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PDBsum entry 1gjz
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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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Structure and properties of a dimeric n-Terminal fragment of human ubiquitin.
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Authors
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D.Bolton,
P.A.Evans,
K.Stott,
R.W.Broadhurst.
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Ref.
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J Mol Biol, 2001,
314,
773-787.
[DOI no: ]
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PubMed id
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Abstract
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Previous peptide dissection and kinetic experiments have indicated that in vitro
folding of ubiquitin may proceed via transient species in which native-like
structure has been acquired in the first 45 residues. A peptide fragment,
UQ(1-51), encompassing residues 1 to 51 of ubiquitin was produced in order to
test whether this portion has propensity for independent self-assembly.
Surprisingly, the construct formed a folded symmetrical dimer that was
stabilised by 0.8 M sodium sulphate at 298 K (the S state). The solution
structure of the UQ(1-51) dimer was determined by multinuclear NMR spectroscopy.
Each subunit of UQ(1-51) consists of an N-terminal beta-hairpin followed by an
alpha-helix and a final beta-strand, with orientations similar to intact
ubiquitin. The dimer is formed by the third beta-strand of one subunit
interleaving between the hairpin and third strand of the other to give a
six-stranded beta-sheet, with the two alpha-helices sitting on top. The
helix-helix and strand portions of the dimer interface also mimic related
features in the structure of ubiquitin. The structural specificity of the
UQ(1-51) peptide is tuneable: as the concentration of sodium sulphate is
decreased, near-native alternative conformations are populated in slow chemical
exchange. Magnetization transfer experiments were performed to characterize the
various species present in 0.35 M sodium sulphate, namely the S state and two
minor forms. Chemical shift differences suggest that one minor form is very
similar to the S state, while the other experiences a significant conformational
change in the third strand. A segmental rearrangement of the third strand in one
subunit of the S state would render the dimer asymmetric, accounting for most of
our results. Similar small-scale transitions in proteins are often invoked to
explain solvent exchange at backbone amide proton sites that have an
intermediate level of protection.
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Figure 3.
Figure 3. (a) Stereo view of a superposition of backbone
traces from the final ensemble of 16 solution structures of the
S state dimer of UQ(1-51), with one subunit in red and the other
in blue. (b) A representation of the fold of the S state dimer,
with b-strands labelled. (c) A representation of the fold of
wild-type ubiquitin with b-strands labelled.
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Figure 5.
Figure 5. Comparison of details of the structures of
wild-type ubiquitin (left) and the S state of UQ(1-51) (right).
(a) Interaction between strand U[2] from the N-terminal hairpin
and the a-helix. (b) Interface between the a-helix and the
3[10]-helix in ubiquitin and between the two a-helices of
UQ(1-51). (c) Arrangement of strands U[1], U[5] and U[3] of
ubiquitin and strands U[3], U'[3] and U[1]of UQ(1-51).
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2001,
314,
773-787)
copyright 2001.
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