Probing protein dynamics and protein-protein interaction by NMR spectroscopy

Abstract

In the first part of this thesis, a novel method for probing methyl dynamics based on dipole-dipole cross-correlated transverse relaxation and auto-correlated longitudinal relaxation is presented. The excellent agreement between dynamics parameters of methyl groups in ubiquitin and those derived previously from &178;H relaxation data, demonstrates the reliability and validity of this method. Subsequently, the method was applied to the study of methyl dynamics of Huntingtin interacting protein 2. In the second part of this thesis, a new strategy to map protein- protein interfaces on the basis of the dependence of NMR relaxation on proton density is presented. The method was demonstrated by the identification of interfaces between human adult hemoglobin (Hb A) subunits. The amino acids involved in Hb A inter-subunits interactions were unambiguously identified and the upper limit of the effective distance between an amide proton and its proximal protons was estimated to build docking models of Hb A dimer and tetramer in solution.