Dynamic correlation between pressure-induced protein structural transition and water penetration.
Water penetration into the hydrophobic interior of proteins has been postulated to be a primary force driving pressure-induced denaturation of proteins. The water penetration model is supported by several theoretical and simulation studies, although its direct evidence is lacking. In this study, 1 micros all-atom molecular dynamics simulations of ubiquitin in explicit water at high and low pressures are performed to examine the water penetration model. The high-pressure simulation starts from a crystal structure at atmospheric pressure and successfully reproduces the main characteristics of a high-pressure structure obtained by NMR. Water penetrates into a specific hydrophobic core of the protein and is ejected from the interior several times. The structural transition results from the relative stabilization of a preexisting metastable structure by applying pressure. A time correlation analysis demonstrates that the transition is accompanied by the penetration of water within a time scale comparable to the relaxation time of water itself. Simultaneous water penetration only occurs above a certain high pressure.
Imai
Takashi
T
Computational Science Research Program and Advanced Science Institute, RIKEN, Wako, Saitama 351-0112, Japan. takashi.imai@riken.jp
Sugita
Yuji
Y
D057927:Hydrophobic and Hydrophilic Interactions; D009682:Magnetic Resonance Spectroscopy; D056004:Molecular Dynamics Simulation; D011312:Pressure; D011487:Protein Conformation; D011489:Protein Denaturation; D025801:Ubiquitin / Q000737:chemistry*; D014867:Water / Q000737:chemistry*
D025801:Ubiquitin; D014867:Water