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PDBsum entry 1dds
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Oxidoreductase
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PDB id
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1dds
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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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The effect of denaturants on protein structure.
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Authors
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J.Dunbar,
H.P.Yennawar,
S.Banerjee,
J.Luo,
G.K.Farber.
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Ref.
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Protein Sci, 1997,
6,
1727-1733.
[DOI no: ]
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PubMed id
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Abstract
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Virtually all studies of the protein-folding reaction add either heat, acid, or
a chemical denaturant to an aqueous protein solution in order to perturb the
protein structure. When chemical denaturants are used, very high concentrations
are usually necessary to observe any change in protein structure. In a solution
with such high denaturant concentrations, both the structure of the protein and
the structure of the solvent around the protein can be altered. X-ray
crystallography is the obvious experimental technique to probe both types of
changes. In this paper, we report the crystal structures of dihydrofolate
reductase with urea and of ribonuclease A with guanidinium chloride. These two
classic denaturants have similar effects on the native structure of the protein.
The most important change that occurs is a reduction in the overall thermal
factor. These structures offer a molecular explanation for the reduction in
mobility. Although the reduction is observed only with the native enzyme in the
crystal, a similar decrease in mobility has also been observed in the unfolded
state in solution (Makhatadze G, Privalov PL. 1992. Protein interactions with
urea and guanidinium chloride: A calorimetric study.
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Figure 1.
Fig. 1. A: A artoon of the guanidinium 132- and 133-binding sites in
ribonuclease. Gua forms a bond to Tyr 76, and Gua 132
forms a bond to Glu 9. In these cartoons, water molecules have
been omitted for clarity. B: The urea 21 I-binding site in
reductase. The A and designations refer to hetwo monomers in the
asymmetric unit. As described n the text both urea and guanidinium form
strong interactions which reduce the mobility of protein.
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Figure 2.
Fig. 2. Electrondensityfor a guanidinium133intheribonucleasestruc-
ture is shown.The 2F,, ~ F, mapwascontouredatthestandarddeviation
ofthemap,andthemodel used togeneratethephasescontained no ua-
nidinium. he distancebetweentheoxygenof Tyr 76andtheguanidinium
nitrogen is only 2.5 A. Te distancebetweentheclosestnitrogensinGua
133 andGua132 s 3.3 A. The peptidebond of residue 62, whch is shown
below Gua 133 inthisfigure, is further away. Thedistancesfor all ofthe
proteininteractions with Gua 133areshon in Figure A.
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The above figures are
reprinted
by permission from the Protein Society:
Protein Sci
(1997,
6,
1727-1733)
copyright 1997.
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