Calculation and measurement of the dipole moment of small proteins: use of protein data base.
The dipole moments of small protein molecules were determined experimentally in order to validate the calculated dipole moments by previous investigators. We found that the agreements are satisfactory for some proteins. There are, however, many proteins for which the agreement is less than satisfactory. In order to find the cause of the disagreement, the dipole moments of these proteins were recalculated using the Brookhaven Protein Data Bank. We calculated the dipole moment due to fixed surface charges and the bond moments of all the carbonyl groups in main chain and side chains. The calculation consists of the mean moments and their mean square fluctuations. In addition, we investigated the effect of electrostatic interactions between charged sites for several proteins. These results show that incorporation of the interactions does not affect substantially the calculated dipole moments. The rms fluctuation of the dipole moment is found to be small but not negligible. In conclusion, recalculated dipole moments are in good agreement with the observed values.
Takashima
S
S
Department of Bioengineering, University of Pennsylvania, Philadelphia 19104-6392.
Asami
K
K
D001703:Biophysics / Q000379:methods; D016206:Databases, Bibliographic; D004798:Enzymes / Q000737:chemistry*; D008433:Mathematics; D008958:Models, Molecular; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*
D004798:Enzymes; D011506:Proteins