Three-dimensional structure of acyl carrier protein determined by NMR pseudoenergy and distance geometry calculations

Biochemistry. 1988 Aug 9;27(16):6135-42. doi: 10.1021/bi00416a046.

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.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Acyl Carrier Protein* / metabolism
  • Algorithms
  • Binding Sites
  • Escherichia coli / metabolism
  • Magnetic Resonance Spectroscopy
  • Models, Molecular
  • Protein Conformation
  • Thermodynamics

Substances

  • Acyl Carrier Protein