Representation of end-to-end and micelle-like BMAP27 oligomer interaction.

<p>(A) End-to-end arrangement, and (B) micelle-like arrangement. The all-atom and coarse-grained models of peptide oligomers are shown as a cartoon and spheres, respectively, and are colored by chains. The relative peptide penetration is calculated from its center of mass to the outer leaflet lipid phosphate atoms as a function of time. The peptide and lipid phosphate atoms are shown in red and blue VDW formats, respectively, in VMD program. Vertical dotted lines divide both leaflets symmetrically and the black arrows indicate the membrane groove formation upon peptide binding. The abbreviations OL and IL denote outer-leaflet and inner-leaflets, respectively. The cyan arrows indicate monomer formation in the end-to-end model system.</p

Average number of hydrogen bonds between membrane lipids and BMAP27 residues.

<p>Average number of hydrogen bonds between membrane lipids and BMAP27 residues.</p

Conformational analysis of BMAP27 in aqueous and model lipid-bilayer environments.

<p>BMAP27 folding studied in (A) AMBER99SB-ILDN, and (B) CHARMM36 force field on a 0.5 μs time scale. The peptide and solvent molecules are represented as schematic and lines in Discovery studio visualizer 3.5, respectively. The peptide is colored by its hydrophobicity where hydrophobic and hydrophilic residues are shown as brown and blue, respectively. The partial density changes across the corresponding simulation boxes are shown in the central column. The z-coordinate represents the peptide position inside the simulation box. BMAP27 interaction with (C) zwitterionic (POPC), and (D) anionic (DOPG) membrane model systems. The peptide conformation is shown as a cartoon, lipid in blue line and water as red lines in VMD program. The relative BMAP27 membrane penetration is calculated by plotting the center of mass of peptide and lipid head phosphates present in the outer leaflets.</p

Interaction of BMAP27 with TLM and LLM systems in all-atom MD simulation.

<p>(A) The graph illustrates the center of mass of BMAP27 (full-length), helix (3–16), C-terminal residues (17–26) and lipid phosphate atoms. (B) Illustration of interaction of BMAP27 with the LLM. The peptide and lipids are shown as a cartoon and line in PyMOL. The hydrogen bonds between BMAP27 and lipid molecules are shown in black dotted lines. The hydrophobic residues and their solvent exposed side chains are shown in blue. The crucial kink position at F10 is shown as bold and red. (C) Center of mass analysis of BMAP27 in the TLM system. (D) Conformational alternation of BMAP27 and its interaction with the TLM model.</p

Membrane Mediated Antimicrobial and Antitumor Activity of Cathelicidin 6: Structural Insights from Molecular Dynamics Simulation on Multi-Microsecond Scale

<div><p>The cathelicidin derived bovine antimicrobial peptide BMAP27 exhibits an effective microbicidal activity and moderate cytotoxicity towards erythrocytes. Irrespective of its therapeutic and multidimensional potentiality, the structural studies are still elusive. Moreover, the mechanism of BMAP27 mediated pore formation in heterogeneous lipid membrane systems is poorly explored. Here, we studied the effect of BMAP27 in model cell-membrane systems such as zwitterionic, anionic, thymocytes-like (TLM) and leukemia-like membranes (LLM) by performing molecular dynamics (MD) simulation longer than 100 μs. All-atom MD studies revealed a stable helical conformation in the presence of anionic lipids, however, significant loss of helicity was identified in TLM and zwitterionic systems. A peptide tilt (~45˚) and central kink (at residue F10) was found in anionic and LLM models, respectively, with an average membrane penetration of < 0.5 nm. Coarse-grained (CG) MD analysis on a multi-μs scale shed light on the membrane-dependent peptide and lipid organization. Stable micelle and end-to-end like oligomers were formed in zwitterionic and TLM models, respectively. In contrast, unstable oligomer formation and monomeric BMAP27 penetration were observed in anionic and LLM systems with selective anionic lipid aggregation (in LLM). Peptide penetration up to ~1.5 nm was observed in CG-MD systems with the BMAP27 C-terminal oriented towards the bilayer core. Structural inspection suggested membrane penetration by micelle/end-to-end like peptide oligomers (carpet-model like) in the zwitterionic/TLM systems, and transmembrane-mode (toroidal-pore like) in the anionic/LLM systems, respectively. Structural insights and energetic interpretation in BMAP27 mutant highlighted the role of F10 and hydrophobic residues in mediating a membrane-specific peptide interaction. Free energy profiling showed a favorable (-4.58 kcal mol^-1 for LLM) and unfavorable (+0.17 kcal mol^-1 for TLM) peptide insertion in anionic and neutral systems, respectively. This determination can be exploited to regulate cell-specific BMAP27 cytotoxicity for the development of potential drugs and antibiotics.</p></div

Illustration of BMAP27 interaction and penetration during the multi-μs coarse-grained MD simulation.

<p>BMAP27 interaction in (A) DPPC, (B) DOPS, (C) TLM, and (D) LLM model systems. The peptide monomers are colored by chain and shown as tan, black, red and green, and the C-terminal residues as yellow in VDW format in VMD program. The outer and inner leaflets of each bilayer system are denoted as OL and IL, respectively. The vertical dotted line drawn indicates the symmetric division of the total distance between the OL and IL. The center of mass graphs representing the peptide penetration is shown with respect to the lipid head atoms for individual systems and are presented below their corresponding molecular structures.</p

Measurement of bilayer thickness in coarse-grained systems using GridMAT-MD program.

<p>The graphics were generated by gnuplot 4.6 using a 20 x 20 matrix distribution. The thickness change monitored through the different colors in the graph are correlated with the distance scale (nanometer) given on the right-hand side of the individual systems. For each system two graphs are shown representing the bilayer thickness before MD (in absence of peptide) and after MD (with peptide) simulation.</p

Summary of molecular dynamics simulation systems.

<p>Summary of molecular dynamics simulation systems.</p

Variation of H-bonds participated in interaction during 50 ns simulation in zNOD-NACHT complexes.

<p>(A) Complex I for zNOD1-NACHT, (B) Complex II for zNOD1-NACHT, (C) Complex III for zNOD1-NACHT, (D) Complex I for zNOD2-NACHT, (E) Complex II for zNOD2-NACHT and (F) Complex III for zNOD2-NACHT (G) mNLRC4-NACHT complex. The y-axis represents the number of H-bond formed during the course of MD simulation and the simulation time (in ns) is depicted in x-axis. All graphs are generates using Grace 5.1.23 plotting program.</p

Interaction analysis (hydrogen bond, hydrophobic contacts, electrostatics and van der Waals contact) of NOD1-NACHT-ATP and NOD2-NACHT-ATP complexes before molecular dynamics simulation.

<p>Interaction analysis (hydrogen bond, hydrophobic contacts, electrostatics and van der Waals contact) of NOD1-NACHT-ATP and NOD2-NACHT-ATP complexes before molecular dynamics simulation.</p