Structure-Based Statistical Mechanical Model Accounts for the Causality and Energetics of Allosteric Communication
Fig 6
Free energy profiles and structural representations of the D-3-phosphoglycerate dehydrogenase PGDH.
The profiles Δgi(0 → 8×SER) are based on calculations performed on two protein forms, 1psd and 1yba, respectively. Protein structures are shown using a colored tube-like representation with both colors, and radius of the tube scaled according to the configurational work exerted per corresponding residue (the radius ρi per residue i is scaled according to the functionρi = (Δgi − mini Δgi)/(maxi Δgi − mini Δgi)). Structures in the middle represent two forms of the protein analyzed in this work: inactive (1psd, top) and active (1yba, bottom). The structure in the right panel illustrates locations of the protein’s ligands: SER (red), NAD (green), and AKG (blue).