Protegrin‐1 orientation and physicochemical properties in membrane bilayers studied by potential of mean force calculations

Protegrin‐1 (PG‐1) belongs to the family of antimicrobial peptides. It interacts specifically with the membrane of a pathogen and kills the pathogen by releasing its cellular contents. To fully understand the energetics governing the orientation of PG‐1 in different membrane environments and its effects on the physicochemical properties of the peptide and membrane bilayers, we have performed the potential of mean force (PMF) calculations as a function of its tilt angle at four distinct rotation angles in explicit membranes composed of either DLPC (1,2‐dilauroylphosphatidylcholine) or POPC (1‐palmitoyl‐2‐oleoylphosphatidylcholine) lipid molecules. The resulting PMFs in explicit lipid bilayers were then used to search for the optimal hydrophobic thickness of the EEF1/IMM1 implicit membrane model in which a two‐dimensional PMF in the tilt and rotation space was calculated. The PMFs in explicit membrane systems clearly reveal that the energetically favorable tilt angle is affected by both the membrane hydrophobic thickness and the PG‐1 rotation angle. Local thinning of the membrane around PG‐1 is observed upon PG‐1 tilting. The thinning is caused by both hydrophobic mismatch and arginine‐lipid head group interactions. The two‐dimensional PMF in the implicit membrane is in good accordance with those from the explicit membrane simulations. The ensemble‐averaged Val16 ¹⁵N and ¹³CO chemical shifts weighted by the two‐dimensional PMF agree fairly well with the experimental values, suggesting the importance of peptide dynamics in calculating such ensemble properties for direct comparison with experimental observables. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010