2rks

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{{STRUCTURE_2rks| PDB=2rks | SCENE= }}
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'''Crystal structure of Staphylococcal nuclease variant PHS L38K at cryogenic temperature'''
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===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.
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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]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri Jul 4 16:57:44 2008''

Revision as of 13:57, 4 July 2008

Image:2rks.png

Template:STRUCTURE 2rks

Crystal structure of Staphylococcal nuclease variant PHS L38K at cryogenic temperature

Template:ABSTRACT PUBMED 18369193

About this Structure

2RKS is a Single protein structure of sequence from Staphylococcus aureus. Full crystallographic information is available from OCA.

Reference

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 MJ, Schlessman JL, Chimenti MS, Sue GR, Damjanovic A, Garcia-Moreno E B, Protein Sci. 2008 Mar 27;. PMID:18369193

Page seeded by OCA on Fri Jul 4 16:57:44 2008

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