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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

Michael J. Harms¹, Jamie L. Schlessman^1,2, Michael S. Chimenti¹, Gloria R. Sue¹, Ana Damjanovi¹, and Bertrand García-Moreno E.¹

¹ Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, USA
² Chemistry Department, U.S. Naval Academy, Annapolis, Maryland 21402, USA

(RECEIVED December 9, 2007; FINAL REVISION February 14, 2008; ACCEPTED February 20, 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 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 7 Å 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.

Keywords: electrostatics; pK_a ; staphylococcal nuclease; buried residues; water penetration; flexibility; dynamics

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