1
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Kell DB, Pretorius E. Proteomic Evidence for Amyloidogenic Cross-Seeding in Fibrinaloid Microclots. Int J Mol Sci 2024; 25:10809. [PMID: 39409138 PMCID: PMC11476703 DOI: 10.3390/ijms251910809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2024] [Revised: 10/01/2024] [Accepted: 10/03/2024] [Indexed: 10/20/2024] Open
Abstract
In classical amyloidoses, amyloid fibres form through the nucleation and accretion of protein monomers, with protofibrils and fibrils exhibiting a cross-β motif of parallel or antiparallel β-sheets oriented perpendicular to the fibre direction. These protofibrils and fibrils can intertwine to form mature amyloid fibres. Similar phenomena can occur in blood from individuals with circulating inflammatory molecules (and also some originating from viruses and bacteria). Such pathological clotting can result in an anomalous amyloid form termed fibrinaloid microclots. Previous proteomic analyses of these microclots have shown the presence of non-fibrin(ogen) proteins, suggesting a more complex mechanism than simple entrapment. We thus provide evidence against such a simple entrapment model, noting that clot pores are too large and centrifugation would have removed weakly bound proteins. Instead, we explore whether co-aggregation into amyloid fibres may involve axial (multiple proteins within the same fibril), lateral (single-protein fibrils contributing to a fibre), or both types of integration. Our analysis of proteomic data from fibrinaloid microclots in different diseases shows no significant quantitative overlap with the normal plasma proteome and no correlation between plasma protein abundance and their presence in fibrinaloid microclots. Notably, abundant plasma proteins like α-2-macroglobulin, fibronectin, and transthyretin are absent from microclots, while less abundant proteins such as adiponectin, periostin, and von Willebrand factor are well represented. Using bioinformatic tools, including AmyloGram and AnuPP, we found that proteins entrapped in fibrinaloid microclots exhibit high amyloidogenic tendencies, suggesting their integration as cross-β elements into amyloid structures. This integration likely contributes to the microclots' resistance to proteolysis. Our findings underscore the role of cross-seeding in fibrinaloid microclot formation and highlight the need for further investigation into their structural properties and implications in thrombotic and amyloid diseases. These insights provide a foundation for developing novel diagnostic and therapeutic strategies targeting amyloidogenic cross-seeding in blood clotting disorders.
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Affiliation(s)
- Douglas B. Kell
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Crown St., Liverpool L69 7ZB, UK
- The Novo Nordisk Foundation Centre for Biosustainability, Building 220, Søltofts Plads 200, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Private Bag X1 Matieland, Stellenbosch 7602, South Africa
| | - Etheresia Pretorius
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Crown St., Liverpool L69 7ZB, UK
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Private Bag X1 Matieland, Stellenbosch 7602, South Africa
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2
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Cervilla-Martínez JF, Rodríguez-Gotor JJ, Wypijewski KJ, Fontán-Lozano Á, Wang T, Santamaría E, Fuller W, Mejías R. Altered Cortical Palmitoylation Induces Widespread Molecular Disturbances in Parkinson's Disease. Int J Mol Sci 2022; 23:ijms232214018. [PMID: 36430497 PMCID: PMC9696982 DOI: 10.3390/ijms232214018] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/01/2022] [Accepted: 11/04/2022] [Indexed: 11/16/2022] Open
Abstract
The relationship between Parkinson's disease (PD), the second-most common neurodegenerative disease after Alzheimer's disease, and palmitoylation, a post-translational lipid modification, is not well understood. In this study, to better understand the role of protein palmitoylation in PD and the pathways altered in this disease, we analyzed the differential palmitoyl proteome (palmitome) in the cerebral cortex of PD patients compared to controls (n = 4 per group). Data-mining of the cortical palmitome from PD patients and controls allowed us to: (i) detect a set of 150 proteins with altered palmitoylation in PD subjects in comparison with controls; (ii) describe the biological pathways and targets predicted to be altered by these palmitoylation changes; and (iii) depict the overlap between the differential palmitome identified in our study with protein interactomes of the PD-linked proteins α-synuclein, LRRK2, DJ-1, PINK1, GBA and UCHL1. In summary, we partially characterized the altered palmitome in the cortex of PD patients, which is predicted to impact cytoskeleton, mitochondrial and fibrinogen functions, as well as cell survival. Our study suggests that protein palmitoylation could have a role in the pathophysiology of PD, and that comprehensive palmitoyl-proteomics offers a powerful approach for elucidating novel cellular pathways modulated in this neurodegenerative disease.
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Affiliation(s)
- Juan F. Cervilla-Martínez
- Department of Physiology, School of Biology, University of Seville, Avenida de la Reina Mercedes, 6, 41012 Sevilla, Spain
| | - Juan J. Rodríguez-Gotor
- Department of Physiology, School of Biology, University of Seville, Avenida de la Reina Mercedes, 6, 41012 Sevilla, Spain
- Instituto de Neurociencias CSIC-UMH, Avenida Santiago Ramón y Cajal s/n, San Juan de Alicante, 03550 Alicante, Spain
| | - Krzysztof J. Wypijewski
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow G12 8QQ, UK
- School of Life Sciences, University of Dundee, Dundee DD2 5DA, UK
| | - Ángela Fontán-Lozano
- Department of Physiology, School of Biology, University of Seville, Avenida de la Reina Mercedes, 6, 41012 Sevilla, Spain
- Instituto de Biomedicina de Sevilla, Campus Hospital Universitario Virgen del Rocío, Avda. Manuel Siurot, s/n, 41013 Sevilla, Spain
| | - Tao Wang
- McKusick—Nathans Institute of Genetic Medicine and Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Enrique Santamaría
- Clinical Neuroproteomics Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), IDISNA, Irunlarrea Street, 3, 31008 Pamplona, Spain
| | - William Fuller
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Rebeca Mejías
- Department of Physiology, School of Biology, University of Seville, Avenida de la Reina Mercedes, 6, 41012 Sevilla, Spain
- Instituto de Biomedicina de Sevilla, Campus Hospital Universitario Virgen del Rocío, Avda. Manuel Siurot, s/n, 41013 Sevilla, Spain
- Correspondence: ; Tel.: +34-954-559-549
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3
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Characterization of Plasma SDS-Protein Aggregation Profile of Patients with Heart Failure with Preserved Ejection Fraction. J Cardiovasc Transl Res 2022:10.1007/s12265-022-10334-w. [PMID: 36271180 DOI: 10.1007/s12265-022-10334-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 10/13/2022] [Indexed: 10/24/2022]
Abstract
This study characterizes the plasma levels and composition of SDS-resistant aggregates (SRAs) in patients with heart failure with preserved ejection fraction (HFpEF) to infer molecular pathways associated with disease and/or proteostasis disruption. Twenty adults (ten with HFpEF and ten age-matched individuals) were included. Circulating SRAs were resolved by diagonal two-dimensional SDS-PAGE, and their protein content was identified by mass spectrometry. Protein carbonylation, ubiquitination and ficolin-3 were evaluated. Patients with HFpEF showed higher SRA/total (36.6 ± 4.9% vs 29.6 ± 2.2%, p = 0.009) and SRA/soluble levels (58.6 ± 12.7% vs 40.6 ± 5.8%, p = 0.008). SRAs were carbonylated and ubiquitinated, suggesting they are composed of dysfunctional proteins resistant to degradation. SRAs were enriched in proteins associated with cardiovascular function/disease and with proteostasis machinery. Total ficolin-3 levels were decreased (0.77 ± 0.22, p = 0.041) in HFpEF, suggesting a reduced proteostasis capacity to clear circulating SRA. Thus, the higher accumulation of SRA in HFpEF may result from a failure or overload of the protein clearance machinery.
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4
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Yamamoto N, Chatani E. Multistep growth of amyloid intermediates and its inhibition toward exploring therapeutic way: A case study using insulin B chain and fibrinogen. Biophys Physicobiol 2022; 19:1-10. [PMID: 35797403 PMCID: PMC9173859 DOI: 10.2142/biophysico.bppb-v19.0017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 05/02/2022] [Indexed: 12/01/2022] Open
Abstract
It is crucial to understand the mechanism of amyloid fibril formation for the development of the therapeutic ways against amyloidoses and neurodegenerative diseases. Prefibrillar intermediates, which emerge prior to the fibril formation, seem to play a key role to the occurrence of nuclei of amyloid fibrils. We have focused on an insulin-derived peptide, B chain, to precisely clarify the mechanism of the fibril formation via prefibrillar intermediates. Various kinds of methods such as circular dichroism spectroscopy, dynamic light scattering, small-angle X-ray scattering, and atomic force microscopy were employed to track the structural changes in prefibrillar intermediates. The prefibrillar intermediates possessing rod-shaped structures elongated as a function of time, which led to fibril formation. We have also found that a blood clotting protein, fibrinogen, inhibits the amyloid fibril formation of B chain. This was caused by the stabilization of prefibrillar intermediates and thus the suppression of their elongation by fibrinogen. These findings have not only shed light on detailed mechanisms about how prefibrillar intermediates convert to the amyloid fibril, but also demonstrated that inhibiting the structural development of prefibrillar intermediates is an effective strategy to develop therapeutic ways against amyloid-related diseases. This review article is an extended version of the Japanese article, Observing Development of Amyloid Prefibrillar Intermediates and their Interaction with Chaperones for Inhibiting the Fibril Formation, published in SEIBUTSU BUTSURI Vol. 61, p. 236-239 (2021).
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Affiliation(s)
- Naoki Yamamoto
- School of Medicine, Jichi Medical University, Shimotsuke, Tochigi 329-0498, Japan
| | - Eri Chatani
- Graduate School of Science, Kobe University, Kobe, Hyogo 657-8501, Japan
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Najarzadeh Z, Nielsen J, Farzadfard A, Sereikaite V, Strømgaard K, Meyer RL, Otzen DE. Human Fibrinogen Inhibits Amyloid Assembly of Most Phenol-Soluble Modulins from Staphylococcus aureus. ACS OMEGA 2021; 6:21960-21970. [PMID: 34497891 PMCID: PMC8412925 DOI: 10.1021/acsomega.1c02333] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 06/16/2021] [Indexed: 06/13/2023]
Abstract
Functional amyloids are highly organized protein/peptide structures that inter alia promote biofilm formation in different bacteria. One such example is provided by a family of 20-45 residue-long peptides called phenol-soluble modulins (PSMs) from Staphylococcus aureus. External components such as eukaryotic host proteins, which alter self-assembly of bacterial amyloids, can affect the biofilm matrix. Here, we studied the effect of the highly prevalent human plasma protein fibrinogen (Fg) on fibrillation of PSMs. Fg inhibits or suppresses fibrillation of most PSMs tested (PSMα1, PSMβ1, and PSMβ2) except for PSMα3, whose already rapid aggregation is accelerated even further by Fg but leads to amorphous β-rich aggregates rather than fibrils. Fg also induces PSMβ2 to form amorphous aggregates and diverts PSMα1 into off-pathway oligomers which consist of both Fg and PSMα1 and cannot seed fibrillation. Peptide arrays showed that Fg bound to the N-terminus of PSMα1, while it bound to the entire length of PSMα3 (except the C terminus) and to the C-termini of PSMβ1 and PSMβ2. The latter peptides are all positively charged, while Fg is negatively charged at physiological pH. The positive charges complement Fg's net negative charge of -7.6 at pH 7.4. Fg's ability to inhibit PSM fibrillation reveals a potential host-defense mechanism to prevent bacterial biofilm growth and infections in the human body.
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Affiliation(s)
- Zahra Najarzadeh
- Interdisciplinary
Nanoscience Centre (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Janni Nielsen
- Interdisciplinary
Nanoscience Centre (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Azad Farzadfard
- Interdisciplinary
Nanoscience Centre (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Vita Sereikaite
- Department
of Drug Design and Pharmacology, University
of Copenhagen, Universitetsparken 2, 2100 Copenhagen Ø, Denmark
| | - Kristian Strømgaard
- Department
of Drug Design and Pharmacology, University
of Copenhagen, Universitetsparken 2, 2100 Copenhagen Ø, Denmark
| | - Rikke Louise Meyer
- Interdisciplinary
Nanoscience Centre (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Daniel Erik Otzen
- Interdisciplinary
Nanoscience Centre (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
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6
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Yamamoto N, Akai T, Inoue R, Sugiyama M, Tamura A, Chatani E. Structural Insights into the Inhibition of Amyloid Fibril Formation by Fibrinogen via Interaction with Prefibrillar Intermediates. Biochemistry 2019; 58:2769-2781. [DOI: 10.1021/acs.biochem.9b00439] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Naoki Yamamoto
- Graduate School of Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
| | - Taiki Akai
- Graduate School of Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
| | - Rintaro Inoue
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2, Asashiro-Nishi, Kumatori-cho, Sennan-gun, Osaka 590-0494, Japan
| | - Masaaki Sugiyama
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2, Asashiro-Nishi, Kumatori-cho, Sennan-gun, Osaka 590-0494, Japan
| | - Atsuo Tamura
- Graduate School of Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
| | - Eri Chatani
- Graduate School of Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
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7
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Niemietz C, Fleischhauer L, Sandfort V, Guttmann S, Zibert A, Schmidt HHJ. Hepatocyte-like cells reveal novel role of SerpinA1 in transthyretin amyloidosis. J Cell Sci 2018; 131:jcs.219824. [DOI: 10.1242/jcs.219824] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 09/18/2018] [Indexed: 01/07/2023] Open
Abstract
Transthyretin (TTR)-related familial amyloid polyneuropathy (ATTR) results from aggregation and extracellular disposition of misfolded TTR variants. Growing evidence suggests the importance of hepatic chaperones for modulation of pathogenesis. We took advantage of iPSC-derived hepatocyte-like cells (HLCs) derived from ATTR patients (ATTR-HLCs) to compare chaperone gene expression to healthy individuals (H-HLCs). From the set of genes analyzed, chaperones that are predominantly located extracellularly were differently expressed. Expression of the chaperones showed a high correlation with TTR in both ATTR-HLCs and H-HLCs. In contrast, after TTR knockdown, the correlation was mainly affected in ATTR-HLCs suggesting that variant TTR expression triggers abberant chaperone expression. Serpin peptidase inhibitor clade A member 1 (SERPINA1/alpha-1 antitrypsin) was the only extracellular chaperone that was markedly upregulated after TTR knockdown in ATTR-HLCs. Co-immunoprecipitation revealed that SerpinA1 physically interacts with TTR. In vitro assays indicated that SerpinA1 can interfere with TTR aggregation. Taken together, our results suggest that extracellular chaperones play a crucial role in ATTR pathogenesis, in particular SerpinA1, which may affect amyloid formation.
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Affiliation(s)
- Christoph Niemietz
- Medizinische Klinik B für Gastroenterologie und Hepatologie, Universitätsklinikum Münster, Münster, Germany
| | - Lutz Fleischhauer
- Medizinische Klinik B für Gastroenterologie und Hepatologie, Universitätsklinikum Münster, Münster, Germany
- Present address: Fakultät für angewandte Naturwissenschaften und Mechatronik, Hochschule München, München, Germany
| | - Vanessa Sandfort
- Medizinische Klinik B für Gastroenterologie und Hepatologie, Universitätsklinikum Münster, Münster, Germany
| | - Sarah Guttmann
- Medizinische Klinik B für Gastroenterologie und Hepatologie, Universitätsklinikum Münster, Münster, Germany
| | - Andree Zibert
- Medizinische Klinik B für Gastroenterologie und Hepatologie, Universitätsklinikum Münster, Münster, Germany
| | - Hartmut H.-J. Schmidt
- Medizinische Klinik B für Gastroenterologie und Hepatologie, Universitätsklinikum Münster, Münster, Germany
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8
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VanSchouwen B, Ahmed R, Milojevic J, Melacini G. Functional dynamics in cyclic nucleotide signaling and amyloid inhibition. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1529-1543. [PMID: 28911813 DOI: 10.1016/j.bbapap.2017.09.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 08/29/2017] [Accepted: 09/07/2017] [Indexed: 12/28/2022]
Abstract
It is now established that understanding the molecular basis of biological function requires atomic resolution maps of both structure and dynamics. Here, we review several illustrative examples of functional dynamics selected from our work on cyclic nucleotide signaling and amyloid inhibition. Although fundamentally diverse, a central aspect common to both fields is that function can only be rationalized by considering dynamic equilibria between distinct states of the accessible free energy landscape. The dynamic exchange between ground and excited states of signaling proteins is essential to explain auto-inhibition and allosteric activation. The dynamic exchange between non-toxic monomeric species and toxic oligomers of amyloidogenic proteins provides a foundation to understand amyloid inhibition. NMR ideally probes both types of dynamic exchange at atomic resolution. Specifically, we will show how NMR was utilized to reveal the dynamical basis of cyclic nucleotide affinity, selectivity, agonism and antagonism in multiple eukaryotic cAMP and cGMP receptors. We will also illustrate how NMR revealed the mechanism of action of plasma proteins that act as extracellular chaperones and inhibit the self-association of the prototypical amyloidogenic Aβ peptide. The examples outlined in this review illustrate the widespread implications of functional dynamics and the power of NMR as an indispensable tool in molecular pharmacology and pathology.
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Affiliation(s)
- Bryan VanSchouwen
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada
| | - Rashik Ahmed
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Julijana Milojevic
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada
| | - Giuseppe Melacini
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada.
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9
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The role of fibrinogen glycation in ATTR: evidence for chaperone activity loss in disease. Biochem J 2016; 473:2225-37. [DOI: 10.1042/bcj20160290] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 05/12/2016] [Indexed: 12/14/2022]
Abstract
Transthyretin amyloidosis (ATTR) belongs to a class of disorders caused by protein misfolding and aggregation. ATTR is a disabling disorder of autosomal dominant trait, where transthyretin (TTR) forms amyloid deposits in different organs, causing dysfunction of the peripheral nervous system. We previously discovered that amyloid fibrils from ATTR patients are glycated by methylglyoxal. Even though no consensus has been reached about the actual role of methylglyoxal-derived advanced glycation end-products in amyloid diseases, evidence collected so far points to a role for protein glycation in conformational abnormalities, being ubiquitously found in amyloid deposits in Alzheimer's disease, dialysis-related amyloidosis and Parkinson's diseases. Human fibrinogen, an extracellular chaperone, was reported to specifically interact with a wide spectrum of stressed proteins and suppress their aggregation, being an interacting protein with TTR. Fibrinogen is differentially glycated in ATTR, leading to its chaperone activity loss. Here we show the existence of a proteostasis imbalance in ATTR linked to fibrinogen glycation by methylglyoxal.
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10
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da Costa G, Ribeiro-Silva C, Ribeiro R, Gilberto S, Gomes RA, Ferreira A, Mateus É, Barroso E, Coelho AV, Freire AP, Cordeiro C. Transthyretin Amyloidosis: Chaperone Concentration Changes and Increased Proteolysis in the Pathway to Disease. PLoS One 2015; 10:e0125392. [PMID: 26147092 PMCID: PMC4492746 DOI: 10.1371/journal.pone.0125392] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 03/24/2015] [Indexed: 11/18/2022] Open
Abstract
Transthyretin amyloidosis is a conformational pathology characterized by the extracellular formation of amyloid deposits and the progressive impairment of the peripheral nervous system. Point mutations in this tetrameric plasma protein decrease its stability and are linked to disease onset and progression. Since non-mutated transthyretin also forms amyloid in systemic senile amyloidosis and some mutation bearers are asymptomatic throughout their lives, non-genetic factors must also be involved in transthyretin amyloidosis. We discovered, using a differential proteomics approach, that extracellular chaperones such as fibrinogen, clusterin, haptoglobin, alpha-1-anti-trypsin and 2-macroglobulin are overrepresented in transthyretin amyloidosis. Our data shows that a complex network of extracellular chaperones are over represented in human plasma and we speculate that they act synergistically to cope with amyloid prone proteins. Proteostasis may thus be as important as point mutations in transthyretin amyloidosis.
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Affiliation(s)
- Gonçalo da Costa
- Centro de Química e Bioquímica, FCUL, Campo Grande, Lisboa, Portugal
| | | | - Raquel Ribeiro
- Centro de Química e Bioquímica, FCUL, Campo Grande, Lisboa, Portugal
| | - Samuel Gilberto
- Centro de Química e Bioquímica, FCUL, Campo Grande, Lisboa, Portugal
| | - Ricardo A Gomes
- Instituto de Tecnologia Química e Biológica, Av. da República Estação Agronómica Nacional, Oeiras, Portugal
| | - António Ferreira
- Centro de Química e Bioquímica, FCUL, Campo Grande, Lisboa, Portugal
| | - Élia Mateus
- Unidade de Transplantação, Hospital Curry Cabral, Lisboa, Portugal
| | - Eduardo Barroso
- Unidade de Transplantação, Hospital Curry Cabral, Lisboa, Portugal
| | - Ana V Coelho
- Instituto de Tecnologia Química e Biológica, Av. da República Estação Agronómica Nacional, Oeiras, Portugal
| | - Ana Ponces Freire
- Centro de Química e Bioquímica, FCUL, Campo Grande, Lisboa, Portugal
| | - Carlos Cordeiro
- Centro de Química e Bioquímica, FCUL, Campo Grande, Lisboa, Portugal
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de Castro Brás LE, Cates CA, DeLeon-Pennell KY, Ma Y, Iyer RP, Halade GV, Yabluchanskiy A, Fields GB, Weintraub ST, Lindsey ML. Citrate synthase is a novel in vivo matrix metalloproteinase-9 substrate that regulates mitochondrial function in the postmyocardial infarction left ventricle. Antioxid Redox Signal 2014; 21:1974-85. [PMID: 24382150 PMCID: PMC4208600 DOI: 10.1089/ars.2013.5411] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
AIM To evaluate the role of matrix metalloproteinase (MMP)-9 deletion on citrate synthase (CS) activity postmyocardial infarction (MI). RESULTS We fractionated left ventricle (LV) samples using a differential solubility-based approach. The insoluble protein fraction was analyzed by mass spectrometry, and we identified CS as a potential intracellular substrate of MMP-9 in the MI setting. CS protein levels increased in the insoluble fraction at day 1 post-MI in both genotypes (p<0.05) but not in the noninfarcted remote region. The CS activity decreased in the infarcted tissue of wild-type (WT) mice at day 1 post-MI (p<0.05), but this was not observed in the MMP-9 null mice, suggesting that MMP-9 deletion helps to maintain the mitochondrial activity post-MI. Additionally, inflammatory gene transcription was increased post-MI in the WT mice and attenuated in the MMP-9 null mice. MMP-9 cleaved CS in vitro, generating an ∼20 kDa fragment. INNOVATION By applying a sample fractionation and proteomics approach, we were able to identify a novel MMP-9-related altered mitochondrial metabolic activity early post-MI. CONCLUSION Our data suggest that MMP-9 deletion improves mitochondrial function post-MI.
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12
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Molecular dynamics studies on the NMR and X-ray structures of rabbit prion proteins. J Theor Biol 2013; 342:70-82. [PMID: 24184221 DOI: 10.1016/j.jtbi.2013.10.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 08/25/2013] [Accepted: 10/09/2013] [Indexed: 12/27/2022]
Abstract
Prion diseases, traditionally referred to as transmissible spongiform encephalopathies (TSEs), are invariably fatal and highly infectious neurodegenerative diseases that affect a wide variety of mammalian species, manifesting as scrapie in sheep and goats, bovine spongiform encephalopathy (BSE or mad-cow disease) in cattle, chronic wasting disease in deer and elk, and Creutzfeldt-Jakob diseases, Gerstmann-Sträussler-Scheinker syndrome, fatal familial insomnia, and kulu in humans, etc. These neurodegenerative diseases are caused by the conversion from a soluble normal cellular prion protein (PrP(C)) into insoluble abnormally folded infectious prions (PrP(Sc)), and the conversion of PrP(C) to PrP(Sc) is believed to involve conformational change from a predominantly α-helical protein to one rich in β-sheet structure. Such a conformational change may be amenable to study by molecular dynamics (MD) techniques. For rabbits, classical studies show that they have a low susceptibility to be infected by PrP(Sc), but recently it was reported that rabbit prions can be generated through saPMCA (serial automated Protein Misfolding Cyclic Amplification) in vitro and the rabbit prion is infectious and transmissible. In this paper, we first do a detailed survey on the research advances of rabbit prion protein (RaPrP) and then we perform MD simulations on the NMR and X-ray molecular structures of rabbit prion protein wild-type and mutants. The survey shows to us that rabbits were not challenged directly in vivo with other known prion strains and the saPMCA result did not pass the test of the known BSE strain of cattle. Thus, we might still look rabbits as a prion resistant species. MD results indicate that the three α-helices of the wild-type are stable under the neutral pH environment (but under low pH environment the three α-helices have been unfolded into β-sheets), and the three α-helices of the mutants (I214V and S173N) are unfolded into rich β-sheet structures under the same pH environment. In addition, we found an interesting result that the salt bridges such as ASP201-ARG155, ASP177-ARG163 contribute greatly to the structural stability of RaPrP.
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13
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Affiliation(s)
- Amy R. Wyatt
- School of Biological Sciences, University of Wollongong, Wollongong, New South Wales 2522, Australia;
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Justin J. Yerbury
- School of Biological Sciences, University of Wollongong, Wollongong, New South Wales 2522, Australia;
| | - Heath Ecroyd
- School of Biological Sciences, University of Wollongong, Wollongong, New South Wales 2522, Australia;
| | - Mark R. Wilson
- School of Biological Sciences, University of Wollongong, Wollongong, New South Wales 2522, Australia;
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15
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Roles of Extracellular Chaperones in Amyloidosis. J Mol Biol 2012; 421:499-516. [DOI: 10.1016/j.jmb.2012.01.004] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Revised: 01/02/2012] [Accepted: 01/03/2012] [Indexed: 01/24/2023]
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16
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Beyond genetic factors in familial amyloidotic polyneuropathy: protein glycation and the loss of fibrinogen's chaperone activity. PLoS One 2011; 6:e24850. [PMID: 22053176 PMCID: PMC3203866 DOI: 10.1371/journal.pone.0024850] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Accepted: 08/19/2011] [Indexed: 02/06/2023] Open
Abstract
Familial amyloidotic polyneuropathy (FAP) is a systemic conformational disease characterized by extracellular amyloid fibril formation from plasma transthyretin (TTR). This is a crippling, fatal disease for which liver transplantation is the only effective therapy. More than 80 TTR point mutations are associated with amyloidotic diseases and the most widely accepted disease model relates TTR tetramer instability with TTR point mutations. However, this model fails to explain two observations. First, native TTR also forms amyloid in systemic senile amyloidosis, a geriatric disease. Second, age at disease onset varies by decades for patients bearing the same mutation and some mutation carrier individuals are asymptomatic throughout their lives. Hence, mutations only accelerate the process and non-genetic factors must play a key role in the molecular mechanisms of disease. One of these factors is protein glycation, previously associated with conformational diseases like Alzheimer's and Parkinson's. The glycation hypothesis in FAP is supported by our previous discovery of methylglyoxal-derived glycation of amyloid fibrils in FAP patients. Here we show that plasma proteins are differentially glycated by methylglyoxal in FAP patients and that fibrinogen is the main glycation target. Moreover, we also found that fibrinogen interacts with TTR in plasma. Fibrinogen has chaperone activity which is compromised upon glycation by methylglyoxal. Hence, we propose that methylglyoxal glycation hampers the chaperone activity of fibrinogen, rendering TTR more prone to aggregation, amyloid formation and ultimately, disease.
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17
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Abstract
The maintenance of the levels and correct folding state of proteins (proteostasis) is a fundamental prerequisite for life. Life has evolved complex mechanisms to maintain proteostasis and many of these that operate inside cells are now well understood. The same cannot yet be said of corresponding processes in extracellular fluids of the human body, where inappropriate protein aggregation is known to underpin many serious diseases such as Alzheimer's disease, type II diabetes and prion diseases. Recent research has uncovered a growing family of abundant extracellular chaperones in body fluids which appear to selectively bind to exposed regions of hydrophobicity on misfolded proteins to inhibit their toxicity and prevent them from aggregating to form insoluble deposits. These extracellular chaperones are also implicated in clearing the soluble, stabilized misfolded proteins from body fluids via receptor-mediated endocytosis for subsequent lysosomal degradation. Recent work also raises the possibility that extracellular chaperones may play roles in modulating the immune response. Future work will better define the in vivo functions of extracellular chaperones in proteostasis and immunology and pave the way for the development of new treatments for serious diseases.
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18
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Gawinecka J, Dieks J, Asif AR, Carimalo J, Heinemann U, Streich JH, Dihazi H, Schulz-Schaeffer W, Zerr I. Codon 129 polymorphism specific cerebrospinal fluid proteome pattern in sporadic Creutzfeldt-Jakob disease and the implication of glycolytic enzymes in prion-induced pathology. J Proteome Res 2010; 9:5646-57. [PMID: 20866111 DOI: 10.1021/pr1004604] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Cerebrospinal fluid (CSF) contains a dynamic and complex mixture of proteins, which can reflect a physiological and pathological state of the central nervous system. In our present study, we show CSF protein patterns from patients with the two most frequent subtypes of sporadic Creutzfeldt-Jakob disease (sCJD) defined by the codon 129 genotype (MM, MV, and VV) and the protease-resistant form of prion protein (type 1 and type 2). The densitometric analysis of 2D gels showed up-regulation of 27 and down-regulation of 3 proteins in the MM-sCJD as well as the up-regulation of 24 proteins in the VV-sCJD as compared to nondemented control. Almost 40% of sCJD specific regulated proteins in CSF are involved in glucose metabolism, regardless of the codon 129 polymorphism. The increase in CSF levels of lactate dehydrogenase (LDH), glucose-6-phosphate isomerase (G6PI), and fructose-bisphosphate aldolase A (ALDOA) were validated on a larger group of sCJD patients including three possible codon 129 polymorphism carriers and three control groups consisting of nondemented, neurological cases as well as patients suffering from Alzheimer's disease or vascular dementia. Subsequently, the abundance of these glycolytic enzymes in the brain as well as their cellular localization were determined. This study demonstrates for the first time the implication of G6PI in prion-induced pathology as well as its cellular translocalization in sCJD. The identification of sCJD-regulated proteins in CSF of living symptomatic patients in our study can broaden our knowledge about pathological processes occurring in sCJD, as they are still not fully understood.
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Affiliation(s)
- Joanna Gawinecka
- Department of Clinical Chemistry, Medical Center Georg-August University, Goettingen, Germany
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19
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Dabbs RA, Wyatt AR, Yerbury JJ, Ecroyd H, Wilson MR. Extracellular Chaperones. Top Curr Chem (Cham) 2010. [PMID: 21516385 DOI: 10.1007/128_2010_85] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The maintenance of the levels and correct folding state of proteins (proteostasis) is a fundamental prerequisite for life. Life has evolved complex mechanisms to maintain proteostasis and many of these that operate inside cells are now well understood. The same cannot yet be said of corresponding processes in extracellular fluids of the human body, where inappropriate protein aggregation is known to underpin many serious diseases such as Alzheimer's disease, type II diabetes and prion diseases. Recent research has uncovered a growing family of abundant extracellular chaperones in body fluids which appear to selectively bind to exposed regions of hydrophobicity on misfolded proteins to inhibit their toxicity and prevent them from aggregating to form insoluble deposits. These extracellular chaperones are also implicated in clearing the soluble, stabilized misfolded proteins from body fluids via receptor-mediated endocytosis for subsequent lysosomal degradation. Recent work also raises the possibility that extracellular chaperones may play roles in modulating the immune response. Future work will better define the in vivo functions of extracellular chaperones in proteostasis and immunology and pave the way for the development of new treatments for serious diseases.
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20
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Two novel fibrinogen variants in the C-terminus of the Bβ-chain: fibrinogen Rokycany and fibrinogen Znojmo. J Thromb Thrombolysis 2010; 30:311-8. [DOI: 10.1007/s11239-010-0505-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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21
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Zsila F. Chaperone-like activity of the acute-phase component human serum α1-acid glycoprotein: Inhibition of thermal- and chemical-induced aggregation of various proteins. Bioorg Med Chem Lett 2010; 20:1205-9. [DOI: 10.1016/j.bmcl.2009.11.132] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2009] [Revised: 11/25/2009] [Accepted: 11/30/2009] [Indexed: 10/20/2022]
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22
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Wyatt A, Yerbury J, Poon S, Dabbs R, Wilson M. Chapter 6: The chaperone action of Clusterin and its putative role in quality control of extracellular protein folding. Adv Cancer Res 2010; 104:89-114. [PMID: 19878774 DOI: 10.1016/s0065-230x(09)04006-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The function(s) of clusterin may depend upon its topological location. A variety of intracellular "isoforms" of clusterin have been reported but further work is required to better define their identity. The secreted form of clusterin has a potent ability to inhibit both amorphous and amyloid protein aggregation. In the case of amorphous protein aggregation, clusterin forms stable, soluble high-molecular-weight complexes with misfolded client proteins. Clusterin expression is increased during many types of physiological and pathological stresses and is thought to function as an extracellular chaperone (EC). The pathology of a variety of serious human diseases is thought to arise as a consequence of the inappropriate aggregation of specific extracellular proteins (e.g., Abeta peptide in Alzheimer's disease and beta(2)-microglobulin in dialysis-related amyloidosis). We have proposed that together with other abundant ECs (e.g., haptoglobin and alpha(2)-macroglobulin), clusterin forms part of a previously unknown quality-control (QC) system for protein folding that mediates the recognition and disposal of extracellular misfolded proteins via receptor-mediated endocytosis and lysosomal degradation. Characterizing the mechanisms of this extracellular QC system will thus have major implications for our understanding of diseases of this type and may eventually lead to the development of new therapies.
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Affiliation(s)
- Amy Wyatt
- School of Biological Sciences, University of Wollongong, Wollongong, New South Wales 2522, Australia
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Tang H, Fu Y, Zhan S, Luo Y. αEC, the C-Terminal Extension of Fibrinogen, Has Chaperone-like Activity. Biochemistry 2009; 48:3967-76. [DOI: 10.1021/bi900015n] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Huadong Tang
- National Engineering Laboratory for Anti-tumor Protein Therapeutics
- Beijing Key Laboratory for Protein Therapeutics
- Cancer Biology Laboratory, Department of Biological Sciences and Biotechnology
| | - Yan Fu
- National Engineering Laboratory for Anti-tumor Protein Therapeutics
- Beijing Key Laboratory for Protein Therapeutics
- Cancer Biology Laboratory, Department of Biological Sciences and Biotechnology
| | - Shunli Zhan
- National Engineering Laboratory for Anti-tumor Protein Therapeutics
| | - Yongzhang Luo
- National Engineering Laboratory for Anti-tumor Protein Therapeutics
- Beijing Key Laboratory for Protein Therapeutics
- Cancer Biology Laboratory, Department of Biological Sciences and Biotechnology
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24
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Tang H, Fu Y, Lei Q, Han Q, Ploplis VA, Castellino FJ, Li L, Luo Y. Fibrinogen facilitates the anti-tumor effect of nonnative endostatin. Biochem Biophys Res Commun 2009; 380:249-53. [PMID: 19167351 PMCID: PMC2676347 DOI: 10.1016/j.bbrc.2009.01.045] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2008] [Accepted: 01/12/2009] [Indexed: 11/23/2022]
Abstract
Endostatin is a potent inhibitor of tumor angiogenesis. Interestingly, nonnative endostatin also exhibits an anti-tumor effect, which remains a mystery so far. Here, we show that intravenous injection of nonnative endostatin results in tumor inhibition effect. Soluble and active endostatin is isolated from human blood after the addition of nonnative endostatin in vitro. By fractionation of the whole blood, we surprisingly identify fibrinogen specifically binding to and inhibiting the aggregation of nonnative endostatin. Moreover, the anti-tumor activity of nonnative endostatin is substantially impaired in fibrinogen-deficient mice. Our studies demonstrate that fibrinogen facilitates the anti-tumor effect of nonnative endostatin, which also provides new insights into the novel physiological function of fibrinogen.
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Affiliation(s)
- Huadong Tang
- Laboratory of Protein Chemistry, Department of Biological Sciences & Biotechnology, Tsinghua University, Beijing 100084, P. R. China
- National Engineering Laboratory for Anti-tumor Protein Therapeutics, Beijing 100084, P. R. China
- Beijing Key Laboratory for Protein Therapeutics, Beijing 100084, P. R. China
| | - Yan Fu
- Laboratory of Protein Chemistry, Department of Biological Sciences & Biotechnology, Tsinghua University, Beijing 100084, P. R. China
- National Engineering Laboratory for Anti-tumor Protein Therapeutics, Beijing 100084, P. R. China
- Beijing Key Laboratory for Protein Therapeutics, Beijing 100084, P. R. China
| | - Qingxin Lei
- Laboratory of Protein Chemistry, Department of Biological Sciences & Biotechnology, Tsinghua University, Beijing 100084, P. R. China
| | - Qing Han
- Laboratory of Protein Chemistry, Department of Biological Sciences & Biotechnology, Tsinghua University, Beijing 100084, P. R. China
| | - Victoria A. Ploplis
- W. M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Francis J. Castellino
- W. M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Ling Li
- Laboratory of Protein Chemistry, Department of Biological Sciences & Biotechnology, Tsinghua University, Beijing 100084, P. R. China
- National Engineering Laboratory for Anti-tumor Protein Therapeutics, Beijing 100084, P. R. China
- Beijing Key Laboratory for Protein Therapeutics, Beijing 100084, P. R. China
| | - Yongzhang Luo
- Laboratory of Protein Chemistry, Department of Biological Sciences & Biotechnology, Tsinghua University, Beijing 100084, P. R. China
- National Engineering Laboratory for Anti-tumor Protein Therapeutics, Beijing 100084, P. R. China
- Beijing Key Laboratory for Protein Therapeutics, Beijing 100084, P. R. China
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