Molecular Dynamics Simulation of Bombolitin II in the Dipalmitoylphosphatidylcholine Membrane Bilayer

Abstract

The orientation behavior of Bombolitin II (BLT2) in the dipalmitoylphosphatidylcholine membrane bilayer was investigated by using molecular-dynamics simulation. During the 20-ns simulation, the BLT2 began to tilt and finally reached the angle of 51° from the membrane-normal. The structure of the peptide formed the amphipathic α-helical structure during the entire simulation time. The peptide tilts with its hydrophobic side faced to the hydrophobic core of the bilayer. We analyzed the mechanism of the tilting behavior of the peptide associated with the membrane in detail. The analysis showed that the hydrogen-bond interaction and the electrostatic interaction were found to exist between Lys(12) and a lipid molecule. These interactions are considered to work as an important factor in tilting the peptide to the membrane-normal.

Computational study on the interactions and orientation of monoclonal human immunoglobulin G on a polystyrene surface

“…The MD simulation was carried out with isobaric-isothermal (NPT) ensemble with 1 femtosecond time step. The details of the calculation procedure were the same as our previous simulations; 26,27 ie, nonbonded interactions were calculated using a group-based cutoff with a switching function 20 and were updated every five time steps. The switching function was turned on at 1.2 nm and turned off at 1.35 nm.…”

Recent Solid-State NMR Studies of Membrane-Bound Peptides and Proteins

“…MD simulation studies were performed to investigate whether the dynamic structures of various antimicrobial, antibacterial, and antibiotic peptides in membrane lipid-bilayer systems agree with those determined in solidstate NMR studies [55,[244][245][246][247][248][249][250]. MD simulation has been used to investigate the orientation of membrane-bound antimicrobial peptides (MB21 [244], indolicidin [245], BLT2 [246], CM15 [247], piscidin-1 [248], δ-lysin [249]), an antibacterial peptide (bovine LFampin [55]), neuropeptides (neuropeptides B and W [250]), human immunodeficiency virus fusion peptides (T-1249 [251], FP-16 and -23 [252], and VP1 [253]), and transmembrane peptides (gramicidin A [254], M2 [255], carnobacteriocin B2 [256], TM2 [257], human islet amyloid polypeptide [258], human serum paraoxonase 1 [259], and gaduscidin-1 and -2 [260]) in zwitterionic or anionic membrane lipid bilayers.…”

“…The result clearly shows that the helical axis of BLT2 is tilted in the equilibrium state at an angle of 51°relative to the membrane normal. Although the tilt angle determined by MD simulation was a slightly larger than that determined from solid-state NMR experiments, the tilting behavior of BLT2 in a DPPC membrane was nevertheless clearly revealed by both NMR analysis [54] and MD simulation [246]. The secondary structure of BLT2 in the membrane bilayer was investigated by analyzing the main-chain torsion angles ϕ and ψ (Fig.…”

“…MD simulation has been used to investigate the orientation of membrane-bound antimicrobial peptides (MB21 [244], indolicidin [245], BLT2 [246], CM15 [247], piscidin-1 [248], δ-lysin [249]), an antibacterial peptide (bovine LFampin [55]), neuropeptides (neuropeptides B and W [250]), human immunodeficiency virus fusion peptides (T-1249 [251], FP-16 and -23 [252], and VP1 [253]), and transmembrane peptides (gramicidin A [254], M2 [255], carnobacteriocin B2 [256], TM2 [257], human islet amyloid polypeptide [258], human serum paraoxonase 1 [259], and gaduscidin-1 and -2 [260]) in zwitterionic or anionic membrane lipid bilayers. The membrane-bound peptides were inserted into the membrane perpendicular to the membrane surface, with the C-or N-terminus toward the inside of the membrane.…”

“…An MD simulation of insertion of the antimicrobial peptide BLT2 in a DPPC bilayer was performed to investigate the peptide's dynamics structure [246]. BLT2 maintained a helical structure throughout the MD simulation time.…”