Translocation of Human β Defensin Type 3 through a Neutrally Charged Lipid Membrane: A Free Energy Study

Human β defensin type 3 (hBD-3) is a cationic (+11 charged) antimicrobial peptide. It has three pairs of intramolecular disulfide bonds which can break under reducing conditions to convert hBD-3 into the linear analog form. hBD-3 can disrupt both Gram-positive and Gram-negative cell membranes, and even the mammalian cell membrane at high concentrations. However, the structural basis for the membrane-disrupting function of hBD-3 is still unknown. In order to understand the interaction mechanism of hBD-3 with a neutrally charged lipid membrane, explicit solvent and lipid umbrella-sampling simulations were performed using the NAMD program on the hBD-3 wild-type and the linear analog, in both the monomer and dimer forms. During the insertion and translocation process, most of the protein structure changes take place near the membrane–solvent interface, while the membrane interior appears to stabilize and rigidify the native-like hBD-3 structure. An energy barrier of 20 kcal/mol (domain unit) should be overcome by hBD-3 dimer in wild-type to cross the POPC bilayer but only 13 kcal/mol (domain unit) to insert into the bilayer center, and 20 kcal/mol for hBD-3 monomers to insert into the membrane center. Significant reorientation of lipids around hBD-3 inside the membranes was observed, which suggests a toroidal model for the membrane disruption process