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Updated: Dec 1, 2025

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
Visualization of structural dynamics of protein disulfide isomerase enzymes in catalysis of oxidative folding and
Masaki Okumura1, Kentaro Noi2, Kenji Inaba3
1Frontier Research Institute for Interdisciplinary Sciences, Aramaki aza Aoba 6-3, Aoba-ku, Sendai 980-8578, Japan.
Abstract:
Time-resolved single-molecule observations by high-speed atomic force microscopy (HS-AFM), have greatly advanced our understanding of how proteins operate to fulfill their unique functions. Using this device, we succeeded in visualizing two members of the protein disulfide isomerase family (PDIs) that act to catalyze oxidative folding and reductive unfolding in the endoplasmic reticulum (ER). ERdj5, an ER-resident disulfide reductase that promotes ER-associated degradation, reduces nonnative disulfide bonds of misfolded proteins utilizing the dynamics of its N-terminal and C-terminal clusters. With unfolded substrates, canonical PDI assembles to form a face-to-face dimer with a central hydrophobic cavity and multiple redox-active sites to accelerate oxidative folding inside the cavity. Altogether, PDIs exert highly dynamic mechanisms to ensure the protein quality control in the ER.
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