The molecular mechanism of selective ion binding and following modulation of protein function has interested researchers for decades. It is known that cells require metal ions for virtually any imaginable biochemical activity. There are many potential applications of selective ion binding in biology and in bio- and nano-technology, such as cell volume management or proper electric signalling. A particularly important example of selective ion binding can be found in secondary membrane transporters. Secondary transporters are a very large family of integral membrane proteins utilizing electrochemically driven transport of cargo against its concentration gradient. Secondary transporters can be found in every tissue type participating in cell signaling, control of synaptic transmission, cell volume and delivery of key nutrients. With a number of readily available crystal structures, this family of membrane proteins represent an ideal and medically important grounds for studies of selective ion transport. Current understanding of the underlying complex thermodynamics of the ligand or ion binding and the subsequent transport across the cellular membrane is very limited. I used available theoretical methods (Molecular Dynamics, Free Energy and Monte-Carlo simulations) to study different factors, which govern ion binding to secondary transporters. The Free Energy Simulations together with the developed statistical-mechanical model were used to explain the role of the protein matrix in ion binding and selectivity of the sodium-dependent aspartate transporter (GltPh) crystallographic sites Na1 and Na2. I was able to show that only one site is functionally important and capable of selective ion binding. I quantify different factors (cavity size, chemical composition, surrounding protein residues, polarization effects) in defining selective binding. The findings are important for a general design of Na-selective sites with potential applications ranging far beyond single transporter protein. I have extended Grand-Canonical Monte-Carlo simulations to the problem of finding functional ion sites, which may be missing in the low-resolution crystal structures. The problem represents a significant challenge, since many of the functionally important sites have very low binding affinity and thus may be missing in available structures. Theoretical results were blind-tested by experimental work in the collaborating lab of Peter Larsson in Miami. From these computations and experimental measurements a new selective binding site was identified and a transport mechanism has been proposed. The quantum effects have been proposed to be important for selective ion binding to protein sites in secondary transporters. I was the first to develop Quantum Mechanics/Molecular Mechanics (QM/MM) for Free Energy Simulations of selective ion binding to model sites. The method was developed in collaboration with the Dennis Salahub group. A proof-of-principles QM/MM FEP study of ion selectivity with CHARMM-deMon was done in collaboration with Dr. Benoît Roux. This methodological section of my thesis extends the available arsenal to studies of selective binding to membrane proteins.