Thermodynamic analysis of a hydrophobic binding site: probing the PDZ domain with nonproteinogenic peptide ligands.
[structure: see text] Isothermal titration calorimetry (ITC) is used to study the thermodynamic consequences of systematically modifying the hydrophobic character of a single residue in a series of protein-binding ligands. By substituting standard and nonproteinogenic aliphatic amino acids for the C-terminal valine of the hexapeptide KKETEV, binding to the third PDZ domain (PDZ3) of the PSD-95 protein is characterized by distinct changes in the Gibbs free energy (DeltaG), enthalpy (DeltaH), and entropy (TDeltaS) parameters. One notable observation is that peptide binding affinity can be improved with a nonstandard residue.
Saro
Dorina
D
Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.
Klosi
Edvin
E
Paredes
Azrael
A
Spaller
Mark R
MR
D000596:Amino Acids / Q000737:chemistry*; D001665:Binding Sites; D002151:Calorimetry / Q000379:methods; D020650:Combinatorial Chemistry Techniques; D008024:Ligands; D015394:Molecular Structure; D009419:Nerve Tissue Proteins / Q000737:chemistry* / Q000378:metabolism; D010455:Peptides / Q000737:chemistry* / Q000378:metabolism; D011487:Protein Conformation; D013816:Thermodynamics
D000596:Amino Acids; D008024:Ligands; D009419:Nerve Tissue Proteins; D010455:Peptides; C033652:postsynaptic density proteins