Prediction of secondary ionization of the phosphate group in phosphotyrosine peptides.
A computational approach, based on a continuum molecular electrostatics model, for the calculation of the pK(a) values of secondary ionization of the phosphate group in phenyl phosphate derivatives is described. The method uses the ESP atomic charges of the mono-anionic and di-anionic forms of the ionizable phosphate group, computed with the use of the density functional method, and applies a new concept of the model group, being the reference state for the pK(a) calculations. Both conformational flexibility and tautomeric degrees of freedom are taken into account in the calculations. The method was parameterized using experimentally available pK(a) values of four derivatives of phenyl phosphates, and phosphotyrosine. Subsequently this parameterization was used to predict pK(a) of the phosphate group in a short peptide Gly-Gly-Tyr(P)-Ala, and in a longer peptide consisting of 12 residues, the latter in water, and in a complex with a protein-phospholipase. The agreement between the computed and the experimental pK(a) values is better than +/-0.3 pH units for the optimized solute dielectric constant of 11-13. This approach is promising and its extension to other phospho-amino acids is in progress.
Wojciechowski
M
M
Department of Biophysics, Warsaw University, Zwirki i Wigury 93, 02-089 Warsaw, Poland.
Grycuk
T
T
Antosiewicz
J M
JM
Lesyng
B
B
D003198:Computer Simulation; D007477:Ions / Q000737:chemistry; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry; D010710:Phosphates / Q000737:chemistry*; D010766:Phosphorylation; D019000:Phosphotyrosine / Q000737:chemistry*; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D012680:Sensitivity and Specificity; D055672:Static Electricity
D007477:Ions; D010455:Peptides; D010710:Phosphates; D019000:Phosphotyrosine