Umbrella Sampling Simulations of Human β Defensin Type 1 and 3 Crossing Model Bacterial Membranes

Human β defensins (hBDs) are cationic, cysteine-rich antimicrobial peptides that exert antibacterial effects by disrupting the integrity of bacterial cell membranes. Two popular hBDs, hBD type 1 (hBD-1) and type 3 (hBD-3), exhibit different activities against Gram-negative (G-) and Gram-positive (G+) bacteria. In order to understand the reasons for their different potencies, a comparative study on hBD-1 and hBD-3 in both monomer and dimer forms was conducted. Their translocation through simple model G- (represented by POPE/POPG = 3/1) and G+ (POPG/POPE = 3/1) bacterial membranes was investigated using coarse-grained umbrella sampling simulations, followed by brief all-atom molecular dynamics simulations. It was found that both hBD-3 and hBD-1 need to overcome a lower energy barrier to cross model G+ membranes than G- membranes. Additionally, hBDs in the dimer form encounter a significantly lower energy barrier when crossing model bacterial membranes than in the monomer form. To find out the reason for that, the structures and interactions between hBDs and membranes were calculated. It was found that hBD-3 adopts a more disordered secondary structure than hBD-1 when embedded in model membranes and in solvent. As the net charge of hBDs decreases from hBD-3 to hBD-1, the number of hydrogen bonds formed between hBDs and bacterial membranes decreases. Meanwhile, hBD-3 disrupts POPG and POPE lipids more significantly than hBD-1 in both kinds of bacterial membrane systems, especially in the dimer form. Both hBDs exhibit a larger nonpolar surface area than polar surface area in solvent and in membranes, and hBD-1 has a higher proportion of nonpolar surface area than hBD-3 in membranes, particularly in the monomer form. In the dimer form, hBDs can rearrange their structures to bury polar atoms or residues at the binding interface, thereby reducing the proportion of polar surface area exposed at the membrane center. In summary, these results suggest that factors, such as charge densities, hydrophobic effects, structural flexibility, and oligomerization state, influence the translocation capability of hBDs through simple model bacterial membranes.