Influence of hydrostatic pressure on dynamics and spatial distribution of protein partial molar volume: time-resolved surficial Kirkwood-Buff approach.
The influence of hydrostatic pressure on the partial molar volume (PMV) of the protein apomyoglobin (AMb) was investigated by all-atom molecular dynamics (MD) simulations. Using the time-resolved Kirkwood-Buff (KB) approach, the dynamic behavior of the PMV was identified. The simulated time average value of the PMV and its reduction by 3000 bar pressurization correlated with experimental data. In addition, with the aid of the surficial KB integral method, we obtained the spatial distributions of the components of PMV to elucidate the detailed mechanism of the PMV reduction. New R-dependent PMV profiles identified the regions that increase or decrease the PMV under the high pressure condition. The results indicate that besides the hydration in the vicinity of the protein surface, the outer space of the first hydration layer also significantly influences the total PMV change. These results provide a direct and detailed picture of pressure induced PMV reduction.
Yu
Isseki
I
Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Sagamihara, Kanagawa 229-8558, Japan. yu@chem.aoyama.ac.jp
Tasaki
Tomohiro
T
Nakada
Kyoko
K
Nagaoka
Masataka
M
D001059:Apoproteins / Q000737:chemistry*; D006874:Hydrostatic Pressure; D056004:Molecular Dynamics Simulation; D009211:Myoglobin / Q000737:chemistry*; D013997:Time Factors; D014867:Water / Q000737:chemistry
D001059:Apoproteins; D009211:Myoglobin; C010857:apomyoglobin; D014867:Water