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PDBsum entry 1v80
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Signaling protein
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PDB id
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1v80
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References listed in PDB file
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Key reference
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Title
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Nmr snapshots of a fluctuating protein structure: ubiquitin at 30 bar-3 kbar.
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Authors
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R.Kitahara,
S.Yokoyama,
K.Akasaka.
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Ref.
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J Mol Biol, 2005,
347,
277-285.
[DOI no: ]
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PubMed id
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Abstract
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Conformational fluctuation plays a key role in protein function, but we know
little about the associated structural changes. Here we present a general method
for elucidating, at the atomic level, a large-scale shape change of a protein
molecule in solution undergoing conformational fluctuation. The method utilizes
the intimate relationship between conformation and partial molar volume and
determines three-dimensional structures of a protein at different pressures
using variable pressure NMR technique, whereby NOE distance and torsion angle
constraints are used to create average coordinates. Ubiquitin (pH 4.6 at 20
degrees C) was chosen as the first target, for which structures were determined
at 30 bar and at 3 kbar, giving "NMR snapshots" of a fluctuating
protein structure at atomic resolution. The result reveals that the helix swings
in and out by >3 angstroms with a simultaneous reorientation of the C-terminal
segment, providing an "open" conformer suitable for enzyme
recognition. Spin relaxation analysis indicates that this fluctuation occurs in
the ten microsecond time range with activation volumes -4.2(+/-3.2) and
18.5(+/-3.0) ml/mol for the "closed-to-open" and the
"open-to-closed" transitions, respectively.
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Figure 3.
Figure 3. Molecular surface of ubiquitin at 30 bar (a)
and at 3 kbar (b). Calculation was performed on selected
energy-minimized structures of ubiquitin (pH 4.6, 20 8C)
using the program GRASP
24
with a probe radius of 1.4 Å .
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Figure 4.
Figure 4. Spin relaxation
dynamics of ubiquitin at 30 bar
(open circle) and at 3 kbar (filled
circle). (a)
15
N longitudinal
relaxation rates,
15
N-R1. (b)
15
N
transverse relaxation rates,
15
N-
R2. (c)
1
H-induced
15
N nuclear
Overhauser effect,
15
N{
1
H}-NOE.
(a)--(c) Data are not included for
E24 and G53 (due to severe line-
broadening), for D21 and A28
(due to spectral overlap at
30 bar), for E16 and V26 (due to
spectral overlap at 3 kbar), for I36
(due to signal disappearance at
3 kbar), and for the Pro residues
(P19, P37, P38) with no amide
groups. (d) Order parameters of
N--H vectors, S
2
. (e) Exchange
contribution to
15
N transverse
relaxation rates,
15
N-Rex. Plots in
(d) and (e) were obtained from
the Modelfree analysis
25,26
of the
spin relaxation parameters for
ubiquitin (pH 4.6 at 20 8C) with
the program FAST-Modelfree
26
under the assumption of isotropic
molecular tumbling. The overall
rotational correlation times were
4.7 ns both at 30 bar and at 3 kbar.
Relaxation parameters for resi-
dues 4, 23, 25, 32, 35 and 49 at
30 bar and residues 2, 4, 9, 13, 14,
17, 28, 29, 32, 43 and 54 at 3 kbar
do not show a reasonable fit to the
Modelfree analysis, giving no
data in (d) and (e).
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2005,
347,
277-285)
copyright 2005.
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