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Melo EP, El-Guendouz S, Correia C, Teodoro F, Lopes C, Martel PJ. A Conformational-Dependent Interdomain Redox Relay at the Core of Protein Disulfide Isomerase Activity. Antioxid Redox Signal 2024; 41:181-200. [PMID: 38497737 DOI: 10.1089/ars.2023.0288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Aims: Protein disulfide isomerases (PDIs) are a family of chaperones resident in the endoplasmic reticulum (ER). In addition to holdase function, some members catalyze disulfide bond formation and isomerization, a crucial step for native folding and prevention of aggregation of misfolded proteins. PDIs are characterized by an arrangement of thioredoxin-like domains, with the canonical protein disulfide isomerase A1 (PDIA1) organized as four thioredoxin-like domains forming a horseshoe with two active sites, a and a', at the extremities. We aimed to clarify important aspects underlying the catalytic cycle of PDIA1 in the context of the full pathways of oxidative protein folding operating in the ER. Results: Using two fluorescent redox sensors, redox green fluorescent protein 2 (roGFP2) and HyPer (circularly permutated yellow fluorescent protein containing the regulatory domain of the H2O2-sensing protein OxyR), either unfolded or native, as client substrates, we identified the N-terminal a active site of PDIA1 as the main oxidant of thiols. From there, electrons can flow to the C-terminal a' active site, with the redox-dependent conformational flexibility of PDIA1 allowing the formation of an interdomain disulfide bond. The a' active site then acts as a crossing point to redirect electrons to ER downstream oxidases or back to client proteins to reduce scrambled disulfide bonds. Innovation and Conclusions: The two active sites of PDIA1 work cooperatively as an interdomain redox relay mechanism that explains PDIA1 oxidative activity to form native disulfides and PDIA1 reductase activity to resolve scrambled disulfides. This mechanism suggests a new rationale for shutting down oxidative protein folding under ER redox imbalance. Whether it applies to physiological substrates in cells remains to be shown.
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Affiliation(s)
- Eduardo P Melo
- Centro de Ciências do Mar (CCMAR), University of Algarve, Faro, Portugal
| | | | - Cátia Correia
- Centro de Ciências do Mar (CCMAR), University of Algarve, Faro, Portugal
| | - Fernando Teodoro
- Centro de Ciências do Mar (CCMAR), University of Algarve, Faro, Portugal
| | - Carlos Lopes
- Centro de Ciências do Mar (CCMAR), University of Algarve, Faro, Portugal
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2
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Vu TL, Nguyen TKO, Song JA, Chong S, Choe H. Enhanced prokaryotic expression, purification, and biological activities of human keratinocyte growth factor. J Biotechnol 2024; 386:42-51. [PMID: 38552676 DOI: 10.1016/j.jbiotec.2024.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 03/19/2024] [Accepted: 03/24/2024] [Indexed: 04/04/2024]
Abstract
Keratinocyte growth factor (KGF), also known as fibroblast growth factor 7 (FGF7), plays a critical role in embryonic development, cell proliferation, and differentiation. However, efficient production of recombinant KGF remains a challenge due to its low expression levels and high tendency for aggregation in Escherichia coli. This study aimed to enhance the expression and solubility of KGF by employing different protein tags-PDIb'a', MBP, and His-fused to the N-terminus of KGF. Among these, H-PDIb'a'-KGF demonstrated superior stability and was selected for large-scale production and purification. The purified KGF was confirmed through liquid chromatography with tandem mass spectrometry analysis, which showed an 81% fragment mass identification coverage. Biological activity assessments using human breast cancer MCF-7 cells indicated that purified KGF significantly increased cell proliferation, with an EC50 of 6.4 ± 0.5 pM. Interestingly, PDIb'a' alone also exhibited a stimulatory effect on MCF-7 cells. Furthermore, the purified KGF enhanced the wound healing of HaCaT keratinocytes in a dose-dependent manner. These findings provide valuable insights into the efficient production and functional characterization of recombinant KGF for potential applications in therapeutic interventions.
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Affiliation(s)
- Thi Luong Vu
- Department of Physiology, University of Ulsan College of Medicine, Asan Medical Center, Seoul 05505, South Korea
| | - Thi Kieu Oanh Nguyen
- Department of Physiology, University of Ulsan College of Medicine, Asan Medical Center, Seoul 05505, South Korea
| | - Jung-A Song
- Department of Physiology, University of Ulsan College of Medicine, Asan Medical Center, Seoul 05505, South Korea
| | - Seonha Chong
- Department of Physiology, University of Ulsan College of Medicine, Asan Medical Center, Seoul 05505, South Korea
| | - Han Choe
- Department of Physiology, University of Ulsan College of Medicine, Asan Medical Center, Seoul 05505, South Korea.
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3
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Yagi-Utsumi M, Miura H, Ganser C, Watanabe H, Hiranyakorn M, Satoh T, Uchihashi T, Kato K, Okazaki KI, Aoki K. Molecular Design of FRET Probes Based on Domain Rearrangement of Protein Disulfide Isomerase for Monitoring Intracellular Redox Status. Int J Mol Sci 2023; 24:12865. [PMID: 37629048 PMCID: PMC10454184 DOI: 10.3390/ijms241612865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/14/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
Multidomain proteins can exhibit sophisticated functions based on cooperative interactions and allosteric regulation through spatial rearrangements of the multiple domains. This study explored the potential of using multidomain proteins as a basis for Förster resonance energy transfer (FRET) biosensors, focusing on protein disulfide isomerase (PDI) as a representative example. PDI, a well-studied multidomain protein, undergoes redox-dependent conformational changes, enabling the exposure of a hydrophobic surface extending across the b' and a' domains that serves as the primary binding site for substrates. Taking advantage of the dynamic domain rearrangements of PDI, we developed FRET-based biosensors by fusing the b' and a' domains of thermophilic fungal PDI with fluorescent proteins as the FRET acceptor and donor, respectively. Both experimental and computational approaches were used to characterize FRET efficiency in different redox states. In vitro and in vivo evaluations demonstrated higher FRET efficiency of this biosensor in the oxidized form, reflecting the domain rearrangement and its responsiveness to intracellular redox environments. This novel approach of exploiting redox-dependent domain dynamics in multidomain proteins offers promising opportunities for designing innovative FRET-based biosensors with potential applications in studying cellular redox regulation and beyond.
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Affiliation(s)
- Maho Yagi-Utsumi
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki 444-8787, Japan
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki 444-8585, Japan
- The Graduate University for Advanced Studies, SOKENDAI, Okazaki 444-8787, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 465-8603, Japan
| | - Haruko Miura
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki 444-8787, Japan
- National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki 444-8787, Japan
| | - Christian Ganser
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki 444-8787, Japan
| | - Hiroki Watanabe
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki 444-8787, Japan
| | - Methanee Hiranyakorn
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki 444-8787, Japan
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki 444-8585, Japan
- The Graduate University for Advanced Studies, SOKENDAI, Okazaki 444-8787, Japan
| | - Tadashi Satoh
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 465-8603, Japan
| | - Takayuki Uchihashi
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki 444-8787, Japan
- Department of Physics, Nagoya University, Nagoya 464-8602, Japan
- Institute for Glyco-Core Research (iGCORE), Nagoya University, Nagoya 464-8601, Japan
| | - Koichi Kato
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki 444-8787, Japan
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki 444-8585, Japan
- The Graduate University for Advanced Studies, SOKENDAI, Okazaki 444-8787, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 465-8603, Japan
| | - Kei-ichi Okazaki
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki 444-8585, Japan
- The Graduate University for Advanced Studies, SOKENDAI, Okazaki 444-8787, Japan
| | - Kazuhiro Aoki
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki 444-8787, Japan
- The Graduate University for Advanced Studies, SOKENDAI, Okazaki 444-8787, Japan
- National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki 444-8787, Japan
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Chetot T, Serfaty X, Carret L, Kriznik A, Sophie-Rahuel-Clermont, Grand L, Jacolot M, Popowycz F, Benoit E, Lambert V, Lattard V. Splice variants of protein disulfide isomerase - identification, distribution and functional characterization in the rat. Biochim Biophys Acta Gen Subj 2023; 1867:130280. [PMID: 36423740 DOI: 10.1016/j.bbagen.2022.130280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 10/28/2022] [Accepted: 11/13/2022] [Indexed: 11/23/2022]
Abstract
BACKGROUND Protein Disulfide Isomerase (PDI) enzyme is an emerging therapeutic target in oncology and hematology. Although PDI reductase activity has been studied with isolated fragments of the protein, natural structural variations affecting reductase activity have not been addressed. METHODS In this study, we discovered four coding splice variants of the Pdi pre-mRNA in rats. In vitro Michaelis constants and apparent maximum steady-state rate constants after purification and distribution in different rat tissues were determined. RESULTS The consensus sequence was found to be the most expressed splice variant while the second most expressed variant represents 15 to 35% of total Pdi mRNA. The third variant shows a quasi-null expression profile and the fourth was not quantifiable. The consensus sequence splice variant and the second splice variant are widely expressed (transcription level) in the liver and even more present in males. Measurements of the reductase activity of recombinant PDI indicate that the consensus sequence and third splice variant are fully active variants. The second most expressed variant, differing by a lack of signal peptide, was found active but less than the consensus sequence. GENERAL SIGNIFICANCE Our work emphasizes the importance of taking splice variants into account when studying PDI-like proteins to understand the full biological functionalities of PDI.
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Affiliation(s)
- Thomas Chetot
- USC 1233 RS2GP, VetAgro Sup, INRAe, Université de Lyon, 69280 Marcy l'étoile, France
| | - Xavier Serfaty
- USC 1233 RS2GP, VetAgro Sup, INRAe, Université de Lyon, 69280 Marcy l'étoile, France
| | - Léna Carret
- USC 1233 RS2GP, VetAgro Sup, INRAe, Université de Lyon, 69280 Marcy l'étoile, France
| | | | | | - Lucie Grand
- Univ Lyon, INSA Lyon, Université Lyon 1, CNRS, CPE Lyon, UMR 5246, ICBMS, 69621 Villeurbanne Cedex, France
| | - Maïwenn Jacolot
- Univ Lyon, INSA Lyon, Université Lyon 1, CNRS, CPE Lyon, UMR 5246, ICBMS, 69621 Villeurbanne Cedex, France
| | - Florence Popowycz
- Univ Lyon, INSA Lyon, Université Lyon 1, CNRS, CPE Lyon, UMR 5246, ICBMS, 69621 Villeurbanne Cedex, France
| | - Etienne Benoit
- USC 1233 RS2GP, VetAgro Sup, INRAe, Université de Lyon, 69280 Marcy l'étoile, France
| | - Véronique Lambert
- USC 1233 RS2GP, VetAgro Sup, INRAe, Université de Lyon, 69280 Marcy l'étoile, France
| | - Virginie Lattard
- USC 1233 RS2GP, VetAgro Sup, INRAe, Université de Lyon, 69280 Marcy l'étoile, France.
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5
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Wang L, Wang CC. Oxidative protein folding fidelity and redoxtasis in the endoplasmic reticulum. Trends Biochem Sci 2023; 48:40-52. [PMID: 35871147 DOI: 10.1016/j.tibs.2022.06.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 06/16/2022] [Accepted: 06/29/2022] [Indexed: 02/09/2023]
Abstract
In eukaryotic cells, oxidative protein folding occurs in the lumen of the endoplasmic reticulum (ER), catalyzed by ER sulfhydryl oxidase 1 (Ero1) and protein disulfide isomerase (PDI). The efficiency and fidelity of oxidative protein folding are vital for the function of secretory cells. Here, we summarize oxidative protein folding in yeast, plants, and mammals, and discuss how the conformation and activity of human Ero1-PDI machinery is regulated through various post-translational modifications (PTMs). We propose that oxidative protein folding fidelity and ER redox homeostasis are maintained by both the precise control of Ero1 oxidase activity and the division of labor between PDI family members. We also discuss how deregulated Ero1-PDI functions contribute to human diseases and can be leveraged for therapeutic interventions.
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Affiliation(s)
- Lei Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Chih-Chen Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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6
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Crystal structure of the collagen prolyl 4-hydroxylase (C-P4H) catalytic domain complexed with PDI: Toward a model of the C-P4H α 2β 2 tetramer. J Biol Chem 2022; 298:102614. [PMID: 36265586 PMCID: PMC9676403 DOI: 10.1016/j.jbc.2022.102614] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 10/12/2022] [Accepted: 10/14/2022] [Indexed: 11/05/2022] Open
Abstract
Collagen prolyl 4-hydroxylases (C-P4H) are α2β2 tetramers, which catalyze the prolyl 4-hydroxylation of procollagen, allowing for the formation of the stable triple-helical collagen structure in the endoplasmic reticulum. The C-P4H α-subunit provides the N-terminal dimerization domain, the middle peptide-substrate-binding (PSB) domain, and the C-terminal catalytic (CAT) domain, whereas the β-subunit is identical to the enzyme protein disulfide isomerase (PDI). The structure of the N-terminal part of the α-subunit (N-terminal region and PSB domain) is known, but the structures of the PSB-CAT linker region and the CAT domain as well as its mode of assembly with the β/PDI subunit, are unknown. Here, we report the crystal structure of the CAT domain of human C-P4H-II complexed with the intact β/PDI subunit, at 3.8 Å resolution. The CAT domain interacts with the a, b', and a' domains of the β/PDI subunit, such that the CAT active site is facing bulk solvent. The structure also shows that the C-P4H-II CAT domain has a unique N-terminal extension, consisting of α-helices and a β-strand, which is the edge strand of its major antiparallel β-sheet. This extra region of the CAT domain interacts tightly with the β/PDI subunit, showing that the CAT-PDI interface includes an intersubunit disulfide bridge with the a' domain and tight hydrophobic interactions with the b' domain. Using this new information, the structure of the mature C-P4H-II α2β2 tetramer is predicted. The model suggests that the CAT active-site properties are modulated by α-helices of the N-terminal dimerization domains of both subunits of the α2-dimer.
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7
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Functions and mechanisms of protein disulfide isomerase family in cancer emergence. Cell Biosci 2022; 12:129. [PMID: 35965326 PMCID: PMC9375924 DOI: 10.1186/s13578-022-00868-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 08/03/2022] [Indexed: 11/13/2022] Open
Abstract
The endoplasmic reticulum (ER) is a multi-layered organelle that is essential for the synthesis, folding, and structural maturation of almost one-third of the cellular proteome. It houses several resident proteins for these functions including the 21 members of the protein disulfide isomerase (PDI) family. The signature of proteins belonging to this family is the presence of the thioredoxin domain which mediates the formation, and rearrangement of disulfide bonds of substrate proteins in the ER. This process is crucial not only for the proper folding of ER substrates but also for maintaining a balanced ER proteostasis. The inclusion of new PDI members with a wide variety of structural determinants, size and enzymatic activity has brought additional epitomes of how PDI functions. Notably, some of them do not carry the thioredoxin domain and others have roles outside the ER. This also reflects that PDIs may have specialized functions and their functions are not limited within the ER. Large-scale expression datasets of human clinical samples have identified that the expression of PDI members is elevated in pathophysiological states like cancer. Subsequent functional interrogations using structural, molecular, cellular, and animal models suggest that some PDI members support the survival, progression, and metastasis of several cancer types. Herein, we review recent research advances on PDIs, vis-à-vis their expression, functions, and molecular mechanisms in supporting cancer growth with special emphasis on the anterior gradient (AGR) subfamily. Last, we posit the relevance and therapeutic strategies in targeting the PDIs in cancer.
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8
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Liang C, Cai M, Xu Y, Fu W, Wu J, Liu Y, Liao X, Ning J, Li J, Huang M, Yuan C. Identification of Antithrombotic Natural Products Targeting the Major Substrate Binding Pocket of Protein Disulfide Isomerase. JOURNAL OF NATURAL PRODUCTS 2022; 85:1332-1339. [PMID: 35471830 DOI: 10.1021/acs.jnatprod.2c00080] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Protein disulfide isomerase (PDI) is a vital oxidoreductase. Extracellular PDI promotes thrombus formation but does not affect physiological blood hemostasis. Inhibition of extracellular PDI has been demonstrated as a promising strategy for antithrombotic treatment. Herein, we focused on the major substrate binding site, a unique pocket in the PDI b' domain, and identified four natural products binding to PDI by combining virtual screening with tryptophan fluorescence-based assays against a customized natural product library. These hits all directly bound to the PDI-b' domain and inhibited the reductase activity of PDI. Among them, galangin showed the most prominent potency (5.9 μM) against PDI and as a broad-spectrum inhibitor for vascular thiol isomerases. In vivo studies manifested that galangin delayed the time of blood vessel occlusion in an electricity-induced mouse thrombosis model. Molecular docking and dynamics simulation further revealed that the hydroxyl-substituted benzopyrone moiety of galangin deeply inserted into the interface between the PDI-b' substrate-binding pocket and the a' domain. Together, these findings provide a potential antithrombotic drug candidate and demonstrate that the PDI b' domain is a critical domain for inhibitor development. Besides, we also report an innovative high-throughput screening method for the rapid discovery of PDI b' targeted inhibitors.
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Affiliation(s)
- Chenghui Liang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, 350108, Fujian, China
| | - Meiqin Cai
- College of Chemistry, Fuzhou University, Fuzhou, 350108, Fujian, China
| | - Yanyan Xu
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, 350108, Fujian, China
| | - Wei Fu
- College of Chemistry, Fuzhou University, Fuzhou, 350108, Fujian, China
| | - Juhong Wu
- College of Chemistry, Fuzhou University, Fuzhou, 350108, Fujian, China
| | - Yurong Liu
- College of Chemistry, Fuzhou University, Fuzhou, 350108, Fujian, China
| | - Xinyuan Liao
- College of Chemistry, Fuzhou University, Fuzhou, 350108, Fujian, China
| | - Jiamin Ning
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, 350108, Fujian, China
| | - Jinyu Li
- College of Chemistry, Fuzhou University, Fuzhou, 350108, Fujian, China
| | - Mingdong Huang
- College of Chemistry, Fuzhou University, Fuzhou, 350108, Fujian, China
| | - Cai Yuan
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, 350108, Fujian, China
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Yang M, Flaumenhaft R. Oxidative Cysteine Modification of Thiol Isomerases in Thrombotic Disease: A Hypothesis. Antioxid Redox Signal 2021; 35:1134-1155. [PMID: 34121445 PMCID: PMC8817710 DOI: 10.1089/ars.2021.0108] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Significance: Oxidative stress is a characteristic of many systemic diseases associated with thrombosis. Thiol isomerases are a family of oxidoreductases important in protein folding and are exquisitely sensitive to the redox environment. They are essential for thrombus formation and represent a previously unrecognized layer of control of the thrombotic process. Yet, the mechanisms by which thiol isomerases function in thrombus formation are unknown. Recent Advances: The oxidoreductase activity of thiol isomerases in thrombus formation is controlled by the redox environment via oxidative changes to active site cysteines. Specific alterations can now be detected owing to advances in the chemical biology of oxidative cysteine modifications. Critical Issues: Understanding of the role of thiol isomerases in thrombus formation has focused largely on identifying single disulfide bond modifications in isolated proteins (e.g., αIIbβ3, tissue factor, vitronectin, or glycoprotein Ibα [GPIbα]). An alternative approach is to conceptualize thiol isomerases as effectors in redox signaling pathways that control thrombotic potential by modifying substrate networks. Future Directions: Cysteine-based chemical biology will be employed to study thiol-dependent dynamics mediated by the redox state of thiol isomerases at the systems level. This approach could identify thiol isomerase-dependent modifications of the disulfide landscape that are prothrombotic.
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Affiliation(s)
- Moua Yang
- Division of Hemostasis and Thrombosis, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
| | - Robert Flaumenhaft
- Division of Hemostasis and Thrombosis, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
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10
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Jha V, Kumari T, Manickam V, Assar Z, Olson KL, Min JK, Cho J. ERO1-PDI Redox Signaling in Health and Disease. Antioxid Redox Signal 2021; 35:1093-1115. [PMID: 34074138 PMCID: PMC8817699 DOI: 10.1089/ars.2021.0018] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Significance: Protein disulfide isomerase (PDI) and endoplasmic reticulum oxidoreductase 1 (ERO1) are crucial for oxidative protein folding in the endoplasmic reticulum (ER). These enzymes are frequently overexpressed and secreted, and they contribute to the pathology of neurodegenerative, cardiovascular, and metabolic diseases. Recent Advances: Tissue-specific knockout mouse models and pharmacologic inhibitors have been developed to advance our understanding of the cell-specific functions of PDI and ERO1. In addition to their roles in protecting cells from the unfolded protein response and oxidative stress, recent studies have revealed that PDI and ERO1 also function outside of the cells. Critical Issues: Despite the well-known contributions of PDI and ERO1 to specific disease pathology, the detailed molecular and cellular mechanisms underlying these activities remain to be elucidated. Further, although PDI and ERO1 inhibitors have been identified, the results from previous studies require careful evaluation, as many of these agents are not selective and may have significant cytotoxicity. Future Directions: The functions of PDI and ERO1 in the ER have been extensively studied. Additional studies will be required to define their functions outside the ER.
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Affiliation(s)
- Vishwanath Jha
- Division of Hematology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Tripti Kumari
- Division of Hematology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Vijayprakash Manickam
- Division of Hematology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Zahra Assar
- Cayman Chemical Company, Inc., Ann Arbor, Michigan, USA
| | - Kirk L Olson
- Cayman Chemical Company, Inc., Ann Arbor, Michigan, USA
| | - Jeong-Ki Min
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea.,Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon, Republic of Korea
| | - Jaehyung Cho
- Division of Hematology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA.,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
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11
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Pei Y, Liu X, Cheng K, Xu G, Jiang L, Li C. Backbone resonance assignment of PDI b'xa' domain construct. BIOMOLECULAR NMR ASSIGNMENTS 2021; 15:409-413. [PMID: 34169459 DOI: 10.1007/s12104-021-10038-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/17/2021] [Indexed: 06/13/2023]
Abstract
Human protein disulfide isomerase (PDI), a protein containing 4 domains a, b, b', a', disordered x linker and C-terminus, plays critical roles in disulfide bond reactions and proper protein folding in the endoplasmic reticulum. The bb' domain contributes to client binding, the a, a' domain catalyse the rearrangement of the disulfide bonds. The x linker and a' domain were the main dynamics region for full-length PDI and the b'xa' construct has the minimum functional domain within full-length PDI. Herein, we report a new preparation strategy with 1, 6-hexandiol and backbone NMR chemical shift assignments for the monomer b'xa' domain.
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Affiliation(s)
- Yunshan Pei
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China
- Graduate University of Chinese Academy of Science, Beijing, 100049, People's Republic of China
| | - Xiaoli Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China
| | - Kai Cheng
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China
| | - Guohua Xu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China
| | - Ling Jiang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China
| | - Conggang Li
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China.
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12
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Nguyen TKO, Vu TL, Nguyen MQ, Ta HKK, Park KS, Kim SH, Kim CJ, Jang YJ, Choe H. Soluble Prokaryotic Overexpression and Purification of Human GM-CSF Using the Protein Disulfide Isomerase b'a' Domain. Int J Mol Sci 2021; 22:ijms22105267. [PMID: 34067755 PMCID: PMC8156066 DOI: 10.3390/ijms22105267] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/06/2021] [Accepted: 05/15/2021] [Indexed: 12/30/2022] Open
Abstract
Granulocyte-macrophage colony-stimulating factor (GM-CSF) is a member of the colony-stimulating factor (CSF) family, which functions to enhance the proliferation and differentiation of hematopoietic stem cells and other hematopoietic lineages such as neutrophils, dendritic cells, or macrophages. These proteins have thus generated considerable interest in clinical therapy research. A current obstacle to the prokaryotic production of human GM-CSF (hGM-CSF) is its low solubility when overexpressed and subsequent complex refolding processes. In our present study, the solubility of hGM-CSF was examined when combined with three N-terminal fusion tags in five E. coli strains at three different expression temperatures. In the five E. coli strains BL21 (DE3), ClearColi BL21 (DE3), LOBSTR, SHuffle T7 and Origami2 (DE3), the hexahistidine-tagged hGM-CSF showed the best expression but was insoluble in all cases at each examined temperature. Tagging with the maltose-binding protein (MBP) and the b'a' domain of protein disulfide isomerase (PDIb'a') greatly improved the soluble overexpression of hGM-CSF at 30 °C and 18 °C. The solubility was not improved using the Origami2 (DE3) and SHuffle T7 strains that have been engineered for disulfide bond formation. Two conventional chromatographic steps were used to purify hGM-CSF from the overexpressed PDIb'a'-hGM-CSF produced in ClearColi BL21 (DE3). In the experiment, 0.65 mg of hGM-CSF was isolated from a 0.5 L flask culture of these E. coli and showed a 98% purity by SDS-PAGE analysis and silver staining. The bioactivity of this purified hGM-CSF was measured at an EC50 of 16.4 ± 2 pM by a CCK8 assay in TF-1 human erythroleukemia cells.
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Affiliation(s)
- Thi Kieu Oanh Nguyen
- Department of Physiology, Bio-Medical Institute of Technology, University of Ulsan College of Medicine, Asan Medical Center, Seoul 05505, Korea; (T.K.O.N.); (T.L.V.); (M.Q.N.); (H.K.K.T.); (Y.J.J.)
| | - Thi Luong Vu
- Department of Physiology, Bio-Medical Institute of Technology, University of Ulsan College of Medicine, Asan Medical Center, Seoul 05505, Korea; (T.K.O.N.); (T.L.V.); (M.Q.N.); (H.K.K.T.); (Y.J.J.)
| | - Minh Quan Nguyen
- Department of Physiology, Bio-Medical Institute of Technology, University of Ulsan College of Medicine, Asan Medical Center, Seoul 05505, Korea; (T.K.O.N.); (T.L.V.); (M.Q.N.); (H.K.K.T.); (Y.J.J.)
| | - Huynh Kim Khanh Ta
- Department of Physiology, Bio-Medical Institute of Technology, University of Ulsan College of Medicine, Asan Medical Center, Seoul 05505, Korea; (T.K.O.N.); (T.L.V.); (M.Q.N.); (H.K.K.T.); (Y.J.J.)
| | - Kyoung Sun Park
- Wide River Institute of Immunology, Seoul National University College of Medicine, Seoul 25159, Korea; (K.S.P.); (S.H.K.)
| | - Soo Hyeon Kim
- Wide River Institute of Immunology, Seoul National University College of Medicine, Seoul 25159, Korea; (K.S.P.); (S.H.K.)
| | - Chong Jai Kim
- Department of Pathology, Asan-Minnesota Institute for Innovating Transplantation, University of Ulsan College of Medicine, Asan Medical Center, Seoul 05505, Korea;
| | - Yeon Jin Jang
- Department of Physiology, Bio-Medical Institute of Technology, University of Ulsan College of Medicine, Asan Medical Center, Seoul 05505, Korea; (T.K.O.N.); (T.L.V.); (M.Q.N.); (H.K.K.T.); (Y.J.J.)
| | - Han Choe
- Department of Physiology, Bio-Medical Institute of Technology, University of Ulsan College of Medicine, Asan Medical Center, Seoul 05505, Korea; (T.K.O.N.); (T.L.V.); (M.Q.N.); (H.K.K.T.); (Y.J.J.)
- Correspondence: ; Tel.: +82-2-3010-4292
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13
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Hirayama C, Machida K, Noi K, Murakawa T, Okumura M, Ogura T, Imataka H, Inaba K. Distinct roles and actions of protein disulfide isomerase family enzymes in catalysis of nascent-chain disulfide bond formation. iScience 2021; 24:102296. [PMID: 33855279 PMCID: PMC8024706 DOI: 10.1016/j.isci.2021.102296] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 01/13/2021] [Accepted: 03/05/2021] [Indexed: 12/04/2022] Open
Abstract
The mammalian endoplasmic reticulum (ER) harbors more than 20 members of the protein disulfide isomerase (PDI) family that act to maintain proteostasis. Herein, we developed an in vitro system for directly monitoring PDI- or ERp46-catalyzed disulfide bond formation in ribosome-associated nascent chains of human serum albumin. The results indicated that ERp46 more efficiently introduced disulfide bonds into nascent chains with a short segment exposed outside the ribosome exit site than PDI. Single-molecule analysis by high-speed atomic force microscopy further revealed that PDI binds nascent chains persistently, forming a stable face-to-face homodimer, whereas ERp46 binds for a shorter time in monomeric form, indicating their different mechanisms for substrate recognition and disulfide bond introduction. Thus, ERp46 serves as a more potent disulfide introducer especially during the early stages of translation, whereas PDI can catalyze disulfide formation when longer nascent chains emerge out from ribosome. We developed an in vitro system for monitoring nascent-chain disulfide formation High-speed AFM visualized PDI and ERp46 molecules acting on nascent chains PDI persistently holds nascent chains via dimerization for disulfide introduction ERp46 rapidly introduces disulfide bonds to nascent chains via short-time binding
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Affiliation(s)
- Chihiro Hirayama
- Institute of Multidisciplinary Research for Advanced Materials, Katahira 2-1-1, Aoba-ku, Tohoku University, Sendai, Miyagi 980-8577, Japan
| | - Kodai Machida
- Graduate School of Engineering, University of Hyogo, Himeji, Hyogo 671-2280, Japan
| | - Kentaro Noi
- Institute for NanoScience Design, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Tadayoshi Murakawa
- Graduate School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa, 226-8503, Japan
| | - Masaki Okumura
- Institute of Multidisciplinary Research for Advanced Materials, Katahira 2-1-1, Aoba-ku, Tohoku University, Sendai, Miyagi 980-8577, Japan.,Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Teru Ogura
- Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Kumamoto 860-0811, Japan.,Faculty of Life Sciences, Kumamoto University, Kumamoto, Kumamoto 862-0973, Japan
| | - Hiroaki Imataka
- Graduate School of Engineering, University of Hyogo, Himeji, Hyogo 671-2280, Japan
| | - Kenji Inaba
- Institute of Multidisciplinary Research for Advanced Materials, Katahira 2-1-1, Aoba-ku, Tohoku University, Sendai, Miyagi 980-8577, Japan
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14
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PDI-Regulated Disulfide Bond Formation in Protein Folding and Biomolecular Assembly. Molecules 2020; 26:molecules26010171. [PMID: 33396541 PMCID: PMC7794689 DOI: 10.3390/molecules26010171] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/25/2020] [Accepted: 12/28/2020] [Indexed: 02/06/2023] Open
Abstract
Disulfide bonds play a pivotal role in maintaining the natural structures of proteins to ensure their performance of normal biological functions. Moreover, biological molecular assembly, such as the gluten network, is also largely dependent on the intermolecular crosslinking via disulfide bonds. In eukaryotes, the formation and rearrangement of most intra- and intermolecular disulfide bonds in the endoplasmic reticulum (ER) are mediated by protein disulfide isomerases (PDIs), which consist of multiple thioredoxin-like domains. These domains assist correct folding of proteins, as well as effectively prevent the aggregation of misfolded ones. Protein misfolding often leads to the formation of pathological protein aggregations that cause many diseases. On the other hand, glutenin aggregation and subsequent crosslinking are required for the formation of a rheologically dominating gluten network. Herein, the mechanism of PDI-regulated disulfide bond formation is important for understanding not only protein folding and associated diseases, but also the formation of functional biomolecular assembly. This review systematically illustrated the process of human protein disulfide isomerase (hPDI) mediated disulfide bond formation and complemented this with the current mechanism of wheat protein disulfide isomerase (wPDI) catalyzed formation of gluten networks.
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15
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Wang L, Yu J, Wang CC. Protein disulfide isomerase is regulated in multiple ways: Consequences for conformation, activities, and pathophysiological functions. Bioessays 2020; 43:e2000147. [PMID: 33155310 DOI: 10.1002/bies.202000147] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 10/13/2020] [Accepted: 10/15/2020] [Indexed: 12/13/2022]
Abstract
Protein disulfide isomerase (PDI) is one of the most abundant and critical protein folding catalysts in the endoplasmic reticulum of eukaryotic cells. PDI consists of four thioredoxin domains and interacts with a wide range of substrate and partner proteins due to its intrinsic conformational flexibility. PDI plays multifunctional roles in a variety of pathophysiological events, both as an oxidoreductase and a molecular chaperone. Recent studies have revealed that the conformation and activity of PDI can be regulated in multiple ways, including posttranslational modification and substrate/ligand binding. Here, we summarize recent advances in understanding the function and regulation of PDI in different pathological and physiological events. We propose that the multifunctional roles of PDI are regulated by multiple mechanisms. Furthermore, we discuss future directions for the study of PDI, emphasizing how different regulatory modes are linked to the conformational changes and biological functions of PDI in the context of diverse pathophysiologies.
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Affiliation(s)
- Lei Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jiaojiao Yu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Chih-Chen Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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16
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Protein disulfide isomerase in cardiovascular disease. Exp Mol Med 2020; 52:390-399. [PMID: 32203104 PMCID: PMC7156431 DOI: 10.1038/s12276-020-0401-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 01/20/2020] [Accepted: 02/04/2020] [Indexed: 01/07/2023] Open
Abstract
Protein disulfide isomerase (PDI) participates in the pathogenesis of numerous diseases. Increasing evidence indicates that intravascular cell-derived PDI plays an important role in the initiation and progression of cardiovascular diseases, including thrombosis and vascular inflammation. Recent studies with PDI conditional knockout mice have advanced our understanding of the function of cell-specific PDI in disease processes. Furthermore, the identification and development of novel small-molecule PDI inhibitors has led into a new era of PDI research that transitioned from the bench to bedside. In this review, we will discuss recent findings on the regulatory role of PDI in cardiovascular disease. Efforts to untangle the functions of a large family of enzymes could lead researchers to new therapies for diverse cardiovascular diseases. Members of the protein disulfide isomerase (PDI) family chemically modify other proteins in ways that can alter both their structure and biological activity. Jaehyung Cho of the University of Illinois at Chicago, USA and coworkers have reviewed numerous studies linking PDI with cardiovascular diseases, including thrombosis, heart attack, vascular inflammation, and stroke. The authors also report progress in developing small-molecule PDI inhibitors that could yield the treatment for these conditions.
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17
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Yu J, Li T, Liu Y, Wang X, Zhang J, Wang X, Shi G, Lou J, Wang L, Wang CC, Wang L. Phosphorylation switches protein disulfide isomerase activity to maintain proteostasis and attenuate ER stress. EMBO J 2020; 39:e103841. [PMID: 32149426 DOI: 10.15252/embj.2019103841] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 02/07/2020] [Accepted: 02/11/2020] [Indexed: 12/11/2022] Open
Abstract
Accumulated unfolded proteins in the endoplasmic reticulum (ER) trigger the unfolded protein response (UPR) to increase ER protein folding capacity. ER proteostasis and UPR signaling need to be regulated in a precise and timely manner. Here, we identify phosphorylation of protein disulfide isomerase (PDI), one of the most abundant and critical folding catalysts in the ER, as an early event during ER stress. The secretory pathway kinase Fam20C phosphorylates Ser357 of PDI and responds rapidly to various ER stressors. Phosphorylation of Ser357 induces an open conformation of PDI and turns it from a "foldase" into a "holdase", which is critical for preventing protein misfolding in the ER. Phosphorylated PDI also binds to the lumenal domain of IRE1α, a major UPR signal transducer, and attenuates excessive IRE1α activity. Importantly, PDI-S359A knock-in mice display enhanced IRE1α activation and liver damage under acute ER stress. We conclude that the Fam20C-PDI axis constitutes a post-translational response to maintain ER proteostasis and plays a vital role in protecting against ER stress-induced cell death.
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Affiliation(s)
- Jiaojiao Yu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Tao Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Xi Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jianchao Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xi'e Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Guizhi Shi
- Laboratory Animal Center of Institute of Biophysics, Chinese Academy of Sciences, Aviation General Hospital of Beijing, University of Chinese Academy of Sciences, Beijing, China
| | - Jizhong Lou
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Likun Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Chih-Chen Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Lei Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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18
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Guyette J, Evangelista B, Tatulian SA, Teter K. Stability and Conformational Resilience of Protein Disulfide Isomerase. Biochemistry 2019; 58:3572-3584. [PMID: 31393106 PMCID: PMC6876119 DOI: 10.1021/acs.biochem.9b00405] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein disulfide isomerase (PDI) is a redox-dependent protein with oxidoreductase and chaperone activities. It is a U-shaped protein with an abb'xa' structural organization in which the a and a' domains have CGHC active sites, the b and b' domains are involved with substrate binding, and x is a flexible linker. PDI exhibits substantial flexibility and undergoes cycles of unfolding and refolding in its interaction with cholera toxin, suggesting PDI can regain a folded, functional conformation after exposure to stress conditions. To determine whether this unfolding-refolding cycle is a substrate-induced process or an intrinsic physical property of PDI, we used circular dichroism to examine the structural properties of PDI subjected to thermal denaturation. PDI exhibited remarkable conformational resilience that is linked to its redox status. In the reduced state, PDI exhibited a 54 °C unfolding transition temperature (Tm) and regained 85% of its native structure after nearly complete thermal denaturation. Oxidized PDI had a lower Tm of 48-50 °C and regained 70% of its native conformation after 75% denaturation. Both reduced PDI and oxidized PDI were functional after refolding from these denatured states. Additional studies documented increased stability of a PDI construct lacking the a' domain and decreased thermal stability of a construct lacking the a domain. Furthermore, oxidation of the a domain limited the ability of PDI to refold. The stability and conformational resilience of PDI are thus linked to both redox-dependent and domain-specific effects. These findings document previously unrecognized properties of PDI and provide insight into the physical foundation of its biological function.
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Affiliation(s)
- Jessica Guyette
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32816 USA
| | - Baggio Evangelista
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32816 USA
| | - Suren A. Tatulian
- Department of Physics, University of Central Florida, Orlando, FL 32816 USA
| | - Ken Teter
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32816 USA
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19
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Abstract
This study provides a structure for microsomal triglyceride transfer protein, a key protein in lipid metabolism and transport. Microsomal triglyceride transfer protein is linked to a human disease state, abetalipoproteinemia. The structure helps us to understand how this protein functions and gives a rationale for how previously reported mutations result in loss of function of the protein and hence, cause disease. The structure also provides a means for rational drug design to treat cardiovascular disease, hypercholesterolemia, and obesity. Microsomal triglyceride transfer protein is composed of 2 subunits. The β-subunit, protein disulfide isomerase (PDI), also acts independently as a protein folding catalyst. The structure that we present here gives insights into how PDI functions in protein folding. Microsomal triglyceride transfer protein (MTP) plays an essential role in lipid metabolism, especially in the biogenesis of very low-density lipoproteins and chylomicrons via the transfer of neutral lipids and the assembly of apoB-containing lipoproteins. Our understanding of the molecular mechanisms of MTP has been hindered by a lack of structural information of this heterodimeric complex comprising an MTPα subunit and a protein disulfide isomerase (PDI) β-subunit. The structure of MTP presented here gives important insights into the potential mechanisms of action of this essential lipid transfer molecule, structure-based rationale for previously reported disease-causing mutations, and a means for rational drug design against cardiovascular disease and obesity. In contrast to the previously reported structure of lipovitellin, which has a funnel-like lipid-binding cavity, the lipid-binding site is encompassed in a β-sandwich formed by 2 β-sheets from the C-terminal domain of MTPα. The lipid-binding cavity of MTPα is large enough to accommodate a single lipid. PDI independently has a major role in oxidative protein folding in the endoplasmic reticulum. Comparison of the mechanism of MTPα binding by PDI with previously published structures gives insights into large protein substrate binding by PDI and suggests that the previous structures of human PDI represent the “substrate-bound” and “free” states rather than differences arising from redox state.
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20
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Özcelik D, Seto A, Rakic B, Farzam A, Supek F, Pezacki JP. Gene Expression Profiling of Endoplasmic Reticulum Stress in Hepatitis C Virus-Containing Cells Treated with an Inhibitor of Protein Disulfide Isomerases. ACS OMEGA 2018; 3:17227-17235. [PMID: 30775641 PMCID: PMC6369735 DOI: 10.1021/acsomega.8b02676] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Accepted: 11/23/2018] [Indexed: 05/30/2023]
Abstract
Protein disulfide isomerases (PDIs) catalyze disulfide bond formation between protein cysteine residues during protein folding in the endoplasmic reticulum (ER) lumen and are essential for maintaining ER homoeostasis. The life cycle of the hepatitis C virus (HCV) is closely associated with the ER. Synthesis and maturation of HCV proteins occur in the ER membrane and are mediated by multiple host cell factors that include also PDI. Here, we present a study investigating the effect of PDI inhibition on Huh7 human hepatoma cells harboring an HCV subgenomic replicon using the abscisic acid-derived PDI inhibitor origamicin. Transcriptional profiling shows that origamicin changed the expression levels of genes involved in the oxidative and ER stress responses and the unfolded protein response, as indicated by the upregulation of antioxidant enzymes and chaperone proteins, the downregulation of cell-cycle proteins, and induction of apoptosis-associated genes. Our data suggest that origamicin negatively impacts HCV replication by causing an imbalance in cellular homoeostasis and induction of stress responses. These insights suggest that inhibition of PDIs by low-molecular-weight inhibitors could be a promising approach to the discovery of novel antiviral compounds.
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Affiliation(s)
- Dennis Özcelik
- Department
of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie Street, Ottawa, Ontario K1N 6N5, Canada
| | - Andrew Seto
- Department
of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie Street, Ottawa, Ontario K1N 6N5, Canada
| | - Bojana Rakic
- Department
of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie Street, Ottawa, Ontario K1N 6N5, Canada
| | - Ali Farzam
- Department
of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie Street, Ottawa, Ontario K1N 6N5, Canada
| | - Frantisek Supek
- Department
of Genetics & Neglected Diseases, Genomics
Institute of the Novartis Research Foundation, San Diego, California 92121, United States
| | - John Paul Pezacki
- Department
of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie Street, Ottawa, Ontario K1N 6N5, Canada
- Department
of Biochemistry, Microbiology, and Immunology, Ottawa Institute for Systems Biology, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
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21
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Morris G, Puri BK, Walder K, Berk M, Stubbs B, Maes M, Carvalho AF. The Endoplasmic Reticulum Stress Response in Neuroprogressive Diseases: Emerging Pathophysiological Role and Translational Implications. Mol Neurobiol 2018; 55:8765-8787. [PMID: 29594942 PMCID: PMC6208857 DOI: 10.1007/s12035-018-1028-6] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 03/20/2018] [Indexed: 02/07/2023]
Abstract
The endoplasmic reticulum (ER) is the main cellular organelle involved in protein synthesis, assembly and secretion. Accumulating evidence shows that across several neurodegenerative and neuroprogressive diseases, ER stress ensues, which is accompanied by over-activation of the unfolded protein response (UPR). Although the UPR could initially serve adaptive purposes in conditions associated with higher cellular demands and after exposure to a range of pathophysiological insults, over time the UPR may become detrimental, thus contributing to neuroprogression. Herein, we propose that immune-inflammatory, neuro-oxidative, neuro-nitrosative, as well as mitochondrial pathways may reciprocally interact with aberrations in UPR pathways. Furthermore, ER stress may contribute to a deregulation in calcium homoeostasis. The common denominator of these pathways is a decrease in neuronal resilience, synaptic dysfunction and even cell death. This review also discusses how mechanisms related to ER stress could be explored as a source for novel therapeutic targets for neurodegenerative and neuroprogressive diseases. The design of randomised controlled trials testing compounds that target aberrant UPR-related pathways within the emerging framework of precision psychiatry is warranted.
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Affiliation(s)
- Gerwyn Morris
- Tir Na Nog, Bryn Road seaside 87, Llanelli, Wales, SA15 2LW, UK
- IMPACT Strategic Research Centre, School of Medicine, Deakin University, Geelong, Australia
| | - Basant K Puri
- Department of Medicine, Imperial College London, Hammersmith Hospital, London, England, W12 0HS, UK.
| | - Ken Walder
- The Centre for Molecular and Medical Research, School of Medicine, Deakin University, P.O. Box 291, Geelong, 3220, Australia
| | - Michael Berk
- IMPACT Strategic Research Centre, School of Medicine, Deakin University, Geelong, Australia
- Department of Psychiatry, University of Melbourne, Melbourne, Australia
- Orygen, the National Centre of Excellence in Youth Mental Health, Parkville, Australia
- Centre for Youth Mental Health, University of Melbourne, Melbourne, Australia
- Florey Institute for Neuroscience and Mental Health, Melbourne, Australia
| | - Brendon Stubbs
- Physiotherapy Department, South London and Maudsley NHS Foundation Trust, London, UK
- Health Service and Population Research Department, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- Faculty of Health, Social Care and Education, Anglia Ruskin University, Chelmsford, UK
| | - Michael Maes
- IMPACT Strategic Research Centre, School of Medicine, Deakin University, Geelong, Australia
- Department of Psychiatry, Chulalongkorn University, Bangkok, Thailand
| | - André F Carvalho
- Department of Psychiatry, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Centre for Addiction & Mental Health (CAMH), Toronto, ON, Canada
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22
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Li H, Yang K, Wang W, Niu Y, Li J, Dong Y, Liu Y, Wang CC, Wang L, Liang H. Crystal and solution structures of human protein-disulfide isomerase-like protein of the testis (PDILT) provide insight into its chaperone activity. J Biol Chem 2018; 293:1192-1202. [PMID: 29203529 PMCID: PMC5787798 DOI: 10.1074/jbc.m117.797290] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 12/01/2017] [Indexed: 01/07/2023] Open
Abstract
Protein-disulfide isomerase-like protein of the testis (PDILT), a member of the protein-disulfide isomerase family, is a chaperone essential for the folding of spermatogenesis-specific proteins in male postmeiotic germ cells. However, the structural mechanisms that regulate the chaperone function of PDILTs are unknown. Here, we report the structures of human PDILT (hPDILT) determined by X-ray crystallography to 2.4 Å resolution and small-angle X-ray scattering (SAXS). Distinct from previously reported U-like structures of related PDI family proteins, our structures revealed that hPDILT folds into a compact L-like structure in crystals and into an extended chain-like structure in solution. The hydrophobic regions and the hydrophobic pockets in hPDILT, which are important for substrate recognition, were clearly delineated in the crystal structure. Moreover, our results of the SAXS analysis and of structure-based substitutions and truncations indicated that the C-terminal tail in hPDILT is required for suppression of aggregation of denatured proteins, suggesting that the tail is crucial for the chaperone activity of PDILT. Taken together, our findings have identified the critical regions and conformational changes of PDILT that enable and control its activity. These results advance our understanding of the structural mechanisms involved in the chaperone activity of PDILT.
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Affiliation(s)
- Huanhuan Li
- From the National Laboratory of Biomacromolecules, ,the College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, and
| | - Kai Yang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, ,the College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, and
| | - Wenjia Wang
- the Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences and
| | - Yingbo Niu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, ,the College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, and
| | - Jun Li
- From the National Laboratory of Biomacromolecules, ,the College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, and
| | - Yuhui Dong
- the Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences and
| | - Yingfang Liu
- From the National Laboratory of Biomacromolecules, ,the School of Medicine and
| | - Chih-chen Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, ,the College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, and
| | - Lei Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, ,the College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, and , To whom correspondence may be addressed. E-mail:
| | - Huanhuan Liang
- From the National Laboratory of Biomacromolecules, ,School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Guangzhou 510275, China, To whom correspondence may be addressed. E-mail:
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23
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Wang X, Xue G, Song M, Xu P, Chen D, Yuan C, Lin L, Flaumenhaft R, Li J, Huang M. Molecular basis of rutin inhibition of protein disulfide isomerase (PDI) by combinedin silicoand experimental methods. RSC Adv 2018; 8:18480-18491. [PMID: 35541126 PMCID: PMC9080521 DOI: 10.1039/c8ra02683a] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 05/02/2018] [Indexed: 01/13/2023] Open
Abstract
Protein disulfide isomerase (PDI) is a founding member of the thiol isomerase family, and is recently found to play critical roles in thrombus formation. The development of effective PDI inhibitors is of great significance, and attracts strong interest. We previously showed that rutin bound directly to PDI and inhibited PDI activities, leading to the suppression of platelet aggregation and fibrin generation in a mouse model. A close analog of rutin, isoquercetin, is currently in advanced phase clinical trials. However, the molecular interaction between rutin and PDI is unknown and is difficult to study by X-ray crystallography due to the weak interaction. Here, we generated a molecular model of PDI:rutin complex by molecular docking and thorough molecular dynamics (MD) simulations. We then validated the complex model through a number of different experimental methods. We mutated the key residues predicted by the model and analyzed the mutants by an optimized isothermal titration calorimetry (ITC) method and a functional assay (insulin reduction assay). The results consistently showed that the PDI residues H354, L355 and E359 are important in the binding of rutin. These residues are next to the canonical major substrate binding site of the b′ domain, and were not conserved across the members of thiol isomerases, explaining the specificity of rutin for PDI among vascular thiol isomerases. Furthermore, the inhibitory activities of three rutin analogues were evaluated using an insulin reduction assay. The results supported that the second sugar ring at the side chain of rutin was not necessary for the binding to PDI. Together, this work provides the structural basis for the inhibitory mechanism of rutin to PDI, and offers a promising strategy for the design of new generation inhibitors with higher binding affinity to PDI for therapeutic applications. Rutin binds and inhibits PDI at b′x domain, H354 is one of the main binding sites.![]()
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Affiliation(s)
- Xu Wang
- State Key Laboratory of Structural Chemistry
- Fujian Institute of Research on the Structure of Matter
- Chinese Academy of Sciences
- Fuzhou 350002
- China
| | - Guangpu Xue
- College of Chemistry
- Fuzhou University
- Fuzhou 350116
- China
| | - Meiru Song
- College of Chemistry
- Fuzhou University
- Fuzhou 350116
- China
| | - Peng Xu
- State Key Laboratory of Structural Chemistry
- Fujian Institute of Research on the Structure of Matter
- Chinese Academy of Sciences
- Fuzhou 350002
- China
| | - Dan Chen
- College of Chemistry
- Fuzhou University
- Fuzhou 350116
- China
| | - Cai Yuan
- College of Biological Science and Engineering
- Fuzhou University
- Fuzhou 350116
- China
| | - Lin Lin
- Beth Israel Deaconess Medical Center
- Harvard Medical School
- Boston
- USA
| | | | - Jinyu Li
- College of Chemistry
- Fuzhou University
- Fuzhou 350116
- China
| | - Mingdong Huang
- State Key Laboratory of Structural Chemistry
- Fujian Institute of Research on the Structure of Matter
- Chinese Academy of Sciences
- Fuzhou 350002
- China
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24
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'Something in the way she moves': The functional significance of flexibility in the multiple roles of protein disulfide isomerase (PDI). BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1383-1394. [PMID: 28844745 PMCID: PMC5654723 DOI: 10.1016/j.bbapap.2017.08.014] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 05/30/2017] [Accepted: 08/10/2017] [Indexed: 01/15/2023]
Abstract
Protein disulfide isomerase (PDI) has diverse functions in the endoplasmic reticulum as catalyst of redox transfer, disulfide isomerization and oxidative protein folding, as molecular chaperone and in multi-subunit complexes. It interacts with an extraordinarily wide range of substrate and partner proteins, but there is only limited structural information on these interactions. Extensive evidence on the flexibility of PDI in solution is not matched by any detailed picture of the scope of its motion. A new rapid method for simulating the motion of large proteins provides detailed molecular trajectories for PDI demonstrating extensive changes in the relative orientation of its four domains, great variation in the distances between key sites and internal motion within the core ligand-binding domain. The review shows that these simulations are consistent with experimental evidence and provide insight into the functional capabilities conferred by the extensive flexible motion of PDI.
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25
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Karamzadeh R, Karimi-Jafari MH, Sharifi-Zarchi A, Chitsaz H, Salekdeh GH, Moosavi-Movahedi AA. Machine Learning and Network Analysis of Molecular Dynamics Trajectories Reveal Two Chains of Red/Ox-specific Residue Interactions in Human Protein Disulfide Isomerase. Sci Rep 2017. [PMID: 28623339 PMCID: PMC5473932 DOI: 10.1038/s41598-017-03966-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The human protein disulfide isomerase (hPDI), is an essential four-domain multifunctional enzyme. As a result of disulfide shuffling in its terminal domains, hPDI exists in two oxidation states with different conformational preferences which are important for substrate binding and functional activities. Here, we address the redox-dependent conformational dynamics of hPDI through molecular dynamics (MD) simulations. Collective domain motions are identified by the principal component analysis of MD trajectories and redox-dependent opening-closing structure variations are highlighted on projected free energy landscapes. Then, important structural features that exhibit considerable differences in dynamics of redox states are extracted by statistical machine learning methods. Mapping the structural variations to time series of residue interaction networks also provides a holistic representation of the dynamical redox differences. With emphasizing on persistent long-lasting interactions, an approach is proposed that compiled these time series networks to a single dynamic residue interaction network (DRIN). Differential comparison of DRIN in oxidized and reduced states reveals chains of residue interactions that represent potential allosteric paths between catalytic and ligand binding sites of hPDI.
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Affiliation(s)
- Razieh Karamzadeh
- Department of Biophysics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.,Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | | | - Ali Sharifi-Zarchi
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.,Computer Engineering Department, Sharif University of Technology, Tehran, Iran.,Computer Science Department, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Hamidreza Chitsaz
- Computer Science Department, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Ghasem Hosseini Salekdeh
- Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.,Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, and Extension Organization, Karaj, Iran
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26
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Red/ox states of human protein disulfide isomerase regulate binding affinity of 17 beta-estradiol. Arch Biochem Biophys 2017; 619:35-44. [DOI: 10.1016/j.abb.2017.02.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 02/15/2017] [Accepted: 02/27/2017] [Indexed: 01/16/2023]
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27
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Perri E, Parakh S, Atkin J. Protein Disulphide Isomerases: emerging roles of PDI and ERp57 in the nervous system and as therapeutic targets for ALS. Expert Opin Ther Targets 2016; 21:37-49. [PMID: 27786579 DOI: 10.1080/14728222.2016.1254197] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
INTRODUCTION There is increasing evidence that endoplasmic reticulum (ER) chaperones Protein Disulphide Isomerase (PDI) and ERp57 (endoplasmic reticulum protein 57) are protective against neurodegenerative diseases related to protein misfolding, including Amyotrophic Lateral Sclerosis (ALS). PDI and ERp57 also possess disulphide interchange activity, in which protein disulphide bonds are oxidized, reduced and isomerized, to form their native conformation. Recently, missense and intronic variants of PDI and ERp57 were associated with ALS, implying that PDI proteins are relevant to ALS pathology. Areas covered: Here, we discuss possible implications of the PDI and ERp57 variants, as well as recent studies describing previously unrecognized roles for PDI and ERp57 in the nervous system. Therapeutics based on PDI may therefore be attractive candidates for ALS. However, in addition to its protective functions, aberrant, toxic roles for PDI have recently been described. These functions need to be fully characterized before effective therapeutic strategies can be designed. Expert opinion: These disease-associated variants of PDI and ERp57 provide additional evidence for an important role for PDI proteins in ALS. However, there are many questions remaining unanswered that need to be addressed before the potential of the PDI family in relation to ALS can be fully realized.
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Affiliation(s)
- Emma Perri
- a Department of Biomedical Sciences, Faculty of Medicine and Health Sciences , Macquarie University , Sydney , Australia
| | - Sonam Parakh
- a Department of Biomedical Sciences, Faculty of Medicine and Health Sciences , Macquarie University , Sydney , Australia
| | - Julie Atkin
- a Department of Biomedical Sciences, Faculty of Medicine and Health Sciences , Macquarie University , Sydney , Australia.,b Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science , La Trobe University , Melbourne , Australia
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28
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Römer RA, Wells SA, Emilio Jimenez‐Roldan J, Bhattacharyya M, Vishweshwara S, Freedman RB. The flexibility and dynamics of protein disulfide isomerase. Proteins 2016; 84:1776-1785. [PMID: 27616289 PMCID: PMC5111589 DOI: 10.1002/prot.25159] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 07/29/2016] [Accepted: 08/24/2016] [Indexed: 01/01/2023]
Abstract
We have studied the mobility of the multidomain folding catalyst, protein disulfide isomerase (PDI), by a coarse‐graining approach based on flexibility. We analyze our simulations of yeast PDI (yPDI) using measures of backbone movement, relative positions and orientations of domains, and distances between functional sites. We find that there is interdomain flexibility at every interdomain junction but these show very different characteristics. The extent of interdomain flexibility is such that yPDI's two active sites can approach much more closely than is found in crystal structures—and indeed hinge motion to bring these sites into proximity is the lowest energy normal mode of motion of the protein. The flexibility predicted for yPDI (based on one structure) includes the other known conformation of yPDI and is consistent with (i) the mobility observed experimentally for mammalian PDI and (ii) molecular dynamics. We also observe intradomain flexibility and clear differences between the domains in their propensity for internal motion. Our results suggest that PDI flexibility enables it to interact with many different partner molecules of widely different sizes and shapes, and highlights considerable similarities of yPDI and mammalian PDI. Proteins 2016; 84:1776–1785. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Rudolf A. Römer
- Department of Physics and Centre for Scientific ComputingThe University of WarwickCoventryCV4 7ALUnited Kingdom
| | - Stephen A. Wells
- Department of Chemical EngineeringUniversity of BathBathBA2 7AYUnited Kingdom
| | - J. Emilio Jimenez‐Roldan
- Department of Physics and Centre for Scientific ComputingThe University of WarwickCoventryCV4 7ALUnited Kingdom
| | - Moitrayee Bhattacharyya
- Molecular Biophysics Unit, Indian Institute of ScienceBangalore560012India
- Present address: Moitrayee Bhattacharyya's current address is Department of Molecular and Cell BiologyUniversity of California BerkeleyCalifornia94720.
| | | | - Robert B. Freedman
- School of Life SciencesThe University of WarwickCoventryCV4 7ALUnited Kingdom
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29
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Bekendam RH, Bendapudi PK, Lin L, Nag PP, Pu J, Kennedy DR, Feldenzer A, Chiu J, Cook KM, Furie B, Huang M, Hogg PJ, Flaumenhaft R. A substrate-driven allosteric switch that enhances PDI catalytic activity. Nat Commun 2016; 7:12579. [PMID: 27573496 PMCID: PMC5013553 DOI: 10.1038/ncomms12579] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 07/14/2016] [Indexed: 01/01/2023] Open
Abstract
Protein disulfide isomerase (PDI) is an oxidoreductase essential for folding proteins in the endoplasmic reticulum. The domain structure of PDI is a–b–b′–x–a′, wherein the thioredoxin-like a and a′ domains mediate disulfide bond shuffling and b and b′ domains are substrate binding. The b′ and a′ domains are connected via the x-linker, a 19-amino-acid flexible peptide. Here we identify a class of compounds, termed bepristats, that target the substrate-binding pocket of b′. Bepristats reversibly block substrate binding and inhibit platelet aggregation and thrombus formation in vivo. Ligation of the substrate-binding pocket by bepristats paradoxically enhances catalytic activity of a and a′ by displacing the x-linker, which acts as an allosteric switch to augment reductase activity in the catalytic domains. This substrate-driven allosteric switch is also activated by peptides and proteins and is present in other thiol isomerases. Our results demonstrate a mechanism whereby binding of a substrate to thiol isomerases enhances catalytic activity of remote domains. Protein Disulfide Isomerase (PDI) is a prothrombotic, multidomain enzyme with separate substrate binding and catalytic domains. Here, the authors identify a new class of compounds that target the PDI substrate binding site, inducing a conformational change in the catalytic domains and inhibiting thrombosis.
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Affiliation(s)
- Roelof H Bekendam
- Division of Hemostasis and Thrombosis, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Pavan K Bendapudi
- Division of Hemostasis and Thrombosis, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Lin Lin
- Division of Hemostasis and Thrombosis, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Partha P Nag
- Department of Pharmaceutical and Administrative Sciences, The Broad Institute Probe Development Center, Cambridge, Massachusetts 02142, USA.,Center for the Science of Therapeutics, Broad Institute, Cambridge, Massachusetts 02142, USA
| | - Jun Pu
- Department of Pharmaceutical and Administrative Sciences, The Broad Institute Probe Development Center, Cambridge, Massachusetts 02142, USA
| | - Daniel R Kennedy
- College of Pharmacy, Western New England University, Springfield, Massachusetts 01119, USA
| | - Alexandra Feldenzer
- College of Pharmacy, Western New England University, Springfield, Massachusetts 01119, USA
| | - Joyce Chiu
- The Centenary Institute, Newtown, Sydney, New South Wales 2050, Australia.,National Health and Medical Research Council Clinical Trials Centre, University of Sydney, Sydney, New South Wales 2050, Australia
| | - Kristina M Cook
- The Centenary Institute, Newtown, Sydney, New South Wales 2050, Australia
| | - Bruce Furie
- Division of Hemostasis and Thrombosis, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Mingdong Huang
- Division of Hemostasis and Thrombosis, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Philip J Hogg
- The Centenary Institute, Newtown, Sydney, New South Wales 2050, Australia.,National Health and Medical Research Council Clinical Trials Centre, University of Sydney, Sydney, New South Wales 2050, Australia
| | - Robert Flaumenhaft
- Division of Hemostasis and Thrombosis, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02115, USA
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30
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Woehlbier U, Colombo A, Saaranen MJ, Pérez V, Ojeda J, Bustos FJ, Andreu CI, Torres M, Valenzuela V, Medinas DB, Rozas P, Vidal RL, Lopez-Gonzalez R, Salameh J, Fernandez-Collemann S, Muñoz N, Matus S, Armisen R, Sagredo A, Palma K, Irrazabal T, Almeida S, Gonzalez-Perez P, Campero M, Gao FB, Henny P, van Zundert B, Ruddock LW, Concha ML, Henriquez JP, Brown RH, Hetz C. ALS-linked protein disulfide isomerase variants cause motor dysfunction. EMBO J 2016; 35:845-65. [PMID: 26869642 PMCID: PMC4972141 DOI: 10.15252/embj.201592224] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Revised: 12/27/2015] [Accepted: 01/05/2016] [Indexed: 12/11/2022] Open
Abstract
Disturbance of endoplasmic reticulum (ER) proteostasis is a common feature of amyotrophic lateral sclerosis (ALS). Protein disulfide isomerases (PDIs) areERfoldases identified as possibleALSbiomarkers, as well as neuroprotective factors. However, no functional studies have addressed their impact on the disease process. Here, we functionally characterized fourALS-linked mutations recently identified in two majorPDIgenes,PDIA1 andPDIA3/ERp57. Phenotypic screening in zebrafish revealed that the expression of thesePDIvariants induce motor defects associated with a disruption of motoneuron connectivity. Similarly, the expression of mutantPDIs impaired dendritic outgrowth in motoneuron cell culture models. Cellular and biochemical studies identified distinct molecular defects underlying the pathogenicity of thesePDImutants. Finally, targetingERp57 in the nervous system led to severe motor dysfunction in mice associated with a loss of neuromuscular synapses. This study identifiesERproteostasis imbalance as a risk factor forALS, driving initial stages of the disease.
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Affiliation(s)
- Ute Woehlbier
- Biomedical Neuroscience Institute, Faculty of Medicine, University of Chile, Santiago, Chile Program of Cellular and Molecular Biology, Center for Molecular Studies of the Cell, Institute of Biomedical Sciences, University of Chile, Santiago, Chile Center for Genomics and Bioinformatics, Universidad Mayor, Santiago, Chile
| | - Alicia Colombo
- Program of Anatomy and Developmental Biology, Institute of Biomedical Sciences, University of Chile, Santiago, Chile Department of Pathological Anatomy, Hospital Clínico, University of Chile, Santiago, Chile
| | - Mirva J Saaranen
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Viviana Pérez
- Department of Cell Biology, Faculty of Biological Sciences, Millennium Nucleus of Regenerative Biology, Center for Advanced Microscopy (CMA Bio-Bio), Universidad de Concepción, Concepción, Chile
| | - Jorge Ojeda
- Department of Cell Biology, Faculty of Biological Sciences, Millennium Nucleus of Regenerative Biology, Center for Advanced Microscopy (CMA Bio-Bio), Universidad de Concepción, Concepción, Chile
| | - Fernando J Bustos
- Faculty of Biological Sciences and Faculty of Medicine, Center for Biomedical Research, Universidad Andres Bello, Santiago, Chile
| | - Catherine I Andreu
- Biomedical Neuroscience Institute, Faculty of Medicine, University of Chile, Santiago, Chile Program of Cellular and Molecular Biology, Center for Molecular Studies of the Cell, Institute of Biomedical Sciences, University of Chile, Santiago, Chile
| | - Mauricio Torres
- Biomedical Neuroscience Institute, Faculty of Medicine, University of Chile, Santiago, Chile Program of Cellular and Molecular Biology, Center for Molecular Studies of the Cell, Institute of Biomedical Sciences, University of Chile, Santiago, Chile
| | - Vicente Valenzuela
- Biomedical Neuroscience Institute, Faculty of Medicine, University of Chile, Santiago, Chile Program of Cellular and Molecular Biology, Center for Molecular Studies of the Cell, Institute of Biomedical Sciences, University of Chile, Santiago, Chile Center for Geroscience, Brain Health and Metabolism, Santiago, Chile
| | - Danilo B Medinas
- Biomedical Neuroscience Institute, Faculty of Medicine, University of Chile, Santiago, Chile Program of Cellular and Molecular Biology, Center for Molecular Studies of the Cell, Institute of Biomedical Sciences, University of Chile, Santiago, Chile Center for Geroscience, Brain Health and Metabolism, Santiago, Chile
| | - Pablo Rozas
- Biomedical Neuroscience Institute, Faculty of Medicine, University of Chile, Santiago, Chile Program of Cellular and Molecular Biology, Center for Molecular Studies of the Cell, Institute of Biomedical Sciences, University of Chile, Santiago, Chile
| | - Rene L Vidal
- Biomedical Neuroscience Institute, Faculty of Medicine, University of Chile, Santiago, Chile Center for Geroscience, Brain Health and Metabolism, Santiago, Chile Neurounion Biomedical Foundation, CENPAR, Santiago, Chile
| | | | - Johnny Salameh
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA
| | | | - Natalia Muñoz
- Biomedical Neuroscience Institute, Faculty of Medicine, University of Chile, Santiago, Chile Center for Geroscience, Brain Health and Metabolism, Santiago, Chile Neurounion Biomedical Foundation, CENPAR, Santiago, Chile
| | - Soledad Matus
- Biomedical Neuroscience Institute, Faculty of Medicine, University of Chile, Santiago, Chile Center for Geroscience, Brain Health and Metabolism, Santiago, Chile Neurounion Biomedical Foundation, CENPAR, Santiago, Chile
| | - Ricardo Armisen
- Program of Cellular and Molecular Biology, Center for Molecular Studies of the Cell, Institute of Biomedical Sciences, University of Chile, Santiago, Chile
| | - Alfredo Sagredo
- Program of Cellular and Molecular Biology, Center for Molecular Studies of the Cell, Institute of Biomedical Sciences, University of Chile, Santiago, Chile
| | - Karina Palma
- Biomedical Neuroscience Institute, Faculty of Medicine, University of Chile, Santiago, Chile Program of Cellular and Molecular Biology, Center for Molecular Studies of the Cell, Institute of Biomedical Sciences, University of Chile, Santiago, Chile
| | - Thergiory Irrazabal
- Biomedical Neuroscience Institute, Faculty of Medicine, University of Chile, Santiago, Chile Program of Cellular and Molecular Biology, Center for Molecular Studies of the Cell, Institute of Biomedical Sciences, University of Chile, Santiago, Chile
| | - Sandra Almeida
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Paloma Gonzalez-Perez
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Mario Campero
- Department of Neurology and Neurosurgery, Faculty of Medicine, University of Chile, Santiago, Chile Faculty of Medicine, Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Fen-Biao Gao
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Pablo Henny
- Department of Anatomy, Medical School, Universidad Católica de Chile, Santiago, Chile
| | - Brigitte van Zundert
- Faculty of Biological Sciences and Faculty of Medicine, Center for Biomedical Research, Universidad Andres Bello, Santiago, Chile
| | - Lloyd W Ruddock
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Miguel L Concha
- Biomedical Neuroscience Institute, Faculty of Medicine, University of Chile, Santiago, Chile Program of Anatomy and Developmental Biology, Institute of Biomedical Sciences, University of Chile, Santiago, Chile Center for Geroscience, Brain Health and Metabolism, Santiago, Chile
| | - Juan P Henriquez
- Department of Cell Biology, Faculty of Biological Sciences, Millennium Nucleus of Regenerative Biology, Center for Advanced Microscopy (CMA Bio-Bio), Universidad de Concepción, Concepción, Chile
| | - Robert H Brown
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Claudio Hetz
- Biomedical Neuroscience Institute, Faculty of Medicine, University of Chile, Santiago, Chile Program of Cellular and Molecular Biology, Center for Molecular Studies of the Cell, Institute of Biomedical Sciences, University of Chile, Santiago, Chile Center for Geroscience, Brain Health and Metabolism, Santiago, Chile Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, USA
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31
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Bekendam RH, Flaumenhaft R. Inhibition of Protein Disulfide Isomerase in Thrombosis. Basic Clin Pharmacol Toxicol 2016; 119 Suppl 3:42-48. [DOI: 10.1111/bcpt.12573] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 02/19/2016] [Indexed: 01/07/2023]
Affiliation(s)
- Roelof H. Bekendam
- Division of Hemostasis and Thrombosis; Department of Medicine; BIDMC; Harvard Medical School; Boston MA USA
| | - Robert Flaumenhaft
- Division of Hemostasis and Thrombosis; Department of Medicine; BIDMC; Harvard Medical School; Boston MA USA
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32
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Rapid expansion of the protein disulfide isomerase gene family facilitates the folding of venom peptides. Proc Natl Acad Sci U S A 2016; 113:3227-32. [PMID: 26957604 DOI: 10.1073/pnas.1525790113] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Formation of correct disulfide bonds in the endoplasmic reticulum is a crucial step for folding proteins destined for secretion. Protein disulfide isomerases (PDIs) play a central role in this process. We report a previously unidentified, hypervariable family of PDIs that represents the most diverse gene family of oxidoreductases described in a single genus to date. These enzymes are highly expressed specifically in the venom glands of predatory cone snails, animals that synthesize a remarkably diverse set of cysteine-rich peptide toxins (conotoxins). Enzymes in this PDI family, termed conotoxin-specific PDIs, significantly and differentially accelerate the kinetics of disulfide-bond formation of several conotoxins. Our results are consistent with a unique biological scenario associated with protein folding: The diversification of a family of foldases can be correlated with the rapid evolution of an unprecedented diversity of disulfide-rich structural domains expressed by venomous marine snails in the superfamily Conoidea.
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33
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Richards KL, Rowe ML, Hudson PB, Williamson RA, Howard MJ. Combined ligand-observe (19)F and protein-observe (15)N,(1)H-HSQC NMR suggests phenylalanine as the key Δ-somatostatin residue recognized by human protein disulfide isomerase. Sci Rep 2016; 6:19518. [PMID: 26786784 PMCID: PMC4726260 DOI: 10.1038/srep19518] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 12/09/2015] [Indexed: 01/27/2023] Open
Abstract
Human protein disulphide isomerase (hPDI) is an endoplasmic reticulum (ER) based isomerase and folding chaperone. Molecular detail of ligand recognition and specificity of hPDI are poorly understood despite the importance of the hPDI for folding secreted proteins and its implication in diseases including cancer and lateral sclerosis. We report a detailed study of specificity, interaction and dissociation constants (Kd) of the peptide-ligand Δ-somatostatin (AGSKNFFWKTFTSS) binding to hPDI using 19F ligand-observe and 15N,1H-HSQC protein-observe NMR methods. Phe residues in Δ-somatostatin are hypothesised as important for recognition by hPDI therefore, step-wise peptide Phe-to-Ala changes were progressively introduced and shown to raise the Kd from 103 + 47 μM until the point where binding was abolished when all Phe residues were modified to Ala. The largest step-changes in Kd involved the F11A peptide modification which implies the C-terminus of Δ-somatostatin is a prime recognition region. Furthermore, this study also validated the combined use of 19F ligand-observe and complimentary 15N,1H-HSQC titrations to monitor interactions from the protein’s perspective. 19F ligand-observe NMR was ratified as mirroring 15N protein-observe but highlighted the advantage that 19F offers improved Kd precision due to higher spectrum resolution and greater chemical environment sensitivity.
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Affiliation(s)
- Kirsty L Richards
- Protein Science Group, School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | - Michelle L Rowe
- Protein Science Group, School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | - Paul B Hudson
- Protein Science Group, School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | - Richard A Williamson
- Protein Science Group, School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | - Mark J Howard
- Protein Science Group, School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
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Yagi-Utsumi M, Satoh T, Kato K. Structural basis of redox-dependent substrate binding of protein disulfide isomerase. Sci Rep 2015; 5:13909. [PMID: 26350503 PMCID: PMC4563560 DOI: 10.1038/srep13909] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 08/13/2015] [Indexed: 01/09/2023] Open
Abstract
Protein disulfide isomerase (PDI) is a multidomain enzyme, operating as an essential folding catalyst, in which the b′ and a′ domains provide substrate binding sites and undergo an open–closed domain rearrangement depending on the redox states of the a′ domain. Despite the long research history of this enzyme, three-dimensional structural data remain unavailable for its ligand-binding mode. Here we characterize PDI substrate recognition using α-synuclein (αSN) as the model ligand. Our nuclear magnetic resonance (NMR) data revealed that the substrate-binding domains of PDI captured the αSN segment Val37–Val40 only in the oxidized form. Furthermore, we determined the crystal structure of an oxidized form of the b′–a′ domains in complex with an undecapeptide corresponding to this segment. The peptide-binding mode observed in the crystal structure with NMR validation, was characterized by hydrophobic interactions on the b′ domain in an open conformation. Comparison with the previously reported crystal structure indicates that the a′ domain partially masks the binding surface of the b′ domain, causing steric hindrance against the peptide in the reduced form of the b′–a′ domains that exhibits a closed conformation. These findings provide a structural basis for the mechanism underlying the redox-dependent substrate binding of PDI.
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Affiliation(s)
- Maho Yagi-Utsumi
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
| | - Tadashi Satoh
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan.,JST, PRESTO, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
| | - Koichi Kato
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
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35
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Lin L, Gopal S, Sharda A, Passam F, Bowley SR, Stopa J, Xue G, Yuan C, Furie BC, Flaumenhaft R, Huang M, Furie B. Quercetin-3-rutinoside Inhibits Protein Disulfide Isomerase by Binding to Its b'x Domain. J Biol Chem 2015; 290:23543-52. [PMID: 26240139 DOI: 10.1074/jbc.m115.666180] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Indexed: 01/30/2023] Open
Abstract
Quercetin-3-rutinoside inhibits thrombus formation in a mouse model by inhibiting extracellular protein disulfide isomerase (PDI), an enzyme required for platelet thrombus formation and fibrin generation. Prior studies have identified PDI as a potential target for novel antithrombotic agents. Using a fluorescence enhancement-based assay and isothermal calorimetry, we show that quercetin-3-rutinoside directly binds to the b' domain of PDI with a 1:1 stoichiometry. The binding of quercetin-3-rutinoside to PDI induces a more compact conformation and restricts the conformational flexibility of PDI, as revealed by small angle x-ray scattering. The binding sites of quercetin-3-rutinoside to PDI were determined by studying its interaction with isolated fragments of PDI. Quercetin-3-rutinoside binds to the b'x domain of PDI. The infusion of the b'x fragment of PDI rescued thrombus formation that was inhibited by quercetin-3-rutinoside in a mouse thrombosis model. This b'x fragment does not possess reductase activity and, in the absence of quercetin-3-rutinoside, does not affect thrombus formation in vivo. The isolated b' domain of PDI has potential as an antidote to reverse the antithrombotic effect of quercetin-3-rutinoside by binding and neutralizing quercetin-3-rutinoside.
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Affiliation(s)
- Lin Lin
- From the Division of Hemostasis and Thrombosis, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts 02115 and
| | - Srila Gopal
- From the Division of Hemostasis and Thrombosis, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts 02115 and
| | - Anish Sharda
- From the Division of Hemostasis and Thrombosis, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts 02115 and
| | - Freda Passam
- From the Division of Hemostasis and Thrombosis, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts 02115 and
| | - Sheryl R Bowley
- From the Division of Hemostasis and Thrombosis, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts 02115 and
| | - Jack Stopa
- From the Division of Hemostasis and Thrombosis, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts 02115 and
| | - Guangpu Xue
- the Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
| | - Cai Yuan
- the Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
| | - Barbara C Furie
- From the Division of Hemostasis and Thrombosis, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts 02115 and
| | - Robert Flaumenhaft
- From the Division of Hemostasis and Thrombosis, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts 02115 and
| | - Mingdong Huang
- From the Division of Hemostasis and Thrombosis, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts 02115 and
| | - Bruce Furie
- From the Division of Hemostasis and Thrombosis, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts 02115 and
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Gonzalez-Perez P, Woehlbier U, Chian RJ, Sapp P, Rouleau GA, Leblond CS, Daoud H, Dion PA, Landers JE, Hetz C, Brown RH. Identification of rare protein disulfide isomerase gene variants in amyotrophic lateral sclerosis patients. Gene 2015; 566:158-65. [PMID: 25913742 PMCID: PMC5553116 DOI: 10.1016/j.gene.2015.04.035] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 04/12/2015] [Accepted: 04/13/2015] [Indexed: 11/17/2022]
Abstract
Disruption of endoplasmic reticulum (ER) proteostasis is a salient feature of amyotrophic lateral sclerosis (ALS). Upregulation of ER foldases of the protein disulfide isomerase (PDI) family has been reported in ALS mouse models and spinal cord tissue and body fluids derived from sporadic ALS cases. Although in vitro studies suggest a neuroprotective role of PDIs in ALS, the possible contribution of genetic mutations of these ER foldases in the disease process remains unknown. Interestingly, intronic variants of the PDIA1 gene were recently reported as a risk factor for ALS. Here, we initially screened for mutations in two major PDI genes (PDIA1/P4HB and PDIA3/ERp57) in a US cohort of 96 familial and 96 sporadic ALS patients using direct DNA sequencing. Then, 463 familial and 445 sporadic ALS patients from two independent cohorts were also screened for mutations in these two genes using whole exome sequencing. A total of nine PDIA1 missense variants and seven PDIA3 missense variants were identified in 16 ALS patients. We have identified several novel and rare single nucleotide polymorphisms (SNPs) in both genes that are enriched in ALS cases compared with a large group of control subjects showing a frequency of around 1% in ALS cases. The possible biological and structural impact of these ALS-linked PDI variants is also discussed.
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Affiliation(s)
- Paloma Gonzalez-Perez
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Ute Woehlbier
- Biomedical Neuroscience Institute, Faculty of Medicine, University of Chile, Santiago, Chile; Institute of Biomedical Sciences, Center for Molecular Studies of the Cell, Program of Cellular and Molecular Biology, University of Chile, Santiago, Chile; Center for Genomics and Bioinformatics, Faculty of Science, Universidad Mayor, Santiago, Chile
| | - Ru-Ju Chian
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Peter Sapp
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Guy A Rouleau
- Montreal Neurological Institute and Hospital, Department of Neurology and Neurosurgery, McGill University, 3801 rue University, Montreal, QC H3A 2B4, Canada
| | - Claire S Leblond
- Montreal Neurological Institute and Hospital, Department of Neurology and Neurosurgery, McGill University, 3801 rue University, Montreal, QC H3A 2B4, Canada
| | - Hussein Daoud
- Montreal Neurological Institute and Hospital, Department of Neurology and Neurosurgery, McGill University, 3801 rue University, Montreal, QC H3A 2B4, Canada
| | - Patrick A Dion
- Montreal Neurological Institute and Hospital, Department of Neurology and Neurosurgery, McGill University, 3801 rue University, Montreal, QC H3A 2B4, Canada
| | - John E Landers
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Claudio Hetz
- Biomedical Neuroscience Institute, Faculty of Medicine, University of Chile, Santiago, Chile; Institute of Biomedical Sciences, Center for Molecular Studies of the Cell, Program of Cellular and Molecular Biology, University of Chile, Santiago, Chile; Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, USA.
| | - Robert H Brown
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA.
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Wang L, Wang X, Wang CC. Protein disulfide-isomerase, a folding catalyst and a redox-regulated chaperone. Free Radic Biol Med 2015; 83:305-13. [PMID: 25697778 DOI: 10.1016/j.freeradbiomed.2015.02.007] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 02/04/2015] [Accepted: 02/07/2015] [Indexed: 01/08/2023]
Abstract
Protein disulfide-isomerase (PDI) was the first protein-folding catalyst to be characterized, half a century ago. It plays critical roles in a variety of physiological events by displaying oxidoreductase and redox-regulated chaperone activities. This review provides a brief history of the identification of PDI as both an enzyme and a molecular chaperone and of the recent advances in studies on the structure and dynamics of PDI, the substrate binding and release, and the cooperation with its partners to catalyze oxidative protein folding and maintain ER redox homeostasis. In this review, we highlight the structural features of PDI, including the high interdomain flexibility, the multiple binding sites, the two synergic active sites, and the redox-dependent conformational changes.
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Affiliation(s)
- Lei Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xi Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Chih-chen Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
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38
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Parakh S, Atkin JD. Novel roles for protein disulphide isomerase in disease states: a double edged sword? Front Cell Dev Biol 2015; 3:30. [PMID: 26052512 PMCID: PMC4439577 DOI: 10.3389/fcell.2015.00030] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 04/28/2015] [Indexed: 12/14/2022] Open
Abstract
Protein disulphide isomerase (PDI) is a multifunctional redox chaperone of the endoplasmic reticulum (ER). Since it was first discovered 40 years ago the functions ascribed to PDI have evolved significantly and recent studies have recognized its distinct functions, with adverse as well as protective effects in disease. Furthermore, post translational modifications of PDI abrogate its normal functional roles in specific disease states. This review focusses on recent studies that have identified novel functions for PDI relevant to specific diseases.
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Affiliation(s)
- Sonam Parakh
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University Sydney, NSW, Australia
| | - Julie D Atkin
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University Sydney, NSW, Australia ; Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University Bundoora, VIC, Australia
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39
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Curtis-Marof R, Doko D, Rowe ML, Richards KL, Williamson RA, Howard MJ. 19F NMR spectroscopy monitors ligand binding to recombinantly fluorine-labelled b'x from human protein disulphide isomerase (hPDI). Org Biomol Chem 2015; 12:3808-12. [PMID: 24796794 PMCID: PMC4157668 DOI: 10.1039/c4ob00699b] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a protein-observe (19)F NMR-based ligand titration binding study of human PDI b'x with Δ-somatostatin that also emphasises the need to optimise recombinant protein fluorination when using 5- or 6-fluoroindole. This study highlights a recombinant preference for 5-fluoroindole over 6-fluoroindole; most likely due to the influence of fluorine atomic packing within the folded protein structure. Fluorination affords a single (19)F resonance probe to follow displacement of the protein x-linker as ligand is titrated and provides a dissociation constant of 23 ± 4 μM.
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Affiliation(s)
- Rose Curtis-Marof
- Protein Science Group, School of Biosciences, University of Kent, Giles Lane, Canterbury, Kent CT2 7NJ, UK.
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40
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Conway ME, Harris M. S-nitrosylation of the thioredoxin-like domains of protein disulfide isomerase and its role in neurodegenerative conditions. Front Chem 2015; 3:27. [PMID: 25932462 PMCID: PMC4399332 DOI: 10.3389/fchem.2015.00027] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 03/30/2015] [Indexed: 12/14/2022] Open
Abstract
Correct protein folding and inhibition of protein aggregation is facilitated by a cellular “quality control system” that engages a network of protein interactions including molecular chaperones and the ubiquitin proteasome system. Key chaperones involved in these regulatory mechanisms are the protein disulfide isomerases (PDI) and their homologs, predominantly expressed in the endoplasmic reticulum of most tissues. Redox changes that disrupt ER homeostasis can lead to modification of these enzymes or chaperones with the loss of their proposed neuroprotective role resulting in an increase in protein misfolding. Misfolded protein aggregates have been observed in several disease states and are considered to play a pivotal role in the pathogenesis of neurodegenerative conditions such as Alzheimer's disease, Parkinson's disease, and Amyotrophic Lateral sclerosis. This review will focus on the importance of the thioredoxin-like CGHC active site of PDI and how our understanding of this structural motif will play a key role in unraveling the pathogenic mechanisms that underpin these neurodegenerative conditions.
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Affiliation(s)
- Myra E Conway
- Department of Applied Sciences, University of the West of England Bristol, UK
| | - Matthew Harris
- Department of Applied Sciences, University of the West of England Bristol, UK
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41
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Inagaki K, Satoh T, Itoh SG, Okumura H, Kato K. Redox-dependent conformational transition of catalytic domain of protein disulfide isomerase indicated by crystal structure-based molecular dynamics simulation. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2014.11.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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42
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Zhang L, Niu Y, Zhu L, Fang J, Wang X, Wang L, Wang CC. Different interaction modes for protein-disulfide isomerase (PDI) as an efficient regulator and a specific substrate of endoplasmic reticulum oxidoreductin-1α (Ero1α). J Biol Chem 2014; 289:31188-99. [PMID: 25258311 DOI: 10.1074/jbc.m114.602961] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Protein-disulfide isomerase (PDI) and sulfhydryl oxidase endoplasmic reticulum oxidoreductin-1α (Ero1α) constitute the pivotal pathway for oxidative protein folding in the mammalian endoplasmic reticulum (ER). Ero1α oxidizes PDI to introduce disulfides into substrates, and PDI can feedback-regulate Ero1α activity. Here, we show the regulatory disulfide of Ero1α responds to the redox fluctuation in ER very sensitively, relying on the availability of redox active PDI. The regulation of Ero1α is rapidly facilitated by either a or a' catalytic domain of PDI, independent of the substrate binding domain. On the other hand, activated Ero1α specifically binds to PDI via hydrophobic interactions and preferentially catalyzes the oxidation of domain a'. This asymmetry ensures PDI to function simultaneously as an oxidoreductase and an isomerase. In addition, several PDI family members are also characterized to be potent regulators of Ero1α. The novel modes for PDI as a competent regulator and a specific substrate of Ero1α govern efficient and faithful oxidative protein folding and maintain the ER redox homeostasis.
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Affiliation(s)
- Lihui Zhang
- From the National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yingbo Niu
- From the National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Zhu
- From the National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingqi Fang
- From the National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xi'e Wang
- From the National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China and
| | - Lei Wang
- From the National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China and
| | - Chih-chen Wang
- From the National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China and
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Okumura M, Kadokura H, Hashimoto S, Yutani K, Kanemura S, Hikima T, Hidaka Y, Ito L, Shiba K, Masui S, Imai D, Imaoka S, Yamaguchi H, Inaba K. Inhibition of the functional interplay between endoplasmic reticulum (ER) oxidoreduclin-1α (Ero1α) and protein-disulfide isomerase (PDI) by the endocrine disruptor bisphenol A. J Biol Chem 2014; 289:27004-27018. [PMID: 25122773 PMCID: PMC4175339 DOI: 10.1074/jbc.m114.564104] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bisphenol A (BPA) is an endocrine disruptor that may have adverse effects on human health. We recently isolated protein-disulfide isomerase (PDI) as a BPA-binding protein from rat brain homogenates and found that BPA markedly inhibited PDI activity. To elucidate mechanisms of this inhibition, detailed structural, biophysical, and functional analyses of PDI were performed in the presence of BPA. BPA binding to PDI induced significant rearrangement of the N-terminal thioredoxin domain of PDI, resulting in more compact overall structure. This conformational change led to closure of the substrate-binding pocket in b' domain, preventing PDI from binding to unfolded proteins. The b' domain also plays an essential role in the interplay between PDI and ER oxidoreduclin 1α (Ero1α), a flavoenzyme responsible for reoxidation of PDI. We show that BPA inhibited Ero1α-catalyzed PDI oxidation presumably by inhibiting the interaction between the b' domain of PDI and Ero1α; the phenol groups of BPA probably compete with a highly conserved tryptophan residue, located in the protruding β-hairpin of Ero1α, for binding to PDI. Consistently, BPA slowed down the reoxidation of PDI and caused the reduction of PDI in HeLa cells, indicating that BPA has a great impact on the redox homeostasis of PDI within cells. However, BPA had no effect on the interaction between PDI and peroxiredoxin-4 (Prx4), another PDI family oxidase, suggesting that the interaction between Prx4 and PDI is different from that of Ero1α and PDI. These results indicate that BPA, a widely distributed and potentially harmful chemical, inhibits Ero1-PDI-mediated disulfide bond formation.
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Affiliation(s)
- Masaki Okumura
- School of Science and Technology, Kwansei Gakuin University, Gakuen 2-1, Sanda, Hyogo 669-1337, Japan,; Division of Protein Chemistry, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan,; RIKEN SPring-8 Center, RIKEN, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan,; School Faculty of Science and Engineering, Kinki University, Kowakae 3-4-1, Higashi-Osaka, Osaka 577-8502, Japan,; Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan.
| | - Hiroshi Kadokura
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Shoko Hashimoto
- School of Science and Technology, Kwansei Gakuin University, Gakuen 2-1, Sanda, Hyogo 669-1337, Japan
| | - Katsuhide Yutani
- RIKEN SPring-8 Center, RIKEN, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Shingo Kanemura
- School of Science and Technology, Kwansei Gakuin University, Gakuen 2-1, Sanda, Hyogo 669-1337, Japan,; RIKEN SPring-8 Center, RIKEN, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan,; Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Takaaki Hikima
- RIKEN SPring-8 Center, RIKEN, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Yuji Hidaka
- School Faculty of Science and Engineering, Kinki University, Kowakae 3-4-1, Higashi-Osaka, Osaka 577-8502, Japan
| | - Len Ito
- School of Science and Technology, Kwansei Gakuin University, Gakuen 2-1, Sanda, Hyogo 669-1337, Japan
| | - Kohei Shiba
- ProCube Business Division, Sysmex Corporation, 1-1-2, Murotani, Nishi-ku, Kobe, Hyogo, 651-2241, Japan, and
| | - Shoji Masui
- Division of Protein Chemistry, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan,; Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Daiki Imai
- School of Science and Technology, Kwansei Gakuin University, Gakuen 2-1, Sanda, Hyogo 669-1337, Japan,; RIKEN SPring-8 Center, RIKEN, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Susumu Imaoka
- School of Science and Technology, Kwansei Gakuin University, Gakuen 2-1, Sanda, Hyogo 669-1337, Japan
| | - Hiroshi Yamaguchi
- School of Science and Technology, Kwansei Gakuin University, Gakuen 2-1, Sanda, Hyogo 669-1337, Japan,; RIKEN SPring-8 Center, RIKEN, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan,.
| | - Kenji Inaba
- Division of Protein Chemistry, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan,; Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan.
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Abstract
Disulfide formation within the endoplasmic reticulum is a complex process requiring a disulfide exchange protein such as PDI (protein disulfide-isomerase) and a mechanism to form disulfides de novo. In mammalian cells, the major pathway for de novo disulfide formation involves the enzyme Ero1α (endoplasmic reticulum oxidase 1α) which couples oxidation of thiols to the reduction of molecular oxygen to form hydrogen peroxide (H2O2). Ero1α activity is tightly regulated by a mechanism that requires the formation of regulatory disulfides. These regulatory disulfides are reduced to activate and reform to inactivate the enzyme. To investigate the mechanism of inactivation we analysed regulatory disulfide formation in the presence of various oxidants under controlled oxygen concentration. Neither molecular oxygen nor H2O2 was able to oxidize Ero1α efficiently to form the correct regulatory disulfides. However, specific members of the PDI family, such as PDI or ERp46 (endoplasmic reticulum-resident protein 46), were able to catalyse this process. Further studies showed that both active sites of PDI contribute to the formation of regulatory disulfides in Ero1α and that the PDI substrate-binding domain is crucial to allow electron transfer between the two enzymes. The results of the present study demonstrate a simple feedback mechanism of re-gulation of mammalian Ero1α involving its primary substrate. The formation of disulfides in proteins that enter the endoplasmic reticulum is essential for their folding. We show in the present study that a key component of the machinery for disulfide formation is negatively regulated by the product of its catalytic activity.
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45
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Yang S, Wang X, Cui L, Ding X, Niu L, Yang F, Wang C, Wang CC, Lou J. Compact conformations of human protein disulfide isomerase. PLoS One 2014; 9:e103472. [PMID: 25084354 PMCID: PMC4118876 DOI: 10.1371/journal.pone.0103472] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 06/29/2014] [Indexed: 11/19/2022] Open
Abstract
Protein disulfide isomerase (PDI) composed of four thioredoxin-like domains a, b, b', and a', is a key enzyme catalyzing oxidative protein folding in the endoplasmic reticulum. Large scale molecular dynamics simulations starting from the crystal structures of human PDI (hPDI) in the oxidized and reduced states were performed. The results indicate that hPDI adopts more compact conformations in solution than in the crystal structures, which are stabilized primarily by inter-domain interactions, including the salt bridges between domains a and b' observed for the first time. A prominent feature of the compact conformations is that the two catalytic domains a and a' can locate close enough for intra-molecular electron transfer, which was confirmed by the characterization of an intermediate with a disulfide between the two domains. Mutations, which disrupt the inter-domain interactions, lead to decreased reductase activity of hPDI. Our molecular dynamics simulations and biochemical experiments reveal the intrinsic conformational dynamics of hPDI and its biological impact.
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Affiliation(s)
- Shang Yang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Xi Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Lei Cui
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Xiang Ding
- Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Lili Niu
- Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Fuquan Yang
- Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Chao Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Chih-chen Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- * E-mail: (CW); (JL)
| | - Jizhong Lou
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- * E-mail: (CW); (JL)
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46
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Peng L, Rasmussen MI, Chailyan A, Houen G, Højrup P. Probing the structure of human protein disulfide isomerase by chemical cross-linking combined with mass spectrometry. J Proteomics 2014; 108:1-16. [PMID: 24792702 DOI: 10.1016/j.jprot.2014.04.037] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 04/07/2014] [Accepted: 04/24/2014] [Indexed: 11/18/2022]
Abstract
UNLABELLED Protein disulfide-isomerase (PDI) is a four-domain flexible protein that catalyzes the formation of disulfide bonds in the endoplasmic reticulum. Here we have analyzed native PDI purified from human placenta by chemical cross-linking followed by mass spectrometry (CXMS). In addition to PDI the sample contained soluble calnexin and ERp72. Extensive cross-linking was observed within the PDI molecule, both intra- and inter-domain, as well as between the different components in the mixture. The high sensitivity of the analysis in the current experiments, combined with a likely promiscuous interaction pattern of the involved proteins, revealed relatively densely populated cross-link heat maps. The established X-ray structure of the monomeric PDI could be confirmed; however, the dimer as presented in the existing models does not seem to be prevalent in solution as modeling on the observed cross-links revealed new models of dimeric PDI. The observed inter-protein cross-links confirmed the existence of a peptide binding area on calnexin that binds strongly both PDI and ERp72. On the other hand, interaction sites on PDI and ERp72 could not be uniquely identified, indicating a more non-specific interaction pattern. BIOLOGICAL SIGNIFICANCE The present work demonstrates the use of chemical cross-linking and mass spectrometry (CXMS) for the determination of a solution structure of natural human PDI and its interaction with the chaperones ERp72 and calnexin. The data shows that the dimeric structure of PDI may be more diverse than indicated by present models. We further observe that the temperature influences the cross-linking pattern of PDI, but this does not influence the overall folding pattern of the molecule.
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Affiliation(s)
- Li Peng
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Morten Ib Rasmussen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Anna Chailyan
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Gunnar Houen
- Department of Clinical Biochemistry, Immunology and Genetics, Statens Serum Institut, Copenhagen, Denmark
| | - Peter Højrup
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark.
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Bastos-Aristizabal S, Kozlov G, Gehring K. Structural insight into the dimerization of human protein disulfide isomerase. Protein Sci 2014; 23:618-26. [PMID: 24549644 DOI: 10.1002/pro.2444] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Revised: 02/07/2014] [Accepted: 02/10/2014] [Indexed: 01/03/2023]
Abstract
Protein disulfide isomerases (PDIs) are responsible for catalyzing the proper oxidation and isomerization of disulfide bonds of newly synthesized proteins in the endoplasmic reticulum (ER). Here, it is shown that human PDI (PDIA1) dimerizes in vivo and proposed that the dimerization of PDI has physiological relevance by autoregulating its activity. The crystal structure of the dimeric form of noncatalytic bb' domains of human PDIA1 determined to 2.3 Å resolution revealed that the formation of dimers occludes the substrate binding site and may function as a mechanism to regulate PDI activity in the ER.
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Affiliation(s)
- Sara Bastos-Aristizabal
- Department of Biochemistry, Groupe de recherche axé sur la structure des protéines, McGill University, 3649 Promenade Sir William Osler, Montréal, Québec, H3G 0B1, Canada
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48
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Protein disulfide isomerase: a promising target for cancer therapy. Drug Discov Today 2014; 19:222-40. [DOI: 10.1016/j.drudis.2013.10.017] [Citation(s) in RCA: 168] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 09/12/2013] [Accepted: 10/22/2013] [Indexed: 12/15/2022]
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49
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Irvine AG, Wallis AK, Sanghera N, Rowe ML, Ruddock LW, Howard MJ, Williamson RA, Blindauer CA, Freedman RB. Protein disulfide-isomerase interacts with a substrate protein at all stages along its folding pathway. PLoS One 2014; 9:e82511. [PMID: 24465374 PMCID: PMC3896340 DOI: 10.1371/journal.pone.0082511] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 10/25/2013] [Indexed: 02/06/2023] Open
Abstract
In contrast to molecular chaperones that couple protein folding to ATP hydrolysis, protein disulfide-isomerase (PDI) catalyzes protein folding coupled to formation of disulfide bonds (oxidative folding). However, we do not know how PDI distinguishes folded, partly-folded and unfolded protein substrates. As a model intermediate in an oxidative folding pathway, we prepared a two-disulfide mutant of basic pancreatic trypsin inhibitor (BPTI) and showed by NMR that it is partly-folded and highly dynamic. NMR studies show that it binds to PDI at the same site that binds peptide ligands, with rapid binding and dissociation kinetics; surface plasmon resonance shows its interaction with PDI has a Kd of ca. 10−5 M. For comparison, we characterized the interactions of PDI with native BPTI and fully-unfolded BPTI. Interestingly, PDI does bind native BPTI, but binding is quantitatively weaker than with partly-folded and unfolded BPTI. Hence PDI recognizes and binds substrates via permanently or transiently unfolded regions. This is the first study of PDI's interaction with a partly-folded protein, and the first to analyze this folding catalyst's changing interactions with substrates along an oxidative folding pathway. We have identified key features that make PDI an effective catalyst of oxidative protein folding – differential affinity, rapid ligand exchange and conformational flexibility.
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Affiliation(s)
- Alistair G. Irvine
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- Department of Chemistry, University of Warwick, Coventry, United Kingdom
| | - A. Katrine Wallis
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Narinder Sanghera
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Michelle L. Rowe
- School of Biosciences, University of Kent, Canterbury, United Kingdom
| | | | - Mark J. Howard
- School of Biosciences, University of Kent, Canterbury, United Kingdom
| | | | | | - Robert B. Freedman
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- * E-mail:
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50
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Cho J. Protein disulfide isomerase in thrombosis and vascular inflammation. J Thromb Haemost 2013; 11:2084-91. [PMID: 24118938 PMCID: PMC4076787 DOI: 10.1111/jth.12413] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Indexed: 12/14/2022]
Abstract
Protein disulfide isomerase (PDI) catalyzes disulfide bond oxidation, reduction and isomerization during protein synthesis in the endoplasmic reticulum (ER). In addition to its critical role in the ER, in vitro and in vivo studies with blocking antibodies and conditional knockout mice have demonstrated that cell surface PDI is required for thrombosis, hemostasis and vascular inflammation in a manner dependent on its isomerase activity. This review will focus on our current understanding of the pathophysiologic role of PDI in regulating integrin-mediated platelet and neutrophil functions during vascular disease.
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Affiliation(s)
- J Cho
- Departments of Pharmacology and Anesthesiology, University of Illinois College of Medicine, Chicago, IL, USA
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