Simulations for Synthetic Biology: Mapping Biological Switches

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Our bodies are made up of many small building blocks called cells. Each cell is constantly drawing in nutrients, receive signals from elsewhere in the body and export waste and products. These vital functions are performed by large molecules, called proteins, that are made within each cell. The cell controls these functions by switching the proteins on and off. We do not understand very well how proteins are able to switch between these states. Researchers in the synthetic biology and bionanotechnology fields have been inspired by this complexity and are trying to design and build their own molecules that do certain things. They also want their synthetic molecules to be able to switch between different states. In this study we plan to investigate how parts of proteins, called alpha-helices, are able to adopt different structures by kinking in the middle. This has been looked at by other researchers, however, we plan to compute maps showing where each of the switched states is and how easily the alpha-helix can move between the two states. This has not been possible until now because a very large number of fast computers are required to run all the necessary simulations. We plan to use HPCx, one of the UK's national supercomputers, to run these simulations. We shall also study how changing the environment around each alpha-helix affects its ability to switch. Our study will therefore not only shed light on how proteins are able to switch between states but will also help other researchers design and build synthetic molecules.