Atomistic Study of Structural and Functional Properties of Membrane Proteins

Living cells exploit membrane proteins to carry out crucial functions like transport of nutrients, signal transduction, energy conversion, etc. Recently, the remarkable and continuous improvement of computational algorithms and power allowed simulating and investigating relevant aspects of the mechanisms of this important class of proteins. In this thesis we focused on the study of two membrane proteins: a transporter and an ion channel. Firstly, we investigated the bacterial homologue of Sodium Galactose Transporter (SGLT), which plays an important role in the accumulation of sugars (i.e. glucose or galactose) inside cells, assuring a correct intestinal absorption and renal re-absorption. Using enhanced sampling techniques, we focused in understanding selected aspects of its transport mechanism. First, we identified a stable Na+ ion binding site, which was not solved crystallographically. Second, based on the results of the first study, we investigated the mechanism of the binding/release of both ligands to/from the protein in the inward-facing conformation and their interplay during this process. Finally, we also worked on another membrane protein: the Cyclic Nucleotide-Gated (CNG) channel. Using a chimera, the NaK2CNG mimic, we investigated the structural basis of the linkage among gating and permeation and of the voltage dependence shown by this channel. Large-scale molecular dynamics (MD) simulations, together with electrophysiology and X-ray crystallography, have been used to study the permeation mechanism of this mimic as a model system of CNG in presence of different alkalications.