Probing the Origin of Structural Stability of Single and Double Stapled P53 Peptide Analogs Bound to MDM2

Abstract

The alpha-helical conformation and structural stability of single and double stapled all-hydrocarbon cross-linked p53 peptides in solution and when bound to MDM2 are investigated. We determined the effects of the peptide sequence, the stereochemistry of the cross-linker, the conformation of the double bond in the alkene bridge, and the length of the bridge, and the relative stability of the alpha-helix structure. The conformation population distribution indicates a fully helical state and several partially folded states. The distribution of dihedral pairs of the stapled peptides in the bound state indicates a significant population around the alpha-helical region. Peptide residues over which the linker spans tend to have the highest helical occupancy. WaterMap simulations yielded over hundred hydration sites identifying regions with water density greater than twice that of the bulk. The free energy released by displacing the hydration sites populating the staple-binding pocket was determined. The three hydrophobic pockets, which bind Phe19, Trp23 and Leu26, provide a large positive contribution to the binding free energy for all peptides studied. In agreement with experimental data, potential of mean forces and weighted histogram analysis methods indicated the order of peptides from lowest to highest binding affinity to be cis-sah3, WT, cis-sah8 and cis-sah4.Work done in collaboration with Z. Guo, K. Streu, G. Krilov. UM thanks Guggenheim Foundation for Fellowship.