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PDBsum entry 1c3t
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De novo protein
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PDB id
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1c3t
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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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Rotamer strain as a determinant of protein structural specificity.
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Authors
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G.A.Lazar,
E.C.Johnson,
J.R.Desjarlais,
T.M.Handel.
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Ref.
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Protein Sci, 1999,
8,
2598-2610.
[DOI no: ]
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PubMed id
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Abstract
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We present direct evidence for a change in protein structural specificity due to
hydrophobic core packing. High resolution structural analysis of a designed core
variant of ubiquitin reveals that the protein is in slow exchange between two
conformations. Examination of side-chain rotamers indicates that this dynamic
response and the lower stability of the protein are coupled to greater strain
and mobility in the core. The results suggest that manipulating the level of
side-chain strain may be one way of fine tuning the stability and specificity of
proteins.
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Secondary reference #1
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Title
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De novo design of the hydrophobic core of ubiquitin.
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Authors
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G.A.Lazar,
J.R.Desjarlais,
T.M.Handel.
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Ref.
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Protein Sci, 1997,
6,
1167-1178.
[DOI no: ]
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PubMed id
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Figure 1.
Fig. 1. Molscript diagram (Kraulis, 1991) of human WT ubiquitin back-
bone with the 14 chosencore side chains. The s based on the
X-ray coordinates (Vijay-Kumar et al., 1987).
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Figure 9.
Wig. 9. tructuralcomparisonofthe WT ubiquitincorepredictedbyROC*
to that from theX-ray stnicture (Vijay-Kumar et dl., 1987). X-ray structure
corsi&chains are in lack andpredictedcoresidechainsare in Side
hainswhichhaveincorrectlypredicted rotamers in the predicted structure
re shown in blue.Hydrogens ate not shown forclarity. The figure s
isplayedusingthe program INSIGHT II (BiosymTechnologies, San Di-
go,California).
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The above figures are
reproduced from the cited reference
which is an Open Access publication published by the Protein Society
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Secondary reference #2
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Title
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Solution structure and dynamics of a designed hydrophobic core variant of ubiquitin.
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Authors
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E.C.Johnson,
G.A.Lazar,
J.R.Desjarlais,
T.M.Handel.
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Ref.
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Structure Fold Des, 1999,
7,
967-976.
[DOI no: ]
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PubMed id
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Figure 1.
Figure 1. Structures of 1D7 versus WT. (a) Stereoview of an
ensemble of the 20 lowest energy structures of 1D7. Sidechains
of core residues are displayed in green and the N and C termini
are labeled. (b) Superposition of the structure of 1D7 closest
to the mean (blue) with the crystal structure (red; accession
code 1UBI [15]) the coordinates of which were used for the
design. (c) Residual dipolar NH couplings of partially oriented
1D7 (y axis) versus WT ubiquitin (x axis) in DMPC:DHPC bicelles
[16]. WT dipolar couplings were taken from Cornilescu et al.
[25]. The difference in the range of dipolar couplings between
the two samples is due to differences in bicelle content.
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The above figure is
reproduced from the cited reference
with permission from Cell Press
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