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| {{STRUCTURE_2rks| PDB=2rks | SCENE= }} | | {{STRUCTURE_2rks| PDB=2rks | SCENE= }} |
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| '''Crystal structure of Staphylococcal nuclease variant PHS L38K at cryogenic temperature'''
| | ===Crystal structure of Staphylococcal nuclease variant PHS L38K at cryogenic temperature=== |
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| ==Overview==
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| 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.
| | The line below this paragraph, {{ABSTRACT_PUBMED_18369193}}, adds the Publication Abstract to the page |
| | (as it appears on PubMed at http://www.pubmed.gov), where 18369193 is the PubMed ID number. |
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| | {{ABSTRACT_PUBMED_18369193}} |
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| ==About this Structure== | | ==About this Structure== |
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| [[Category: Internal ion pair]] | | [[Category: Internal ion pair]] |
| [[Category: Staphylococcal nuclease]] | | [[Category: Staphylococcal nuclease]] |
| ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 16 23:06:12 2008'' | | |
| | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri Jul 4 16:57:44 2008'' |
