Identification Of The Millisecond Dynamical Behaviors Of Protein-Peptide Interaction By NMR

NMR (Nuclear Magnetic Resonance) relaxation is the process that brings a system of nuclear spin back to the equilibrium state. NMR relaxation studies have become routine for analysis of protein intramolecular motions. In the beginning of the development of the NMR methods, people tried to probe the dynamics of biomolecules by NMR relaxation. With the development of the NMR theory and technologies, people can analyse the dynamics of biomolecules at different timescales by several NMR methods. In recent years, the NMR technology can provide information of the protein motions on timescale from picosecond to seconds. This article introduces our works about using NMR technologies to analyse the dynamical behaviors of the AF-6 PDZ domain when it interacts with the Bcr peptide, and discusses its relationship with the allostery. This article comprises three parts:The first part introduces the theories and the methods of using NMR technologies to probe the protein motions on timescale from picosecond to nanosecond.The second part introduces the theories and the methods of using NMR technologies to probe the protein motions on timescale from microsecond to millisecond, and introduces recent works about the application of these technologies to analyse the functional processes of proteins.The third part introduces our work about using NMR technologies to analyse the dynamical behaviors of the AF-6 PDZ domain when it interacts with the Bcr peptide. PDZ (postsynaptic density-95, disks large, zonula occludens-1) domains are small, protein-protein binding modules that can use multiple surfaces for docking diverse molecules. These domains can propagate signals from ligand-binding site to distal regions of the structure through allosteric communication. Recent works have revealed that picosecond to nanosecond timescale dynamics play a potential role in propagating long-range signals within a protein. Comparison of structures of AF-6 PDZ domain in free and complexed shows a rearrangement of the conformation in distal surface 2 far away from the peptide binding groove. We performed the NMR relaxation dispersion experiments on AF-6 PDZ domain at three states (the free state, the low saturation state and the complex state). We found that besides the equilibrium shifting between the free and the complex states, there are others millisecond dynamical behavior changes. And those dynamical behavior changes have correlation with the dynamical and thermodynamic couplings indentified in other PDZ domains previously. When the AF-6 PDZ domain is saturated by Bcr peptide, we observed the similar millisecond dynamical behaviors as the side-chain ps-ns dynamics in PDZ2 in distal surface 1. These results provide the evidences that intrinsic millisecond dynamic network provide a mechanism for the transmission of allosteric signals throughout a protein. Interestingly, the two distal surfaces of PDZ domain make different responses to peptide binding with changes in millisecond motions and structure rearrangement, respectively. The role of the different response patterns in signaling pathway and the second step of the cooperative binding process should be further studied.