The role of the backbone torsion in protein folding

Background: The set of forces and sequence of events that govern the transition from an unfolded polypeptide chain to a functional protein with correct spatial structure remain incompletely known, despite the importance of the problem and decades of theory development, computer simulations, and laboratory experiments. Information about the correctly folded state of most proteins is likely to be present in their sequences, and yet many proteins fail to attain native structure after overexpression in a non-native environment or upon experimental denaturation and refolding. Presentation of the hypothesis: We hypothesize that correct protein folding in vivo is an active, energy-dependent process that most likely applies torque force co-translationally to all proteins and possibly also post-translationally to many proteins in every cell. When a site on an unfolded polypeptide is rotationally constrained, torsion applied at another site would induce twisting of the main chain, which would initiate the formation of a local secondary structure, such as an alpha-helical turn or a beta-turn/beta-hairpin. The nucleation of structural elements is a rate-limiting, energetically unfavorable step in the process of protein folding, and energy-dependent chain torsion is likely to help overcome this barrier in vivo. Several molecular machines in a cell, primarily ribosomes, but also possibly signal recognition particles and chaperone systems, may play a role in applying torque to an unfolded protein chain, using the energy of GTP or ATP hydrolysis. Lack of such force in the in vitro systems may be the main reason of the failure of many longer proteins to attain the correct functional conformation. Testing the hypothesis: The hypothesis can be tested using single-molecule approaches, by measuring directly the forces applied to polypeptide chains under controlled conditions in vitro, and in bulk, by assessing folding rates and extent of misfolding in proteins that are engineered to experience transient spatial constraint during their synthesis. Implications of the hypothesis: Learning about the role of main chain torsion in protein folding will improve our understanding of folding mechanisms and may lead to bioengineering solutions that would enhance the yields of correctly folded proteins in heterologous expression systems.