Three-dimensional structure of acyl carrier protein determined by NMR pseudoenergy and distance geometry calculations.
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Holak TA, Kearsley SK, Kim Y, Prestegard JH
Three-dimensional structure of acyl carrier protein determined by NMR pseudoenergy and distance geometry calculations.
Biochemistry. 1988 Aug 9;27(16):6135-42.
- PubMed ID
- 3056520 [ View in PubMed]
- Abstract
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.