Three-dimensional structure of acyl carrier protein determined by NMR pseudoenergy and distance geometry calculations.
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.
Holak
T A
TA
Department of Chemistry, Yale University, New Haven, Connecticut 06511.
Kearsley
S K
SK
Kim
Y
Y
Prestegard
J H
JH
D000213:Acyl Carrier Protein / Q000378:metabolism; D000465:Algorithms; D001665:Binding Sites; D004926:Escherichia coli / Q000378:metabolism; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D011487:Protein Conformation; D013816:Thermodynamics
D000213:Acyl Carrier Protein