pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model.
A macroscopic electrostatic model is used to calculate the pKa values of the titratable groups in lysozyme. The model makes use of detailed structural information and treats solvation self-energies and interactions arising from permanent partial charges and titratable charges. Both the tetragonal and triclinic crystal structures are analyzed. Half of the experimentally observed pKa shifts (11 out of 21) are well reproduced by calculations for both structures; this includes the unusually high pKa of Glu 35 in the active site. For more than half the pKa's (13 out of 21), there is a large difference (1-3.3 pK units) between the results from the two structures. Many of these correspond to the titrating groups for which the calculations are in error. Since for an ionic strength of 0.1 M the Debye screening between titratable groups leads to a very high effective dielectric constant (the average value for all pairs of titrating groups is approximately 900), near-neighbor interactions dominate the pKa perturbations. Thus, the pKa values are very sensitive to the details of the local protein conformation, and it is likely that side-chain mobility has an important role in determining the observed pKa shifts.
Bashford
D
D
Department of Chemistry, Harvard University, Cambridge, Massachusetts 02138.
Karplus
M
M
D003198:Computer Simulation; D007700:Kinetics; D008956:Models, Chemical; D008958:Models, Molecular; D009113:Muramidase / Q000378:metabolism; D011487:Protein Conformation; D011506:Proteins / Q000378:metabolism*; D012996:Solutions
D011506:Proteins; D012996:Solutions; D009113:Muramidase