Molecular dynamics free energy calculations to assess the possibility of water existence in protein nonpolar cavities.
Are protein nonpolar cavities filled with water molecules? Although many experimental and theoretical investigations have been done, particularly for the nonpolar cavity of IL-1 beta, the results are still conflicting. To study this problem from the thermodynamic point of view, we calculated hydration free energies of four protein nonpolar cavities by means of the molecular dynamics thermodynamic integration method. In addition to the IL-1 beta cavity (69 A(3)), we selected the three largest nonpolar cavities of AvrPphB (81 A(3)), Trp repressor (87 A(3)), and hemoglobin (108 A(3)) from the structural database, in view of the simulation result from another study that showed larger nonpolar cavities are more likely to be hydrated. The calculations were performed with flexible and rigid protein models. The calculated free energy changes were all positive; hydration of the nonpolar cavities was energetically unfavorable for all four cases. Because hydration of smaller cavities should happen more rarely, we conclude that existing protein nonpolar cavities are not likely to be hydrated. Although a possibility remains for much larger nonpolar cavities, such cases are not found experimentally. We present a hypothesis to explain this: hydrated nonpolar cavities are quite unstable and the conformation could not be maintained.
Oikawa
Masataka
M
Computational Biology Group, Quantum Beam Science Directorate, Japan Atomic Energy Agency, Kyoto, Japan. oikawa@cp.kyoto-u.ac.jp
Yonetani
Yoshiteru
Y
D016880:Anisotropy; D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D009068:Movement; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D013816:Thermodynamics; D014867:Water / Q000737:chemistry*
D011506:Proteins; D014867:Water