The enzyme prostaglandin H2 synthase-1 (PGHS-1) catalyzes the transformation of the essential fatty acid, arachidonic acid (AA), to prostaglandin H2 [17]. Aspirin, flurbiprofen, and other non-steroidal anti-inflammatory drugs directly target PGHS-1 and inhibit the first step of its transformation by preventing access of AA to the cyclooxygenase active site. Based on the crystal structure of PGHS-1, with flurbiprofen bound at the active site, a model for AA embedded in the enzyme has been suggested, in which AA replaces the inhibitor [18].
The aim of the investigation is to elucidate the folding of AA into the narrow hydrophobic binding channel of the cyclooxygenase site, and to identify key residues guiding AA binding. Steered Molecular Dynamics calculations (SMD) [3-8, 103, 104] of enforced unbinding were carried out on one monomer (9,000 atoms) of the PGHS-1 homo-dimer with AA bound in its putative cyclooxygenation site, leading to the exit of the ligand from its narrow hydrophobic binding channel*. AA contains four rigid cis double bonds connected to each other by a pair of conformationally flexible single bonds. The unbinding mechanism can be described as a series of rotations around these single bonds that leave the """"""""rigid backbone"""""""" of the fatty acid formed by the conformationally inflexible cis double bonds relatively unaffected. Our hypothesis is that this type of concerted motion is specific for the chemical structure of AA and is important for the binding and recognition mechanism. Another set of simulations was carried out with the Targeted Molecular Dynamics (TMD) method [105]. A comparison of the SMD and TMD simulations revealed that the pathways generated by both methods show very similar modes of concerted rotations around single bonds during the unbinding of AA.
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