Simulated (un)binding of arachidonic acid in the cyclooxygenase site of prostaglandin H-2 synthase-1

Molecular dynamics simulations with external forces are employed to study t he unbinding and binding of arachidonic acid (AA) in the cyclooxygenase (CO X) site of prostaglandin H-2 synthase-l. Simulations with AA inside the COX binding channel reveal sequences of concerted bond rotations in the fatty acid alkyl chain which obviate the need for gross conformational changes in the protein and substrate during unbinding and binding. The all-cia struct ure of AA, with double bonds separated by two single bonds, facilitates eas y access to the COX channel and correct positioning inside the active site for the COX chemistry to occur. Two derivatives of AA, one with a cia doubl e bond changed to a trans configuration and the other with a double bond re duced to a single bend, are also studied. In both cases the concertedness o f bond rotations in the fatty acid chain is diminished and larger forces ar e required to move the fatty acid inside the COX channel. Important motions of residues near the mouth of the COX channel are found and analyzed. In p articular, a conformational "switch" involving Arg83, Glu524 and Arg120 is seen to mediate the movement of the substrate from the membrane to the chan nel.