The binding of proteins to various substrates in a biological system is a basic but essential process to maintain the function of living things. The mechanisms underlying protein binding have been the focus of theoretical and experimental research for many years. Many mechanisms have been proposed and characterized, including "lock and key", "induced fit", "population shift" and "fly-casting". The recently discovered "fly-casting" mechanism allows a protein chain to unfold and extend to reach substrates a long distance away from the protein. This mechanism compensates for diffusive entropy by enlarging the "capture radius" of binding process, and consequently accelerates the binding process.
Based on a theoretical model of fly-casting binding, Dr. Chang and colleagues found that temperature, an important component of the entropic term in free energy, influences the capture radius of fly-casting binding. Their results indicate that the transition temperature of protein folding and unfolding is the most suitable condition for fly-casting binding, since the capture radius is greatest at that temperature. Their work, entitled "Influence of temperature and diffusive entropy on the capture radius of fly-casting binding", was published in SCIENCE CHINA Physics, Mechanics & Astronomy, 2011, 54(12).
According to their theory, free energy contains two components. One is related to protein folding and binding, and the other is related to the diffusion of a protein in space. During binding, the first component of free energy decreases as the protein approaches the specific substrate, while the second component increases. The points at which the two free energy curves crosses defines the capture radius for protein binding. These free energy curves agree with those derived from molecular dynamic simulations.
The capture radius of fly-casting binding could be affected by many factors, including protein binding affinity and limitations of protein folding. Their theory, which introduces a term for diffusive entropy, indicates that environmental temperature, an important entropic factor, also influences the capture radius. The maximum capture radius is obtained at the transition temperature between folding and unfolding. The results represent a balance between the energetic and entropic terms in the free energy function. Their theory and results provide a valuable reference for future research on protein binding.
See the article: Chang L, Guo X L, Zhang J, et al. Influence of temperature and diffusive entropy on the capture radius of fly-casting binding. SCI CHINA Phys Mech Astron, 2011, 54(12):2237�