Figure 6.11 A Gated Channel Protein Opens in Response to a Stimulus The channel protein has a pore of polar amino acids and water. It is anchored in the hydrophobic bilayer by its outer coating of nonpolar R groups. The protein changes its three-dimensional shape when a stimulus molecule (ligand) binds to it, opening the pore so that specific hydrophilic substances can pass through. Other channels open in response to an electric potential (voltage) or mechanical stimuli.