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PDBsum entry 1bac
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Photoreceptor
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PDB id
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1bac
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References listed in PDB file
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Key reference
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Title
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An energy-Based approach to packing the 7-Helix bundle of bacteriorhodopsin.
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Authors
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K.C.Chou,
L.Carlacci,
G.M.Maggiora,
L.A.Parodi,
M.W.Schulz.
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Ref.
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Protein Sci, 1992,
1,
810-827.
[DOI no: ]
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PubMed id
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Abstract
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Based on the heavy-atom coordinates determined by the electron microscopy for
the seven main helical regions of bacteriorhodopsin with the all-trans retinal
isomer, energy optimizations were carried out for helix bundles containing the
all-trans retinal and 13-cis retinal chromophores, respectively. A combination
of simulated annealing and energy minimization was utilized during the process
of energy optimization. It was found that the 7-helix bundle containing the
all-trans isomer is about 10 kcal/mol lower in conformational energy than that
containing the 13-cis isomer. An energetic analysis indicates that such a
difference in energy is consistent with the observation that absorption of a
570-nm proton is required for the conversion of a bacteriorhodopsin from its
all-trans to 13-cis form. It was also found that the above conversion process is
accompanied by a significant conformational perturbation around the chromophore,
as reflected by the fact that the beta-ionone ring of retinal moves about 5.6 A
along the direction perpendicular to the membrane plane. This is consistent with
the observation by Fodor et al. (Fodor, S.P.A., Ames, J.B., Gebhard, R., van der
Berg, E.M.M., Stoeckenius, W., Lugtenburg, J., & Mathies, R.A., 1988,
Biochemistry 27, 7097-7101). Furthermore, it is interesting to observe that
although the retinal chromophore undergoes a significant change in its spatial
position, the orientation of its transition dipole changes only slightly, in
accord with experimental observations. In other words, even though orientation
of the retinal transition dipole is very restricted, there is sufficient room,
and degrees of freedom, for the retinal chromophore to readjust its position
considerably. This finding provides new insight into the subtle change of the
retinal microenvironment, which may be important for revealing the
proton-pumping mechanism of bacteriorhodopsin. The importance of electrostatic
and nonbonded interactions in stabilizing the 7-helix bundle structure has also
been analyzed. Electrostatic interactions favor an antiparallel arrangement
among adjacent helices. Nonbonded interactions, however, drive most of the
closely packed helices into an arrangement in which the packing angles lie
around -160 degrees, a value very near the -154 degrees value computed earlier
as the most favorable packing arrangement of two poly(Ala) alpha-helices (Chou,
K.-C., Némethy, G., & Scheraga, H.A., 1983, J. Phys. Chem. 87, 2869-2881).
The structural features of the 7-helix bundle and their relationship to those
found in typical 4-helix bundle proteins are also discussed.(ABSTRACT TRUNCATED
AT 400 WORDS)
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Secondary reference #1
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Title
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Geometric and energy parameters in lysine-Retinal chromophores.
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Authors
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L.Carlacci,
M.W.Schulz,
K.C.Chou.
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Ref.
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Protein Eng, 1991,
4,
885-889.
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PubMed id
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Secondary reference #2
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Title
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Model for the structure of bacteriorhodopsin based on high-Resolution electron cryo-Microscopy.
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Authors
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R.Henderson,
J.M.Baldwin,
T.A.Ceska,
F.Zemlin,
E.Beckmann,
K.H.Downing.
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Ref.
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J Mol Biol, 1990,
213,
899-929.
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PubMed id
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Secondary reference #3
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Title
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Energetic approach to the packing of alpha-Helices. 2. General treatment of nonequivalent and nonregular helices
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Authors
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K.-C.Chou,
G.Nemethy,
H.A.Scheraga.
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Ref.
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j am chem soc, 1984,
106,
3161.
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