Energetic consequences of structural features and dynamics changes upon nucleotide binding to ribonuclease SA

摘要: Proteins are often able to distinguish between closely related ligands, thus achieving specificity. A major goal in biophysical chemistry is understand the molecular basis for protein-ligand recognition. This level of understanding necessary developing methods accurately predict binding energetics from structural data. The this thesis was identify features interactions that may not be adequately accounted structure calculations order improve our ability these interactions. Specifically, protein-nucleotide were studied using small, guanine-specific ribonuclease, RNase Sa two nucleotide inhibitors, guanosine-3’-monophosphate (3’GMP) and inosine-3’-monophosphate (3’IMP) as a model system. Comparing inhibitors isothermal titration calorimetry (ITC), x-ray crystallography, NMR dynamics (MD) simulations has revealed important determinants guanine base recognition by proteins, specifically role exocyclic amino group (N2) base. Importantly, due high conservation sites observations can potentially extended other systems. In addition, provided well-defined system investigation changes heat capacity backbone upon ligand binding. All data presented here support idea fluctuations protein contribute significantly even an apparently rigid-body interaction. These make significant contribution enthalpy, entropy, associated with Sa-nucleotide implies fast time-scale motions must optimize structure-based use