Interaction of Human β Defensin Type 3 (hBD-3) with Different PIP2-Containing Membranes, a Molecular Dynamics Simulation Study

Abstract

Human β defensin type 3 (hBD-3) is a cysteine-rich small antibacterial peptide. It belongs to the human innate immune system. hBD-3 has six cysteine residues, which form three pairs of disulfide bonds, and those bonds break in the reducing condition. It is known that hBD-3 can interact with bacterial membrane, and even eukaryotic cell membrane, which has a low concentration of phosphatidylinositol 4,5-bisphosphate (PIP2) lipids. PIP2 is a vital component in cell membranes and has been found to play important roles during antimicrobial peptide (AMP) interaction with membranes. To understand the functional mechanism of hBD-3 interacting with PIP2-containing membranes, the binding structures of hBD-3 on 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayers mixed with 10% of PIP2 were predicted using two kinds of methods. The first one is by placing the hBD-3 monomer in different orientations above the POPC + 10%PIP2 membrane to set up five different initial simulation systems and performing long-term simulations on each to predict the most stable binding structure. It was found that hBD-3 analogue binds on the mixed lipid membrane on the two loop regions. The second method is by running long-term simulations on one or nine hBD-3 dimers binding on POPC mixed with 10%PIP2 lipid bilayer starting from the solid-state NMR (ssNMR)-suggested orientation. The dimer dissociated, and the most stable binding of hBD-3 in wild-type on the mixed membrane is also through the two loop regions, which agrees with the prediction from both the first method and the lipid self-assembly result. The PIP2 lipids can form long-lasting hydrogen bonds with positively charged residues such as Arg and Lys on hBD-3, thus forming clusters with hBD-3. As a comparison, hBD-3 dimers binding with a combined bilayer having 1,2-palmitoyl-oleoyl-sn-glycero-3-phosphoserine (POPS) on the upper and POPC on the lower leaflets and the combined POPS + POPC bilayer mixing with 10%PIP2 were also studied. The long-term simulation result shows that hBD-3 can bind with the heads of negatively charged POPS and PIP2 lipids and form hydrogen bonds. The stable binding sites of hBD-3 on PIP2 or POPS mixed bilayers are still on the two loop regions. On the combined POPS + POPC mixed with 10%PIP2 bilayer, the binding of hBD-3 with PIP2 lipids became less stable and fewer because of the competition of binding with the POPS lipids. Besides that, binding with hBD-3 can decrease the membrane thickness of the POPC + PIP2, POPS + POPC, and POPS + POPC + PIP2 bilayers and make POPS and PIP2 lipids more flexible based on the order parameter calculations. Our results supply molecular insight on AMP binding with different membranes and can help understand the functional mechanism of hBD-3 disrupting PIP2-containing membranes.

Phosphatidylinositol (PI) Lipids Modulate the Binding of Tau Fibrils on Lipid Bilayers

“…24 PIP 2 is also involved in the generation of messenger molecules, membrane trafficking, membrane protein interaction, protein -protein interactions and protein oligomerization. [25][26][27][28] PI lipids are found to significantly influence the dynamics and the structure of the PC membranes. 29 Molecular dynamics simulations have paved the way to study the interaction of lipid bilayers with amyloid fibrils.…”

Machine learning assisted rational design of antimicrobial peptides based on human endogenous proteins and their applications for cosmetic preservative system optimization

“…Human β defensin type 3 (hBD-3) is a cysteine-rich small antibacterial peptide with broad-spectrum antimicrobial activity and may play an important role in innate epithelial defense. Because hBD-3 kills bacteria by disrupting the cell membrane, which is relatively stable in chemical composition, its antibacterial activity will not cause drug resistance 22 . Thus, hBD-3 could serve as a potential AMP for designing novel preservatives.…”

Antimicrobial Peptide Recognition Motif of the Substrate Binding Protein SapA from Nontypeable Haemophilus influenzae

“…AMPs are conserved across species and selectively target pathogen cell membranes to disrupt membrane integrity. − The two main classes of AMPs in humans, defensins and cathelicidins, are positively charged amphipathic peptides consisting of 20 to 50 amino acids. , Defensins are cysteine-rich AMPs with three intramolecular disulfide bridges, forming a conserved γ-core motif composed of a β-hairpin in an antiparallel β-sheet. , Additionally, each defensin includes an unstructured loop between Cys-2 to Cys-4 which contains charged and hydrophobic residues important for membrane interaction (Figure ). − The alpha helical peptide LL-37, the only member of the cathelicidin family found in humans, is produced by a variety of cell types, including the epithelial cells of the airway . Defensins, including α-defensin 1 (hNP-1), β-defensin 2 (hBD-2), and β-defensin 3 (hBD-3), are prevalent in the epithelial cells of mucosal surfaces including the nasopharynx and are considered potent AMPs in response to NTHi infections. ,− …”

“… 26 , 28 Additionally, each defensin includes an unstructured loop between Cys-2 to Cys-4 which contains charged and hydrophobic residues important for membrane interaction ( Figure 1 ). 29 − 31 The alpha helical peptide LL-37, the only member of the cathelicidin family found in humans, is produced by a variety of cell types, including the epithelial cells of the airway. 27 Defensins, including α-defensin 1 (hNP-1), β-defensin 2 (hBD-2), and β-defensin 3 (hBD-3), are prevalent in the epithelial cells of mucosal surfaces including the nasopharynx and are considered potent AMPs in response to NTHi infections.…”