1
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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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2
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Sheng Y, Deng Y, Li X, Ji P, Sun X, Liu B, Zhu J, Zhao J, Nan Y, Zhou EM, Hiscox JA, Stewart JP, Sun Y, Zhao Q. Hepatitis E virus ORF3 protein hijacking thioredoxin domain-containing protein 5 (TXNDC5) for its stability to promote viral particle release. J Virol 2024; 98:e0164923. [PMID: 38548704 PMCID: PMC11019958 DOI: 10.1128/jvi.01649-23] [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: 01/10/2024] [Accepted: 03/06/2024] [Indexed: 04/17/2024] Open
Abstract
Hepatitis E virus (HEV) is the most common cause of acute viral hepatitis worldwide, responsible for approximately 20 million infections annually. Among the three open reading frames (ORFs) of the HEV genome, the ORF3 protein is involved in virus release. However, the host proteins involved in HEV release need to be clarified. In this study, a host protein, thioredoxin domain-containing protein 5 (TXNDC5), interacted with the non-palmitoylated ORF3 protein by co-immunoprecipitation analysis. We determined that the overexpression or knockdown of TXNDC5 positively regulated HEV release from the host cells. The 17FCL19 mutation of the ORF3 protein lost the ability to interact with TXNDC5. The releasing amounts of HEV with the ORF3 mutation (FCL17-19SSP) were decreased compared with wild-type HEV. The overexpression of TXNDC5 can stabilize and increase ORF3 protein amounts, but not the TXNDC5 mutant with amino acids 1-88 deletion. Meanwhile, we determined that the function of TXNDC5 on the stabilization of ORF3 protein is independent of the Trx-like domains. Knockdown of TXNDC5 could lead to the degradation of ORF3 protein by the endoplasmic reticulum (ER)-associated protein degradation-proteasome system. However, the ORF3 protein cannot be degraded in the knockout-TXNDC5 stable cells, suggesting that it may hijack other proteins for its stabilization. Subsequently, we found that the other members of protein disulfide isomerase (PDI), including PDIA1, PDIA3, PDIA4, and PDIA6, can increase ORF3 protein amounts, and PDIA3 and PDIA6 interact with ORF3 protein. Collectively, our study suggested that HEV ORF3 protein can utilize TXNDC5 for its stability in ER to facilitate viral release. IMPORTANCE Hepatitis E virus (HEV) infection is the leading cause of acute viral hepatitis worldwide. After the synthesis and modification in the cells, the mature ORF3 protein is essential for HEV release. However, the host protein involved in this process has yet to be determined. Here, we reported a novel host protein, thioredoxin domain-containing protein 5 (TXNDC5), as a chaperone, contributing to HEV release by facilitating ORF3 protein stability in the endoplasmic reticulum through interacting with non-palmitoylated ORF3 protein. However, we also found that in the knockout-TXNDC5 stable cell lines, the HEV ORF3 protein may hijack other proteins for its stabilization. For the first time, our study demonstrated the involvement of TXNDC5 in viral particle release. These findings provide some new insights into the process of the HEV life cycle, the interaction between HEV and host factors, and a new direction for antiviral design.
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Affiliation(s)
- Yamin Sheng
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Yingying Deng
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiaoxuan Li
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Pinpin Ji
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Xuwen Sun
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Baoyuan Liu
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Jiahong Zhu
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Jiakai Zhao
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Yuchen Nan
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - En-Min Zhou
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Julian A. Hiscox
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - James P. Stewart
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Yani Sun
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Qin Zhao
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
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3
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Sanyasi C, Balakrishnan SS, Chinnasamy T, Venugopalan N, Kandavelu P, Batra-Safferling R, Muthuvel SK. Insights on the dynamic behavior of protein disulfide isomerase in the solution environment through the SAXS technique. In Silico Pharmacol 2024; 12:23. [PMID: 38584776 PMCID: PMC10997565 DOI: 10.1007/s40203-024-00198-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 02/17/2024] [Indexed: 04/09/2024] Open
Abstract
The dynamic behavior of Protein Disulfide Isomerase (PDI) in an aqueous solution environment under physiologically active pH has been experimentally verified in this study using Small Angle X-ray Scattering (SAXS) technique. The structural mechanism of dimerization for full-length PDI molecules and co-complex with two renowned substrates has been comprehensively discussed. The structure models obtained from the SAXS data of PDI purified from bovine liver display behavior duality between unaccompanied-enzyme and after engaged with substrates. The analysis of SAXS data revealed that PDI exists as a homo-dimer in the solution environment, and substrate induction provoked its segregation into monomer to enable the enzyme to interact systematically with incoming clients. Supplementary Information The online version contains supplementary material available at 10.1007/s40203-024-00198-0.
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Affiliation(s)
- Chandrasekar Sanyasi
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry, 605014 India
| | - Susmida Seni Balakrishnan
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry, 605014 India
| | - Thirunavukkarasu Chinnasamy
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Pondicherry, 605014 India
| | - Nagarajan Venugopalan
- GMCA Structural Biology Facility, X-Ray Science Division, Argonne National Laboratory, Argonne, IL USA
| | - Palani Kandavelu
- SER-CAT and The Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30601 USA
| | - Renu Batra-Safferling
- Institute of Complex Systems (ICS-6: Structural Biochemistry), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Suresh Kumar Muthuvel
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry, 605014 India
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4
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Doharey PK, Verma P, Dubey A, Singh SK, Kumar M, Tripathi T, Alonazi M, Siddiqi NJ, Sharma B. Biophysical and in-silico studies on the structure-function relationship of Brugia malayi protein disulfide isomerase. J Biomol Struct Dyn 2024; 42:1533-1543. [PMID: 37079006 DOI: 10.1080/07391102.2023.2201849] [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: 11/14/2022] [Accepted: 04/03/2023] [Indexed: 04/21/2023]
Abstract
Human Lymphatic filariasis is caused by parasitic nematodes Wuchereria bancrofti, Brugia malayi, and Brugia timori. Protein disulfide isomerase (PDI), a redox-active enzyme, helps to form and isomerize the disulfide bonds, thereby acting as a chaperone. Such activity is essential for activating many essential enzymes and functional proteins. Brugia malayi protein disulfide isomerase (BmPDI) is crucial for parasite survival and an important drug target. Here, we used a combination of spectroscopic and computational analysis to study the structural and functional changes in the BmPDI during unfolding. Tryptophan fluorescence data revealed two well-separated transitions during the unfolding process, suggesting that the unfolding of the BmPDI is non-cooperative. The binding of the fluorescence probe 8-anilino-1-naphthalene sulfonic acid dye (ANS) validated the results obtained by the pH unfolding. The dynamics of molecular simulation performed at different pH conditions revealed the structural basis of BmPDI unfolding. Detailed analysis suggested that under different pH, both the global structure and the conformational dynamics of the active site residues were differentially altered. Our multiparametric study reveals the differential dynamics and collective motions of BmPDI unfolding, providing insights into its structure-function relationship.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Pravesh Verma
- Biochemistry Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Amit Dubey
- Computational Chemistry and Drug discovery Division, Quanta calculus Pvt. Ltd, Kushinagar, India
- Department of Pharmacology, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai, India
| | - Sudhir Kumar Singh
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Manish Kumar
- Department of Biochemistry, University of Allahabad, Allahabad, India
| | - Timir Tripathi
- Department of Biochemistry, North-Eastern Hill University, Umshing, India
| | - Mona Alonazi
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Nikhat Jamal Siddiqi
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Bechan Sharma
- Department of Biochemistry, University of Allahabad, Allahabad, India
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5
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Li Y, Xiao C, Pan Y, Qin L, Zheng L, Zhao M, Huang M. Optimization of Protein Folding for Improved Secretion of Human Serum Albumin Fusion Proteins in Saccharomyces cerevisiae. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:18414-18423. [PMID: 37966975 DOI: 10.1021/acs.jafc.3c05330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2023]
Abstract
The successful expression and secretion of recombinant proteins in cell factories significantly depend on the correct folding of nascent peptides, primarily achieved through disulfide bond formation. Thus, optimizing cellular protein folding is crucial, especially for proteins with complex spatial structures. In this study, protein disulfide isomerases (PDIs) from various species were introduced into Saccharomyces cerevisiae to facilitate proper disulfide bond formation and enhance recombinant protein secretion. The impacts of these PDIs on recombinant protein production and yeast growth metabolism were evaluated by substituting the endogenous PDI1. Heterologous PDIs cannot fully compensate the endogenous PDI. Furthermore, protein folding mediators, PDI and ER oxidoreductase 1 (Ero1), from different species were used to increase the production of complex human serum albumin (HSA) fusion proteins. The validated folding mediators were then introduced into unfolded protein response (UPR)-optimized strains, resulting in a 7.8-fold increase in amylase-HSA and an 18.2-fold increase in albiglutide compared with the control strain. These findings provide valuable insights for optimizing protein folding and expressing HSA-based drugs.
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Affiliation(s)
- Yanling Li
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China
- Guangdong Food Green Processing and Nutrition Regulation Technologies Research Center, Guangzhou 510650, China
| | - Chufan Xiao
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China
- Guangdong Food Green Processing and Nutrition Regulation Technologies Research Center, Guangzhou 510650, China
| | - Yuyang Pan
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China
- Guangdong Food Green Processing and Nutrition Regulation Technologies Research Center, Guangzhou 510650, China
| | - Ling Qin
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China
- Guangdong Food Green Processing and Nutrition Regulation Technologies Research Center, Guangzhou 510650, China
| | - Lin Zheng
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China
- Guangdong Food Green Processing and Nutrition Regulation Technologies Research Center, Guangzhou 510650, China
| | - Mouming Zhao
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China
- Guangdong Food Green Processing and Nutrition Regulation Technologies Research Center, Guangzhou 510650, China
| | - Mingtao Huang
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China
- Guangdong Food Green Processing and Nutrition Regulation Technologies Research Center, Guangzhou 510650, China
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6
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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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7
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Jiang H, Thapa P, Hao Y, Ding N, Alshahrani A, Wei Q. Protein Disulfide Isomerases Function as the Missing Link Between Diabetes and Cancer. Antioxid Redox Signal 2022; 37:1191-1205. [PMID: 36000195 PMCID: PMC9805878 DOI: 10.1089/ars.2022.0098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 08/11/2022] [Indexed: 01/13/2023]
Abstract
Significance: Diabetes has long been recognized as an independent risk factor for cancer, but there is insufficient mechanistic understanding of biological mediators that bridge two disorders together. Understanding the pathogenic association between diabetes and cancer has become the focus of many studies, and findings are potentially valuable for the development of effective preventive or therapeutic strategies for both disorders. Recent Advances: A summary of literature reveals a possible connection between diabetes and cancer through the family of protein disulfide isomerase (PDI). Historical as well as the most recent findings on the structure, biochemistry, and biology of the PDI family were summarized in this review. Critical Issues: PDIs in general function as redox enzymes and protein chaperones to control the quality of proteins by correcting or otherwise eliminating misfolded proteins in conditions of oxidative stress and endoplasmic reticulum stress, respectively. However, individual members of the PDI family may contribute uniquely to the pathogenesis of diabetes and cancer. Studies of exemplary members such as protein disulfide isomerase-associated (PDIA) 1, PDIA6, and PDIA15 were reviewed to highlight their contributions in the pathogenesis of diabetes and cancer and how they can be potential links bridging the two disorders through the cross talk of signaling pathways. Future Directions: Apparently ubiquitous presence of the PDIs creates difficulties and challenges for scientific community to develop targeted therapeutics for the treatment of diabetes and cancer simultaneously. Understanding molecular contribution of individual PDI in the context of specific disease may provide some insights into the development of mechanism-based target-directed therapeutics. Antioxid. Redox Signal. 37, 1191-1205.
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Affiliation(s)
- Hong Jiang
- Department of Toxicology and Cancer Biology, University of Kentucky College of Medicine, Lexington, Kentucky, USA
| | - Pratik Thapa
- Department of Toxicology and Cancer Biology, University of Kentucky College of Medicine, Lexington, Kentucky, USA
| | - Yanning Hao
- Department of Toxicology and Cancer Biology, University of Kentucky College of Medicine, Lexington, Kentucky, USA
| | - Na Ding
- Department of Toxicology and Cancer Biology, University of Kentucky College of Medicine, Lexington, Kentucky, USA
| | - Aziza Alshahrani
- Department of Toxicology and Cancer Biology, University of Kentucky College of Medicine, Lexington, Kentucky, USA
| | - Qiou Wei
- Department of Toxicology and Cancer Biology, University of Kentucky College of Medicine, Lexington, Kentucky, USA
- Markey Cancer Center, University of Kentucky College of Medicine, Lexington, Kentucky, USA
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8
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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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9
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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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10
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Tian Z, Wang Z, Munawar M, Zheng J. Identification and Characterization of a Novel Protein Disulfide Isomerase Gene ( MgPDI2) from Meloidogyne graminicola. Int J Mol Sci 2020; 21:E9586. [PMID: 33339262 PMCID: PMC7767112 DOI: 10.3390/ijms21249586] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/04/2020] [Accepted: 12/04/2020] [Indexed: 01/05/2023] Open
Abstract
Protein disulfide isomerase (PDI) is a multifunctional enzyme that catalyzes rate-limiting reactions such as disulfide bond formation, isomerization, and reduction. There is some evidence that indicates that PDI is also involved in host-pathogen interactions in plants. In this study, we show that the rice root-knot nematode, Meloidogyne graminicola, has evolved a secreted effector, MgPDI2, which is expressed in the subventral esophageal glands and up-regulated during the early parasitic stage of M. graminicola. Purified recombinant MgPDI2 functions as an insulin disulfide reductase and protects plasmid DNA from nicking. As an effector, MgPDI2 contributes to nematode parasitism. Silencing of MgPDI2 by RNA interference in the pre-parasitic second-stage juveniles (J2s) reduced M. graminicola multiplication and also increased M. graminicola mortality under H2O2 stress. In addition, an Agrobacterium-mediated transient expression assay found that MgPDI2 caused noticeable cell death in Nicotiana benthamiana. An intact C-terminal region containing the first catalytic domain (a) with an active motif (Cys-Gly-His-Cys, CGHC) and the two non-active domains (b and b') is required for cell death induction in N. benthamiana. This research may provide a promising target for the development of new strategies to combat M. graminicola infections.
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Affiliation(s)
- Zhongling Tian
- Laboratory of Plant Nematology, Institute of Biotechnology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China; (Z.T.); (M.M.)
| | - Zehua Wang
- Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China;
| | - Maria Munawar
- Laboratory of Plant Nematology, Institute of Biotechnology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China; (Z.T.); (M.M.)
| | - Jingwu Zheng
- Laboratory of Plant Nematology, Institute of Biotechnology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China; (Z.T.); (M.M.)
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Hangzhou 310058, China
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11
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Robinson RM, Reyes L, Duncan RM, Bian H, Strobel ED, Hyman SL, Reitz AB, Dolloff NG. Tuning isoform selectivity and bortezomib sensitivity with a new class of alkenyl indene PDI inhibitor. Eur J Med Chem 2019; 186:111906. [PMID: 31787362 DOI: 10.1016/j.ejmech.2019.111906] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 11/07/2019] [Accepted: 11/20/2019] [Indexed: 02/07/2023]
Abstract
Protein disulfide isomerase (PDI, PDIA1) is an emerging therapeutic target in oncology. PDI inhibitors have demonstrated a unique propensity to selectively induce apoptosis in cancer cells and overcome resistance to existing therapies, although drug candidates have not yet progressed to the stage of clinical development. We recently reported the discovery of lead indene compound E64FC26 as a potent pan-PDI inhibitor that enhances the cytotoxic effects of proteasome inhibitors in panels of Multiple Myeloma (MM) cells and MM mouse models. An extensive medicinal chemistry program has led to the generation of a diverse library of indene-containing molecules with varying degrees of proteasome inhibitor potentiating activity. These compounds were generated by a novel nucleophilic aromatic ring cyclization and dehydration reaction from the precursor ketones. The results provide detailed structure activity relationships (SAR) around this indene pharmacophore and show a high degree of correlation between potency of PDI inhibition and bortezomib (Btz) potentiation in MM cells. Inhibition of PDI leads to ER and oxidative stress characterized by the accumulation of misfolded poly-ubiquitinated proteins and the induction of UPR biomarkers ATF4, CHOP, and Nrf2. This work characterizes the synthesis and SAR of a new chemical class and further validates PDI as a therapeutic target in MM as a single agent and in combination with proteasome inhibitors.
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Affiliation(s)
- Reeder M Robinson
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, College of Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Leticia Reyes
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, College of Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Ravyn M Duncan
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, College of Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Haiyan Bian
- Fox Chase Chemical Diversity Center, Inc, Doylestown, PA, USA
| | - Eric D Strobel
- Fox Chase Chemical Diversity Center, Inc, Doylestown, PA, USA
| | - Sarah L Hyman
- Fox Chase Chemical Diversity Center, Inc, Doylestown, PA, USA
| | - Allen B Reitz
- Fox Chase Chemical Diversity Center, Inc, Doylestown, PA, USA
| | - Nathan G Dolloff
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, College of Medicine, Medical University of South Carolina, Charleston, SC, USA.
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12
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A comparative analysis of secreted protein disulfide isomerases from the tropical co-endemic parasites Schistosoma mansoni and Leishmania major. Sci Rep 2019; 9:9568. [PMID: 31267027 PMCID: PMC6606611 DOI: 10.1038/s41598-019-45709-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 06/10/2019] [Indexed: 12/19/2022] Open
Abstract
The human parasites Schistosoma mansoni and Leishmania major are co-endemic and a major threat to human health. Though displaying different tissue tropisms, they excrete/secrete similar subsets of intracellular proteins that, interacting with the host extracellular matrix (ECM), help the parasites invading the host. We selected one of the most abundant proteins found in the secretomes of both parasites, protein disulfide isomerase (PDI), and performed a comparative screening with surface plasmon resonance imaging (SPRi), looking for ECM binding partners. Both PDIs bind heparan sulfate; none of them binds collagens; each of them binds further ECM components, possibly linked to the different tropisms. We investigated by small-angle X-ray scattering both PDIs structures and those of a few complexes with host partners, in order to better understand the differences within this conserved family fold. Furthermore, we highlighted a previously undisclosed moonlighting behaviour of both PDIs, namely a concentration-dependent switch of function from thiol-oxidoreductase to holdase. Finally, we have tried to exploit the differences to look for possible compounds able to interfere with the redox activity of both PDI.
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13
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Dynamic assembly of protein disulfide isomerase in catalysis of oxidative folding. Nat Chem Biol 2019; 15:499-509. [PMID: 30992562 DOI: 10.1038/s41589-019-0268-8] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 03/07/2019] [Indexed: 11/08/2022]
Abstract
Time-resolved direct observations of proteins in action provide essential mechanistic insights into biological processes. Here, we present mechanisms of action of protein disulfide isomerase (PDI)-the most versatile disulfide-introducing enzyme in the endoplasmic reticulum-during the catalysis of oxidative protein folding. Single-molecule analysis by high-speed atomic force microscopy revealed that oxidized PDI is in rapid equilibrium between open and closed conformations, whereas reduced PDI is maintained in the closed state. In the presence of unfolded substrates, oxidized PDI, but not reduced PDI, assembles to form a face-to-face dimer, creating a central hydrophobic cavity with multiple redox-active sites, where substrates are likely accommodated to undergo accelerated oxidative folding. Such PDI dimers are diverse in shape and have different lifetimes depending on substrates. To effectively guide proper oxidative protein folding, PDI regulates conformational dynamics and oligomeric states in accordance with its own redox state and the configurations or folding states of substrates.
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14
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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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15
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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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16
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A shape-shifting redox foldase contributes to Proteus mirabilis copper resistance. Nat Commun 2017; 8:16065. [PMID: 28722010 PMCID: PMC5524982 DOI: 10.1038/ncomms16065] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 05/24/2017] [Indexed: 01/11/2023] Open
Abstract
Copper resistance is a key virulence trait of the uropathogen Proteus mirabilis. Here we show that P. mirabilis ScsC (PmScsC) contributes to this defence mechanism by enabling swarming in the presence of copper. We also demonstrate that PmScsC is a thioredoxin-like disulfide isomerase but, unlike other characterized proteins in this family, it is trimeric. PmScsC trimerization and its active site cysteine are required for wild-type swarming activity in the presence of copper. Moreover, PmScsC exhibits unprecedented motion as a consequence of a shape-shifting motif linking the catalytic and trimerization domains. The linker accesses strand, loop and helical conformations enabling the sampling of an enormous folding landscape by the catalytic domains. Mutation of the shape-shifting motif abolishes disulfide isomerase activity, as does removal of the trimerization domain, showing that both features are essential to foldase function. More broadly, the shape-shifter peptide has the potential for ‘plug and play’ application in protein engineering. Bacterial disulfide isomerases shuffle incorrect disulfide bonds. Here, the authors structurally characterize the disulfide isomerase ScsC from Proteus mirabilis and identify a functionally important shape-shifting motif that allows ScsC to adopt a diverse range of conformations and enable swarming in the presence of copper stress.
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17
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Maegawa KI, Watanabe S, Noi K, Okumura M, Amagai Y, Inoue M, Ushioda R, Nagata K, Ogura T, Inaba K. The Highly Dynamic Nature of ERdj5 Is Key to Efficient Elimination of Aberrant Protein Oligomers through ER-Associated Degradation. Structure 2017; 25:846-857.e4. [PMID: 28479060 DOI: 10.1016/j.str.2017.04.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 03/08/2017] [Accepted: 04/10/2017] [Indexed: 12/12/2022]
Abstract
ERdj5, composed of an N-terminal J domain followed by six thioredoxin-like domains, is the largest protein disulfide isomerase family member and functions as an ER-localized disulfide reductase that enhances ER-associated degradation (ERAD). Our previous studies indicated that ERdj5 comprises two regions, the N- and C-terminal clusters, separated by a linker loop and with distinct functional roles in ERAD. We here present a new crystal structure of ERdj5 with a largely different cluster arrangement relative to that in the original crystal structure. Single-molecule observation by high-speed atomic force microscopy visualized rapid cluster movement around the flexible linker loop, indicating the highly dynamic nature of ERdj5 in solution. ERdj5 mutants with a fixed-cluster orientation compromised the ERAD enhancement activity, likely because of less-efficient reduction of aberrantly formed disulfide bonds and prevented substrate transfer in the ERdj5-mediated ERAD pathway. We propose a significant role of ERdj5 conformational dynamics in ERAD of disulfide-linked oligomers.
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Affiliation(s)
- Ken-Ichi Maegawa
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan; CREST, JST, Japan
| | - Satoshi Watanabe
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan; CREST, JST, Japan
| | - Kentaro Noi
- Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan; CREST, JST, Japan
| | - Masaki Okumura
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Yuta Amagai
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Michio Inoue
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan; CREST, JST, Japan
| | - Ryo Ushioda
- Department of Molecular Biosciences, Kyoto Sangyo University, Kyoto 603-8455, Japan; CREST, JST, Japan
| | - Kazuhiro Nagata
- Department of Molecular Biosciences, Kyoto Sangyo University, Kyoto 603-8455, Japan; CREST, JST, Japan
| | - Teru Ogura
- Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan; CREST, JST, Japan
| | - Kenji Inaba
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan; CREST, JST, Japan.
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18
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Assembly of the elongated collagen prolyl 4-hydroxylase α2β2 heterotetramer around a central α2 dimer. Biochem J 2017; 474:751-769. [DOI: 10.1042/bcj20161000] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 01/05/2017] [Accepted: 01/16/2017] [Indexed: 11/17/2022]
Abstract
Collagen prolyl 4-hydroxylase (C-P4H), an α2β2 heterotetramer, is a crucial enzyme for collagen synthesis. The α-subunit consists of an N-terminal dimerization domain, a central peptide substrate-binding (PSB) domain, and a C-terminal catalytic (CAT) domain. The β-subunit [also known as protein disulfide isomerase (PDI)] acts as a chaperone, stabilizing the functional conformation of C-P4H. C-P4H has been studied for decades, but its structure has remained elusive. Here, we present a three-dimensional small-angle X-ray scattering model of the entire human C-P4H-I heterotetramer. C-P4H is an elongated, bilobal, symmetric molecule with a length of 290 Å. The dimerization domains from the two α-subunits form a protein–protein dimer interface, assembled around the central antiparallel coiled-coil interface of their N-terminal α-helices. This region forms a thin waist in the bilobal tetramer. The two PSB/CAT units, each complexed with a PDI/β-subunit, form two bulky lobes pointing outward from this waist region, such that the PDI/β-subunits locate at the far ends of the βααβ complex. The PDI/β-subunit interacts extensively with the CAT domain. The asymmetric shape of two truncated C-P4H-I variants, also characterized in the present study, agrees with this assembly. Furthermore, data from these truncated variants show that dimerization between the α-subunits has an important role in achieving the correct PSB–CAT assembly competent for catalytic activity. Kinetic assays with various proline-rich peptide substrates and inhibitors suggest that, in the competent assembly, the PSB domain binds to the procollagen substrate downstream from the CAT domain.
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19
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Synthesis and Experimental Validation of New PDI Inhibitors with Antiproliferative Activity. J CHEM-NY 2017. [DOI: 10.1155/2017/2370359] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Protein disulfide isomerase (PDI) is a member of the thioredoxin superfamily of redox enzymes. PDI is a multifunctional protein that catalyzes disulfide bond formation, cleavage, and rearrangement in unfolded or misfolded proteins and functions as a chaperone in the endoplasmic reticulum. Besides acting as a protein folding catalyst, several evidences have suggested that PDI can bind small molecules containing, for example, a phenolic structure, which includes the estrogenic one. Increasing studies indicate that PDI is involved in both physiology and pathophysiology of cells and tissues and is involved in the survival and proliferation of different cancers. Propionic acid carbamoyl methyl amides (PACMAs) showed anticancer activity in human ovarian cancer, both in vitro and in vivo, by inhibiting PDI. The inhibition of PDI’s activity may have a therapeutic role, in various diseases, including cancer. In the present study, we designed and synthesized a diversified small library of compounds with the aim of identifying a new class of PDI inhibitors. Most of synthesized compounds showed a good inhibitory potency against PDI and particularly 4-methyl substituted 2,6-di-tert-butylphenol derivatives (8–10) presented an antiproliferative activity in a wide panel of human cancer cell lines, including ovarian ones.
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20
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Murugan R, Ravi G, Vijayaprasath G, Rajendran S, Thaiyan M, Nallappan M, Gopalan M, Hayakawa Y. Ni–CeO2 spherical nanostructures for magnetic and electrochemical supercapacitor applications. Phys Chem Chem Phys 2017; 19:4396-4404. [DOI: 10.1039/c6cp08281e] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ni–CeO2 spherical nano structures prepared using microwave assisted method and a specific capacitance of 577 F g−1 was achieved at 2 A g−1 in 1 M KOH.
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Affiliation(s)
| | - Ganesan Ravi
- Department of Physics
- Alagappa University
- Karaikudi-630 003
- India
| | | | | | | | - Maheswari Nallappan
- Department of Physics
- Gandhigram Rural Institute
- Gandhigram-Deemed University
- India
| | - Muralidharan Gopalan
- Department of Physics
- Gandhigram Rural Institute
- Gandhigram-Deemed University
- India
| | - Yasuhiro Hayakawa
- Research Institute of Electronics
- Shizuoka University
- Hamamatsu-432-8011
- Japan
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21
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Soares Moretti AI, Martins Laurindo FR. Protein disulfide isomerases: Redox connections in and out of the endoplasmic reticulum. Arch Biochem Biophys 2016; 617:106-119. [PMID: 27889386 DOI: 10.1016/j.abb.2016.11.007] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 11/08/2016] [Accepted: 11/21/2016] [Indexed: 12/13/2022]
Abstract
Protein disulfide isomerases are thiol oxidoreductase chaperones from thioredoxin superfamily. As redox folding catalysts from the endoplasmic reticulum (ER), their roles in ER-related redox homeostasis and signaling are well-studied. PDIA1 exerts thiol oxidation/reduction and isomerization, plus chaperone effects. Also, substantial evidence indicates that PDIs regulate thiol-disulfide switches in other cell locations such as cell surface and possibly cytosol. Subcellular PDI translocation routes remain unclear and seem Golgi-independent. The list of signaling and structural proteins reportedly regulated by PDIs keeps growing, via thiol switches involving oxidation, reduction and isomerization, S-(de)nytrosylation, (de)glutathyonylation and protein oligomerization. PDIA1 is required for agonist-triggered Nox NADPH oxidase activation and cell migration in vascular cells and macrophages, while PDIA1-dependent cytoskeletal regulation appears a converging pathway. Extracellularly, PDIs crucially regulate thiol redox signaling of thrombosis/platelet activation, e.g., integrins, and PDIA1 supports expansive caliber remodeling during injury repair via matrix/cytoskeletal organization. Some proteins display regulatory PDI-like motifs. PDI effects are orchestrated by expression levels or post-translational modifications. PDI is redox-sensitive, although probably not a mass-effect redox sensor due to kinetic constraints. Rather, the "all-in-one" organization of its peculiar redox/chaperone properties likely provide PDIs with precision and versatility in redox signaling, making them promising therapeutic targets.
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Affiliation(s)
- Ana Iochabel Soares Moretti
- Vascular Biology Laboratory, Heart Institute (InCor), University of São Paulo, School of Medicine, São Paulo, Brazil
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22
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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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23
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Role of Disulfide Bonds in Stabilizing the Conformation of Selected Enzymes—An Approach Based on Divergence Entropy Applied to the Structure of Hydrophobic Core in Proteins. ENTROPY 2016. [DOI: 10.3390/e18030067] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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24
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Neubert P, Halim A, Zauser M, Essig A, Joshi HJ, Zatorska E, Larsen ISB, Loibl M, Castells-Ballester J, Aebi M, Clausen H, Strahl S. Mapping the O-Mannose Glycoproteome in Saccharomyces cerevisiae. Mol Cell Proteomics 2016; 15:1323-37. [PMID: 26764011 PMCID: PMC4824858 DOI: 10.1074/mcp.m115.057505] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Indexed: 11/17/2022] Open
Abstract
O-Mannosylation is a vital protein modification conserved from fungi to humans. Yeast is a perfect model to study this post-translational modification, because in contrast to mammals O-mannosylation is the only type of O-glycosylation. In an essential step toward the full understanding of protein O-mannosylation we mapped the O-mannose glycoproteome in baker's yeast. Taking advantage of an O-glycan elongation deficient yeast strain to simplify sample complexity, we identified over 500 O-glycoproteins from all subcellular compartments for which over 2300 O-mannosylation sites were mapped by electron-transfer dissociation (ETD)-based MS/MS. In this study, we focus on the 293 O-glycoproteins (over 1900 glycosylation sites identified by ETD-MS/MS) that enter the secretory pathway and are targets of ER-localized protein O-mannosyltransferases. We find that O-mannosylation is not only a prominent modification of cell wall and plasma membrane proteins, but also of a large number of proteins from the secretory pathway with crucial functions in protein glycosylation, folding, quality control, and trafficking. The analysis of glycosylation sites revealed that O-mannosylation is favored in unstructured regions and β-strands. Furthermore, O-mannosylation is impeded in the proximity of N-glycosylation sites suggesting the interplay of these types of post-translational modifications. The detailed knowledge of the target proteins and their O-mannosylation sites opens for discovery of new roles of this essential modification in eukaryotes, and for a first glance on the evolution of different types of O-glycosylation from yeast to mammals.
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Affiliation(s)
- Patrick Neubert
- From the ‡Centre for Organismal Studies (COS), Department of Cell Chemistry, Heidelberg University, Im Neuenheimer Feld 360, D-69120 Heidelberg, Germany
| | - Adnan Halim
- §Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Martin Zauser
- From the ‡Centre for Organismal Studies (COS), Department of Cell Chemistry, Heidelberg University, Im Neuenheimer Feld 360, D-69120 Heidelberg, Germany
| | - Andreas Essig
- ¶Institute of Microbiology, Department of Biology, Swiss Federal Institute of Technology, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Hiren J Joshi
- §Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Ewa Zatorska
- From the ‡Centre for Organismal Studies (COS), Department of Cell Chemistry, Heidelberg University, Im Neuenheimer Feld 360, D-69120 Heidelberg, Germany
| | - Ida Signe Bohse Larsen
- §Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Martin Loibl
- From the ‡Centre for Organismal Studies (COS), Department of Cell Chemistry, Heidelberg University, Im Neuenheimer Feld 360, D-69120 Heidelberg, Germany
| | - Joan Castells-Ballester
- From the ‡Centre for Organismal Studies (COS), Department of Cell Chemistry, Heidelberg University, Im Neuenheimer Feld 360, D-69120 Heidelberg, Germany
| | - Markus Aebi
- ¶Institute of Microbiology, Department of Biology, Swiss Federal Institute of Technology, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Henrik Clausen
- §Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Sabine Strahl
- From the ‡Centre for Organismal Studies (COS), Department of Cell Chemistry, Heidelberg University, Im Neuenheimer Feld 360, D-69120 Heidelberg, Germany;
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25
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Kenche H, Ye ZW, Vedagiri K, Richards DM, Gao XH, Tew KD, Townsend DM, Blumental-Perry A. Adverse Outcomes Associated with Cigarette Smoke Radicals Related to Damage to Protein-disulfide Isomerase. J Biol Chem 2016; 291:4763-78. [PMID: 26728460 DOI: 10.1074/jbc.m115.712331] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Indexed: 12/19/2022] Open
Abstract
Identification of factors contributing to the development of chronic obstructive pulmonary disease (COPD) is crucial for developing new treatments. An increase in the levels of protein-disulfide isomerase (PDI), a multifaceted endoplasmic reticulum resident chaperone, has been demonstrated in human smokers, presumably as a protective adaptation to cigarette smoke (CS) exposure. We found a similar increase in the levels of PDI in the murine model of COPD. We also found abnormally high levels (4-6 times) of oxidized and sulfenilated forms of PDI in the lungs of murine smokers compared with non-smokers. PDI oxidation progressively increases with age. We begin to delineate the possible role of an increased ratio of oxidized PDI in the age-related onset of COPD by investigating the impact of exposure to CS radicals, such as acrolein (AC), hydroxyquinones (HQ), peroxynitrites (PN), and hydrogen peroxide, on their ability to induce unfolded protein response (UPR) and their effects on the structure and function of PDIs. Exposure to AC, HQ, PN, and CS resulted in cysteine and tyrosine nitrosylation leading to an altered three-dimensional structure of the PDI due to a decrease in helical content and formation of a more random coil structure, resulting in protein unfolding, inhibition of PDI reductase and isomerase activity in vitro and in vivo, and subsequent induction of endoplasmic reticulum stress response. Addition of glutathione prevented the induction of UPR, and AC and HQ induced structural changes in PDI. Exposure to PN and glutathione resulted in conjugation of PDI possibly at active site tyrosine residues. The findings presented here propose a new role of PDI in the pathogenesis of COPD and its age-dependent onset.
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Affiliation(s)
- Harshavardhan Kenche
- From the Anderson Cancer Institute, Memorial Health University Medical Center, Savannah, Georgia 31404
| | - Zhi-Wei Ye
- the College of Pharmacy, Medical University of South Carolina, Charleston, South Carolina 29425
| | - Kokilavani Vedagiri
- From the Anderson Cancer Institute, Memorial Health University Medical Center, Savannah, Georgia 31404
| | - Dylan M Richards
- From the Anderson Cancer Institute, Memorial Health University Medical Center, Savannah, Georgia 31404
| | - Xing-Huang Gao
- Genetics, Case Western Reserve University, Cleveland, Ohio 44106, and
| | - Kenneth D Tew
- the College of Pharmacy, Medical University of South Carolina, Charleston, South Carolina 29425
| | - Danyelle M Townsend
- the College of Pharmacy, Medical University of South Carolina, Charleston, South Carolina 29425
| | - Anna Blumental-Perry
- From the Anderson Cancer Institute, Memorial Health University Medical Center, Savannah, Georgia 31404, the Department of Biomedical Sciences, Mercer University School of Medicine, Savannah, Georgia 31404, the Departments of Surgery and
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26
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Albesa-Jové D, Comino N, Tersa M, Mohorko E, Urresti S, Dainese E, Chiarelli LR, Pasca MR, Manganelli R, Makarov V, Riccardi G, Svergun DI, Glockshuber R, Guerin ME. The Redox State Regulates the Conformation of Rv2466c to Activate the Antitubercular Prodrug TP053. J Biol Chem 2015; 290:31077-89. [PMID: 26546681 DOI: 10.1074/jbc.m115.677039] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Indexed: 11/06/2022] Open
Abstract
Rv2466c is a key oxidoreductase that mediates the reductive activation of TP053, a thienopyrimidine derivative that kills replicating and non-replicating Mycobacterium tuberculosis, but whose mode of action remains enigmatic. Rv2466c is a homodimer in which each subunit displays a modular architecture comprising a canonical thioredoxin-fold with a Cys(19)-Pro(20)-Trp(21)-Cys(22) motif, and an insertion consisting of a four α-helical bundle and a short α-helical hairpin. Strong evidence is provided for dramatic conformational changes during the Rv2466c redox cycle, which are essential for TP053 activity. Strikingly, a new crystal structure of the reduced form of Rv2466c revealed the binding of a C-terminal extension in α-helical conformation to a pocket next to the active site cysteine pair at the interface between the thioredoxin domain and the helical insertion domain. The ab initio low-resolution envelopes obtained from small angle x-ray scattering showed that the fully reduced form of Rv2466c adopts a "closed" compact conformation in solution, similar to that observed in the crystal structure. In contrast, the oxidized form of Rv2466c displays an "open" conformation, where tertiary structural changes in the α-helical subdomain suffice to account for the observed conformational transitions. Altogether our structural, biochemical, and biophysical data strongly support a model in which the formation of the catalytic disulfide bond upon TP053 reduction triggers local structural changes that open the substrate binding site of Rv2466c allowing the release of the activated, reduced form of TP053. Our studies suggest that similar structural changes might have a functional role in other members of the thioredoxin-fold superfamily.
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Affiliation(s)
- David Albesa-Jové
- From the Unidad de Biofísica, Centro Mixto Consejo Superior de Investigaciones Científicas, Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC,UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia 48940, Spain, the Departamento de Bioquímica, Universidad del País Vasco, Leioa, Bizkaia 48940, Spain, the IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Natalia Comino
- From the Unidad de Biofísica, Centro Mixto Consejo Superior de Investigaciones Científicas, Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC,UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia 48940, Spain, the Departamento de Bioquímica, Universidad del País Vasco, Leioa, Bizkaia 48940, Spain
| | - Montse Tersa
- From the Unidad de Biofísica, Centro Mixto Consejo Superior de Investigaciones Científicas, Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC,UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia 48940, Spain, the Departamento de Bioquímica, Universidad del País Vasco, Leioa, Bizkaia 48940, Spain
| | - Elisabeth Mohorko
- the Institute for Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
| | - Saioa Urresti
- From the Unidad de Biofísica, Centro Mixto Consejo Superior de Investigaciones Científicas, Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC,UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia 48940, Spain, the Departamento de Bioquímica, Universidad del País Vasco, Leioa, Bizkaia 48940, Spain
| | | | - Laurent R Chiarelli
- Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, 27100 Pavia, Italy
| | - Maria Rosalia Pasca
- Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, 27100 Pavia, Italy
| | | | - Vadim Makarov
- the A. N. Bakh Institute of Biochemistry, Russian Academy of Science, 119071 Moscow, Russia, and
| | - Giovanna Riccardi
- Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, 27100 Pavia, Italy
| | - Dmitri I Svergun
- the European Molecular Biology Laboratory, Hamburg Outstation, c/o Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, D-22603 Hamburg, Germany
| | - Rudi Glockshuber
- the Institute for Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
| | - Marcelo E Guerin
- From the Unidad de Biofísica, Centro Mixto Consejo Superior de Investigaciones Científicas, Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC,UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia 48940, Spain, the Departamento de Bioquímica, Universidad del País Vasco, Leioa, Bizkaia 48940, Spain, the IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain,
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27
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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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28
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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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29
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Sapra A, Ramadan D, Thorpe C. Multivalency in the inhibition of oxidative protein folding by arsenic(III) species. Biochemistry 2014; 54:612-21. [PMID: 25506675 PMCID: PMC4303313 DOI: 10.1021/bi501360e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
The
renewed use of arsenicals as chemotherapeutics has rekindled
interest in the biochemistry of As(III) species. In this work, simple
bis- and tris-arsenical derivatives were synthesized with the aim
of exploiting the chelate effect in the inhibition of thiol-disulfide
oxidoreductases (here, Quiescin sulfhydryl oxidase, QSOX, and protein
disulfide isomerase, PDI) that utilize two or more CxxC motifs in
the catalysis of oxidative protein folding. Coupling 4-aminophenylarsenoxide
(APAO) to acid chloride or anhydride derivatives yielded two bis-arsenical
prototypes, BA-1 and BA-2, and a tris-arsenical, TA-1. Unlike the
monoarsenical, APAO, these new reagents proved to be strong inhibitors
of oxidative protein folding in the presence of a realistic intracellular
concentration of competing monothiol (here, 5 mM reduced glutathione,
GSH). However, this inhibition does not reflect direct inactivation
of QSOX or PDI, but avid binding of MVAs to the reduced unfolded protein
substrates themselves. Titrations of reduced riboflavin-binding protein
with MVAs show that all 18 protein −SH groups can be captured
by these arsenicals. With reduced RNase, addition of substoichiometric
levels of MVAs is accompanied by the formation of Congo Red- and Thioflavin
T-positive fibrillar aggregates. Even with Kd values of ∼50 nM, MVAs are ineffective inhibitors
of PDI in the presence of millimolar levels of competing GSH. These
results underscore the difficulties of designing effective and specific
arsenical inhibitors for folded enzymes and proteins. Some of the
cellular effects of arsenicals likely reflect their propensity to
associate very tightly and nonspecifically to conformationally mobile
cysteine-rich regions of proteins, thereby interfering with folding
and/or function.
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Affiliation(s)
- Aparna Sapra
- Department of Chemistry and Biochemistry, University of Delaware , Newark, Delaware 19716, United States
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30
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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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31
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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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32
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Abstract
SIGNIFICANCE The thioredoxin (Trx) superfamily proteins, including protein disulfide isomerases (PDI) and Dsb protein family, are major players in oxidative protein folding, which involves native disulfide bond formation. These proteins contain Trx folds with CXXC active sites and fulfill their physiological functions in oxidative cellular compartments such as the endoplasmic reticulum (ER) or the bacterial periplasm. RECENT ADVANCES The structure of the Trx superfamily protein PDI has been solved by X-ray crystallography and shown to be a flexible molecule, having a horseshoe shape with a closed reduced and an open oxidized conformation, which is important for exerting its catalytic activity. Atomic force microscopy revealed that PDI works as a placeholder to prevent early non-native disulfide bond formation and further misfolding. S-nitrosylation of the active site of PDI inhibits the PDI activity and links protein misfolding to neurodegenerative diseases like Alzheimer's and Parkinson's diseases. CRITICAL ISSUES Electron transfer pathways of the oxidative protein folding show conserved Trx-like thiol-disulfide chemistry. Overall, mammalian cells have a large number of disulfide-containing proteins, the folding of which involves non-native disulfide bond isomerization. The process is sensitive to oxidative stress and ER stress. FUTURE DIRECTIONS The correct oxidative protein folding is critical for the substrate protein stability and function, and protein misfolding is linked to, for example, neurodegenerative diseases. Further understanding on the mechanisms and specific roles of Trx superfamily proteins in oxidative protein folding may lead to drug development for the treatment of bacterial infection and various human diseases in aging and neurodegeneration.
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Affiliation(s)
- Jun Lu
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet , Stockholm, Sweden
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33
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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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34
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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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35
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Substrate-induced unfolding of protein disulfide isomerase displaces the cholera toxin A1 subunit from its holotoxin. PLoS Pathog 2014; 10:e1003925. [PMID: 24516389 PMCID: PMC3916401 DOI: 10.1371/journal.ppat.1003925] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 12/30/2013] [Indexed: 01/05/2023] Open
Abstract
To generate a cytopathic effect, the catalytic A1 subunit of cholera toxin (CT) must be separated from the rest of the toxin. Protein disulfide isomerase (PDI) is thought to mediate CT disassembly by acting as a redox-driven chaperone that actively unfolds the CTA1 subunit. Here, we show that PDI itself unfolds upon contact with CTA1. The substrate-induced unfolding of PDI provides a novel molecular mechanism for holotoxin disassembly: we postulate the expanded hydrodynamic radius of unfolded PDI acts as a wedge to dislodge reduced CTA1 from its holotoxin. The oxidoreductase activity of PDI was not required for CT disassembly, but CTA1 displacement did not occur when PDI was locked in a folded conformation or when its substrate-induced unfolding was blocked due to the loss of chaperone function. Two other oxidoreductases (ERp57 and ERp72) did not unfold in the presence of CTA1 and did not displace reduced CTA1 from its holotoxin. Our data establish a new functional property of PDI that may be linked to its role as a chaperone that prevents protein aggregation. Protein disulfide isomerase (PDI) is a luminal endoplasmic reticulum (ER) protein with related but independent oxidoreductase and chaperone activities. The molecular mechanism of PDI chaperone function remains unidentified. Here, we report that PDI unfolds upon contact with the catalytic A1 subunit of cholera toxin (CT). This unfolding event dislodges CTA1 from the rest of the multimeric toxin, which is a prerequisite for the ER-to-cytosol export of CTA1 and toxin activity against the host cell. The substrate-induced unfolding of PDI is linked to its chaperone activity. Our work has established a new property of PDI that is required for CT disassembly and provides a possible structural basis for the broader role of PDI as a chaperone that prevents protein aggregation.
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Halloran M, Parakh S, Atkin JD. The role of s-nitrosylation and s-glutathionylation of protein disulphide isomerase in protein misfolding and neurodegeneration. Int J Cell Biol 2013; 2013:797914. [PMID: 24348565 PMCID: PMC3852308 DOI: 10.1155/2013/797914] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 08/19/2013] [Accepted: 09/02/2013] [Indexed: 12/13/2022] Open
Abstract
Neurodegenerative diseases involve the progressive loss of neurons, and a pathological hallmark is the presence of abnormal inclusions containing misfolded proteins. Although the precise molecular mechanisms triggering neurodegeneration remain unclear, endoplasmic reticulum (ER) stress, elevated oxidative and nitrosative stress, and protein misfolding are important features in pathogenesis. Protein disulphide isomerase (PDI) is the prototype of a family of molecular chaperones and foldases upregulated during ER stress that are increasingly implicated in neurodegenerative diseases. PDI catalyzes the rearrangement and formation of disulphide bonds, thus facilitating protein folding, and in neurodegeneration may act to ameliorate the burden of protein misfolding. However, an aberrant posttranslational modification of PDI, S-nitrosylation, inhibits its protective function in these conditions. S-nitrosylation is a redox-mediated modification that regulates protein function by covalent addition of nitric oxide- (NO-) containing groups to cysteine residues. Here, we discuss the evidence for abnormal S-nitrosylation of PDI (SNO-PDI) in neurodegeneration and how this may be linked to another aberrant modification of PDI, S-glutathionylation. Understanding the role of aberrant S-nitrosylation/S-glutathionylation of PDI in the pathogenesis of neurodegenerative diseases may provide insights into novel therapeutic interventions in the future.
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Affiliation(s)
- M. Halloran
- Department of Neuroscience in the School of Psychological Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - S. Parakh
- Department of Biochemistry, La Trobe University, Bundoora, VIC 3086, Australia
| | - J. D. Atkin
- Department of Biochemistry, La Trobe University, Bundoora, VIC 3086, Australia
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Xu LR, Liu XL, Chen J, Liang Y. Protein disulfide isomerase interacts with tau protein and inhibits its fibrillization. PLoS One 2013; 8:e76657. [PMID: 24098548 PMCID: PMC3788760 DOI: 10.1371/journal.pone.0076657] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Accepted: 08/30/2013] [Indexed: 01/20/2023] Open
Abstract
Background Tau protein is implicated in the pathogenesis of neurodegenerative disorders such as tauopathies including Alzheimer disease, and Tau fibrillization is thought to be related to neuronal toxicity. Physiological inhibitors of Tau fibrillization hold promise for developing new strategies for treatment of Alzheimer disease. Because protein disulfide isomerase (PDI) is both an enzyme and a chaperone, and implicated in neuroprotection against Alzheimer disease, we want to know whether PDI can prevent Tau fibrillization. In this study, we have investigated the interaction between PDI and Tau protein and the effect of PDI on Tau fibrillization. Methodology/Principal Findings As evidenced by co-immunoprecipitation and confocal laser scanning microscopy, human PDI interacts and co-locates with some endogenous human Tau on the endoplasmic reticulum of undifferentiated SH-SY5Y neuroblastoma cells. The results from isothermal titration calorimetry show that one full-length human PDI binds to one full-length human Tau (or human Tau fragment Tau244–372) monomer with moderate, micromolar affinity at physiological pH and near physiological ionic strength. As revealed by thioflavin T binding assays, Sarkosyl-insoluble SDS-PAGE, and transmission electron microscopy, full-length human PDI remarkably inhibits both steps of nucleation and elongation of Tau244–372 fibrillization in a concentration-dependent manner. Furthermore, we find that two molecules of the a-domain of human PDI interact with one Tau244–372 molecule with sub-micromolar affinity, and inhibit both steps of nucleation and elongation of Tau244–372 fibrillization more strongly than full-length human PDI. Conclusions/Significance We demonstrate for the first time that human PDI binds to Tau protein mainly through its thioredoxin-like catalytic domain a, forming a 1∶1 complex and preventing Tau misfolding. Our findings suggest that PDI could act as a physiological inhibitor of Tau fibrillization, and have applications for developing novel strategies for treatment and early diagnosis of Alzheimer disease.
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Affiliation(s)
- Li-Rong Xu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xiao-Ling Liu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jie Chen
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yi Liang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
- * E-mail:
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38
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Pinto RD, Moreira AR, Pereira PJB, dos Santos NMS. Two thioredoxin-superfamily members from sea bass (Dicentrarchus labrax, L.): characterization of PDI (PDIA1) and ERp57 (PDIA3). FISH & SHELLFISH IMMUNOLOGY 2013; 35:1163-1175. [PMID: 23880452 DOI: 10.1016/j.fsi.2013.07.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Revised: 07/03/2013] [Accepted: 07/14/2013] [Indexed: 06/02/2023]
Abstract
PDI (PDIA1) and ERp57 (PDIA3), members of the PDI family and of the thioredoxin (Trx) superfamily, are multifunctional proteins with wide physiological roles and have been implicated in several pathologies. Importantly, they are both involved in the MHC class I antigen presentation pathway. This paper reports the isolation and characterization of full cDNA and genomic clones from sea bass (Dicentrarchus labrax, L.) PDI (Dila-PDI) and ERp57 (Dila-ERp57). The genes are ~12.4 and ~7.1 kb long, originating 2155 and 2173 bp transcripts and encoding 497 and 484 amino acids mature proteins, for Dila-PDI and -ERp57, respectively. The PDI gene consists of eleven exons and ERp57 of thirteen. As described in other species, both molecules are composed of four Trx-like domains (abb'a') followed by a C-terminal tail, retaining two CGHC active sites and an ER-signalling sequence, suggestive of a conserved function. Additionally, three-dimensional homology models further support Dila-PDI and Dila-ERp57 as orthologs of mammalian PDI and ERp57, respectively. Finally, high similarity is observed to their vertebrate counterparts (>69% identity), especially among the few ones from closely related teleosts (>79% identity). Hence, these results provide relevant primary data and will enable further studies to clarify the roles of PDI and ERp57 in European sea bass immunity.
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Affiliation(s)
- Rute D Pinto
- Fish Immunology and Vaccinology Group, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal.
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39
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Oxidative protein-folding systems in plant cells. Int J Cell Biol 2013; 2013:585431. [PMID: 24187554 PMCID: PMC3800646 DOI: 10.1155/2013/585431] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 08/01/2013] [Indexed: 12/13/2022] Open
Abstract
Plants are unique among eukaryotes in having evolved organelles: the protein storage vacuole, protein body, and chloroplast. Disulfide transfer pathways that function in the endoplasmic reticulum (ER) and chloroplasts of plants play critical roles in the development of protein storage organelles and the biogenesis of chloroplasts, respectively. Disulfide bond formation requires the cooperative function of disulfide-generating enzymes (e.g., ER oxidoreductase 1), which generate disulfide bonds de novo, and disulfide carrier proteins (e.g., protein disulfide isomerase), which transfer disulfides to substrates by means of thiol-disulfide exchange reactions. Selective molecular communication between disulfide-generating enzymes and disulfide carrier proteins, which reflects the molecular and structural diversity of disulfide carrier proteins, is key to the efficient transfer of disulfides to specific sets of substrates. This review focuses on recent advances in our understanding of the mechanisms and functions of the various disulfide transfer pathways involved in oxidative protein folding in the ER, chloroplasts, and mitochondria of plants.
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40
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Wang C, Li W, Ren J, Fang J, Ke H, Gong W, Feng W, Wang CC. Structural insights into the redox-regulated dynamic conformations of human protein disulfide isomerase. Antioxid Redox Signal 2013; 19:36-45. [PMID: 22657537 DOI: 10.1089/ars.2012.4630] [Citation(s) in RCA: 155] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
AIM Human protein disulfide isomerase (hPDI) is a key enzyme and a redox-regulated chaperone responsible for oxidative protein folding in the endoplasmic reticulum. This work aims to reveal the molecular mechanism underlying the redox-regulated functions of hPDI by determining the crystal structures of hPDI in different redox states. RESULTS The structures of hPDI (abb'xa') in both the reduced and oxidized states showed that the four thioredoxin domains of a, b, b', and a' are arranged as a horseshoe shape with two CGHC active sites, respectively, in domains a and a' facing each other at the two ends. In reduced hPDI, domains a, b, and b' line up in the same plane, whereas domain a' twists ∼45° out. The two active sites are 27.6 Å apart. In oxidized hPDI, the four domains are differently organized to stay in the same plane, and the distance between the active sites increases to 40.3 Å. In contrast to the closed conformation of reduced hPDI, oxidized hPDI exists in an open state with more exposed hydrophobic areas and a larger cleft with potential for substrate binding. INNOVATION This is the first report of the high-resolution structures of hPDI containing all four domains in both the reduced and the oxidized states. It reveals the redox-regulated structural dynamic properties of the protein. CONCLUSION The redox-regulated open/closed conformational switch of hPDI endows the protein with versatile target-binding capacities for its enzymatic and chaperone functions.
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Affiliation(s)
- Chao Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
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41
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Benham AM, van Lith M, Sitia R, Braakman I. Ero1-PDI interactions, the response to redox flux and the implications for disulfide bond formation in the mammalian endoplasmic reticulum. Philos Trans R Soc Lond B Biol Sci 2013; 368:20110403. [PMID: 23530257 PMCID: PMC3638393 DOI: 10.1098/rstb.2011.0403] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The protein folding machinery of the endoplasmic reticulum (ER) ensures that proteins entering the eukaryotic secretory pathway acquire appropriate post-translational modifications and reach a stably folded state. An important component of this protein folding process is the supply of disulfide bonds. These are introduced into client proteins by ER resident oxidoreductases, including ER oxidoreductin 1 (Ero1). Ero1 is usually considered to function in a linear pathway, by ‘donating’ a disulfide bond to protein disulfide isomerase (PDI) and receiving electrons that are passed on to the terminal electron acceptor molecular oxygen. PDI engages with a range of clients as the direct catalyst of disulfide bond formation, isomerization or reduction. In this paper, we will consider the interactions of Ero1 with PDI family proteins and chaperones, highlighting the effect that redox flux has on Ero1 partnerships. In addition, we will discuss whether higher order protein complexes play a role in Ero1 function.
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Affiliation(s)
- Adam M Benham
- School of Biological and Biomedical Sciences, Durham University, South Road, Durham DH1 3LE, UK.
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42
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Li S, Zhao H, Li Y, Niu S, Cai B. Complete nucleotide sequence of plasmid pND6-2 from Pseudomonas putida ND6 and characterization of conjugative genes. Gene 2013; 512:148-56. [DOI: 10.1016/j.gene.2012.09.065] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Revised: 07/22/2012] [Accepted: 09/12/2012] [Indexed: 11/27/2022]
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43
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Sato Y, Inaba K. Disulfide bond formation network in the three biological kingdoms, bacteria, fungi and mammals. FEBS J 2012; 279:2262-71. [DOI: 10.1111/j.1742-4658.2012.08593.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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44
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Laurindo FRM, Pescatore LA, Fernandes DDC. Protein disulfide isomerase in redox cell signaling and homeostasis. Free Radic Biol Med 2012; 52:1954-69. [PMID: 22401853 DOI: 10.1016/j.freeradbiomed.2012.02.037] [Citation(s) in RCA: 168] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Revised: 02/23/2012] [Accepted: 02/24/2012] [Indexed: 12/16/2022]
Abstract
Thiol proteins may potentially act as redox signaling adaptor proteins, adjusting reactive oxygen species intermediates to specific signals and redox signals to cell homeostasis. In this review, we discuss redox effects of protein disulfide isomerase (PDI), a thioredoxin superfamily oxidoreductase from the endoplasmic reticulum (ER). Abundantly expressed PDI displays ubiquity, interactions with redox and nonredox proteins, versatile effects, and several posttranslational modifications. The PDI family contains >20 members with at least some apparent complementary actions. PDI has oxidoreductase, isomerase, and chaperone effects, the last not directly dependent on its thiols. PDI is a converging hub for pathways of disulfide bond introduction into ER-processed proteins, via hydrogen peroxide-generating mechanisms involving the oxidase Ero1α, as well as hydrogen peroxide-consuming reactions involving peroxiredoxin IV and the novel peroxidases Gpx7/8. PDI is a candidate pathway for coupling ER stress to oxidant generation. Emerging information suggests a convergence between PDI and Nox family NADPH oxidases. PDI silencing prevents Nox responses to angiotensin II and inhibits Akt phosphorylation in vascular cells and parasite phagocytosis in macrophages. PDI overexpression spontaneously enhances Nox activation and expression. In neutrophils, PDI redox-dependently associates with p47phox and supports the respiratory burst. At the cell surface, PDI exerts transnitrosation, thiol reductase, and apparent isomerase activities toward targets including adhesion and matrix proteins and proteases. Such effects mediate redox-dependent adhesion, coagulation/thrombosis, immune functions, and virus internalization. The route of PDI externalization remains elusive. Such multiple redox effects of PDI may contribute to its conspicuous expression and functional role in disease, rendering PDI family members putative redox cell signaling adaptors.
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Affiliation(s)
- Francisco R M Laurindo
- Vascular Biology Laboratory, Heart Institute (InCor), University of São Paulo School of Medicine, 05403-000 São Paulo, Brazil.
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45
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Jimenez-Roldan JE, Freedman RB, Römer RA, Wells SA. Rapid simulation of protein motion: merging flexibility, rigidity and normal mode analyses. Phys Biol 2012; 9:016008. [PMID: 22313618 DOI: 10.1088/1478-3975/9/1/016008] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Protein function frequently involves conformational changes with large amplitude on timescales which are difficult and computationally expensive to access using molecular dynamics. In this paper, we report on the combination of three computationally inexpensive simulation methods--normal mode analysis using the elastic network model, rigidity analysis using the pebble game algorithm, and geometric simulation of protein motion--to explore conformational change along normal mode eigenvectors. Using a combination of ElNemo and First/Froda software, large-amplitude motions in proteins with hundreds or thousands of residues can be rapidly explored within minutes using desktop computing resources. We apply the method to a representative set of six proteins covering a range of sizes and structural characteristics and show that the method identifies specific types of motion in each case and determines their amplitude limits.
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Affiliation(s)
- J E Jimenez-Roldan
- Department of Physics and Centre for Scientific Computing, University of Warwick, Coventry CV4 7AL, UK.
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46
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Grubb S, Guo L, Fisher EA, Brodsky JL. Protein disulfide isomerases contribute differentially to the endoplasmic reticulum-associated degradation of apolipoprotein B and other substrates. Mol Biol Cell 2011; 23:520-32. [PMID: 22190736 PMCID: PMC3279382 DOI: 10.1091/mbc.e11-08-0704] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
ER-associated degradation (ERAD) rids the early secretory pathway of misfolded or misprocessed proteins. Some members of the protein disulfide isomerase (PDI) family appear to facilitate ERAD substrate selection and retrotranslocation, but a thorough characterization of PDIs during the degradation of diverse substrates has not been undertaken, in part because there are 20 PDI family members in mammals. PDIs can also exhibit disulfide redox, isomerization, and/or chaperone activity, but which of these activities is required for the ERAD of different substrate classes is unknown. We therefore examined the fates of unique substrates in yeast, which expresses five PDIs. Through the use of a yeast expression system for apolipoprotein B (ApoB), which is disulfide rich, we discovered that Pdi1 interacts with ApoB and facilitates degradation through its chaperone activity. In contrast, Pdi1's redox activity was required for the ERAD of CPY* (a misfolded version of carboxypeptidase Y that has five disulfide bonds). The ERAD of another substrate, the alpha subunit of the epithelial sodium channel, was Pdi1 independent. Distinct effects of mammalian PDI homologues on ApoB degradation were then observed in hepatic cells. These data indicate that PDIs contribute to the ERAD of proteins through different mechanisms and that PDI diversity is critical to recognize the spectrum of potential ERAD substrates.
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Affiliation(s)
- Sarah Grubb
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
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47
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Wang C, Yu J, Huo L, Wang L, Feng W, Wang CC. Human protein-disulfide isomerase is a redox-regulated chaperone activated by oxidation of domain a'. J Biol Chem 2011; 287:1139-49. [PMID: 22090031 DOI: 10.1074/jbc.m111.303149] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Protein-disulfide isomerase (PDI), with domains arranged as abb'xa'c, is a key enzyme and chaperone localized in the endoplasmic reticulum (ER) catalyzing oxidative folding and preventing misfolding/aggregation of proteins. It has been controversial whether the chaperone activity of PDI is redox-regulated, and the molecular basis is unclear. Here, we show that both the chaperone activity and the overall conformation of human PDI are redox-regulated. We further demonstrate that the conformational changes are triggered by the active site of domain a', and the minimum redox-regulated cassette is located in b'xa'. The structure of the reduced bb'xa' reveals for the first time that domain a' packs tightly with both domain b' and linker x to form one compact structural module. Oxidation of domain a' releases the compact conformation and exposes the shielded hydrophobic areas to facilitate its high chaperone activity. Thus, the study unequivocally provides mechanistic insights into the redox-regulated chaperone activity of human PDI.
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Affiliation(s)
- Chao Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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48
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Jimenez-Roldan JE, Wells SA, Freedman RB, Roemer RA. Integration of FIRST, FRODA and NMM in a coarse grained method to study Protein Disulphide Isomerase conformational change. ACTA ACUST UNITED AC 2011. [DOI: 10.1088/1742-6596/286/1/012002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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49
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Ramírez-Díaz MI, Díaz-Magaña A, Meza-Carmen V, Johnstone L, Cervantes C, Rensing C. Nucleotide sequence of Pseudomonas aeruginosa conjugative plasmid pUM505 containing virulence and heavy-metal resistance genes. Plasmid 2011; 66:7-18. [PMID: 21421005 DOI: 10.1016/j.plasmid.2011.03.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2010] [Revised: 03/12/2011] [Accepted: 03/14/2011] [Indexed: 12/24/2022]
Abstract
We determined the complete nucleotide sequence of conjugative plasmid pUM505 isolated from a clinical strain of Pseudomonas aeruginosa. The plasmid had a length of 123,322bp and contained 138 complete coding regions, including 46% open reading frames encoding hypothetical proteins. pUM505 can be considered a hybrid plasmid because it presents two well-defined regions. The first region corresponded to a larger DNA segment with homology to a pathogenicity island from virulent Pseudomonas strains; this island in pUM505 was comprised of genes probably involved in virulence and genes encoding proteins implicated in replication, maintenance and plasmid transfer. Sequence analysis identified pil genes encoding a type IV secretion system, establishing pUM505 as a member of the family of IncI1 plasmids. Plasmid pUM505 also contained virB4/virD4 homologues, which are linked to virulence in other plasmids. The second region, smaller in length, contains inorganic mercury and chromate resistance gene clusters both flanked by putative mobile elements. Although no genes for antibiotic resistance were identified, when pUM505 was transferred to a recipient strain of P. aeruginosa it conferred resistance to the fluoroquinolone ciprofloxacin. pUM505 also conferred resistance to the superoxide radical generator paraquat. pUM505 could provide Pseudomonas strains with a wide variety of adaptive traits such as virulence, heavy-metal and antibiotic resistance and oxidative stress tolerance which can be selective factors for the distribution and prevalence of this plasmid in diverse environments, including hospitals and heavy metal contaminated soils.
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Affiliation(s)
- M I Ramírez-Díaz
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana, Morelia, Michoacán, Mexico.
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50
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The endoplasmic reticulum sulfhydryl oxidase Ero1β drives efficient oxidative protein folding with loose regulation. Biochem J 2011; 434:113-21. [PMID: 21091435 DOI: 10.1042/bj20101357] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In eukaryotes, disulfide bonds are formed in the endoplasmic reticulum, facilitated by the Ero1 (endoplasmic reticulum oxidoreductin 1) oxidase/PDI (protein disulfide-isomerase) system. Mammals have two ERO1 genes, encoding Ero1α and Ero1β proteins. Ero1β is constitutively expressed in professional secretory tissues and induced during the unfolded protein response. In the present work, we show that recombinant human Ero1β is twice as active as Ero1α in enzymatic assays. Ero1β oxidizes PDI more efficiently than other PDI family members and drives oxidative protein folding preferentially via the active site in the á domain of PDI. Our results reveal that Ero1β oxidase activity is regulated by long-range disulfide bonds and that Cys130 plays a critical role in feedback regulation. Compared with Ero1α, however, Ero1β is loosely regulated, consistent with its role as a more active oxidase when massive oxidative power is required.
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