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Contents |
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* Residue conservation analysis
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PDB id:
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Membrane protein
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Title:
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Molecular basis of transmenbrane signalling by sensory rhodopsin ii- transducer complex
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Structure:
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Sensory rhodopsin ii. Chain: a. Fragment: residues 1-225. Engineered: yes. Other_details: his-tag. Sensory rhodopsin ii transducer. Chain: b. Fragment: residues 23-82. Synonym: transducer htr ii fragment , htr-ii, methyl-accepting
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Source:
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Natronomonas pharaonis. Organism_taxid: 2257. Expressed in: escherichia coli. Expression_system_taxid: 469008.
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Biol. unit:
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Tetramer (from PDB file)
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Resolution:
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1.93Å
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R-factor:
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0.226
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R-free:
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0.258
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Authors:
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V.I.Gordeliy,J.Labahn,R.Moukhametzianov,R.Efremov,J.Granzin, R.Schlesinger,G.Bueldt,T.Savopol,A.Scheidig,J.P.Klare,M.Engelhard
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Key ref:
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V.I.Gordeliy
et al.
(2002).
Molecular basis of transmembrane signalling by sensory rhodopsin II-transducer complex.
Nature,
419,
484-487.
PubMed id:
DOI:
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Date:
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15-Aug-02
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Release date:
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10-Oct-02
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PROCHECK
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Headers
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References
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DOI no:
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Nature
419:484-487
(2002)
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PubMed id:
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Molecular basis of transmembrane signalling by sensory rhodopsin II-transducer complex.
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V.I.Gordeliy,
J.Labahn,
R.Moukhametzianov,
R.Efremov,
J.Granzin,
R.Schlesinger,
G.Büldt,
T.Savopol,
A.J.Scheidig,
J.P.Klare,
M.Engelhard.
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ABSTRACT
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Microbial rhodopsins, which constitute a family of seven-helix membrane proteins
with retinal as a prosthetic group, are distributed throughout the Bacteria,
Archaea and Eukaryota. This family of photoactive proteins uses a common
structural design for two distinct functions: light-driven ion transport and
phototaxis. The sensors activate a signal transduction chain similar to that of
the two-component system of eubacterial chemotaxis. The link between the
photoreceptor and the following cytoplasmic signal cascade is formed by a
transducer molecule that binds tightly and specifically to its cognate receptor
by means of two transmembrane helices (TM1 and TM2). It is thought that light
excitation of sensory rhodopsin II from Natronobacterium pharaonis (SRII) in
complex with its transducer (HtrII) induces an outward movement of its helix F
(ref. 6), which in turn triggers a rotation of TM2 (ref. 7). It is unclear how
this TM2 transition is converted into a cellular signal. Here we present the
X-ray structure of the complex between N. pharaonis SRII and the
receptor-binding domain of HtrII at 1.94 A resolution, which provides an atomic
picture of the first signal transduction step. Our results provide evidence for
a common mechanism for this process in phototaxis and chemotaxis.
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Selected figure(s)
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Figure 2.
Figure 2: Fold of the receptor -transducer complex a, Ribbon
diagram of the top view from the cytoplasmic side.  -Helices
are in red for the receptor and green for the transducer;  -strands
are in blue and coils in grey.The labels of the symmetry related
complex are marked by a prime. The crystallographic symmetry
axis is located between TM1 -TM2 and TM1' -TM2'. b, Side view of
the complex. The complex is coloured according to B-factor
mobility: light red/green (less mobile), dark red/green
(mobile). ES, extracellular side; CS, cytoplasmic side. The
dotted white lines confine the major hydrophobic core of the
proteins. Of note, the actual membrane boundary will not follow
these straight lines. The arrows indicate the shortened stalk in
HtrI (white) and the site where the helices 1
and 4
of the chemoreceptor domain of H. salinarum HtrII are attached
to the transmembrane helices TM1 and TM2 (blue). All figures
were generated with MOLSCRIPT and Raster3D.
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Figure 3.
Figure 3: Stereo view of the hydrogen bonds and van der Waals
contacts between receptor ( alpha- -helices
in red) and transducer ( alpha--helices
in green). The residues that are involved in hydrogen bonds
are labelled.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nature
(2002,
419,
484-487)
copyright 2002.
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Figures were
selected
by the author.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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J.Holterhues,
E.Bordignon,
D.Klose,
C.Rickert,
J.P.Klare,
S.Martell,
L.Li,
M.Engelhard,
and
H.J.Steinhoff
(2011).
The Signal Transfer from the Receptor NpSRII to the Transducer NpHtrII Is Not Hampered by the D75N Mutation.
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Biophys J,
100,
2275-2282.
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|
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A.Gautier,
H.R.Mott,
M.J.Bostock,
J.P.Kirkpatrick,
and
D.Nietlispach
(2010).
Structure determination of the seven-helix transmembrane receptor sensory rhodopsin II by solution NMR spectroscopy.
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Nat Struct Mol Biol,
17,
768-774.
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PDB code:
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D.L.Farrens
(2010).
What site-directed labeling studies tell us about the mechanism of rhodopsin activation and G-protein binding.
|
| |
Photochem Photobiol Sci,
9,
1466-1474.
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H.Kandori,
Y.Sudo,
and
Y.Furutani
(2010).
Protein-protein interaction changes in an archaeal light-signal transduction.
|
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J Biomed Biotechnol,
2010,
424760.
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and
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(2010).
Membrane domain structures of three classes of histidine kinase receptors by cell-free expression and rapid NMR analysis.
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Proc Natl Acad Sci U S A,
107,
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PDB codes:
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J.Cheung,
and
W.A.Hendrickson
(2010).
Sensor domains of two-component regulatory systems.
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Curr Opin Microbiol,
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J.S.Parkinson
(2010).
Signaling mechanisms of HAMP domains in chemoreceptors and sensor kinases.
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Annu Rev Microbiol,
64,
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K.McLuskey,
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Crystal structures of all-alpha type membrane proteins.
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Eur Biophys J,
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723-755.
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K.R.Vinothkumar,
and
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Structures of membrane proteins.
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Q Rev Biophys,
43,
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M.Dittmann,
J.Sauermann,
R.Seidel,
W.Zimmermann,
and
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(2010).
Native chemical ligation of hydrophobic peptides in organic solvents.
|
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J Pept Sci,
16,
558-562.
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M.Etzkorn,
K.Seidel,
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S.Martell,
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M.Engelhard,
and
M.Baldus
(2010).
Complex formation and light activation in membrane-embedded sensory rhodopsin II as seen by solid-state NMR spectroscopy.
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| |
Structure,
18,
293-300.
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S.D.Goldberg,
G.D.Clinthorne,
M.Goulian,
and
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(2010).
Transmembrane polar interactions are required for signaling in the Escherichia coli sensor kinase PhoQ.
|
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Proc Natl Acad Sci U S A,
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S.Streif,
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A predictive computational model of the kinetic mechanism of stimulus-induced transducer methylation and feedback regulation through CheY in archaeal phototaxis and chemotaxis.
|
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BMC Syst Biol,
4,
27.
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T.Kouyama,
and
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(2010).
Structural divergence and functional versatility of the rhodopsin superfamily.
|
| |
Photochem Photobiol Sci,
9,
1458-1465.
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|
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V.Borshchevskiy,
R.Efremov,
E.Moiseeva,
G.Büldt,
and
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(2010).
Overcoming merohedral twinning in crystals of bacteriorhodopsin grown in lipidic mesophase.
|
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Acta Crystallogr D Biol Crystallogr,
66,
26-32.
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G.Jékely
(2009).
Evolution of phototaxis.
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Philos Trans R Soc Lond B Biol Sci,
364,
2795-2808.
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J.Kriegsmann,
I.Gregor,
I.von der Hocht,
J.Klare,
M.Engelhard,
J.Enderlein,
and
J.Fitter
(2009).
Translational diffusion and interaction of a photoreceptor and its cognate transducer observed in giant unilamellar vesicles by using dual-focus FCS.
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Chembiochem,
10,
1823-1829.
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M.Caffrey
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Annu Rev Biophys,
38,
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V.B.Bergo,
E.N.Spudich,
J.L.Spudich,
and
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(2009).
Active water in protein-protein communication within the membrane: the case of SRII-HtrII signal relay.
|
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Biochemistry,
48,
811-813.
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|
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Y.J.Kim,
I.Chizhov,
and
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(2009).
Functional Expression of the Signaling Complex Sensory Rhodopsin II/Transducer II from Halobacterium salinarum in Escherichia coli.
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Photochem Photobiol,
85,
521-528.
|
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|
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|
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A.B.Wöhri,
L.C.Johansson,
P.Wadsten-Hindrichsen,
W.Y.Wahlgren,
G.Fischer,
R.Horsefield,
G.Katona,
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R.J.Cogdell,
N.J.Fraser,
S.Engström,
and
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(2008).
A lipidic-sponge phase screen for membrane protein crystallization.
|
| |
Structure,
16,
1003-1009.
|
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|
|
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|
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D.A.Cisneros,
L.Oberbarnscheidt,
A.Pannier,
J.P.Klare,
J.Helenius,
M.Engelhard,
F.Oesterhelt,
and
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(2008).
Transducer binding establishes localized interactions to tune sensory rhodopsin II.
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| |
Structure,
16,
1206-1213.
|
|
|
|
|
|
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I.Kawamura,
H.Yoshida,
Y.Ikeda,
S.Yamaguchi,
S.Tuzi,
H.Saitô,
N.Kamo,
and
A.Naito
(2008).
Dynamics change of phoborhodopsin and transducer by activation: study using D75N mutant of the receptor by site-directed solid-state 13C NMR.
|
| |
Photochem Photobiol,
84,
921-930.
|
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|
|
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I.L.Budyak,
O.S.Mironova,
N.Yanamala,
V.Manoharan,
G.Büldt,
R.Schlesinger,
and
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(2008).
Flexibility of the Cytoplasmic Domain of the Phototaxis Transducer II from Natronomonas pharaonis.
|
| |
J Biophys,
2008,
267912.
|
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|
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J.Cheung,
C.A.Bingman,
M.Reyngold,
W.A.Hendrickson,
and
C.D.Waldburger
(2008).
Crystal structure of a functional dimer of the PhoQ sensor domain.
|
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J Biol Chem,
283,
13762-13770.
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PDB codes:
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J.Sasaki,
and
J.L.Spudich
(2008).
Signal transfer in haloarchaeal sensory rhodopsin- transducer complexes.
|
| |
Photochem Photobiol,
84,
863-868.
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M.Doebber,
E.Bordignon,
J.P.Klare,
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L.Li,
M.Engelhard,
and
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(2008).
Salt-driven Equilibrium between Two Conformations in the HAMP Domain from Natronomonas pharaonis: THE LANGUAGE OF SIGNAL TRANSFER?
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| |
J Biol Chem,
283,
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O.A.Sineshchekov,
J.Sasaki,
B.J.Phillips,
and
J.L.Spudich
(2008).
A Schiff base connectivity switch in sensory rhodopsin signaling.
|
| |
Proc Natl Acad Sci U S A,
105,
16159-16164.
|
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|
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S.R.McAllister,
and
C.A.Floudas
(2008).
Alpha-helical topology prediction and generation of distance restraints in membrane proteins.
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| |
Biophys J,
95,
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Y.Furutani,
D.Suzuki,
K.Ihara,
H.Kandori,
M.Homma,
and
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(2008).
Salinibacter Sensory Rhodopsin: SENSORY RHODOPSIN I-LIKE PROTEIN FROM A EUBACTERIUM.
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J Biol Chem,
283,
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|
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W.D.Hoff,
and
J.L.Spudich
(2008).
Single-molecule tour de force: teasing apart a signaling complex.
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| |
Structure,
16,
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X.Jiang,
E.Zaitseva,
M.Schmidt,
F.Siebert,
M.Engelhard,
R.Schlesinger,
K.Ataka,
R.Vogel,
and
J.Heberle
(2008).
Resolving voltage-dependent structural changes of a membrane photoreceptor by surface-enhanced IR difference spectroscopy.
|
| |
Proc Natl Acad Sci U S A,
105,
12113-12117.
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Y.Furutani,
M.Ito,
Y.Sudo,
N.Kamo,
and
H.Kandori
(2008).
Protein-protein interaction of a Pharaonis halorhodopsin mutant forming a complex with Pharaonis halobacterial transducer protein II detected by Fourier-transform infrared spectroscopy.
|
| |
Photochem Photobiol,
84,
874-879.
|
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Y.Sudo,
T.Nishihori,
M.Iwamoto,
K.Shimono,
C.Kojima,
and
N.Kamo
(2008).
A long-lived M-like state of phoborhodopsin that mimics the active state.
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| |
Biophys J,
95,
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A.R.Crofts
(2007).
Life, Information, Entropy, and Time: Vehicles for Semantic Inheritance.
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Complexity,
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J.Sasaki,
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N.Van Eps,
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W.L.Hubbell,
and
J.L.Spudich
(2007).
Different dark conformations function in color-sensitive photosignaling by the sensory rhodopsin I-HtrI complex.
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| |
Biophys J,
92,
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(2007).
Laser-induced transient grating analysis of dynamics of interaction between sensory rhodopsin II D75N and the HtrII transducer.
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Biophys J,
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Crystal structure of the Anabaena sensory rhodopsin transducer.
|
| |
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M.Dhage,
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and
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(2006).
Transmembrane helix-helix association: relative stabilities at low pH.
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| |
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E.N.Spudich,
V.D.Trivedi,
and
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(2006).
Role of the cytoplasmic domain in Anabaena sensory rhodopsin photocycling: vectoriality of Schiff base deprotonation.
|
| |
Biophys J,
91,
4519-4527.
|
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and
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(2006).
Development of the signal in sensory rhodopsin and its transfer to the cognate transducer.
|
| |
Nature,
440,
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|
|
|
PDB codes:
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Y.Sudo,
and
J.L.Spudich
(2006).
Three strategically placed hydrogen-bonding residues convert a proton pump into a sensory receptor.
|
| |
Proc Natl Acad Sci U S A,
103,
16129-16134.
|
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Y.Sudo,
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H.Kandori,
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(2006).
Functional importance of the interhelical hydrogen bond between Thr204 and Tyr174 of sensory rhodopsin II and its alteration during the signaling process.
|
| |
J Biol Chem,
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Biophys J,
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The hydroxylamine reaction of sensory rhodopsin II: light-induced conformational alterations with C13=C14 nonisomerizable pigment.
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Biophys J,
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Photoactivation perturbs the membrane-embedded contacts between sensory rhodopsin II and its transducer.
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The cytoplasmic membrane-proximal domain of the HtrII transducer interacts with the E-F loop of photoactivated Natronomonas pharaonis sensory rhodopsin II.
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PDB code:
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The most recent references are shown first.
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Where a reference describes a PDB structure, the PDB
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