3D hydrophobic moment vectors as a tool to characterize the surface polarity of amphiphilic peptides

Biophys J. 2014 Jun 3;106(11):2385-94. doi: 10.1016/j.bpj.2014.04.020.

Abstract

The interaction of membranes with peptides and proteins is largely determined by their amphiphilic character. Hydrophobic moments of helical segments are commonly derived from their two-dimensional helical wheel projections, and the same is true for β-sheets. However, to the best of our knowledge, there exists no method to describe structures in three dimensions or molecules with irregular shape. Here, we define the hydrophobic moment of a molecule as a vector in three dimensions by evaluating the surface distribution of all hydrophilic and lipophilic regions over any given shape. The electrostatic potential on the molecular surface is calculated based on the atomic point charges. The resulting hydrophobic moment vector is specific for the instantaneous conformation, and it takes into account all structural characteristics of the molecule, e.g., partial unfolding, bending, and side-chain torsion angles. Extended all-atom molecular dynamics simulations are then used to calculate the equilibrium hydrophobic moments for two antimicrobial peptides, gramicidin S and PGLa, under different conditions. We show that their effective hydrophobic moment vectors reflect the distribution of polar and nonpolar patches on the molecular surface and the calculated electrostatic surface potential. A comparison of simulations in solution and in lipid membranes shows how the peptides undergo internal conformational rearrangement upon binding to the bilayer surface. A good correlation with solid-state NMR data indicates that the hydrophobic moment vector can be used to predict the membrane binding geometry of peptides. This method is available as a web application on http://www.ibg.kit.edu/HM/.

MeSH terms

  • Algorithms*
  • Amino Acid Sequence
  • Antimicrobial Cationic Peptides / chemistry*
  • Antimicrobial Cationic Peptides / metabolism
  • Gramicidin / chemistry*
  • Gramicidin / metabolism
  • Hydrophobic and Hydrophilic Interactions
  • Lipid Bilayers / chemistry
  • Lipid Bilayers / metabolism
  • Molecular Dynamics Simulation*
  • Molecular Sequence Data
  • Peptides / chemistry*
  • Peptides / metabolism
  • Protein Binding
  • Static Electricity

Substances

  • Antimicrobial Cationic Peptides
  • Lipid Bilayers
  • Peptides
  • peptide-Gly-Leu-amide
  • Gramicidin