Aminoacid, peptides and cation transporters conform a family of secondary transporters present in both prokaryotic and eukaryotic organism. They play an important role in ion homeostasis, cell's volume regulation, nutrient uptake and even in neurotransmiter recycling processes. Recently, the first crystal structure of a bacterial sodium independent amino acid transporter (ApcT) has been obtained (cite). It has been suggested, rather unconclusively, that ApcT couples substrate uptake to one or more protons. In the mechanism proposed by E. Gouaux and colaborators, LYS 158 plays a key role in the gating mechanism, promoting large amplitude movements upon protonation and deprotonation. However details of this motion, proton stoichoimetry and even how protons get in and out of the core of the protein are unknown. In this work we seek to answer these questions using computational tools: gran canonical monte carlo, molecular dynamic simulation, molecular docking and free enery calculation. Preliminary results seem to confirm the idea that the protonation state of LYS 158 has an important effect on the protein structure. However, results also suggest that the global mechanism can be different from that originaly porposed. We are also interested in the molecular basis for the rather unselective nature of ApcT, a characteristic that sets it appart from most aminoacid transporters, such as LeuT.