Protein folding: An antagonistic reaction of spontaneous folding and diffusion limited aggregation in nature

Protein folding may follow a spontaneous process or a reaction-path directed process, determined by various folding transition boundaries due to intrinsic properties of the protein. A general first-order-like state-transition model predicts that a protein might be trapped in an aggregated state when the folding path crosses the transition boundary. Both experimental study and molecular simulation indicated that protein within this particular transition region might involve intermolecular interactions. Therefore, a direct folding process may have been a combination of an antagonistic reaction of spontaneous folding and a diffusion limited aggregation. In this paper, the protein folding mechanism and the theoretical basis of time limited diffusion/aggregation process are elaborated. The application of auto-correlation function in time dependent biological studies is also discussed.