Prediction of binding free energy for adsorption of antimicrobial peptide lactoferricin B on a POPC membrane.
Molecular dynamics (MD) simulations are used to study the interaction of a zwitterionic palmitoyl-oleoyl-phosphatidylcholine (POPC) bilayer with the cationic antimicrobial peptide bovine lactoferricin (LFCinB) in a 100 mM NaCl solution at 310 K. The interaction of LFCinB with POPC is used as a model system for studying the details of membrane-peptide interactions, with the peptide selected because of its antimicrobial nature. Seventy-two 3 ns MD simulations, with six orientations of LFCinB at 12 different distances from a POPC membrane, are carried out to determine the potential of mean force (PMF) or free energy profile for the peptide as a function of the distance between LFCinB and the membrane surface. To calculate the PMF for this relatively large system a new variant of constrained MD and thermodynamic integration is developed. A simplified method for relating the PMF to the LFCinB-membrane binding free energy is described and used to predict a free energy of adsorption (or binding) of -1.05+/-0.39 kcal/mol , and corresponding maximum binding force of about 20 pN, for LFCinB-POPC. The contributions of the ions-LFCinB and the water-LFCinB interactions to the PMF are discussed. The method developed will be a useful starting point for future work simulating peptides interacting with charged membranes and interactions involved in the penetration of membranes, features necessary to understand in order to rationally design peptides as potential alternatives to traditional antibiotics.
Vivcharuk
Victor
V
Biophysics Interdepartmental Group and Department of Physics, University of Guelph, Guelph, Ontario N1G 2W1, Canada. viv@physics.uoguelph.ca
Tomberli
Bruno
B
Tolokh
Igor S
IS
Gray
C G
CG
D000327:Adsorption; D000465:Algorithms; D000818:Animals; D023181:Antimicrobial Cationic Peptides / Q000737:chemistry*; D001703:Biophysics / Q000379:methods*; D002417:Cattle; D003198:Computer Simulation; D007781:Lactoferrin / Q000737:chemistry*; D015233:Models, Statistical; D008968:Molecular Conformation; D010455:Peptides / Q000737:chemistry; D010713:Phosphatidylcholines / Q000737:chemistry*; D011485:Protein Binding; D013314:Stress, Mechanical; D013816:Thermodynamics
D023181:Antimicrobial Cationic Peptides; D010455:Peptides; D010713:Phosphatidylcholines; C082171:lactoferricin B; D007781:Lactoferrin; C028694:1-palmitoyl-2-oleoylphosphatidylcholine