Alternate pathways for acetic acid and acetate ion release from acetylcholinesterase: a molecular dynamics study

Two competing passageways for the exit of acetic acid and acetate ion in Torpedo californica (Tc) acetylcholinesterase (ACHE) were studied by examining free energies of passage through two potential trajectories using the umbrella sampling technique as implemented in CHARMM. The coordinates for migration were defined as the distance from Se200 O gamma, one through the 20-Angstrom long active-site gorge ending with Trp279 and a 14-Angstrom long route ending at Arg244. The free energies were calculated in successive windows 0.5 Angstrom wide for 40-90 ps. The potential of mean force (PMF) was calculated along the coordinate for migration. The PMF for the migration of acetic acid decreases by similar to 8 kcal/mol after 8-Angstrom travel through the main gorge. The PMF profile for acetate ion migration falls to a 6 kcal/mol lower value than for acetic acid migration in the main gorge. The free energy barrier for the migration of acetate ion is 1.5 kcal/mol due to a constriction formed by Tyr121, Phe290, Phe330, and Phe331 in the main gorge. The interaction between acetic acid/acetate ion and the OH group of Tyr121 appears to guide product release through the main gorge. Acetate ion remains hydrogen-bonded to Tyr121 until it approaches Trp279 when it is expelled into bulk water. Acetic acid encounters a 6 kcal/mol barrier through the alternate pathway, while the PMF for acetate ion drops similar to 27 kcal/mol when it approaches Arg244. This is the lowest energy path. Full molecular dynamics simulations, free of restraint for 170 ps, result in the migration of acetate ion through the short channel but not through the main gorge. The results indicate that if the nascent acetic acid should ionize within 3.5 Angstrom from Ser200 O gamma it would be more likely to exit via the alternate channel than through the main gorge.