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Abstract: Recent single-molecule force measurements on single-domain proteins havehighlighted a three-state folding mechanism where a stabilized intermediatestate I is observed on the folding trajectory between the stretched state andthe native state. Here we investigate on-lattice protein-like heteropolymermodels that lead to a three-state mechanism and show that force experiments canbe useful to determine the structure of I. We have mostly found that I iscomposed of a core stabilized by a high number of native contacts, plus anunstructured extended chain. The lifetime of I is shown to be sensitive tomodifications of the protein that spoil the core. We then propose three typesof modifications-point mutations, cuts, and circular permutations-aiming at:1 confirming the presence of the core and 2 determining its location,within one amino acid accuracy, along the polypeptide chain. We also proposeforce jump protocols aiming to probe the on-off-pathway nature of I.



Author: Ivan Junier, Felix Ritort

Source: https://arxiv.org/







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