Structural studies of organic monolayer and protein -membrane systems via molecular dynamics computer simulations

Great interest exists among chemists, physicists, biologists, materials scientists and others, in learning more about the microscopic structure of organic thin films and protein-membrane complexes. In this work, we undertook structural investigations into two such systems, using molecular dynamics simulations as our tool. On the one hand, we studied different models of an alkane self-assembled monolayer, in order to improve our understanding of the structural effects of such parameters as the chain packing density in the monolayer plane, and the strength of the interactions between the chains and the model substrate surface. We found that the SAM-substrate interaction is very important to the SAM structure, and that by varying the strength of this interaction alone, we could produce SAMs either with or without long-range in-plane order (much like alkylthiol and alkylsilane SAMs, respectively). On the other hand, we performed extensive analysis of a family of model hydrated protein-membrane systems, in order to better understand the structural interrelation of a membrane protein, its associated membrane, and the surrounding solvent. Our basic model was a cytochrome c molecule attached to an alkane SAM and surrounded by water; we explored models with different amounts of water, different SAM endgroups, and differing coordination number of the heme iron atom. We found that the overall protein structure is largely conserved, that a polar-endgroup SAM interacts more strongly with the protein than does a nonpolar SAM, and that increased hydration tends to mitigate the effects of changing other parameters. Structural measurements from our models, such as the electron density profile and the protein\u27s orientation and radius of gyration, were in reasonable agreement with experimental spectroscopic and scattering measurements