The Calcium: where molecular modeling meets nano-scale microscopy.

Calcium is an essential ion for the condensation of biomolecules and for the formation of materials in living organism like bones and teeth. It also estabilizes a DNA mesh present on bacterial biofilm with the function to make bacteria resilient against antibiotic. Despite this enormous impact, the initial steps of calcium-molecule interaction and their impact on the nucleation of biominerals are not well understood. On this project we will describe the first stages of the interaction between Ca2+ and the protein osteopontin (OPN), which has been identified as a key protein regulating the growth of bone mineral. Further, the role of Ca2+ in the organisation of DNA will be investigated. Theoretical predictions will be compared with experiments done at the group of Roland Kroger at the York JEOL Nanocentre. Your project will allow you to:

1) Describe DNA/Osteopontin folding caused by Ca2+ with molecular modelling. This is relevant for tackling the challenge of antibiotic resistence and for the field of bone regeneration. You will learn the most advanced techniques on molecular modelling
2) Detailed description of Ca2+ interaction using QM-based methodologies. A refinement of the interaction will be obtained by DFT with the leading software CASTEP/ONETEP in collaboration with Matt Probert, who is one of the main developers of the code.