PDBsum entry 1acp

Fatty acid synthesis protein

PDB id: 1acp

Contents

Protein chain

77 a.a.

References listed in PDB file

Key reference

• Title: Refinement of the nmr structures for acyl carrier protein with scalar coupling data.
• Authors: Y.Kim, J.H.Prestegard.
• Ref.: Proteins, 1990, 8, 377-385.
• PubMed id: 2091027

Abstract

Structure determination of small proteins using NMR data is most commonly pursued by combining NOE derived distance constraints with inherent constraints based on chemical bonding. Ideally, one would make use of a variety of experimental observations, not just distance constraints. Here, coupling constant constraints have been added to molecular mechanics and molecular dynamics protocols for structure determination in the form of a psuedoenergy function that is minimized in a search for an optimum molecular conformation. Application is made to refinement of a structure for a 77 amino acid protein involved in fatty acid synthesis, Escherichia coli acyl carrier protein (ACP). 54 3JHN alpha coupling constants, 12 coupling constants for stereospecifically assigned side chain protons, and 450 NOE distance constraints were used to calculate the 3-D structure of ACP. A three-step protocol for a molecular dynamics calculation is described, in analogy to the protocol previously used in molecular mechanics calculations. The structures calculated with the molecular mechanics approach and the molecular dynamics approach using a rigid model for the protein show similar molecular energies and similar agreement with experimental distance and coupling constant constraints. The molecular dynamics approach shows some advantage in overcoming local minimum problems, but only when a two-state averaging model for the protein was used, did molecular energies drop significantly.

Secondary reference #1

• Title: A dynamic model for the structure of acyl carrier protein in solution.
• Authors: Y.Kim, J.H.Prestegard.
• Ref.: Biochemistry, 1989, 28, 8792-8797. [DOI no: 10.1021/bi00448a017]
• PubMed id: 2690950

Secondary reference #2

• Title: Three-Dimensional structure of acyl carrier protein determined by nmr pseudoenergy and distance geometry calculations.
• Authors: T.A.Holak, S.K.Kearsley, Y.Kim, J.H.Prestegard.
• Ref.: Biochemistry, 1988, 27, 6135-6142. [DOI no: 10.1021/bi00416a046]
• PubMed id: 3056520