolysaccarides chez Escherichia coli
Dony, Nicolas ULg

Scientific conference (2011, February 25)

Detailed reference viewed: 13 (6 ULg)
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See detailPlant-based production of human lysozyme mutants
Tocquin, Pierre ULg; Dumoulin, Mireille ULg; Dony, Nicolas ULg et al

Poster (2007)

Detailed reference viewed: 20 (11 ULg)