Impala: A Simple Restraint Field To Simulate The Biological Membrane In Molecular Structure Studies

The lipid bilayer is crucial for the folding of integral membrane proteins. This
article presents an empirical method to account for water-lipid interfaces in the
insertion of molecules interacting with bilayers. The interactions between the
molecule and the bilayer are described by restraint functions designed to mimic
the membrane effect. These functions are calculated for each atom and are
proportional to the accessible surface of the latter. The membrane is described
as a continuous medium whose properties are varying along the axis perpendicular
to the bilayer plane. The insertion is analyzed by a Monte Carlo procedure
applied to the restraint functions. The method was successfully applied to small
alpha peptides of known configurations. It provides insights of the behaviors of
the peptide dynamics that cannot be obtained with statistical approaches (e.g.,
hydropathy analysis).