Cells have membranes that create boundaries to the outside world. Proteins that are attached to the membrane make up approximately one-half of the membrane weight, and they are important since they regulate the majority of the transport across the membrane. The membrane proteins have diverse functions in the cell, ranging from collecting signals in the brain to harvesting light in plants. They are also important drug targets and many popular drugs such as losec affect membrane proteins. The drug substance plugs a hole in a membrane protein so that less acid can enter the stomach. In order to make it easier to develop this kind of substance, it is important to know the structure or shape of the protein in question, since it is the structure that determines the function. The three dimensional shape of membrane proteins is only known for less than 100 of them making them underrepresented in the over 15000 structurally determined proteins. In contrast, between 20-30% of all proteins in an organism are membrane proteins. The main reasons for this underrepresentation are the specific properties of the membrane proteins. Since they normally reside inside a membrane, they are difficult to get out from the membrane and to extract enough material needed for the structural determination.

Today there are many methods for making computers calculate the structure of ordinary proteins, but none that work very well. There are fewer methods for membrane proteins, but the gain of succesfully predicting their structure may be of even greater benefit for the scientific community because of the problems that occur when determining their structure. I am using computers for gaining insights about the structure of membrane proteins in order to develop better membrane prediction methods. Since I use computers for solving biological problems I work in the field of Bioinformatics.

The structure of the membrane spanning part of a protein called sensory rhodopsin is shown above. It is involved in signal transduction in response to light stimuli. The blue grid is an approximation of where the cellmembrane is located.