Mjm. Burgering et al., HYDROGEN-EXCHANGE STUDIES OF THE ARC REPRESSOR - EVIDENCE FOR A MONOMERIC FOLDING INTERMEDIATE, Biopolymers, 35(2), 1995, pp. 217-226
The hydrogen exchange rates of the backbone amide and labile side-chai
n protons of the dimeric Arc repressor have been measured. For the slo
wly exchanging amides in the alpha-helical regions, these rates show a
concentration dependence. To account for this dependence, the role of
the monomer-dimer equilibrium was considered. Extrapolating the obser
ved exchange rates to zero dimer concentration provides estimates of t
hese rates in the monomer and shows that they are significantly retard
ed compared to those of an unfolded polypeptide. This suggests that th
e monomer is in a structured ''molten globule'' like state. In particu
lar, the two helices of Arc retain a high degree of their secondary st
ructure and it is proposed that the two amphiphilic helices are packed
together with their hydrophobic faces. Evidence for a partially folde
d structure in the Arc monomer was reported earlier in two other studi
es [J. L. Silva, C. F. Silveira, A. Correia, Jr., and L. Pontes (1992)
Journal of Molecular Biology, Vol. 223, pp. 545-555; X. Peng, J. Jona
s, and J. L. Silva (1993) Proceedings of the National Academy of Scien
ce USA, Vol. 90, pp. 1776-1780]. By combining the results of these stu
dies and ours, a folding pathway of the dimeric Arc repressor involvin
g four different stages is proposed. Due to the low concentration of A
rc repressor in the cell, the protein is present either as a free mono
mer or it is bound to DNA presumably as a tetramer. Therefore the fold
ing pathway can be regarded as an integral part of the overall DNA bin
ding process. (C) John Wiley & Sons, Inc.