A self-consistent, microenvironment modulated screened Coulomb potential approximation to calculate pH-dependent electrostatic effects in proteins

An improved approach is presented for calculating pH-dependent electrostati c effects in proteins using sigmoidally screened Coulomb potentials (SCP). It is hypothesized that a key determinant of seemingly aberrant behavior in pK(a) shifts is due to the properties of the unique microenvironment aroun d each residue. To help demonstrate this proposal, an approach is developed to characterize the microenvironments using the local hydrophobicity/hydro philicity around each residue of the protein. The quantitative characteriza tion of the microenvironments shows that the protein is a complex mosaic of differing dielectric regions that provides a physical basis for modifying the dielectric screening functions: in more hydrophobic microenvironments t he screening decreases whereas the converse applies to more hydrophilic reg ions. The approach was applied to seven proteins providing more than 100 me asured pK(a) values and yielded a root mean square deviation of 0.5 between calculated and experimental values. The incorporation of the local hydroph obicity characteristics into the algorithm allowed the resolution of some o f the more intractable problems in the calculation of pK(a). Thus, the dive rgent shifts of the pK(a) of Glu-35 and Asp-66 in hen egg white lysozyme, w hich are both about 90% buried, was correctly predicted. Mechanistically, t he divergence occurs because Glu-35 is in a hydrophobic microenvironment, w hile Asp-66 is in a hydrophilic microenvironment. Furthermore, because the calculation of the microenvironmental effects takes very little CPU time, t he computational speed of the SCP formulation is conserved. Finally, result s from different crystal structures of a given protein were compared, and i t is shown that the reliability of the calculated pK(a) values is sufficien t to allow identification of conformations that may be more relevant for th e solution structure.