posted on 2007-10-30, 00:00authored byGuanglei Cui, Kenneth M. Merz
Studies aimed at elucidating the reaction mechanism of farnesyltransferase (FTase), which
catalyzes the prenylation of many cellular signaling proteins including Ras, has been an active area of
research. Much is known regarding substrate binding and the impact of various catalytic site residues on
catalysis. However, the molecular level details regarding the conformational rearrangement of farnesyldiphosphate (FPP), which has been proposed via structural analysis and mutagenesis studies to occur
prior to the chemical step, is still poorly understood. Following on our previous computational
characterization of the resting state of the FTase ternary complex, the thermodynamics of the conformational
rearrangement step in the absence of magnesium was investigated for the wild type FTase and the Y300Fβ
mutant complexed with the peptide CVIM. In addition, we also explored the target dependence of the
conformational activation step by perturbing isoleucine into a leucine (CVLM). The calculated free energy
profiles of the proposed conformational transition confirm the presence of a stable intermediate state,
which was identified only when the diphosphate is monoprotonated (FPP2-). The farnesyl group in the
computed intermediate state assumes a conformation similar to that of the product complex, particularly
for the first two isoprene units. We found that Y300β can readily form hydrogen bonds with either of the
phosphates of FPP. Removing the hydroxyl group on Y300β does not significantly alter the thermodynamics
of the conformational transition, but shifts the location of the intermediate farther away from the nucleophile
by 0.5 Å, which suggests that Y300β facilitate the reaction by stabilizing the chemical step. Our results
also showed an increased transition barrier height for CVLM (1.5 kcal/mol higher than that of CVIM).
Although qualitatively consistent with the findings from the recent kinetic isotope experiments by Fierke
and co-workers, the magnitude is not large enough to affect the rate-limiting step.