Molecular Mechanism of Lipid Nanodisk Formation by Styrene-Maleic Acid Copolymers

Abstract

Experimental characterization of membrane proteins often requires solubilization. A recent approach is to use styrene-maleic acid (SMA) copolymers to isolate membrane proteins in nanometer-sized membrane disks, or so-called SMA lipid particles (SMALPs). The approach has the advantage of allowing direct extraction of proteins, keeping their native lipid environment. Despite the growing popularity of using SMALPs, the molecular mechanism behind the process remains poorly understood. Here, we unravel the molecular details of the nanodisk formation by using coarse-grained molecular dynamics simulations. We show how SMA copolymers bind to the lipid bilayer interface, driven by the hydrophobic effect. Due to the concerted action of multiple adsorbed copolymers, large membrane defects appear, including small, water-filled pores. The copolymers can stabilize the rim of these pores, leading to pore growth and membrane disruption. Although complete solubilization is not seen on the timescale of our simulations, self-assembly experiments show that small nanodisks are the thermodynamically preferred end state. Our findings shed light on the mechanism of SMALP formation and on their molecular structure. This can be an important step toward the design of optimized extraction tools for membrane protein research.

Styrene maleic acid copolymer induces pores in biomembranes

“…6). The observation is in principle in agreement with the prediction of Xue et al, 13 and also supported by the finding that adhered DMPC membrane patches dissolve noticeably from the edges (Fig. 1o, p and r, s).…”

“…The work supports the theoretical prediction of SMA copolymer-induced pores, published by Xue et al in 2018. 13 We do not have, however, sufficient data to claim with certainty that the mechanism proposed by the authors is the exact one found in the experimental system. The results altogether confirm that SMA copolymers cause water-filled pores in lipid bilayers, well complementing the recent theoretical predictions.…”

“…12 Very recently, molecular dynamics simulations predicted that SMA copolymers may induce water-filled pores in membranes prior to their solubilization into lipid particles. 13 These pores are nanometer-sized and should allow passage of small watersoluble molecules.…”

Self-Assembly of Polymer-Encased Lipid Nanodiscs and Membrane Protein Reconstitution

“…The MD system was solvated using one bead water and neutralized by adding counter Na + ions under a periodic boundary condition. The SMA-EA-DLPC lipid bilayer (SMA-EA to DLPC ) MD system was next subjected to energy-minimization using the steepest-descent method followed by constant volume and pressure equilibration as described elsewhere 11 . The SMA-EA-DLPC bilayer system was finally simulated for a production run of 10 µs.…”

Coarse-grained implicit solvent lipid force field with a compatible resolution to the Cα protein representation

“…Among others, the MARTINI model has been successfully applied to many targets. [19][20][21][22] Most of these models, with some exceptions 13,17,23 , use explicit solvent molecules, making them computationally demanding compared to the above-mentioned minimal models.…”