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The folding cooperativity of a protein is controlled by its chain topology

2010; Nature Portfolio; Volume: 465; Issue: 7298 Linguagem: Inglês

10.1038/nature09021

1476-4687

Elizabeth A. Shank, Ciro Cecconi, Jesse Dill, Susan Marqusee, Carlos Bustamante,

RNA and protein synthesis mechanisms

Protein molecules often include domains that can be distinguished as relatively separate regions in their three-dimensional structure, but how such domains communicate during folding or enzymatic function is largely unclear. Shank et al. have now developed a new technology to study this using single-molecule optical tweezers acting via DNA 'handles' to pull on a protein from different directions while monitoring the energetics of unfolding and refolding events in regions away from those submitted to mechanical forces. Comparing topological variants of a protein — the two-domain protein T4 lysozyme that is a familiar model for folding studies — they then derive new rules of cooperation between sub-domains and suggest how evolution may select reshuffled gene topologies that bypass folding dead-ends. Proteins often comprise domains that can be distinguished as relatively separate regions in the three-dimensional structure. Communication between these domains is important for catalysis, regulation and folding, but how they communicate is largely unclear. Here, single-molecule optical tweezers were used to pull on a protein while monitoring the energetics of unfolding and refolding events in disparate regions. By comparing topological variations of the same protein, new rules of cooperation between domains were derived. The three-dimensional structures of proteins often show a modular architecture comprised of discrete structural regions or domains. Cooperative communication between these regions is important for catalysis, regulation and efficient folding; lack of coupling has been implicated in the formation of fibrils and other misfolding pathologies1. How different structural regions of a protein communicate and contribute to a protein’s overall energetics and folding, however, is still poorly understood. Here we use a single-molecule optical tweezers approach to induce the selective unfolding of particular regions of T4 lysozyme and monitor the effect on other regions not directly acted on by force. We investigate how the topological organization of a protein (the order of structural elements along the sequence) affects the coupling and folding cooperativity between its domains. To probe the status of the regions not directly subjected to force, we determine the free energy changes during mechanical unfolding using Crooks’ fluctuation theorem. We pull on topological variants (circular permutants) and find that the topological organization of the polypeptide chain critically determines the folding cooperativity between domains and thus what parts of the folding/unfolding landscape are explored. We speculate that proteins may have evolved to select certain topologies that increase coupling between regions to avoid areas of the landscape that lead to kinetic trapping and misfolding.