Kinetic advantage of intrinsically disordered proteins in coupled folding-binding process: a critical assessment of the "fly-casting" mechanism.
Intrinsically disordered proteins (IDPs) are recognized to play important roles in many biological functions such as transcription and translation regulation, cellular signal transduction, protein phosphorylation, and molecular assemblies. The coupling of folding with binding through a "fly-casting" mechanism has been proposed to account for the fast binding kinetics of IDPs. In this article, experimental data from the literature were collated to verify the kinetic advantages of IDPs, while molecular simulations were performed to clarify the origin of the kinetic advantages. The phosphorylated KID-kinase-inducible domain interacting domain (KIX) complex was used as an example in the simulations. By modifying a coarse-grained model with a native-centric Gō-like potential, we were able to continuously tune the degree of disorder of the phosphorylated KID domain and thus investigate the intrinsic role of chain flexibility in binding kinetics. The simulations show that the "fly-casting" effect is not only due to the greater capture radii of IDPs. The coupling of folding with binding of IDPs leads to a significant reduction in binding free-energy barrier. Such a reduction accelerates the binding process. Although the greater capture radius has been regarded as the main factor in promoting the binding rate of IDPs, we found that this parameter will also lead to the slower translational diffusion of IDPs when compared with ordered proteins. As a result, the capture rate of IDPs was found to be slower than that of ordered proteins. The main origin of the faster binding for IDPs are the fewer encounter times required before the formation of the final binding complex. The roles of the interchain native contacts fraction (Q(b)) and the mass-center distance (DeltaR) as reaction coordinates are also discussed.
Huang
Yongqi
Y
College of Chemistry and Molecular Engineering, Center for Theoretical Biology, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Peking University, Beijing 100871, China.
Liu
Zhirong
Z
D000818:Animals; D002417:Cattle; D003198:Computer Simulation; D004058:Diffusion; D006801:Humans; D007700:Kinetics; D008958:Models, Molecular; D018583:Pliability; D011485:Protein Binding; D017510:Protein Folding; D055550:Protein Stability; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D013816:Thermodynamics; D013997:Time Factors
D011506:Proteins