The importance of surface loops for stabilizing an eightfold βα barrel protein

An important step in understanding how a protein folds is to determine those regions of the sequence that are critical to both its stability and its folding pathway. We chose phosphoribosyl anthranilate isomerase from Escherichia coli, which is a monomeric representative of the (βα)8 barrel family of proteins, to construct a variant that carries an internal tandem duplication of the fifth βα module. This (βα)9 variant was enzymically active and therefore must have a wild-type (βα)8 core. It had a choice a priori to fold to three different folding frames, which are distinguished by carrying the duplicated segment as an insert into one out of three different loops. Steady-state kinetic constants, the fluorescence properties of a crucial tryptophan residue, and limited proteolysis showed that the stable (βα)9 variant carries the insertion between β-strand 5 and α-helix 5. This preference can be explained by the important role of loops between α helices and β strands in stabilizing the structure of the enzyme.