MA/MSc Internship for EUGLOH program

Keywords: Molecular dynamics similation, Molecular modeling, Protein, Membrane, Lipids

Internship Duration: 30/11/-1 - 30/11/-1

Flippases are membrane proteins that help maintain transbilayer lipid asymmetry, by actively transporting lipids from the exoplasmic to the cytosolic layer of cell membranes. In humans, mutations of the flippase ATP8B1 cause intrahepatic cholestasis, a hereditary disease (1). Several high-resolution structures of the yeast flippase Drs2p have been determined in the laboratory, providing detailed insights into the regulatory mechanism of these molecular machines (2). Drs2p transports phosphatidylserine lipids and is autoinhibited by its N- and C-termini. Moreover, the activity of Drs2p is regulated by the presence of a phosphoinositide, PI4P (3). Indeed, we have shown that Drs2p is fully active when truncated in N- and C-termini and in the presence of PI4P (4).
We propose to the student to study the mechanisms by which PI4P activates Drs2p by all-atom molecular dynamics (MD) simulations in the presence of a lipid bilayer. Indeed, MD makes it possible to obtain information at the atomic scale on the dynamics of systems and on the interactions between proteins and lipids.
Several systems comprising the flippase Drs2p embedded in a lipid bilayer have been already constructed. Two different membrane types were chosen: a pure POPC bilayer and a mixed bilayer comprising a mixture of lipids mimicking a biological membrane. In each of these two lipid environments, PI4P is either absent or present. The trajectories have already been computed in two replica of one microsecond each. The objective is to analyze and compare the simulations in the presence and absence of PI4P to highlight the role of PI4P in Drs2p-catalyzed lipid transport.

(1) Paulusma, C. C., Elferink, R. P. J. O. & Jansen, P. L. M. Progressive familial intrahepatic
cholestasis type 1. Semin. Liver Dis. 30, 117–124 (2010).
(2) Timcenko M, Lyons JA, Januliene D, Ulstrup JJ, Dieudonné T, Montigny C, Ash MR, Karlsen JL, Boesen T, Kühlbrandt W, Lenoir G, Moeller A, Nissen P. Structure and autoregulation of a P4-ATPase lipid flippase. Nature:366-370 (2019).
(3) Zhou, X., Sebastian, T. T. & Graham, T. R. Auto-inhibition of Drs2p, a yeast phospholipid
flippase, by its carboxyl-terminal tail. J. Biol. Chem. 288, 31807–31815 (2013).
(4) Azouaoui H, Montigny C, Dieudonné T, Champeil P, Jacquot A, Vázquez-Ibar JL, Le Maréchal P, Ulstrup J, Ash MR, Lyons JA, Nissen P, Lenoir G. High phosphatidylinositol 4-phosphate (PI4P)-dependent ATPase activity for the Drs2p-Cdc50p flippase after removal of its N- and C-terminal extensions. J Biol Chem. 292(19):7954-7970 (2017).

Molecular dynamics simulation

Structure and autoregulation of a P4-ATPase lipid flippase.
Timcenko M, Lyons JA, Januliene D, Ulstrup JJ, Dieudonné T, Montigny C, Ash MR, Karlsen JL, Boesen T, Kühlbrandt W, Lenoir G, Moeller A, Nissen P. Nature:366-370 (2019).

Deciphering the Mechanism of Inhibition of SERCA1a by Sarcolipin Using Molecular Simulations.
Barbot T, Beswick V, Montigny C, Quiniou É, Jamin N, Mouawad L. Front Mol Biosci. 2021 Feb 4;7:606254. doi: 10.3389/fmolb.2020.606254

• Medicine and health sciences, Veterinary science
• Pharmacy, Biology, Physics and Chemistry