Fig. 3: Structures and radius profiles along the channel axis of the designed pores.
a Stable DpPorA (cyan) structures are shown in cartoon representation. Basic amino acid residues are highlighted in blue, while acidic residues are depicted in red. b Stable LpPorA (green) and DpPorA (cyan) structures are overlapped in cartoon representation. Basic amino acid residues are highlighted in blue, while acidic residues are depicted in red. c Average radius profiles along the channel axis are based on unbiased trajectories, with the transparent shades indicating standard deviations in the average radius calculations. d Cartoon representations of stable DpPorA DE (cyan) structures of the mutated pPorA. e Overlapped cartoon representations of stable LpPorA DE (green) and DpPorA DE (cyan) structures of the mutated pPorA. f The average radius profiles of the mutated pores along the channel axis from a trajectory, while the transparent shades indicating standard deviations in the average radius calculations. g C-terminal views of the electrostatic potential maps highlight the charged amino residues of DpPorA lining the interior channel wall. The computed electrostatic potential ranges from −188 to +309 kBT/e for DpPorA, where 1 kBT/e equals 26 mV at 300 K. To enhance clarity, the color range for the displayed electrostatic potential maps has been restricted to a range from −100 to +100 kBT/e. h C-terminal electrostatic potential map of DpPorA DE, where the computed electrostatic potential ranges from −299 to +775 kBT/e for DpPorA DE. i The overlapped representation of the C-terminal electrostatic potential map of DpPorA (displayed with a narrower ribbon) and DpPorA DE (displayed with a broader ribbon).
