Dependence of Protein Structure on Environment: FOD Model Applied to Membrane Proteins

Irena Roterman, Katarzyna Stapor, Krzysztof Gądek, Tomasz Gubała , Piotr Nowakowski, Piotr Fabian and Leszek Konieczny

The natural environment of proteins is the polar aquatic environment and the hydrophobic (amphipathic) environment of the membrane. The fuzzy oil drop model (FOD) used to characterize water-soluble proteins, as well as its modified version FOD-M, enables a mathematical description of the presence and influence of diverse environments on protein structure. The present work characterized the structures of membrane proteins, including those that act as channels, and a water-soluble protein for contrast. The purpose of the analysis was to verify the possibility that an external force field can be used in the simulation of the protein-folding process, taking into account the diverse nature of the environment that guarantees a structure showing biological activity.