Research output per year
Research output per year
Abstract
Opioid receptors, whose structures were revealed in 2012, are part of the G-protein coupled receptor (GPCRs), target of 50 % of drugs on the market today [1]. The structural and functional properties of transmembrane proteins are affected by the lipid environment [2].
To understand these processes, classical molecular dynamics (MD) simulations can provide numerous clarifications. We compare the results of CG (coarsegrained, 1 μs) and AA (all-atom, 17 ns) simulations for a patch of membrane with POPC (1-palmitoyl- 2-oleoyl-sn-glycero-3-phosphocholin) and the μ receptor by NAMD (NAnoscale Molecular Dynamic). CG simulations are quick but less accurate than AA simulations. We need them to demonstrate the role of lipids in μ conformations changes. For details and evidences, AA simulations are necessary.
Firstly, we examine the adaptation of the lipids to the receptor and vice versa. To explain such adaptation, we examine precisely the interactions between the amino acids and lipids by calculating the distance between each other and the tilt of the helices of the μ protein during the MD simulation. Then, we study, via POCASA, the possible pockets on the protein to accomodate lipids and determine differents key conformations through the clustering of the pockets.
Ultimately, our goal is to perform MD simulations with the most realistic lipid composition, the simplest and most significant in terms of protein/lipid interactions, in order to guide the docking experiments and show the importance of the interaction of a protein with a lipid towards its structural and functional properties.
Bibliography:
[1] Manglik A., Kruse A., Kobilka T., Thian F., Mathiesen J., Sunahara R., Pardo L., Weis W., Kobilka B., Granier S. (2012) Crystal structure of the mu-opioid receptor bound to a morphinan antagonist Nature 485: 321-7
[2] Jastrzebska B., Debinski A., Filipek S., Palczewski K. (2011) Role of membrane integrity on G protein-coupled receptors: rhodopsin stability and function Progress in Lipid Research 50: 267-77
To understand these processes, classical molecular dynamics (MD) simulations can provide numerous clarifications. We compare the results of CG (coarsegrained, 1 μs) and AA (all-atom, 17 ns) simulations for a patch of membrane with POPC (1-palmitoyl- 2-oleoyl-sn-glycero-3-phosphocholin) and the μ receptor by NAMD (NAnoscale Molecular Dynamic). CG simulations are quick but less accurate than AA simulations. We need them to demonstrate the role of lipids in μ conformations changes. For details and evidences, AA simulations are necessary.
Firstly, we examine the adaptation of the lipids to the receptor and vice versa. To explain such adaptation, we examine precisely the interactions between the amino acids and lipids by calculating the distance between each other and the tilt of the helices of the μ protein during the MD simulation. Then, we study, via POCASA, the possible pockets on the protein to accomodate lipids and determine differents key conformations through the clustering of the pockets.
Ultimately, our goal is to perform MD simulations with the most realistic lipid composition, the simplest and most significant in terms of protein/lipid interactions, in order to guide the docking experiments and show the importance of the interaction of a protein with a lipid towards its structural and functional properties.
Bibliography:
[1] Manglik A., Kruse A., Kobilka T., Thian F., Mathiesen J., Sunahara R., Pardo L., Weis W., Kobilka B., Granier S. (2012) Crystal structure of the mu-opioid receptor bound to a morphinan antagonist Nature 485: 321-7
[2] Jastrzebska B., Debinski A., Filipek S., Palczewski K. (2011) Role of membrane integrity on G protein-coupled receptors: rhodopsin stability and function Progress in Lipid Research 50: 267-77
| Original language | English |
|---|---|
| Publication status | Published - 26 Apr 2016 |
| Event | Jounée-Rencontre des jeunes chimistes de la SRC 2016 - Université Libre de Bruxelles, Bruxelles, Belgium Duration: 26 Apr 2016 → 26 Apr 2016 |
Symposium
| Symposium | Jounée-Rencontre des jeunes chimistes de la SRC 2016 |
|---|---|
| Country/Territory | Belgium |
| City | Bruxelles |
| Period | 26/04/16 → 26/04/16 |
Keywords
- Protein-lipid interaction
- All-atom
- Coarse-grained
- µ opioid receptor
Fingerprint
Dive into the research topics of 'Comparison of Coarse-Grain and All-Atom Methods for the Study of µ Opioid Receptor'. Together they form a unique fingerprint.Research output
- 1 Poster
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Comparison of the effect of membrane lipids on the µ opioid receptor by studying crystallographic, all-atoms and coarse-grained models
Angladon, M-A., Leherte, L. & Vercauteren, D., 21 Feb 2015.Research output: Contribution to conference › Poster
Projects
- 3 Finished
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Etude de l'influence de la membrane plasmique sur les propriétés structurales et fonctionnelles du récepteur opïoide µ
Angladon, M. & Vercauteren, D.
1/10/13 → 30/09/17
Project: PHD
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PAI n°P7/05 - FS2: Functional Supramolecular Systems (FS2)
Champagne, B., De Vos, D., Van der Auweraer, M., Jérôme, C., Lazzaroni, R., Marin, G., Jonas, A., Du Prez, F., Vanderzande, D., Van Tendeloo, G., Van Speybroeck, V., NENON, S. & STAELENS, N.
1/04/12 → 30/09/17
Project: Research
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Equipment
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High Performance Computing Technology Platform
Benoît Champagne (Manager)
Technological Platform High Performance ComputingFacility/equipment: Technological Platform
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Ecole interdisciplinaire pour doctorants - L'alimentation
Marie-Ange Angladon (Poster)
17 May 2016 → 19 May 2016Activity: Participating in or organising an event types › Participation in conference
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Jounée-Rencontre des jeunes chimistes de la SRC 2016
Marie-Ange Angladon (Poster)
26 Apr 2016Activity: Participating in or organising an event types › Participation to a Symposium, a study Day