STRUCTURAL HOMOLOGY OF SPINACH ACYL CARRIER PROTEIN AND ESCHERICHIA-COLI ACYL CARRIER PROTEIN-BASED ON NMR DATA

Acyl carrier proteins (ACPs) from spinach and from Escherichia coli ha ve been used to demonstrate the utility of proton NMR for comparison o f homologous structures. The structure of E. coli ACP had been previou sly determined and modeled as a rapid equilibrium among multiple confo rmational forms (Kim and Prestegard, Biochemistry 28:8792-8797, 1989). Spinach ACP showed two slowly exchanging forms and could be manipulat ed into one form for structural study. Here we compare this single for m to postulated multiple forms of E. coli ACP using the limited amount of NOE data available for the spinach protein. A number of long-range NOE contacts were present between homologous residues in both spinach and E. coli ACP, suggesting tertiary structural homology. To allow a more definitive structural comparison, a method was developed to use s pinach ACP NOE constraints to search for regions of structural diverge nce from two postulated forms of E. coli ACP, The homologous regions o f the two protein sequences were aligned, additional distance constrai nts were extracted from the E. coli structure, and these were mapped o nto the spinach sequence. These distance constraints were combined wit h experimental NOE constraints and a distance geometry simulated annea ling protocol was used to test for compatibility of the constraints. A ll of the experimental spinach NOE constraints could be successfully c ombined with the E. coli data, confirming the general hypothesis of st ructural homology. A better fit was obtained with one form, suggesting a preferential stabilization of that form in the spinach case, Protei ns 27:131-143 (C) 1997 Wiley-Liss, Inc.