Theoretical study of the cosolvent effect on the partial molar volume change of staphylococcal nuclease associated with pressure denaturation.
We explain the molecular mechanism of the effect of urea and glycerol cosolvents on the partial molar volume (PMV) change associated with the pressure denaturation of staphylococcal nuclease (SNase) protein recently observed in experiments. Native and denatured conformations of SNase are produced by using molecular dynamics simulations in water, and the PMV is obtained from the integral equation theory of molecular liquids called 3D-RISM, which is based on statistical mechanics. The PMV of the native SNase in water predicted by 3D-RISM theory is in good agreement with experiment. The PMV changes associated with pressure denaturation in water and in water-urea and water-glycerol mixtures are qualitatively reproduced. By analyzing the results obtained, we found two interesting cosolvent effects on the PMV: (1) both urea and glycerol cosolvents increase the PMVs of both native and denatured SNase compared to those in water and (2) both urea and glycerol cosolvents increase the PMV of denatured SNase more than that of native SNase. We also showed that these two observations can be explained in terms of the thermal volume, which is related to the packing effect of solvent molecules.
Yamazaki
Takeshi
T
Department of Mechanical Engineering, University of Alberta, and National Institute for Nanotechnology, National Research Council of Canada, 11421 Saskatchewan Drive, Edmonton, Alberta T6G 2M9, Canada.
Imai
Takashi
T
Hirata
Fumio
F
Kovalenko
Andriy
A
D003198:Computer Simulation; D005990:Glycerol / Q000737:chemistry / Q000494:pharmacology; D008836:Micrococcal Nuclease / Q000737:chemistry* / Q000187:drug effects; D008958:Models, Molecular; D011312:Pressure; D011487:Protein Conformation; D011489:Protein Denaturation; D017434:Protein Structure, Tertiary; D012997:Solvents / Q000737:chemistry; D013210:Staphylococcus / Q000201:enzymology*; D013329:Structure-Activity Relationship; D013816:Thermodynamics; D014508:Urea / Q000737:chemistry / Q000494:pharmacology
D012997:Solvents; D014508:Urea; D008836:Micrococcal Nuclease; D005990:Glycerol