Determination of the Interfacial Water Content in Protein-Protein Complexes from Free Energy Simulations
| Autor: | Jürgen Brickmann, Thorsten Borosch, Stefan M. Kast, Peter Monecke |
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| Rok vydání: | 2006 |
| Předmět: |
Models
Molecular Macromolecular Substances Protein Conformation Entropy Molecular Conformation Biophysics Antigen-Antibody Complex Biophysical Theory and Modeling Protein structure Protein Interaction Mapping Bound water Molecule Computer Simulation Solubility Databases Protein Water content Canonical ensemble Hydrogen bond Chemistry Water Hydrogen Bonding computer.file_format Models Theoretical Protein Data Bank Chemical physics Calibration Solvents Thermodynamics Physical chemistry computer Software |
| Zdroj: | Biophysical Journal. 90:841-850 |
| ISSN: | 0006-3495 |
| DOI: | 10.1529/biophysj.105.065524 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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