| A better understanding of life at a microscopic level permits the formulation of better drugs, the imitation of biological processes for technological applications, and the prediction of the impact of pathogenic substances. At the heart of biological molecular processes lies the interaction of polypeptides with solvent and lipid environments; technological applications rely on the interaction of polypeptides with inorganic substrates. Molecular dynamics (MD) simulations provide a means by which these interactions may be examined in atomic-level detail, offering increasing speed and accuracy, as well as applicability to progressively larger system sizes and longer simulation times. MD techniques were applied to several systems to study interfacial effects on the conformation of proteins. The interaction of Glycophorin A transmembrane helices in a detergent (sodium dodecyl sulfate, SDS) micelle has been characterized with respect to mutations along the helix-helix interface. It is seen that destabilizing mutations result in a change to the protein structure that are fluidly accommodated by the surrounding micelle. In a long timescale (24 ns) simulation, spontaneous aggregation and organization of SDS molecules into a micelle that surrounds the GpA helix dimer and solubilizes it has been observed. The final structural properties of the system compare well to experimentally observed values, and the dynamics of the aggregation are described by a diffusion model. The simulations elucidate the interaction between GpA and its environment, showing that GpA is unstable in the aqueous environment but regains stability once surrounded by SDS. MD simulations were also used to provide an atomic-level description of the structure and surface-specific adsorption characteristics of a gold-binding protein onto Au surfaces in an aqueous environment. |
