| Abstract
| - Farnesylation is a posttranslational lipid modification in which a 15-carbon farnesyl isoprenoidis linked via a thioether bond to specific cysteine residues of proteins in a reaction catalyzed by proteinfarnesyltransferase (FTase). We synthesized the benzyloxyisoprenyl pyrophosphate (BnPP) series oftransferable farnesyl pyrophosphate (FPP) analogues (1a−e) to test the length dependence of the isoprenoidsubstrate on the FTase-catalyzed transfer of lipid to protein substrate. Kinetic analyses show thatpyrophosphates 1a−e and geranyl pyrophosphate (GPP) transfer with a lower efficiency than FPP whereasgeranylgeranyl pyrophosphate (GGPP) does not transfer at all. While a correlation was found betweenKm and analogue hydrophobicity and length, there was no correlation between kcat and these properties.Potential binding geometries of FPP, GPP, GGPP, and analogues 1a−e were examined by modeling themolecules into the active site of the FTase crystal structure. We found that analogue 1d displacesapproximately the same volume of the active site as does FPP, whereas GPP and analogues 1a−c occupylesser volumes and 1e occupies a slightly larger volume. Modeling also indicated that GGPP adopts adifferent conformation than the farnesyl chain of FPP, partially occluding the space occupied by the Ca1a2Xpeptide in the ternary X-ray crystal structure. Within the confines of the FTase pocket, the double bondsand branched methyl groups of the geranylgeranyl chain significantly restrict the number of possibleconformations relative to the more flexible lipid chain of analogues 1a−e. The modeling results alsoprovide a molecular explanation for the observation that an aromatic ring is a good isostere for the terminalisoprene of FPP.
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