Molecular Dynamics Study of Lipid Bilayer Electroporation with Open/Conductive State KcsA K+ Channel under Nanosecond Pulsed Electric Field

Ion channel proteins (e.g., K + channels) actively participate in external field-induced electroporation (EP), yet the mechanism by which open/conductive (O/O) state K + channels influence bilayer EP remains unclear. Here, we employ molecular dynamics (MD) simulations to investigate the impact of the O/O-state KcsA channels on membrane EP. Two systems─pure POPC bilayers and bilayers embedded with the O/O-state KcsA─were subjected to nanosecond pulsed electric fields (nsPEF) of varying amplitudes and polarities. In addition to lipid pore formation, nsPEF directly triggers pore generation within the selectivity filter (SF) of KcsA, which evolves into complex pores accompanied by protein conformational changes. Negative pulses preferentially initiate SF pore formation, while positive pulses at lower amplitudes favor complex pore development. Poration time ( t ep ) analysis demonstrates that O/O-state KcsA significantly accelerates membrane poration, particularly under negative pulses. To quantitatively characterize the poration, umbrella sampling (US) was applied to compute free energy profiles along reaction coordinates (RC). Biased simulations show that pure membranes exhibit similar free energy barriers for poration under positive and negative pulses, whereas KcsA-containing membranes display lower free energy under negative pulses, corroborating unbiased MD findings. These differences arise from asymmetric channel geometries, enhanced membrane potential heterogeneity, and altered water dipole distributions relative to those of pure membranes. This study advances understanding of field–protein interactions with the O/O-state KcsA channel-containing membranes and offers novel insights into its EP mechanisms.