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PDBsum entry 2bkg
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De novo protein
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PDB id
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2bkg
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References listed in PDB file
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Key reference
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Title
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Crystal structure of a consensus-Designed ankyrin repeat protein: implications for stability.
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Authors
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H.K.Binz,
A.Kohl,
A.Plückthun,
M.G.Grütter.
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Ref.
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Proteins, 2006,
65,
280-284.
[DOI no: ]
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PubMed id
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Abstract
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Consensus-designed ankyrin repeat (AR) proteins are thermodynamically very
stable. The structural analysis of the designed AR protein E3_5 revealed that
this stability is due to a regular fold with highly conserved structural motifs
and H-bonding networks. However, the designed AR protein E3_19 exhibits a
significantly lower stability than E3_5 (9.6 vs. 14.8 kcal/mol), despite 88%
sequence identity. To investigate the structural correlations of this stability
difference between E3_5 and E3_19, we determined the crystal structure of E3_19
at 1.9 A resolution. E3_19 as well has a regular AR domain fold with the
characteristic H-bonding patterns. All structural features of the E3_5 and E3_19
molecules appear to be virtually identical (RMSD(Calpha) approximately 0.7 A).
However, clear differences are observed in the surface charge distribution of
the two AR proteins. E3_19 features clusters of charged residues and more
exposed hydrophobic residues than E3_5. The atomic coordinates of E3_19 have
been deposited in the Protein Data Bank. PDB ID: 2BKG.
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Figure 2.
Figure 2. Structural comparison of of E3_19 and E3_5. (a)
Stereoview of the superposition of E3_19 (B molecule, brown)
with E3_5 (PDB ID: 1MJ0, blue) in ribbon representations. The
N-and C-termini are labeled for orientation. The two proteins
are practically identical, with the biggest differences being
observed in the C-terminal AR, where E3_5 appears to be more
compact than E3_19. The two E3_19 molecules of the asymmetric
unit are virtually identical (b) H-bonding in the C-terminal AR
of E3_19. Asn156 makes H-bonds to Asp122 (residues in stick mode
in blue). (c) H-bonding in the C-terminal AR of E3_5. Asn158
makes H-bonds to Lys122 and Ala121 (residues in stick mode in
magenta).
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Figure 3.
Figure 3. Charge distribution in E3_19 and E3_5. E3_19 is
depicted on the left, E3_5 is depicted on the right. (a)
Negative charges in the  -turn
regions. Negatively charged residues are depicted in stick mode
in red on the backbones in ribbons. For completeness, Asp122 of
E3_19 is also shown. (b) Positively charged residues (stick mode
in blue) in the first three repeats of E3_19 and the first and
fourth repeat of E3_5, respectively, are depicted on the
backbones in ribbons. (c) Surface representations of the
electrostatic potential of E3_19 and E3_5 (red = -0.5, white =
0, blue = +0.5). For orientation identically positioned ribbon
representations are depicted on the left of each surface
representation.
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The above figures are
reprinted
by permission from John Wiley & Sons, Inc.:
Proteins
(2006,
65,
280-284)
copyright 2006.
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