LAUSR

The structural characterization of membrane-associated proteins on fluid lipid bilayers remains a challenge to most modern biophysical techniques. Neutron reflectivity (NR) has emerged as a method that provides sub-nanometer resolution of proteins in a functional lipid environment. Interpretation of NR data gives an envelope structure related to the distribution of protein density along the membrane normal direction and further refinement using structural information may yield a full atomistic description of the protein-membrane complex. However, for flexible or intrinsically disordered protein domains, such information is often not available or multiple conformational states may contribute to the average density profile as resolved by NR. Thus, characterization of such systems requires more elaborate approaches. We previously demonstrated that molecular dynamics (MD) simulations can provide a full atomistic interpretation of NR results in cases where only partial internal protein structure is available, but such simulations are often plagued by long equilibration times. Here we present a procedure to steer MD simulations toward configurations that reproduce experimental NR results. Biasing potentials are calculated through a comparison of the one-dimensional densities from NR data with the evolving density profile derived from the MD trajectory at each time step. This results in steering forces that direct molecular conformations of the protein on the bilayer toward the experimental results. Steering becomes weaker as the density profiles match more closely, disappearing entirely for matched densities. The structure is guided toward the desired configuration, rather than rigidly confined to the experimental density. Here we show the application of our method to model peptide and small protein systems, also discussing the efficiency of the procedure and potential merits and pitfalls in its application.