Proton binding and release are elementary steps for the transfer of protons within proteins, which is a process that is crucial in biochemical catalysis and biological energy transduction. Local electric fields in proteins affect the proton binding energy compared to aqueous solution. In membrane proteins, also the membrane potential affects the local electrostatics and can thus be crucial for protein function. In this paper, we introduce a procedure to calculate the protonation probability of titratable sites of a membrane protein in the presence of a membrane potential. In the framework of continuum electrostatics, we use a modified Poisson-Boltzmann equation to include the influence of the membrane potential. Our method considers that in a transmembrane protein each titratable site is accessible for protons from only one side of the membrane depending on the hydrogen bond pattern of the protein. We show that the protonation of sites receiving their protons from different sides of the membrane is differently influenced by the membrane potential. In addition, the effect of the membrane potential is combined with the effect of the pH gradient resulting from proton pumping. Our method is applied to bacteriorhodopsin, a light-activated proton pump. We find that the proton pumping of this protein might be regulated by Asp115, a conserved residue for which no function has been identified yet. According to our calculations, the interaction of Asp115 with Asp85 leads to the protonation of the latter if the pH gradient or the membrane potential becomes too large. Since Asp85 is the primary proton acceptor in the photocycle, bacteriorhodopsin molecules in which Asp85 is protonated cannot pump protons. Furthermore, we estimate how the membrane potential affects the energetics of the individual proton-transfer reactions of the photocycle. Most reactions, except the initial proton transfer from the Schiff base to Asp85, are influenced. Our calculations give new insights into the mechanism with which bacteriorhodopsin senses the membrane potential and the pH gradient and how the proton pumping is regulated by these parameters.