Observing molecular interactions that determine stability, folding, and functional states of single Na+/H+ antiporters

Selective ion and solute transport across cell membranes is a vital process occurring in all types of cells. Evolutionarily developed transport proteins work as membrane-embedded molecular machines, which alternately open a gate on each side of the membrane to bind and translocate specific ions. Sodium/proton exchange plays a crucial role in maintaining cytoplasmic pH and membrane potential, while, if not regulated, the process causes severe heart diseases in humans. Here I applied single-molecule force spectroscopy to investigate molecular interactions determining the structural stability of the sodium/proton antiporter NhaA of Escherichia coli, which serves as a model system for this class of proteins. Mechanical pulling of NhaA molecules embedded in the native lipid bilayer caused a step-wise unfolding of the protein and provided insights into its stability. Modified experiments allowed observing refolding of NhaA molecules and estimating folding kinetics for individual structural elements, as well as detecting eventual misfolded conformations of the protein. The activity of NhaA increases 2000fold upon switching pH from 6 to 8. Single-molecule force measurements revealed a reversible change in molecular interactions within the ligand-binding site of the transporter at pH 5.5. The effect was enhanced in the presence of sodium ions. The observation suggests an early activation stage of the protein and provides new insights into the functioning mechanism. When studying interactions of NhaA with the inhibitor 2-aminoperimidine, I exploited single-molecule force measurements to validate the binding mechanism and to describe quantitatively formation of the protein:inhibitor complex. The ability of single-molecule force measurements to probe structurally and functionally important interactions of membrane proteins opens new prospects for using the approach in protein science and applied research