关键词:
protein folding
protein binding
staphylococcal nuclease
statistical mechanical model
real-time NMR
摘要:
Protein conformational changes associated with ligand binding, especially those involving intrinsically disordered proteins, are mediated by tightly coupled intra-and intermolecular events. Such reactions are often discussed in terms of two limiting kinetic mech-anisms, conformational selection (CS), where folding precedes binding, and induced fit (IF), where binding precedes folding. It has been shown that coupled folding/binding reactions can pro-ceed along both CS and IF pathways with the flux ratio depending on conditions such as ligand concentration. However, the struc-tural and energetic basis of such complex reactions remains poorly understood. Therefore, we used experimental, theoretical, and computational approaches to explore structural and energetic as-pects of the coupled-folding/binding reaction of staphylococcal nuclease in the presence of the substrate analog adenosine-3 ',5 '-diphosphate. Optically monitored equilibrium and kinetic data, combined with a statistical mechanical model, gave deeper insight into the relative importance of specific and Coulombic protein- ligand interactions in governing the reaction mechanism. We also investigated structural aspects of the reaction at the residue level using NMR and all-atom replica-permutation molecular dynamics simulations. Both approaches yielded clear evidence for accumula-tion of a transient protein-ligand encounter complex early in the reaction under IF-dominant conditions. Quantitative analysis of the equilibrium/kinetic folding revealed that the ligand-dependent CS-to-IF shift resulted from stabilization of the compact transition state primarily by weakly ligand-dependent Coulombic interactions with smaller contributions from specific binding energies. At a more macroscopic level, the CS-to-IF shift was represented as a displace-ment of the reaction "route" on the free energy surface, which was consistent with a flux analysis.