Refined solution structures of the Escherichia coli trp holo- and aporepressor

Abstract

The solution structures of the trp-repressor from Escherichia coli in both the liganded (holo-) and unliganded (apo-) form, have been refined by restrained molecular dynamics with simulated annealing using the program XPLOR and additional experimental constraints. The ensemble of refined holorepressor structures have a root-mean-square deviation (r.m.s.d.) of 0.8 Å relative to the average structure for the backbone of the dimer core (helices A, B, C, A′, B′, C′) and 2.5 Å for the helix-turn-helix DNA-binding domain (helices D and E). The corresponding values for the aporepressor are 0.9 Å for the backbone of the ABC-dimer core and 3.2 Å for the DE helix-turn-helix. The r.m.s.d. of the average structures from the corresponding crystal structures are 2.3 Å for the holorepressor ABC core and 4.2 Å for its DE region; 2.3 Å for the aporepressor core and 5.5 Å for its DE region. The relative disorder of the DNA-binding domain is reflected in a number of experimental parameters including substantially more rapid backbone proton exchange rates, exchange-limited relaxation times and crystallographic B-factors. The stabilizing effect of the L-Trp ligand is evident in these measurements, as it is in the higher precision of the holorepressor structure. © 1993 Academic Press, Inc.