Protein folding: Funnel model revised

The spatial structure of proteins, largely determined by their amino acid sequences, is also dependent on the environmental conditions under which the folding process takes place. In aqueous environments, exposure of polar amino acids is the driving factor, whereas protein stabilization in amphipathic membranes requires exposure to hydrophobic residues. This observation can be extended to all other environmental conditions under which proteins exhibit biological activity and, most importantly, to the folding process. The fuzzy oil drop (FOD) model assumes a centric location of hydrophobic residues (hydrophobic core) with exposure of polar residues towards the aqueous environment, as the influence of the aqueous environment is extended to include the contribution of other non-aqueous factors, enabling the assessment of their influence on protein structuring. The application of the modified FOD model (FOD-M) we have developed allows the environment to be represented as an external force field in the form of a continuum. The role of environmental conditions allows modification of the funnel model expressing the localization of the energy minimum as dependent on external conditions expressed by the K scale, where K measures the degree of other than polar water factors participating in folding process.