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PDBsum entry 2rdf
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References listed in PDB file
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Key reference
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Title
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Electrostatic effects in a network of polar and ionizable groups in staphylococcal nuclease.
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Authors
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K.L.Baran,
M.S.Chimenti,
J.L.Schlessman,
C.A.Fitch,
K.J.Herbst,
B.E.Garcia-Moreno.
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Ref.
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J Mol Biol, 2008,
379,
1045-1062.
[DOI no: ]
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PubMed id
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Abstract
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His121 and His124 are embedded in a network of polar and ionizable groups on the
surface of staphylococcal nuclease. To examine how membership in a network
affects the electrostatic properties of ionizable groups, the tautomeric state
and the pK(a) values of these histidines were measured with NMR spectroscopy in
the wild-type nuclease and in 13 variants designed to disrupt the network. In
the background protein, His121 and His124 titrate with pK(a) values of 5.2 and
5.6, respectively. In the variants, where the network was disrupted, the pK(a)
values range from 4.03 to 6.46 for His121, and 5.04 to 5.99 for His124. The
largest decrease in a pK(a) was observed when the favorable Coulomb interaction
between His121 and Glu75 was eliminated; the largest increase was observed when
Tyr91 or Tyr93 was substituted with Ala or Phe. In all variants, the dominant
tautomeric state at neutral pH was the N(epsilon2) state. At one level the
network behaves as a rigid unit that does not readily reorganize when disrupted:
crystal structures of the E75A or E75Q variants show that even when the pivotal
Glu75 is removed, the overall configuration of the network was unaffected. On
the other hand, a few key hydrogen bonds appear to govern the conformation of
the network, and when these bonds are disrupted the network reorganizes. Coulomb
interactions within the network report an effective dielectric constant of 20,
whereas a dielectric constant of 80 is more consistent with the magnitude of
medium to long-range Coulomb interactions in this protein. The data demonstrate
that when structures are treated as static, rigid bodies, structure-based pK(a)
calculations with continuum electrostatics method are not useful to treat
ionizable groups in cases where pK(a) values are governed by short-range polar
and Coulomb interactions.
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Figure 1.
Fig. 1. (a) Location of the network surrounding His121 and
His124 in the structure of wild-type SNase. (b) A diagram of the
network of interactions around His121 and His124. The distances
that are shown identify the noncovalent interactions that are
most consistent with the experimental data.
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Figure 7.
Fig. 7. (a) 2F[o]–F[c] electron density maps contoured
around significant amino acid side chains in the E75A variant at
1.25  down
triangle, open (light blue). The side chains of Ala75, His121
and His124 are shown in blue and labeled. The neighboring Lys9,
Glu73, Asp77, Tyr91, Tyr93, Glu101, Lys127 and Ser128 are shown
in yellow. (b) The same as a but with the structure of the E75Q
variant. (c) Backbone superposition of wild-type SNase (gray)
(PDB accession code 1stn.pbd), E75A (blue) and E75Q (red). (d)
Stereoview of the superposition of wild-type SNase (gray), E75A
(blue) and E75Q (red). Side chains of Lys7, Glu73, Asp77, Tyr91,
and Tyr93 are shown for comparison. The C^α RMSD of the
structure of E75A or E75Q against the wild type was 0.60 Å.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2008,
379,
1045-1062)
copyright 2008.
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