Multiscale simulation is employed to examine changes in atomistic-level protein structure due to long wavelength membrane undulations and plane stress fields. An ensemble of atomistic-level simulations of a model of a transmembrane influenza A virus M2 proton channel in a dimyristoylphosphatidylcholine (DMPC) bilayer is coupled to a corresponding mesoscopic model of a DMPC bilayer in an explicit mesoscopic solvent. Structural variations in the key proton gating His(37) residues of the M2 channel are examined. Small, but distinct variations in the structure of the His(37) residues are observed in both the open and closed states of the channel as a result of the coupling to mesoscopic-level membrane motions. (c) 2006 Elsevier Inc. All rights reserved.