Conformational analysis of a farnesyltransferase peptide inhibitor, CVIM

Abstract

The conformational states of the peptide Cys-Val-Ile-Met (or CVIM) were computed and characterized. CVIM inhibits farnesylation of the Ras oncogene product, p21^ras, at the cysteine residue of the C-terminal segment. CVIM is active in an extended conformation. A similar peptide (KTKCVFM) appears to bind the enzyme in the Type I bend conformation. In the present study, the conformations of CVIM were computed in an aqueous environment with the peptide in the zwitterionic state. Solvation free energy based on solvent accessible surface area and a distance dependent dielectric were used in the calculations. Final conformations of multiple independent Monte Carlo simulated annealing (MCSA) conformational searches were used as starting points for Metropolis Monte Carlo (MMC) runs. Conformations saved at intervals during MMC runs were analyzed. Conformers were separated by interactive clustering in dihedral angle coordinates. The four lowest energy conformers corresponding to a Type I bend, extended, AB-bend, and BA-bend were within 0.3 kcal/mol of each other, and dominant in terms of population. The Type I bend and extended conformers were supported by the binding studies. The extended conformer was the most populated. In the AB-bend conformer, `A' indicates the α-helix conformation of Val, and `B' indicates the β-strand conformation of Ile. The AB- and BA-bend conformations differed from the extended conformation in the value of Val ψ and Ile ψ, respectively, and from the Type I bend conformation in the value of Ile ψ and Val ψ, respectively. The four lowest energy conformers were characterized in terms of energy, density of low energy conformations (or entropy), structure, side chain rotamer fraction population, and interatomic distances.