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PDBsum entry 1f9c
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Buried charged surface in proteins.
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Authors
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T.Kajander,
P.C.Kahn,
S.H.Passila,
D.C.Cohen,
L.Lehtiö,
W.Adolfsen,
J.Warwicker,
U.Schell,
A.Goldman.
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Ref.
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Structure, 2000,
8,
1203-1214.
[DOI no: ]
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PubMed id
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Abstract
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BACKGROUND: The traditional picture of charged amino acids in globular proteins
is that they are almost exclusively on the outside exposed to the solvent.
Buried charges, when they do occur, are assumed to play an essential role in
catalysis and ligand binding, or in stabilizing structure as, for instance,
helix caps. RESULTS: By analyzing the amount and distribution of buried charged
surface and charges in proteins over a broad range of protein sizes, we show
that buried charge is much more common than is generally believed. We also show
that the amount of buried charge rises with protein size in a manner which
differs from other types of surfaces, especially aromatic and polar uncharged
surfaces. In large proteins such as hemocyanin, 35% of all charges are greater
than 75% buried. Furthermore, at all sizes few charged groups are fully exposed.
As an experimental test, we show that replacement of the buried D178 of muconate
lactonizing enzyme by N stabilizes the enzyme by 4.2 degrees C without any
change in crystallographic structure. In addition, free energy calculations of
stability support the experimental results. CONCLUSIONS: Nature may use charge
burial to reduce protein stability; not all buried charges are fully stabilized
by a prearranged protein environment. Consistent with this view, thermophilic
proteins often have less buried charge. Modifying the amount of buried charge at
carefully chosen sites may thus provide a general route for changing the
thermophilicity or psychrophilicity of proteins.
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Figure 4.
Figure 4. The Structures of the Regions Containing D178,
H181, and D150 in Wild-Type MLE and the D178N VariantWild type,
(a); Di78N, (b). The path of the backbone is shown as a "worm."
D178, H151, and D150, as well as residues that interact with
them, are in ball and stick. Oxygen is red; nitrogen is blue.
Hydrogen bonds are shown as dotted lines. The figure was
prepared using MOLSCRIPT [65] and Raster3D [66]
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The above figure is
reprinted
by permission from Cell Press:
Structure
(2000,
8,
1203-1214)
copyright 2000.
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Secondary reference #1
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Title
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The refined X-Ray structure of muconate lactonizing enzyme from pseudomonas putida prs2000 at 1.85 a resolution.
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Authors
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S.Helin,
P.C.Kahn,
B.L.Guha,
D.G.Mallows,
A.Goldman.
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Ref.
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J Mol Biol, 1995,
254,
918-941.
[DOI no: ]
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PubMed id
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Figure 5.
Figure 5. The fold of MLE monomer A, created using MOLSCRIPT (Kraulis, 1991). a-Helices are shown as spirals,
b-sheets as arrows and the rest as thin stripes. (a) Complete monomer, viewed perpendicular to the ab-barrel axis. The
manganese ion is shown as a red sphere in the centre of the barrel. The N-terminal domain is at the top of the Figure,
coloured yellow, the central barrel domain is coloured blue, and the C-terminal subdomain, behind the rest of the
molecule, is coloured cyan. The chain break between residues Arg20 and Glu30 is drawn as a broken line. (b) The
N-terminal domain, viewed from approximately the same direction as in (a). (c) The central barrel domain, viewed down
the barrel axis. (d) The C-terminal subdomain, viewed from approximately the same direction as in (a). The secondary
structure elements are labelled in (b), (c) and (d).
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Figure 6.
Figure 6. MOLSCRIPT (Kraulis, 1991) Figure of the complicated hydrogen-bonding pattern involving b-strands 4
(N-terminal + barrel), 5 and 11 (barrel), and 13 and 14 (C-terminal). The hydrogen bonds are shown as dotted lines;
carbon atoms are grey, nitrogen black and oxygen white. The very steep crossing angle between strands 4 and 11 can
be seen.
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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