Dynamic and kinetic investigations of SEM-5/SOS peptide interactions

The dynamics of SEM-5 SH3 domain protein can provide an important insight into how structural dynamics contribute to protein function. This is important because solving the structure of protein alone only provides the detail on the population weight average of native ensembles. NMR (Nuclear Magnetic Resonance) is one of the best techniques that can be used to elucidate the conformational fluctuation of SH3 domain under native condition, The hypothesis of this study is that the protein during ligand-free ¬form is undergoing an equilibrium between binding-competent (BC) and binding-incompetent (BI) states(1). In order to test this hypothesis, we apply a Glycine mutation in a solvent exposed and highly dynamic region within RT loop of SH3 domain protein. Through this mutation, we aim to manipulate the dynamics of the protein but preserve the protein-ligand interface. Several NMR methodologies including order parameter and line-shape analysis are applied to observe the correlation of protein dynamics with its function, taking into consideration several thermodynamic and kinetic aspects of the structural changes involved.\r\n\r\n