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Cells have elaborate mechanisms to transport substances such as nutrients and drugs across the cell membrane that forms a barrier between the inside and outside of a cell. ATP-Binding Cassette Transporters form a large class of membrane proteins across all forms of life that play important physiological roles, including nutrient uptake in bacteria, drug resistance in cancer cells, and regulation of processes involved in cystic fibrosis and diabetes. The chemical hydrolysis of ATP, a source of energy, provides the power for ABC transporters to drive transport, but it is not clear how this... Read more...

Cells are surrounded by membranes, thin sheets made up of two layers of molecules that separate the inside from the cell from its environment. These molecules, lipids, have water-loving headgroups and oily tails, so that the membrane has an oil-like interior. Biological membranes contain a vast variety of proteins that are responsible for contact between the cell and the outside world: they transmit signals, transport nutrients and other molecules, and maintain the right conditions for the cell. Lipids also play an important role in these processes.

Among other... Read more...

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... Read more...

The MARTINI force field, developed between the groups of Marrink and Tieleman, is a coarse grained force field suited for molecular dynamics simulations of biomolecular systems. The force field has been parametrized in a systematic way, based on the reproduction of partitioning free energies between polar and apolar phases of a large number of chemical compounds. 

The model uses a four-to-one mapping where, on average, four heavy atoms are represented by a single interaction center. In order to keep the model simple, only four main types of interaction sites are defined: polar (P... Read more...