Michal Stepniewski

University of Helsinki
Supervisor: Henri Xhaard
Funding: ISB
Date: 2010-06-29

Computational methods for the analysis of membrane protein structure of function

Membrane proteins are embedded in lipid bilayers at the interface between the inside and the outside of the cell or in intracellular compartments. It was long speculated that the specific constraints associated with the lipid bilayer, i.e. the need to fold as a bundle of alpha-helices, would make the three-dimensional structure of membrane proteins more amenable to amino acid sequence-based prediction than for their soluble conterparts(1) , e.g. with hydropathy and hydrophobic moment plots (2).

Nonetheless, the vast majority of software that are currently in use for molecular modeling applications do not take any advantage of the many rules(1,2,3) that have been developed since. The first major goal of this project is t todevelop new computational tools specifically adapted to study the three-dimensional structure of membrane proteins. The second major goal of this project is to define new general rules about membrane protein structure that would transcend protein families.