Temperature Driven Shape Transformation of Nanodiscs by Coarse-Grained Molecular Dynamics Simulations

Abstract

Nanodisc, a synthetic lipoprotein composed of a phospholipid bilayer encircled by membrane scaffold proteins, is an encapsulating agent widely used for the study of membrane proteins. In this study, an effect of temperature on the nanodisc shape has been investigated by coarse-grained molecular dynamics (CGMD) simulations to provide insight into its molecular morphology in solution at frozen and ambient temperatures. CGMD simulations were conducted for different temperatures ranging from 200K to 400K with Martini force fields for CG-protein and lipid. Microsecond CG-MD simulations revealed structure and dynamic responses upon a variation of simulation temperature. The simulations showed large-scale motions and changes in solvation property of the nanodiscs as an increasing in temperatures. The deformation from the initial discoidal nanodisc into an oblate shape has been observed. It is anticipated that the shape transformation of nanodiscs upon rising in temperature is associated with the gel to fluid phase transition.