Intriguing role of water in protein-ligand binding studied by neutron crystallography on trypsin complexes

Nat Commun. 2018 Sep 3;9(1):3559. doi: 10.1038/s41467-018-05769-2.


Hydrogen bonds are key interactions determining protein-ligand binding affinity and therefore fundamental to any biological process. Unfortunately, explicit structural information about hydrogen positions and thus H-bonds in protein-ligand complexes is extremely rare and similarly the important role of water during binding remains poorly understood. Here, we report on neutron structures of trypsin determined at very high resolutions ≤1.5 Å in uncomplexed and inhibited state complemented by X-ray and thermodynamic data and computer simulations. Our structures show the precise geometry of H-bonds between protein and the inhibitors N-amidinopiperidine and benzamidine along with the dynamics of the residual solvation pattern. Prior to binding, the ligand-free binding pocket is occupied by water molecules characterized by a paucity of H-bonds and high mobility resulting in an imperfect hydration of the critical residue Asp189. This phenomenon likely constitutes a key factor fueling ligand binding via water displacement and helps improving our current view on water influencing protein-ligand recognition.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Benzamidines / pharmacology
  • Computer Simulation
  • Crystallography*
  • Crystallography, X-Ray
  • Hydrogen Bonding
  • Ligands*
  • Neutron Diffraction*
  • Protein Binding*
  • Serine Proteinase Inhibitors / pharmacology
  • Thermodynamics
  • Trypsin / chemistry*
  • Trypsin / drug effects
  • Trypsin / metabolism
  • Water*


  • Benzamidines
  • Ligands
  • Serine Proteinase Inhibitors
  • Water
  • Trypsin
  • benzamidine