Paper Citing NAMD - Abstract
Harms, Michael J.; Schlessman, Jamie L.; Chimenti, Michael S.; Sue, Gloria R.; Damjanovic, Ana; Garcia-Moreno E, Bertrand
A buried lysine that titrates with a normal pK(a): Role of conformational flexibility at the protein-water interface as a determinant of pK(a)values
PROTEIN SCIENCE, 17:833-845, MAY 2008
Previously we reported that Lys, Asp, and Glu residues at positions 66 and 92 in staphylococcal nuclease ( SNase) titrate with pK(a) values shifted by up to 5 pKa units in the direction that promotes the neutral state. In contrast, the internal Lys-38 in SNase titrates with a normal pKa. The crystal structure of the L38K variant shows that the side chain of Lys-38 is buried. The ionizable moiety is; 7 A from solvent and ion paired with Glu-122. This suggests that the pKa value of Lys-38 is normal because the energetic penalty for dehydration is offset by a favorable Coulomb interaction. However, the pKa of Lys-38 was also normal when Glu-122 was replaced with Gln or with Ala. Continuum electrostatics calculations were unable to reproduce the pKa of Lys-38 unless the protein was treated with an artificially high dielectric constant, consistent with structural reorganization being responsible for the normal pKa value of Lys-38. This reorganization must be local because circular dichroism and NMR spectroscopy indicate that the L38K protein is native-like under all conditions studied. In molecular dynamics simulations, the ion pair between Lys-38 and Glu-122 is unstable. The simulations show that a minor rearrangement of a loop is sufficient to allow penetration of water to the amino moiety of Lys-38. This illustrates both the important roles of local flexibility and water penetration as determinants of pKa values of ionizable groups buried near the protein-water interface, and the challenges faced by structure-based pKa calculations in reproducing these effects.
