In accordance with our general approach to biological processes, here too we chose to elaborate on the following basic aspects, which we believe to be crucial for the understanding of these processes: structure, energetics, and dynamics. ese are covered by the –rst part

FIGURE 8.1. Examples of biologically important protein-ligand interactions. (a) Enzyme substrate/cofactor binding. Here, L-phenylalanine dehydrogenase is the enzyme (in blue ribbon representation), bound to both substrate (colored by atom type) and cofactor (NADH, colored in orange) (PDB entry 1c1d). (b) Allosteric regulators. e –gure shows the protein fructose-1,6-bisphosphatase with 2,5-anhydro-d-glucitol-1,6-bisphosphate (AHG, an analogue of its substrate), and AMP (an allosteric inhibitor) (PDB entry 1fpd). As clearly seen, the allosteric ligand occupies a distinct binding site, which is quite distant from the catalytic site.