Unknown

Dataset Information

0

A buried lysine that titrates with a normal pKa: role of conformational flexibility at the protein-water interface as a determinant of pKa values.


ABSTRACT: 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 pK(a) units in the direction that promotes the neutral state. In contrast, the internal Lys-38 in SNase titrates with a normal pK(a). The crystal structure of the L38K variant shows that the side chain of Lys-38 is buried. The ionizable moiety is approximately 7 A from solvent and ion paired with Glu-122. This suggests that the pK(a) value of Lys-38 is normal because the energetic penalty for dehydration is offset by a favorable Coulomb interaction. However, the pK(a) of Lys-38 was also normal when Glu-122 was replaced with Gln or with Ala. Continuum electrostatics calculations were unable to reproduce the pK(a) of Lys-38 unless the protein was treated with an artificially high dielectric constant, consistent with structural reorganization being responsible for the normal pK(a) 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 pK(a) values of ionizable groups buried near the protein-water interface, and the challenges faced by structure-based pK(a) calculations in reproducing these effects.

SUBMITTER: Harms MJ 

PROVIDER: S-EPMC2327280 | biostudies-literature | 2008 May

REPOSITORIES: biostudies-literature

altmetric image

Publications

A buried lysine that titrates with a normal pKa: role of conformational flexibility at the protein-water interface as a determinant of pKa values.

Harms Michael J MJ   Schlessman Jamie L JL   Chimenti Michael S MS   Sue Gloria R GR   Damjanović Ana A   García-Moreno Bertrand B  

Protein science : a publication of the Protein Society 20080327 5


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 pK(a) units in the direction that promotes the neutral state. In contrast, the internal Lys-38 in SNase titrates with a normal pK(a). The crystal structure of the L38K variant shows that the side chain of Lys-38 is buried. The ionizable moiety is approximately 7 A from solvent and ion paired with Glu-122. This suggests that the pK(a) value  ...[more]

Similar Datasets

| S-EPMC3069169 | biostudies-literature
| S-EPMC3562795 | biostudies-literature
| S-EPMC2203286 | biostudies-literature
| S-EPMC2736131 | biostudies-literature
| S-EPMC3009415 | biostudies-literature
| S-EPMC1538816 | biostudies-literature
| S-EPMC3048411 | biostudies-literature
| S-EPMC2475499 | biostudies-literature
| S-EPMC7176579 | biostudies-literature
| S-EPMC3414879 | biostudies-other