Determination of the interfacial water content in protein-protein complexes from free energy simulations.
The question as to how many tightly or weakly bound water molecules are located in interfaces between protein-protein complex constituents is addressed from a phase equilibrium point of view by developing a theory in the canonical ensemble. A fast method based on free energy simulations is described for computing the number of water molecules in the interface regions. Results are given for 211 interfacial cavities of 26 antigen-antibody complexes for which experimentally determined structures are found in the Protein Data Bank. The accuracy of the method is assessed and the computational water content is compared with experimental data, revealing the amount of water molecules not resolved by experimental approaches.
Monecke
Peter
P
Eduard Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, 64287 Darmstadt, Germany.
Borosch
Thorsten
T
Brickmann
Jürgen
J
Kast
Stefan M
SM
D000936:Antigen-Antibody Complex; D001703:Biophysics / Q000379:methods*; D002138:Calibration; D003198:Computer Simulation; D030562:Databases, Protein; D019277:Entropy; D006860:Hydrogen Bonding; D046911:Macromolecular Substances; D008958:Models, Molecular; D008962:Models, Theoretical; D008968:Molecular Conformation; D011487:Protein Conformation; D025941:Protein Interaction Mapping; D012984:Software; D012995:Solubility; D012997:Solvents; D013816:Thermodynamics; D014867:Water / Q000737:chemistry*
D000936:Antigen-Antibody Complex; D046911:Macromolecular Substances; D012997:Solvents; D014867:Water