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PDBsum entry 1idy
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DNA binding protein
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PDB id
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1idy
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Contents |
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* Residue conservation analysis
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Proc Natl Acad Sci U S A
93:13583-13588
(1996)
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PubMed id:
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A small engineered protein lacks structural uniqueness by increasing the side-chain conformational entropy.
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K.Furukawa,
M.Oda,
H.Nakamura.
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ABSTRACT
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A small globular protein, the third repeat of the c-Myb DNA-binding domain,
which is composed of 54 amino acid residues, was engineered so as to understand
the structural uniqueness of native proteins. This small protein has three
alpha-helices that form a helix-turn-helix structure, which is maintained by the
hydrophobic core with three Ile residues. One of the mutant proteins, with two
of the buried Ile (Ile-155 and Ile-181) substituted with Leu residues, showed
multiple conformations, as monitored by heteronuclear magnetic resonance
spectroscopy for 13C- and 15N-labeled proteins. The increase in the side-chain
conformational entropy, caused by changing the Ile to a Leu residue on an
alpha-helix, could engender the lack of structural uniqueness. In native
proteins, the conformations of not only the beta-branched side chains, but also
those of the neighboring bulky side chains, can be greatly restricted, depending
upon the local backbone structure.
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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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B.G.Wensley,
M.Gärtner,
W.X.Choo,
S.Batey,
and
J.Clarke
(2009).
Different members of a simple three-helix bundle protein family have very different folding rate constants and fold by different mechanisms.
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J Mol Biol,
390,
1074-1085.
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J.López de la Osa,
D.A.Bateman,
S.Ho,
C.González,
A.Chakrabartty,
and
D.V.Laurents
(2007).
Getting specificity from simplicity in putative proteins from the prebiotic earth.
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Proc Natl Acad Sci U S A,
104,
14941-14946.
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PDB codes:
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S.Gianni,
N.R.Guydosh,
F.Khan,
T.D.Caldas,
U.Mayor,
G.W.White,
M.L.DeMarco,
V.Daggett,
and
A.R.Fersht
(2003).
Unifying features in protein-folding mechanisms.
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Proc Natl Acad Sci U S A,
100,
13286-13291.
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S.Takada
(2001).
Protein folding simulation with solvent-induced force field: folding pathway ensemble of three-helix-bundle proteins.
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Proteins,
42,
85-98.
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O.V.Galzitskaya,
A.K.Surin,
and
H.Nakamura
(2000).
Optimal region of average side-chain entropy for fast protein folding.
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Protein Sci,
9,
580-586.
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Y.Isogai,
A.Ishii,
T.Fujisawa,
M.Ota,
and
K.Nishikawa
(2000).
Redesign of artificial globins: effects of residue replacements at hydrophobic sites on the structural properties.
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Biochemistry,
39,
5683-5690.
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Y.Isogai,
M.Ota,
T.Fujisawa,
H.Izuno,
M.Mukai,
H.Nakamura,
T.Iizuka,
and
K.Nishikawa
(1999).
Design and synthesis of a globin fold.
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Biochemistry,
38,
7431-7443.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
codes are
shown on the right.
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Links
