Gramicidin A is a small but highly selective ion channel, an antibiotic protein embedded in the cell membrane, whose inner pore conducts cations in a single-file geometry. Given the difficulties in describing the energetics of its ion transport using classical potentials, a full density-functional theory study was conducted using the linear-scaling code CONQUEST. This code computes electronic structure through the conventional exact diagonalisation method, but also an approximate method of variable accuracy, which scales linearly with system size and makes it possible to apply quantum mechanics to large numbers of atoms.

Since the function of this channel is closely related to structure, two experimental structures featuring slightly different helix properties and peptide residue orientation were selected for comparison in an initial, isolated channel investigation performed using the diagonalisation method. Comprehensive structural optimisations led to geometries that are close to respective initial structures, and situated in different local minima of the Born-Oppenheimer surface. The lower energy experimental structure was also closer to an energy minimum and notably more stable during optimisation, while the other geometry underwent an expansion in helix pitch that is difficult to reconcile with other experiments. Despite the lack of channel environment in this preliminary study, the relative stability trend is in agreement with that predicted by long-time classical potential molecular dynamics of fully solvated channels.

Electronic properties of the isolated channel were explored with respect to changes in its helix characteristics and peptide residues and found to be more sensitive to helix features. Order-N calculations of the isolated channel agree very well with the diagonalisation result. Future order-N studies of this system will probe gramicidin A in a phospholipid membrane and explore the interactions between the channel and its environment.

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