Protein Folding with a Little Help: Annealing Action of the Chaperonin Biological Nanomachine

George Stan

National Institutes of Health

Protein folding is the process through which an initially extended protein chain acquires its unique and stable native (biologically active) conformation. In the conformational free energy landscape description, protein folding translates into the search for a global minimum along a rough energy surface. Protein chains that are kinetically trapped into low energy minima (misfolded states) are rescued by chaperonin proteins. Chaperonins are biological nanomachines that employ a spectacular mechanism for simulated annealing. During the chaperonin cycle, concerted, large scale, rigid body conformational changes, ultimately driven by ATP hydrolysis, result in a dramatically expanded chaperonin cavity serving as folding chamber. Chaperonins repeatedly bind misfolded proteins, randomly disrupt their structure, and release them in less folded states, allowing these substrate proteins multiple opportunities to find pathways leading to the native state. Important questions related to the annealing function of GroEL, the most studied chaperonin molecule are: What is the fate of the non-native protein during the chaperonin cycle? What proteins are natural substrates for GroEL? What conformations of natural substrates are recognized by GroEL? Is there redundancy built into the chaperonin annealing mechanism? To address these questions, I used structural and bioinformatic techniques, as well as coarse-grained and all-atom molecular dynamics simulations. I will show that the fundamental annealing function of GroEL consists of forced unfolding and refolding of the substrate protein. The annealing action is related to the change in the nature of the interaction between the substrate protein and the GroEL particle from predominantly hydrophobic to largely hydrophilic. Natural GroEL substrates are those that contain patterns of residues similar to those in the co-chaperonin GroES mobile loop. GroEL recognizes non-native conformations of natural substrates with accessible binding regions. Molecular dynamics simulations of a peptide interacting with the apical domain fragment of GroEL show that the minimal annealing action is a transient binding and release of the substrate.