Dynamics and Thermodynamics of Ligand–Protein Interactions

Abstract

Protein-ligand interactions are of fundamental importance in a great many biological processes. However, despite enormous advances in the speed and accuracy of the three-dimensional structure determination of proteins and their complexes, our ability to predict binding affinity from structure remains severely limited. One reason for this dilemma is that affinities are governed not only by energetic considerations arising from the precise spatial disposition of interacting groups (loosely, enthalpy), but also by the dynamics of these groups (loosely, entropy) including solvent effects. In this work I will review current methodology for unravelling this complex problem, including X-ray crystallography, NMR, isothermal titration calorimetry and theoretical free energy perturbation methods. © 2007 Springer-Verlag Berlin Heidelberg.