MOLECULAR-DYNAMICS SIMULATIONS OF A PROTEIN ON HYDROPHOBIC AND HYDROPHILIC SURFACES

Molecular dynamics simulations have been used to investigate the behav ior of the peripheral membrane protein, cytochrome c, covalently tethe red to hydrophobic (methyl-terminated) and hydrophilic (thiol-terminat ed) self-assembled monolayers (SAMs). The simulations predict that the protein will undergo minor structural changes when it is tethered to either surface, and the structures differ qualitatively on the two sur faces: the protein is less spherical on the hydrophilic SAM where the polar surface residues reach out to interact with the SAM surface. The protein is completely excluded from the hydrophobic SAM but partially dissolves in the hydrophilic SAM. Consequently, the surface of the th iol-terminated SAM is considerably less ordered than that of the methy l-terminated SAM, although a comparable, high degree of order is maint ained in the bulk of both SAMs: the chains exhibit collective tilts in the nearest-neighbor direction at angles of 20 degrees and 17 degrees with respect to the surface normal in the hydrophobic and the hydroph ilic SAMs, respectively. On the hydrophobic SAM the protein is oriente d so that the heme plane is more nearly parallel to the surface, where as on the hydrophilic surface it is more nearly perpendicular. The sec ondary structure of the protein, dominated by alpha helices, is not si gnificantly affected, but the structure of the loops as well as the he lix packing is slightly modified by the surfaces.