title: The thermodynamic signature of ligand binding to histone deacetylase-like amidohydrolases is most sensitive to the flexibility in the L2-loop lining the active site pocket.
abstract: The analysis of the thermodynamic driving forces of ligand-protein binding has been suggested to be a key component for the selection and optimization of active compounds into drug candidates. The binding enthalpy as deduced from isothermal titration calorimetry (ITC) is usually interpreted assuming single-step binding of a ligand to one conformation of the target protein. Although successful in many cases, these assumptions are oversimplified approximations of the reality with flexible proteins and complicated binding mechanism in many if not most cases. The relationship between protein flexibility and thermodynamic signature of ligand binding is largely understudied.
  
  
  
  Directed mutagenesis, X-ray crystallography, enzyme kinetics and ITC methods were combined to dissect the influence of loop flexibility on the thermodynamics and mechanism of ligand binding to histone deacetylase (HDAC)-like amidohydrolases.
  
  
  
  The general ligand-protein binding mechanism comprises an energetically demanding gate opening step followed by physical binding. Increased flexibility of the L2-loop in HDAC-like amidohydrolases facilitates access of ligands to the binding pocket resulting in predominantly enthalpy-driven complex formation.
  
  
  
  The study provides evidence for the great importance of flexibility adjacent to the active site channel for the mechanism and observed thermodynamic driving forces of molecular recognition in HDAC like enzymes.
  
  
  
  The flexibility or malleability in regions adjacent to binding pockets should be given more attention when designing better drug candidates. The presented case study also suggests that the observed binding enthalpy of protein-ligand systems should be interpreted with caution, since more complicated binding mechanisms may obscure the significance regarding potential drug likeness.
authors.affiliation: Department of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Haardtring 100, 64295 Darmstadt, Germany.
authors.forename: Christian
authors.initials: C
authors.lastname: Meyners
authors.affiliation: Department of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Haardtring 100, 64295 Darmstadt, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Krämer
authors.affiliation: Department of Structural Biology, Max-Planck-Institute of Biophysics, 60438 Frankfurt, Germany.
authors.forename: Özkan
authors.initials: Ö
authors.lastname: Yildiz
authors.affiliation: Department of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Haardtring 100, 64295 Darmstadt, Germany. Electronic address: franz-josef.meyer-almes@h-da.de.
authors.forename: Franz-Josef
authors.initials: FJ
authors.lastname: Meyer-Almes
mesh_terms: D000581:Amidohydrolases / Q000737:chemistry*; D001665:Binding Sites; D002151:Calorimetry; D018360:Crystallography, X-Ray; D006655:Histone Deacetylases / Q000737:chemistry*; D006860:Hydrogen Bonding; D008024:Ligands; D055503:Protein Multimerization; D055550:Protein Stability; D013816:Thermodynamics
chemical_list: D008024:Ligands; D000581:Amidohydrolases; D006655:Histone Deacetylases
keywords: Binding mechanism; Conformational flexibility; Histone deacetylases; Protein-ligand binding; Thermodynamic signatures