Formation and domain partitioning of H-ras peptide nanoclusters: effects of peptide concentration and lipid composition.

Abstract

Experiments have shown that homologous Ras proteins containing different lipid modification, which is required for membrane binding, form nonoverlapping nanoclusters on the plasma membrane. However, the physical basis for clustering and lateral organization remains poorly understood. We have begun to tackle this issue using coarse-grained molecular dynamics simulations of the H-ras lipid anchor (tH), a triply lipid-modified heptapeptide embedded in a domain-forming mixed lipid bilayer [Janosi L. et al. Proc. Natl. Acad. Sci. U.S.A. 2012, 109, 8097]. Here we use the same simulation approach to investigate the effect of peptide concentration and bilayer composition on the clustering and lateral distribution of tH. We found no major difference in the clustering behavior of tH above a certain concentration. However, the simulations predict the existence of a critical concentration below which tH does not form nanoclusters. Moreover, our data demonstrate that cholesterol enhances the stability of tH nanoclusters but is not required for their formation. Finally, analyses of peptide distributions and partition free energies allowed us to quantitatively describe how clustering facilitates the accumulation of tH at the interface between ordered and disordered domains of the simulated bilayer systems. These thermodynamic insights represent some of the key elements for a comprehensive understanding of the molecular basis for the formation and stability of Ras signaling platforms.