Adsorption of Peptides to A Gold Surface Using Molecular Dynamics Simulations

Using proteins to assemble inorganic particles is of interest to materials scientists who wish to use biomimetic strategies to create well-defined nanometer-scale structures. In order to use biomimetics, it is important to understand how proteins bind to inorganic particles on the molecular level. This project focused on investigating the adsorption of a specific protein onto gold using molecular dynamics simulations. The project was divided into several specific tasks. Firstly, we chose the sequence of a suitable gold binding protein. We then decided to model two proteins composed of three or six repeats of the GBP1 unit: 3GBP1 and 6GBP1. GBP1 stands for ?gold binding peptide 1? and refers to a sequence of amino acids that is known to bind very strongly and with a high degree of specificity to gold. Secondly, the stable structures of 3GBP1 and 6GBP1 were determined using a structure prediction program. Thirdly, the stability of the 3GBP1 and 6GBP1 structures was tested by simulating them in water. Subsequently, MD simulations were performed to check the validity of currently accepted parameters for the gold and water interaction. Finally, we performed simulations in which the 3GBP1 protein was placed next to gold. These simulations were performed initially with no water present, using publicly available software packages called NAMD and VMD. The results of the simulations were analyzed by focusing on the dynamics of the binding process and observing changes in the protein-gold surface interactions. We found that the published Lennard-Jones epsilon parameter describing the interaction of water with gold is incorrect by two orders of magnitude and determined a more correct value for that parameter. Tentative results provide insights into the peptide-gold binding process.