INFLUENCE OF WATER ENVIRONMENT ON PROTEIN FOLDING AND COMPLEXATION

<ns5:p>Background The presence of water for biological systems, which is critical for protein activity, is treated in protein molecular dynamics simulation tools as a collection of individual water molecules in numbers corresponding to the conditions of a given simulation. The presence of water is important for the folding process as well as the structural changes associated with biological activity. Methods This article presents proposals to treat the water environment as a provider of an external force field directing the folding process to achieve the structure expected by the biological system. The external force field can have different forms, e.g. the form of a field derived from the hydrophobic membrane for membrane proteins, or the form of a chaperonin, if the protein acquires an active structural form assisted by support proteins. Results The study is limited to examples of proteins shaped by the water environment, whose presence as an external force field is expressed by a 3D Gaussian function directing the hydrophobic residues toward central part of protein and hydrophilic ones toward the surface. Conclusions The discussed examples of proteins prove the necessary participation of environment – especially water – in folding process. In consequence the funnel model can be expressed in quantitative form visualising the appropriate energy minimum (global or local) to be determined by specificity of external force field.</ns5:p>