In my thesis work, I investigate functional mechanisms of complex molecular machines in the cell membrane that carry out the transport (reuptake) of neurotransmitter molecules into the cell. I apply and develop methods of computational biophysics to reveal and quantify the molecular transport process that is essential for the ability of the cell to continue to signal. Such detailed understanding is highly significant because dysfunction of these transporter proteins is known to relate to depression, epilepsy and strokes, and to be involved in neurodegenerative diseases, such as Alzheimer's or Parkinson's disease. The mechanistic insights gained from the studies presented in this thesis pertain to (1) a conformational transition in the substrate translocation mechanism of glutamate transporters, and (2) allosteric changes in the substrate transport mechanism of the neurotransmitter-sodium symporter protein family: For the family of glutamate transporters, a major finding is that transient exposure of a protein-protein interface to solvent facilitates the conformational transition of the transporter and allows functionally relevant chloride ions to bind to the interface. In the study of neurotransmitter-sodium symporters, a major discovery is the identification of common allosteric pathways of pairwise interaction changes that connect the intra- with the extracellular side of the transporter. The computational approaches that enabled these mechanistic insights include Motion Planning, mixed Elastic Network Models, (targeted) Molecular Dynamics simulations, Free Energy Perturbations, and various statistical analysis methods.