A Multi-Scale Approach to Membrane Remodeling Processes

Abstract

We present a multi-scale simulation procedure to describe membrane-related biological processes that span over a wide range of length scales. At macroscopic length-scale, a membrane is described as a flexible thin film modeled by a dynamic triangulated surface with its spatial conformations governed by an elastic energy containing only a few model parameters. An implicit protein model allows us to include complex effects of membrane-protein interactions in the macroscopic description. The gist of this multi-scale approach is a scheme to calibrate the implicit protein model using finer scale simulation techniques e.g., all atom and coarse grain molecular dynamics. We previously used this approach and properly described the formation of membrane tubular invaginations upon binding of B-subunit of Shiga toxin. Here, we provide a perspective of our multi-scale approach, summarizing its main features and sketching possible routes for future development.

Annexin A4 trimers are recruited by high membrane curvatures in giant plasma membrane vesicles

“…The equilibrium properties of the systems are analyzed by Monte Carlo simulation techniques with 4 MC moves i.e., vertex move (a vertex is moved in a random direction), Alexander move (a mutual link between neighboring triangles is flipped and two new triangles will be generated) and Kawazaki moves (an inclusion jumps to a neighboring vertex) and the membrane projected area change. To each Monte Carlo Sweep (MCS) with a probability of P = 1/(5N v ), the membrane projected area is updated and with probability of 1−P , trial moves corresponding to N v vertex moves, N l Alexander move and N i Kawazaki moves are performed (for more details see [38][39][40] ). To map the simulation results to the experimental setup, d, the simulation length metric, is converted to a physical length.…”

Annexin A4 trimers are recruited by high membrane curvatures in Giant Plasma Membrane Vesicles

“…Kawazaki moves (an inclusion jumps to a neighboring vertex) and the membrane projected area change. To each Monte Carlo Sweep (MCS) with a probability of P = 1/(5N v ), the membrane projected area is updated and with probability of 1−P , trial moves corresponding to N v vertex moves, N l Alexander move and N i Kawazaki moves are performed (for more details see [38][39][40] ). To map the simulation results to the experimental setup, d, the simulation length metric, is converted to a physical length.…”

Molecular architecture and dynamics of SARS-CoV-2 envelope by integrative modeling

“…The initial stage of modeling the entire envelope consisted of a dynamic triangulated surface (DTS) simulation 20,21 to obtain a triangulated envelope shape matching the dimensions of the virion. This model was subsequently converted to a CG representation 22 , placing CG models of the proteins and lipids based on Martini force field model 23 with specified stoichiometries (Supp.…”