From phenotype to protein folding: Characterization of the allele-dependent genetic interactions between chaperonin and co-chaperonin alleles

Chaperonin and cochaperonin proteins function together in the folding of protein substrates in vivo. Many mutant chaperonin and cochaperonin alleles from bacteria and bacteriophage can be categorized into one of two classes based on their in vivo compatibility with other cochaperonin and chaperonin alleles. These two allele classes are predicted to code for cochaperonin or chaperonin proteins that bind either too tightly or too weakly to their partner proteins. The "groEL44" class is assigned to alleles that code for chaperonins/cochaperonins that bind too weakly; and the "groEL515" class corresponds to chaperonins/cochaperonins that bind too strongly. By definition, alleles from the same class are not compatible with each other in vivo, while alleles from opposite classes are compatible. These predictions of chaperonin binding affinity have primarily served to explain phenotypic dichotomy, but have had very little supporting biophysical evidence at the protein level. The work presented here corroborates the hypothesis, and more precisely defines what "tight" and "weak" mean in the context of cochaperonin-chaperonin binding. Also, the importance of moderation in the cochaperonin-chaperonin protein interaction is demonstrated.; The interaction between chaperonins and cochaperonins is facilitated by flexible and structurally disordered mobile loops found in all cochaperonin proteins. These loops undergo a folding transition concomitant to cochaperonin-chaperonin binding. The folding transition and structural character of these loops are integral to the functional binding interaction between cochaperonin and chaperonin proteins. In order to better understand the contributions of mobile-loop folding towards the interaction between cochaperonins and cochaperonins, the structure, dynamics and folding of the mobile loop of the Escherichia coli cochaperonin GroES have been characterized using NMR spectroscopy and other techniques. Furthermore, a specific beta-hairpin conformation of the GroES mobile loop is characterized and proposed to be significant to the interaction between GroES and the chaperonin GroEL. Moreover, the folding propensity and structural stabilization of cochaperonin mobile loops can dictate the strength of the interaction between cochaperonins and chaperonins.; This study attempts to characterize a phenotypic phenomenon and then explain it at the mechanistic level of protein interaction, and then ultimately reveal how this protein interaction depends on folding transitions within the proteins.