Interaction of Human β Defensin Type 3 (hBD-3) with Different PIP2-Containing Membranes, a Molecular Dynamics
1Department of Chemical Engineering, Tennessee Technological University, Cookeville, Tennessee 38505, United States.
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.
Insights
Human β defensin type 3 (hBD-3), an antimicrobial peptide, binds to cell membranes containing PIP2 lipids via its loop regions. This interaction, involving hydrogen bonds, alters membrane thickness and lipid flexibility, offering insights into hBD-3
Area of Science:
- Biochemistry
- Molecular Biology
- Biophysics
Background:
- Human β defensin type 3 (hBD-3) is a key component of the innate immune system, known for its antimicrobial properties.
- hBD-3 interacts with cell membranes, particularly those containing phosphatidylinositol 4,5-bisphosphate (PIP2) lipids, which are crucial for membrane function and antimicrobial peptide (AMP) interactions.
Purpose of the Study:
- To elucidate the molecular mechanisms and binding structures of hBD-3 interacting with PIP2-containing lipid bilayers.
- To understand how hBD-3 binding affects membrane properties like thickness and lipid dynamics.
Main Methods:
- Molecular dynamics simulations were employed to predict the binding structures of hBD-3 monomers and dimers on various lipid bilayers (POPC, POPC+PIP2, POPS+POPC, POPS+POPC+PIP2).
- Analysis of hydrogen bonding, membrane thickness, and lipid order parameters provided insights into the binding interactions and their effects.
Main Results:
- hBD-3 predominantly binds to PIP2-containing membranes through its two loop regions, forming stable hydrogen bonds with PIP2 and POPS lipids.
- The binding of hBD-3 was observed to decrease membrane thickness and increase the flexibility of PIP2 and POPS lipids.
- Competition between PIP2 and POPS lipids affected the stability and extent of hBD-3 binding on mixed bilayers.
Conclusions:
- hBD-3 utilizes its loop regions for stable binding to PIP2-rich membranes, driven by hydrogen bond formation with charged lipid headgroups.
- hBD-3 binding induces significant changes in membrane biophysical properties, contributing to its functional mechanism.
- These findings provide molecular-level understanding of hBD-3's interaction with diverse membranes, aiding in the comprehension of its role in membrane disruption.
