The effect of membrane proteins and peptides on their surrounding lipids is crucial for the structure, dynamics, and function of complex biological membranes as well as the interplay between membrane proteins and their environment. Here, we present a study of the influence of the transmembrane pore region of an ion channel on the physical properties of a phospholipid bilayer. We performed multinanosecond molecular dynamics simulations of the pore-forming aggregate of alpha-helical transmembrane peptides, which constitutes a model for the channel region of the nicotinic acetylcholine receptor, inserted in a simple lipid bilayer at conditions similar to those of the recent NMR experiments [Opella, S. J.; et al. Nature Struct. Biol. 1999, 6, 374]. The results obtained are compared with simulations of the pure lipid bilayer membrane. In particular, we consider here the simplest possible model membrane: a fully hydrated dimyristoyl-sn-glycerophosphocholine lipid bilayer, which is in the biologically relevant fluid lamellar phase at room temperature. Our analysis reveals that the peptides affect the properties of the lipid bilayer in several ways: (1) the bilayer thickness increases, (2) the number of gauche defects of the hydrocarbon chains decreases, (3) the orientational order of the hydrocarbon chains increases, (4) the orientational probability distribution of the lipid headgroup dipole moments becomes broader (more disordered), and (5) the lipid headgroup dipole moments are on average more oriented toward the water phase. Some of these effects depend on the specific properties of the case studied, such as the hydrophobic length of the bundle and the charges at the interface. Interestingly, the pore does not affect the two different sides of the membrane in the same way.