Using computer simulations to study biological problems
Membrane proteins are central to many important processes in cells. About 20% of all human proteins are membrane proteins, and the majority of currently used drugs interacts with them. It would be very helpful for understanding how cells work, for understanding the molecular basis of diseases, and for developing new drugs if the structures of membrane proteins would be known in detail. Unfortunately, it has turned out to be difficult to determine the structure of membrane proteins. Only a few dozen structures are known, compared to more than 15000 structures of water-soluble proteins. A large class of membrane proteins is predominantly build of helices, a common type of basic structure in proteins. It would be an important step towards being able to predict membrane protein structure if it were possible to predict how such helices interact to form larger structures.
In this project, computer simulation methods are used to model the structure of a number of simple designed transmembrane peptides that have been studied in great detail by experimental methods. Studying simple model membrane proteins will help to learn the rules that determine helix-helix interactions. Once it is possible to predict the structure of simple membrane proteins, similar methods can be applied to more complex proteins of medical importance.