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#1 21.05.2013 10:23:29

zaitsev
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Откуда: КНУ, химфак
Здесь с 15.05.2005
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phD proposal- France

PhD subject for your master students

Methodological tools to combine Nuclear Magnetic Resonance of biomembranes and numerical simulations of molecular dynamics for understanding molecules/lipid membrane interactions

This thesis is part of the general context of understanding the mode of action of molecules whose biological activity is related to a special interaction with the plasma membrane. If the anchor of membrane receptors is well accepted and is better studied, more and more molecules are found with their activity not related to a specific receptor. Therefore, understanding these molecules / lipid membrane interactions is essential to elucidate the biological mechanisms involved. For the past few years, several national teams (M. Baaden Paris) and international (P. Tieleman, Canada, R. Efremov, Russia) have been engaged in the theoretical study of membrane complexes and membranes solely, using implicit or explicit models and the development of specific forcefields, and recently using coarse-grained models or large membrane complexes and have then developed methods dedicated for this type of study and interactions.

However, the methodological tools to combine Nuclear Magnetic Resonance of biomembranes and numerical simulations of molecular dynamics remains relatively small and often poorly adapted to specific experimental settings (order parameter and profile, lateral diffusion) and the corresponding theoretical validation. Therefore, the combination of the two approaches allows one to complement the experience by numerical simulation leading to a description of the systems that is both accurate and relevant. In addition to dedicated analytical tools, tools that automate the construction of lipid bilayers / membranotrope molecules mixed systems do not exist and will also be developed.

The robustness of such tools will be tested on a set of molecules studied by both teams and for which data (including NMR) on membrane interactions are already known. Thus, we will focus on the case of lipopeptides (hybrid molecules, both protein and lipid) such as surfactin whose direct interaction with the lipids of the plasma membrane confers antimicrobial properties (via membrane lysis) or elicitation of the organism (bacteria or plant). In addition our local, national and international collaborations will also permit to use other membranotropes molecules: rhamnolipids, acylated peptides (U. Nancy) model peptides and peptides derived from collagen and elastin (U. Conrad, Germany).

The collaboration between the two laboratories, members of both Research Federation Condorcet and CAP Santé of URCA and UPJV universities, will rely on a range of platforms, including the Analytical Platform (PFA-NMR) and Modeling and Scientific Computing (MECs) in Amiens, or regional data center ROMEO and multiscale molecular modeling platform (P3M) in Reims. The latter two platforms got the first NVIDIA CUDA Center and are also recognized in two PIA ( Programme d'Investissement d'Avenir ) registered by GENCI ( Grand Equipement National de Calcul Intensif ) and the RENABI ( Réseau National des Plate-formes BioInformatiques ). Finally, specific contacts with teams of Pr Efremov (Russia), Baaden (Paris) and Conrad (Germany) portend valuable collaborations and leading to the realization of this project.

Application: CV and cover letter to sebastien.buchoux@u-picardie.fr, manuel.dauchez@univ-reims.fr and catherine.sarazin@u-picardie.fr

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