Figure 6.

Steered molecular dynamics (SMD) simulations of the migration of CO₂ and HCO₃⁻ through LCI1. (A) CO₂ trajectory through LCI1 in SMD is shown as blue mesh. LCI1 is oriented with the channel along the z-axis and the position of ligand along the channel is measured as distance from the protein center of mass along the z-axis. (B) Plots of applied forces as a function of ligand positions along the channel (blue, CO₂; red, HCO₃⁻), which indicate that pushing HCO₃⁻ through the channel requires much larger force, suggesting that CO₂ may be the preferred ligand. A black rectangle highlights the region corresponding to the putative CO₂-binding site. The two peaks marked in the CO₂ plot (blue) indicate local electrostatic interactions between (C) putative bound CO₂ and residues E87 and N161; and (D) putative bound CO₂ and residue Q16. (E) Root mean square fluctuations (RMSF) of the LCI1 residues during the SMD simulations with CO₂ (blue) and HCO₃⁻ (red).