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PDBsum entry 1r3p
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Transport protein
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PDB id
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1r3p
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References listed in PDB file
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Key reference
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Title
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Deformation of helix c in the low temperature l-Intermediate of bacteriorhodopsin.
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Authors
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K.Edman,
A.Royant,
G.Larsson,
F.Jacobson,
T.Taylor,
D.Van der spoel,
E.M.Landau,
E.Pebay-Peyroula,
R.Neutze.
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Ref.
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J Biol Chem, 2004,
279,
2147-2158.
[DOI no: ]
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PubMed id
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Abstract
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X-ray and electron diffraction studies of specific reaction intermediates, or
reaction intermediate analogues, have produced a consistent picture of the
structural mechanism of light-driven proton pumping by bacteriorhodopsin. Of
central importance within this picture is the structure of the L-intermediate,
which follows the retinal all-trans to 13-cis photoisomerization step of the
K-intermediate and sets the stage for the primary proton transfer event from the
positively charged Schiff base to the negatively charged Asp-85. Here we report
the structural changes in bacteriorhodopsin following red light illumination at
150 K. Single crystal microspectrophotometry showed that only the L-intermediate
is populated in three-dimensional crystals under these conditions. The
experimental difference Fourier electron density map and refined
crystallographic structure were consistent with those previously presented
(Royant, A., Edman, K., Ursby, T., Pebay-Peyroula, E., Landau, E. M., and
Neutze, R. (2000) Nature 406, 645-648; Royant, A., Edman, K., Ursby, T.,
Pebay-Peyroula, E., Landau, E. M., and Neutze, R. (2001) Photochem. Photobiol.
74, 794-804). Based on the refined crystallographic structures, molecular
dynamic simulations were used to examine the influence of the conformational
change of the protein that is associated with the K-to-L transition on retinal
dynamics. Implications regarding the structural mechanism for proton pumping by
bacteriorhodopsin are discussed.
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Figure 2.
FIG. 2. Long distance overview of the F[exc]-F[gnd]
difference Fourier electron density maps resulting from green
light illumination at 110 K contoured at 4.0  (a), red light
illumination at 150 K contoured at 3.2 (b), and green light
illumination at 170 K contoured at 3.4 (c). Positive electron
density changes are colored blue, and negative electron density
changes are colored yellow. More details of the trapping
protocols are given in the text. Overviews of the difference
density maps depicted in a and c can be found in stereo in Refs.
10 and 1, respectively.
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Figure 6.
FIG. 6. Light-induced changes in the EC H-bond network. a,
the location of water molecules in bR. b, the location of water
molecules in L[LT]. Figs. 2, 3, 4, 5, 6 were drawn using the
Swiss PDB Viewer (102).
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2004,
279,
2147-2158)
copyright 2004.
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