Identification of electroporation sites in the complex lipid organization of the plasma membrane

Abstract

The plasma membrane of a biological cell is a complex assembly of lipids and membrane proteins, which tightly regulate transmembrane transport. When a cell is exposed to a strong electric field, the membrane integrity becomes transiently disrupted by formation of transmembrane pores. This phenomenon, termed electroporation, is already utilized in many rapidly developing applications in medicine including gene therapy, cancer treatment, and treatment of cardiac arrythmias. However, the molecular mechanisms of electroporation are not yet sufficiently well understood; in particular, it is unclear where exactly pores form in the complex organization of the plasma membrane. In this study we combine coarse-grained molecular dynamics simulations, machine learning methods, and Bayesian survival analysis to identify how formation of pores depends on the local lipid organization. We show that pores do not form homogeneously across the membrane, but colocalize with domains that have specific features, the most important being high density of polyunsaturated lipids. We further show that knowing the lipid organization is sufficient to reliably predict poration sites with machine learning. However, by analysing poration kinetics with Bayesian survival analysis we then show that poration does not depend solely on local lipid arrangement, but also on membrane mechanical properties and the polarity of the electric field. Finally, we discuss how the combination of atomistic and coarse-grained molecular dynamics simulations, machine learning methods, and Bayesian survival analysis can guide the design of future experiments and help us to develop an accurate description of plasma membrane electroporation on the whole-cell level. Achieving this will allow us to shift the optimization of electroporation applications from blind trial-and-error approaches to mechanistic-driven design.

Two decades of Martini: Better beads, broader scope

“…Figure 9a also highlights the paradigm shift brought by Ing olfsson et al's simulation of a 63-component plasma membrane of realistic lipid composition. 194 That effort showcased Martini's maturity and suitability to this type of systems and kick-started an entire sub-field in simulations of realistic lipid bilayers 192,195,395,396 (of which the current complexity record, held by Corradi et al on lipid interactions of membrane proteins, 192 is an example; Table 1, Figure 9b). These simulations also underscore the simulation size and time requirements that high complexity can entail: Ing olfsson et al had to simulate a membrane patch of over 70 Â 70 nm 2 so that, at 0.03% mole fraction, the least represented lipid could still be present in multiple copies.…”