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PDBsum entry 2snm
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References listed in PDB file
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Key reference
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Title
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In a staphylococcal nuclease mutant the side-Chain of a lysine replacing valine 66 is fully buried in the hydrophobic core.
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Authors
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W.E.Stites,
A.G.Gittis,
E.E.Lattman,
D.Shortle.
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Ref.
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J Mol Biol, 1991,
221,
7.
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PubMed id
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Abstract
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The crystal structure of the staphylococcal nuclease mutant V66K, in which
valine 66 is replaced by lysine, has been solved at 1.97 A resolution. Unlike
lysine residues in previously reported protein structures, this residue appears
to bury its side-chain in the hydrophobic core without salt bridging, hydrogen
bonding or other forms of electrostatic stabilization. Solution studies of the
free energy of denaturation, delta GH2O, show marked pH dependence and clearly
indicate that the lysine residue must be deprotonated in the folded state. V66K
is highly unstable at neutral pH but only modestly less stable than the
wild-type protein at high pH. The pH dependence of stability for V66K, in
combination with similar measurements for the wild-type protein, allowed
determination of the pKa values of the lysine in both the denatured and native
forms. The epsilon-amine of this residue has a pKa value in the denatured state
of 10.2, but in the native state it must be 6.4 or lower. The epsilon-amine is
thus deprotonated in the folded molecule. These values enabled an estimation of
the epsilon-amine's relative change in free energy of solvation between solvent
and the protein interior at 5.1 kcal/mol or greater. This implies that the value
of the dielectric constant of the protein interior must be less than 12.8.
Lysine is usually found with the methylene groups of its side-chain partly
buried but is nevertheless considered a hydrophilic surface residue. It would
appear that the high pKa value of lysine, which gives it a positive charge at
physiological pH, is the primary reason for its almost exclusive confinement to
the surface proteins. When deprotonated, this amino acid type can be fully
incorporated into the hydrophobic core.
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