title: How Co-translational Folding of Multi-domain Protein Is Affected by Elongation Schedule: Molecular Simulations.
abstract: Co-translational folding (CTF) facilitates correct folding in vivo, but its precise mechanism remains elusive. For the CTF of a three-domain protein SufI, it was reported that the translational attenuation is obligatory to acquire the functional state. Here, to gain structural insights on the underlying mechanisms, we performed comparative molecular simulations of SufI that mimic CTF as well as refolding schemes. A CTF scheme that relied on a codon-based prediction of translational rates exhibited folding probability markedly higher than that by the refolding scheme. When the CTF schedule is speeded up, the success rate dropped. These agree with experiments. Structural investigation clarified that misfolding of the middle domain was much more frequent in the refolding scheme than that in the codon-based CTF scheme. The middle domain is less stable and can fold via interactions with the folded N-terminal domain. Folding pathway networks showed the codon-based CTF gives narrower pathways to the native state than the refolding scheme.
authors.affiliation: Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan.
authors.forename: Tomohiro
authors.initials: T
authors.lastname: Tanaka
authors.affiliation: Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan.
authors.forename: Naoto
authors.initials: N
authors.lastname: Hori
authors.affiliation: Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan.
authors.forename: Shoji
authors.initials: S
authors.lastname: Takada
mesh_terms: D055119:Elastic Modulus; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000235:genetics / Q000648:ultrastructure*; D008956:Models, Chemical; D056004:Molecular Dynamics Simulation; D010441:Peptide Chain Elongation, Translational / Q000235:genetics*; D011487:Protein Conformation; D017510:Protein Folding; D017434:Protein Structure, Tertiary
chemical_list: D029968:Escherichia coli Proteins; C473632:SufI protein, E coli