Evaluation of intrinsic compressibility of proteins by molecular dynamics simulation.
Molecular dynamics simulation has been performed on five native proteins in water to evaluate their intrinsic isothermal compressibilities beta(T,int). To identify physical factors contributing to protein compressibility, a general method is presented for analyzing the compressibility of mechanically inhomogeneous systems. The value of beta(T,int) varies with protein species considerably: beta-lactoglobulin (14.15 x 10(-2) GPa(-1)) is more than twice as compressible as ribonuclease A (6.77 x 10(-2) GPa(-1)). Beta-lactoglobulin and myoglobin (13.95 x 10(-2) GPa(-1)) have similar values of beta(T,int), but the mechanisms responsible for them are significantly different. The volume fluctuations of internal cavities and the magnitudes of the crosscorrelation between them are the key factors determining beta(T,int) of proteins. Though the volume fractions of internal cavity for the five studied proteins are nearly equal to one another, the mean cavity compressibilities beta(T,cav) vary considerably with protein species and range from 0.35 to 0.69 GPa(-1), which are much smaller than those of normal organic liquids such as methanol, ethanol, and benzene and close to that of glycerol (0.55 GPa(-1)), a strongly associated liquid.
Mori
Kazuki
K
Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan.
Seki
Yasutaka
Y
Yamada
Yutaka
Y
Matsumoto
Hiroki
H
Soda
Kunitsugu
K
D000818:Animals; D001703:Biophysics / Q000379:methods*; D002417:Cattle; D002627:Chemistry, Physical / Q000379:methods*; D002645:Chickens; D006736:Horses; D007782:Lactoglobulins / Q000737:chemistry; D009113:Muramidase / Q000737:chemistry; D009211:Myoglobin / Q000737:chemistry; D011312:Pressure; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D012259:Ribonuclease, Pancreatic / Q000737:chemistry; D014907:Whales
D007782:Lactoglobulins; D009211:Myoglobin; D011506:Proteins; D012259:Ribonuclease, Pancreatic; C421864:hen egg lysozyme; D009113:Muramidase