Figure 5.4: A Ligand-Gated Channel Protein Opens in Response to a Stimulus The channel protein is anchored in the lipid bilayer by the nonpolar (hydrophobic) amino acids exposed on the protein’s surface. The protein changes its three-dimensional shape when a stimulus molecule (ligand) binds to it, opening a pore lined with polar amino acids. This allows hydrophilic, polar substances to pass through.