Protein function in extremely acidic conditions: Molecular simulations of a predicted aquaporin and a potassium channel in Acidithiobacillus ferrooxidans

We wish to understand how membrane proteins function in extremely acid conditions (<pH1 - pH3) using, as initial models, a predicted aquaporin and a potassium (K⁺) channel from the acidophile, Acidithiobacillus ferrooxidans ATCC 23270. A fundamental question is how these proteins function when confronted by a proton concentration difference of 6 orders of magnitude across the membrane. Similarity alignments were used to find the most similar three dimensional structure for each protein from crystallized orthologs deposited in the protein database PDB and these were used as templates for molecular simulations. Proteins from A. ferrooxidans were submitted to a molecular modeling strategy and their structural and dynamic properties were determined using molecular dynamics (MD) simulations (20 ns). Aquaporins are a large family of transmembrane channel proteins that allow the passive but selective movement of water, glycerol or CO₂ across cell membranes. MD calculations computed key biophysical features related to permeation parameters. K⁺ channels are membrane proteins that allow voltage-driven potassium flux across cellular membranes. A structural analysis of the A. ferrooxidans K⁺ channel predicts that it does not expose ionizable amino acids to the external surface. This would reduce protonation of residues at pH 1, permitting tertiary structure to be maintained.