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PDBsum entry 1fsd
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Novel sequence
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PDB id
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1fsd
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DOI no:
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Science
278:82-87
(1997)
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PubMed id:
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De novo protein design: fully automated sequence selection.
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B.I.Dahiyat,
S.L.Mayo.
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ABSTRACT
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The first fully automated design and experimental validation of a novel sequence
for an entire protein is described. A computational design algorithm based on
physical chemical potential functions and stereochemical constraints was used to
screen a combinatorial library of 1.9 x 10(27) possible amino acid sequences for
compatibility with the design target, a betabetaalpha protein motif based on the
polypeptide backbone structure of a zinc finger domain. A BLAST search shows
that the designed sequence, full sequence design 1 (FSD-1), has very low
identity to any known protein sequence. The solution structure of FSD-1 was
solved by nuclear magnetic resonance spectroscopy and indicates that FSD-1 forms
a compact well-ordered structure, which is in excellent agreement with the
design target structure. This result demonstrates that computational methods can
perform the immense combinatorial search required for protein design, and it
suggests that an unbiased and quantitative algorithm can be used in various
structural contexts.
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Selected figure(s)
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Figure 2.
Fig. 2. Comparison of Zif268 (9) and computed FSD-1
structures. (A) Stereoview of the second zinc finger module of
Zif268^ showing its buried residues and zinc binding site. (B)
Stereoview of the computed orientations of buried side chains in
FSD-1. For clarity, only side chains from residues 3, 5, 8, 12,
18, 21, 22, and 25 are shown. Color figures were created with
MOLMOL (38).
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Figure 6.
Fig. 6. Comparison of the FSD-1 structure (blue) and the
design target (red). Stereoview of the best-fit superposition of
the restrained^ energy minimized average NMR structure of FSD-1
and the backbone^ of Zif268. Residues 3 to 26 are shown.
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The above figures are
reprinted
by permission from the AAAs:
Science
(1997,
278,
82-87)
copyright 1997.
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Figures were
selected
by an automated process.
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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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PDB codes:
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A.Bazzoli,
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C.Y.Chen,
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J Chem Phys,
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PDB code:
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J.J.Havranek,
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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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