Cooperative Folding Units of Escherichia coli Tryptophan Repressor

Abstract

A previously published computational procedure was used to identify cooperative folding units within tryptophan repressor. The theoretical results predict the existence of distinct stable substructures in the protein chain for the monomer and the dimer. The predictions were compared with experimental data on structure and folding of the repressor and its proteolytic fragments and show excellent agreement for the dimeric form of the protein. The results suggest that the monomer, the structure of which is currently unknown, is likely to have a structure different from the one it has within the context of the highly intertwined dimer. Application of this method to the repressor monomer represents an extension of the computations into the realm of evaluating hypothetical structures such as those produced by threading.

Absence of kinetic thermal stabilization in a hyperthermophile rubredoxin indicated by 40 microsecond folding in the presence of irreversible denaturation

“…Their T m values in the absence of denaturant differ by 39.5°C, which, when compared to the 63°C differential in the optimal growth temperatures of the host organisms, yields a quite typical ratio of 0.63. The hydrogen exchange analysis of Pf rubredoxin10 has been widely cited as demonstrating a multi‐state unfolding process in this hyperthermophile protein 55–66. The present results demonstrate that these hydrogen exchange data are consistent with two‐state folding behavior, indicating that Pf rubredoxin is comparatively ‘normal’ in this regard.…”

E. coli trp Repressor Forms a Domain-Swapped Array in Aqueous Alcohol

“…Dimeric trpR possesses these elements in duplicate. The ds-trpR structure presented here, together with complementary results on the trpR dimer from NMR (Zhao et al, 1993), proteolytic analysis (Carey, 1989), fragment reassembly (Tasayco and Carey, 1992), computational studies (Wallqvist et al, 1999), and crystal structure comparisons of the trpR dimer all support a four-subdomain structural organization for the protein (shown schematically in Fig. 3b), and indicate that the linker is dispensable for folding.…”

An ambiguity principle for assigning protein structural domains

“…Although the best partitioning solution provided by SWORD for this structure is also a one-domain assignment, our algorithm produces two alternative decompositions (Fig. 3X) identifying two domains (in blue and magenta), which have been shown to fold, or partially fold, in an independent manner ( 30 , 31 ). …”