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Title
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Three-dimensional structure of acyl carrier protein determined by NMR pseudoenergy and distance geometry calculations.
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Authors
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T.A.Holak,
S.K.Kearsley,
Y.Kim,
J.H.Prestegard.
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Ref.
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Biochemistry, 1988,
27,
6135-6142.
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PubMed id
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Abstract
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Distance constraints from two-dimensional NMR cross-relaxation data are used to
derive a three-dimensional structure for acyl carrier protein from Escherichia
coli. Several approaches to structure determination are explored. The most
successful proves to be an approach that combines the early stages of a distance
geometry program with energy minimization in the presence of NMR constraints
represented as pseudopotentials. Approximately 450 proton to proton distance
constraints including 50 long-range constraints were included in these programs.
Starting structures were generated at random by the distance geometry program
and energies minimized by a molecular mechanics module to give final structures.
Seven of the structures were deemed acceptable on the basis of agreement with
experimentally determined distances. Root-mean-square deviations from the mean
of these structures for backbone atoms range from 2 to 3 A. All structures show
three roughly parallel helices with hydrophobic residues facing inward and
hydrophilic residues facing outward. A hydrophobic cleft is recognizable and is
identified as a likely site for acyl chain binding.
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