Evolutionary bridges to new protein folds: design of C-terminal Cro protein chameleon sequences

Regions of amino-acid sequence that are compatible with multiple folds may facilitate evolutionary transitions in protein structure. In a previous study, we described a heuristically designed chameleon sequence (SASF1, structurally ambivalent sequence fragment 1) that could adopt either of two naturally occurring conformations (-helical or -sheet) when incorporated as part of the C-terminal dimerization subdomain of two structurally divergent transcription factors, P22 Cro and Cro. Here we describe longer chameleon designs (SASF2 and SASF3) that in the case of SASF3 correspond to the full C-terminal half of the ordered region of a P22 Cro/ Cro sequence alignment (residues 3457). P22-SASF2 and (WDD)-SASF2 show moderate thermal stability in denaturation curves monitored by circular dichroism (T(m) values of 46 and 55C, respectively), while P22-SASF3 and (WDD)-SASF3 have somewhat reduced stability (T(m) values of 33 and 49C, respectively). (13)C and (1)H NMR secondary chemical shift analysis confirms two C-terminal -helices for P22-SASF2 (residues 3645 and 5457) and two C-terminal -strands for (WDD)-SASF2 (residues 4045 and 5052), corresponding to secondary structure locations in the two parent sequences. Backbone relaxation data show that both chameleon sequences have a relatively well-ordered structure. Comparisons of (15)N-(1)H correlation spectra for SASF2 and SASF3-containing proteins strongly suggest that SASF3 retains the chameleonism of SASF2. Both Cro C-terminal conformations can be encoded in a single sequence, showing the plausibility of linking different Cro folds by smooth evolutionary transitions. The N-terminal subdomain, though largely conserved in structure, also exerts an important contextual influence on the structure of the C-terminal region.