Dynamic assembly of protein disulfide isomerase in catalysis of oxidative folding

Okumura, Masaki; Noi, Kentaro; Kanemura, Shingo; Kinoshita, Misaki; Saio, Tomohide; Inoue, Yuichi; Hikima, Takaaki; Akiyama, Shuji; Ogura, Teru; Inaba, Kenji

doi:10.1038/s41589-019-0268-8

Cited by 72 publications

(87 citation statements)

References 49 publications

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“…However, the mode of interaction must still be precise to position cysteines and satisfy the steric requirements for thiol-disulfide exchange to occur [5]. Molecular dynamics simulations and single-molecule studies showed that the catalytic domains of PDI are flexible, which helps to achieve such interactions in structurally diverse substrates [69,70]. When considering the mode of PDI-substrate interaction, it is also important to take into account the accessibility of cysteines in the substrate.…”

Section: Pdi Preferentially Interacts With Unfolded Substrates To Catmentioning

confidence: 99%

Mechanisms of Disulfide Bond Formation in Nascent Polypeptides Entering the Secretory Pathway

Robinson

Bulleid

2020

Cells

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Disulfide bonds are an abundant feature of proteins across all domains of life that are important for structure, stability, and function. In eukaryotic cells, a major site of disulfide bond formation is the endoplasmic reticulum (ER). How cysteines correctly pair during polypeptide folding to form the native disulfide bond pattern is a complex problem that is not fully understood. In this paper, the evidence for different folding mechanisms involved in ER-localised disulfide bond formation is reviewed with emphasis on events that occur during ER entry. Disulfide formation in nascent polypeptides is discussed with focus on (i) its mechanistic relationship with conformational folding, (ii) evidence for its occurrence at the co-translational stage during ER entry, and (iii) the role of protein disulfide isomerase (PDI) family members. This review highlights the complex array of cellular processes that influence disulfide bond formation and identifies key questions that need to be addressed to further understand this fundamental process.

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Section: Pdi Preferentially Interacts With Unfolded Substrates To Catmentioning

confidence: 99%

Mechanisms of Disulfide Bond Formation in Nascent Polypeptides Entering the Secretory Pathway

Robinson

Bulleid

2020

Cells

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“…[26] Protein disulfide isomerase (PDI) is an oxidoreductase family located at ER lumen, assisting protein folding through the catalytic thiol-disulfide exchange reactions. [27] PDIA3 (also ERp57) is amember of PDI family and mediates numerous functions in the cell. [28] It plays important roles as akey molecular player in the quality control of newly synthesized glycoproteins and ar equired component of the peptide loading complex of major histocompatibility complex (MHC) class Im olecules.N umerous human diseases such as cancer, prion disorders,Alzheimersdisease and hepatitis are linked to expression or functions of PDIA3.…”

Section: Resultsmentioning

confidence: 99%

A Gallium(III) Complex that Engages Protein Disulfide Isomerase A3 (PDIA3) as an Anticancer Target

et al. 2020

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Gallium(III)-based drugs have gained momentum in cancer therapyd ue to their iron-dependent anticancer activity.J udicious choice of ligands is critical for improved oral bioavailability,a ntitumor efficacy,a nd distinct mechanisms from simple Ga III salts.Wedescribe Ga III complexes with planar tetradentate salen ligands [salen = 2,3-bis[(4-dialkylamino-2-hydroxybenzylidene)amino]but-2-enedinitrile)] and labile axial solvent ligands,w hich displayt umor growth inhibition in vitro and in vivo comparable to cisplatin. Confocal fluorescence microscopy, western blotting,mRNAprofiling, chemicalp roteomics,a nd surface plasmon resonance (SPR) studies provide compelling evidence that PDIA3, am ember of the protein disulfide isomerase (PDI) family involved in endoplasmic reticulum (ER) stress,isadirect target of Ga-1.T his work offers an ew route to designing and synthesizing Ga-based drugs,and also reveals that PDIA3 is an important anticancer target.

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“…Alternatively, they could enable fast crossing between two "energetically frustrated" enzyme conformations with different catalytic activities (47,48) The discovery that the reduction of PDI redistributes its conformational landscape towards the open ensemble raises important questions as to the molecular mechanism by which PDI couples the chemistry of the active sites with changes in its conformation and how the signal is propagated throughout the molecule. A recent study showed that mutation of the catalytic cysteine residues with alanine mimics the reduced form (24), suggesting that disulfide bonds stabilize the oxidized state. Another study showed that catalytically inactive PDI in which the catalytic cysteine residues were mutated to serine retained chaperone activity similar to oxidized PDI but different from reduced PDI (40).…”

Section: Pdi's Conformational Dynamics Explain Als-linked Loss Of Funmentioning

confidence: 99%

“…Over the past two decades, structural, computational, and biophysical studies have documented large-scale redox-dependent conformational changes in the human enzyme and orthologs (16,(20)(21)(22)(23)(24). experiments, although ideal, are greatly complicated by the relatively large size of PDI (i.e., 58 kDa).…”

Section: Introductionmentioning

confidence: 99%

Reduction of protein disulfide isomerase results in open conformations and stimulates dynamic exchange between structural ensembles

Chinnaraj

Flaumenhaft²,

Pozzi

2020

Preprint

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Cysteine residues provide enzymes involved in signaling and metabolism with an allosteric mechanism to quickly respond to changes in the surrounding redox environment. Yet how thiol modifications impact enzyme structure and dynamics is poorly understood. Here, we apply single-molecule Förster resonance energy transfer (smFRET) to study redox-dependent conformational dynamics of a highly flexible oxidoreductase, protein disulfide isomerase (PDI), in solution. We demonstrate that PDI toggles in the millisecond timescale between two major conformational ensembles, “open” and “closed”, that differ ∼20Å in length due to relocation of the two catalytic domains, whose equilibrium distribution is modulated by the redox state. While reduced PDI predominantly populates the open ensemble, oxidized PDI visits both ensembles with similar probability. We provide evidence that i) transition from the open to the closed ensemble requires loss of free thiols, not disulfide bonding, as previously thought, and ii) exposure to small molecules that alkylate the catalytic cysteines and mutation of cysteines in the N-terminal active site shift PDI to the closed conformation. Finally, using mutational and kinetic analyses, we show that the fraction of open ensemble at equilibrium positively correlates with the reductase activity of PDI. This work forms the basis of a new dynamic mechanism of PDI regulation by a cysteine-based redox switch in which thiol-controlled equilibrium distribution of the open/closed ensembles dictates function.

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Dynamic assembly of protein disulfide isomerase in catalysis of oxidative folding

Cited by 72 publications

References 49 publications

Mechanisms of Disulfide Bond Formation in Nascent Polypeptides Entering the Secretory Pathway

Mechanisms of Disulfide Bond Formation in Nascent Polypeptides Entering the Secretory Pathway

A Gallium(III) Complex that Engages Protein Disulfide Isomerase A3 (PDIA3) as an Anticancer Target

Reduction of protein disulfide isomerase results in open conformations and stimulates dynamic exchange between structural ensembles

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