Modeling of the Open-Channel Structure of Mscl Using Restrained Simulations

Abstract

Mechanosensitive channels are membrane proteins that act as safety valves to protect bacterial cells from sudden osmotic shock. The gating is induced by tension in the surrounding lipid bilayer and results in a a large conformational change. The structure of the mechanosensitive channel of large conductance (MscL) in the closed state has been solved by XRD [1]. The protein has been characterized using EPR [3] and FRET [3] spectroscopy but a detailed structure of the open-channel structure is unknown.In this study we present a method for incorporating structural data from EPR and FRET experiments into a coarse grained model of MscL. The simulations system was modelled using the MARTINI force field [4]. Restraints based on solvent accessibility from EPR data were implemented by altering the interactions of specific residues with water and lipid particles. Distance restraints between specific residues were implemented using harmonic potentials. A series of MD simulations with different combinations of restraints and membrane tension were carried out. Restraints were slowly introduced to induce gating. The simulations produced a set of open channel structures that were analysed using a range of structural features such as pore radius and helix tilt.[1] Chang G et al. (1998). Structure of the MscL Homolog from Mycobacterium tuberculosis: A Gated Mechanosensitive Ion Channel. Science282, 2220-2226[2] Perozo E et al. (2002). Physical principles underlying the transduction of bilayer deformation forces during mechanosensitive channel gating. Nature Structural Biology 9, 696-703[3] Corry B et al. Conformational changes involved in MscL channel gating measured using FRET spectroscopy. Biophysical Journal89, L49-L51[4] Marrink SJ et al. (2007). The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations. Journal of Physical Chemistry B111, 7812-7824