Dielectric properties of proteins from simulation: the effects of solvent, ligands, pH, and temperature.
We have used a standard Fröhlich-Kirkwood dipole moment fluctuation model to calculate the static dielectric permittivity, epsilon(0), for four different proteins, each of which was simulated under at least two different conditions of pH, temperature, solvation, or ligand binding. For the range of proteins and conditions studied, we calculate values for epsilon(0) between 15 and 40. Our results show, in agreement with prior work, that the behavior of charged residues is the primary determinant of the effective permittivity. Furthermore, only environmental changes that alter the properties of charged residues exert a significant effect on epsilon. In contrast, buried water molecules or ligands have little or no effect on protein dielectric properties.
Pitera
J W
JW
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, CH-8092 Zürich, Switzerland.
Falta
M
M
van Gunsteren
W F
WF
D000818:Animals; D002161:Camelids, New World; D002352:Carrier Proteins / Q000737:chemistry* / Q000378:metabolism; D002645:Chickens; D003198:Computer Simulation; D000071438:Fatty Acid-Binding Protein 7; D050556:Fatty Acid-Binding Proteins; D006863:Hydrogen-Ion Concentration; D007143:Immunoglobulin Heavy Chains / Q000737:chemistry* / Q000378:metabolism; D007768:Lactalbumin / Q000737:chemistry* / Q000378:metabolism; D008024:Ligands; D008958:Models, Molecular; D009113:Muramidase / Q000737:chemistry* / Q000378:metabolism; D009363:Neoplasm Proteins; D009419:Nerve Tissue Proteins; D017433:Protein Structure, Secondary; D051381:Rats; D012997:Solvents / Q000378:metabolism; D055672:Static Electricity; D013696:Temperature
D002352:Carrier Proteins; C490174:Fabp7 protein, rat; D000071438:Fatty Acid-Binding Protein 7; D050556:Fatty Acid-Binding Proteins; D007143:Immunoglobulin Heavy Chains; D008024:Ligands; D009363:Neoplasm Proteins; D009419:Nerve Tissue Proteins; D012997:Solvents; D007768:Lactalbumin; D009113:Muramidase