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Kamuda K, Ronzoni R, Majumdar A, Guan FHX, Irving JA, Lomas DA. A novel pathological mutant reveals the role of torsional flexibility in the serpin breach in adoption of an aggregation-prone intermediate. FEBS J 2024; 291:2937-2954. [PMID: 38523412 DOI: 10.1111/febs.17121] [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: 11/24/2023] [Revised: 02/17/2024] [Accepted: 03/07/2024] [Indexed: 03/26/2024]
Abstract
Mutants of alpha-1-antitrypsin cause the protein to self-associate and form ordered aggregates ('polymers') that are retained within hepatocytes, resulting in a predisposition to the development of liver disease. The associated reduction in secretion, and for some mutants, impairment of function, leads to a failure to protect lung tissue against proteases released during the inflammatory response and an increased risk of emphysema. We report here a novel deficiency mutation (Gly192Cys), that we name the Sydney variant, identified in a patient in heterozygosity with the Z allele (Glu342Lys). Cellular analysis revealed that the novel variant was mostly retained as insoluble polymers within the endoplasmic reticulum. The basis for this behaviour was investigated using biophysical and structural techniques. The variant showed a 40% reduction in inhibitory activity and a reduced stability as assessed by thermal unfolding experiments. Polymerisation involves adoption of an aggregation-prone intermediate and paradoxically the energy barrier for transition to this state was increased by 16% for the Gly192Cys variant with respect to the wild-type protein. However, with activation to the intermediate state, polymerisation occurred at a 3.8-fold faster rate overall. X-ray crystallography provided two crystal structures of the Gly192Cys variant, revealing perturbation within the 'breach' region with Cys192 in two different orientations: in one structure it faces towards the hydrophobic core while in the second it is solvent-exposed. This orientational heterogeneity was confirmed by PEGylation. These data show the critical role of the torsional freedom imparted by Gly192 in inhibitory activity and stability against polymerisation.
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Affiliation(s)
- Kamila Kamuda
- Division of Medicine, UCL Respiratory, Rayne Institute, University College London, UK
- Institute of Structural and Molecular Biology, Birkbeck College, University College London, UK
| | - Riccardo Ronzoni
- Division of Medicine, UCL Respiratory, Rayne Institute, University College London, UK
- Institute of Structural and Molecular Biology, Birkbeck College, University College London, UK
| | - Avik Majumdar
- AW Morrow Gastroenterology and Liver Centre, Royal Prince Alfred Hospital, Sydney, Australia
- Victorian Liver Transplant Unit, Austin Health, Melbourne, Australia
- The University of Melbourne, Melbourne, Australia
| | - Fiona H X Guan
- AW Morrow Gastroenterology and Liver Centre, Royal Prince Alfred Hospital, Sydney, Australia
| | - James A Irving
- Division of Medicine, UCL Respiratory, Rayne Institute, University College London, UK
- Institute of Structural and Molecular Biology, Birkbeck College, University College London, UK
| | - David A Lomas
- Division of Medicine, UCL Respiratory, Rayne Institute, University College London, UK
- Institute of Structural and Molecular Biology, Birkbeck College, University College London, UK
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2
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B Fortela DL, Mikolajczyk AP, Carnes MR, Sharp W, Revellame E, Hernandez R, Holmes WE, Zappi ME. Predicting molecular docking of per- and polyfluoroalkyl substances to blood protein using generative artificial intelligence algorithm DiffDock. Biotechniques 2024; 76:14-26. [PMID: 37947020 DOI: 10.2144/btn-2023-0070] [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] [Indexed: 11/12/2023] Open
Abstract
This study computationally evaluates the molecular docking affinity of various perfluoroalkyl and polyfluoroalkyl substances (PFAs) towards blood proteins using a generative machine-learning algorithm, DiffDock, specialized in protein-ligand blind-docking learning and prediction. Concerns about the chemical pathways and accumulation of PFAs in the environment and eventually in the human body has been rising due to empirical findings that levels of PFAs in human blood has been rising. DiffDock may offer a fast approach in determining the fate and potential molecular pathways of PFAs in human body.
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Affiliation(s)
- Dhan Lord B Fortela
- Department of Chemical Engineering, University of Louisiana, Lafayette, LA 70504, USA
- Energy Institute of Louisiana, University of Louisiana, Lafayette, LA 70504, USA
| | - Ashley P Mikolajczyk
- Department of Chemical Engineering, University of Louisiana, Lafayette, LA 70504, USA
- Energy Institute of Louisiana, University of Louisiana, Lafayette, LA 70504, USA
| | - Miranda R Carnes
- Department of Chemical Engineering, University of Louisiana, Lafayette, LA 70504, USA
| | - Wayne Sharp
- Energy Institute of Louisiana, University of Louisiana, Lafayette, LA 70504, USA
- Department of Civil Engineering, University of Louisiana, Lafayette, LA 70504, USA
| | - Emmanuel Revellame
- Department of Chemical Engineering, University of Louisiana, Lafayette, LA 70504, USA
- Energy Institute of Louisiana, University of Louisiana, Lafayette, LA 70504, USA
| | - Rafael Hernandez
- Department of Chemical Engineering, University of Louisiana, Lafayette, LA 70504, USA
- Energy Institute of Louisiana, University of Louisiana, Lafayette, LA 70504, USA
| | - William E Holmes
- Department of Chemical Engineering, University of Louisiana, Lafayette, LA 70504, USA
- Energy Institute of Louisiana, University of Louisiana, Lafayette, LA 70504, USA
| | - Mark E Zappi
- Department of Chemical Engineering, University of Louisiana, Lafayette, LA 70504, USA
- Energy Institute of Louisiana, University of Louisiana, Lafayette, LA 70504, USA
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3
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Denardo A, Ben Khlifa E, Bignotti M, Giuliani R, D'Acunto E, Miranda E, Irving JA, Fra A. Probing of the reactive center loop region of alpha-1-antitrypsin by mutagenesis predicts new type-2 dysfunctional variants. Cell Mol Life Sci 2023; 81:6. [PMID: 38087060 PMCID: PMC11073084 DOI: 10.1007/s00018-023-05059-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 10/25/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023]
Abstract
Lung disease in alpha-1-antitrypsin deficiency (AATD) mainly results from insufficient control of the serine proteases neutrophil elastase (NE) and proteinase-3 due to reduced plasma levels of alpha-1-antitrypsin (AAT) variants. Mutations in the specificity-determining reactive center loop (RCL) of AAT would be predicted to minimally affect protein folding and secretion by hepatocytes but can impair anti-protease activity or alter the target protease. These properly secreted but dysfunctional 'type-2' variants would not be identified by common diagnostic protocols that are predicated on a reduction in circulating AAT. This has potential clinical relevance: in addition to the dysfunctional Pittsburgh and Iners variants reported previously, several uncharacterized RCL variants are present in genome variation databases. To prospectively evaluate the impact of RCL variations on secretion and anti-protease activity, here we performed a systematic screening of amino acid substitutions occurring at the AAT-NE interface. Twenty-three AAT variants that can result from single nucleotide polymorphisms in this region, including 11 present in sequence variation databases, were expressed in a mammalian cell model. All demonstrated unaltered protein folding and secretion. However, when their ability to form stable complexes with NE was evaluated by western blot, enzymatic assays, and a novel ELISA developed to quantify AAT-NE complexes, substrate-like and NE-binding deficient dysfunctional variants were identified. This emphasizes the ability of the RCL to accommodate inactivating substitutions without impacting the integrity of the native molecule and demonstrates that this class of molecule violates a generally accepted paradigm that equates circulating levels with functional protection of lung tissue.
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Affiliation(s)
- Andrea Denardo
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Emna Ben Khlifa
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Mattia Bignotti
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Roberta Giuliani
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Emanuela D'Acunto
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, Rome, Italy
| | - Elena Miranda
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, Rome, Italy
| | - James A Irving
- UCL Respiratory and the Institute of Structural and Molecular Biology, University College London, London, UK
| | - Annamaria Fra
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy.
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4
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Kaur U, Kihn KC, Ke H, Kuo W, Gierasch LM, Hebert DN, Wintrode PL, Deredge D, Gershenson A. The conformational landscape of a serpin N-terminal subdomain facilitates folding and in-cell quality control. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.24.537978. [PMID: 37163105 PMCID: PMC10168285 DOI: 10.1101/2023.04.24.537978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Many multi-domain proteins including the serpin family of serine protease inhibitors contain non-sequential domains composed of regions that are far apart in sequence. Because proteins are translated vectorially from N- to C-terminus, such domains pose a particular challenge: how to balance the conformational lability necessary to form productive interactions between early and late translated regions while avoiding aggregation. This balance is mediated by the protein sequence properties and the interactions of the folding protein with the cellular quality control machinery. For serpins, particularly α 1 -antitrypsin (AAT), mutations often lead to polymer accumulation in cells and consequent disease suggesting that the lability/aggregation balance is especially precarious. Therefore, we investigated the properties of progressively longer AAT N-terminal fragments in solution and in cells. The N-terminal subdomain, residues 1-190 (AAT190), is monomeric in solution and efficiently degraded in cells. More β -rich fragments, 1-290 and 1-323, form small oligomers in solution, but are still efficiently degraded, and even the polymerization promoting Siiyama (S53F) mutation did not significantly affect fragment degradation. In vitro, the AAT190 region is among the last regions incorporated into the final structure. Hydrogen-deuterium exchange mass spectrometry and enhanced sampling molecular dynamics simulations show that AAT190 has a broad, dynamic conformational ensemble that helps protect one particularly aggregation prone β -strand from solvent. These AAT190 dynamics result in transient exposure of sequences that are buried in folded, full-length AAT, which may provide important recognition sites for the cellular quality control machinery and facilitate degradation and, under favorable conditions, reduce the likelihood of polymerization.
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Affiliation(s)
- Upneet Kaur
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA 01003
| | - Kyle C. Kihn
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201
| | - Haiping Ke
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA 01003
| | - Weiwei Kuo
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA 01003
| | - Lila M. Gierasch
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA 01003
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA 01003
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003
| | - Daniel N. Hebert
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA 01003
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA 01003
| | - Patrick L. Wintrode
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201
| | - Daniel Deredge
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201
| | - Anne Gershenson
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA 01003
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA 01003
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5
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Cruz MA, Bohinc D, Andraska EA, Alvikas J, Raghunathan S, Masters NA, van Kleef ND, Bane KL, Hart K, Medrow K, Sun M, Liu H, Haldeman S, Banerjee A, Lessieur EM, Hageman K, Gandhi A, de la Fuente M, Nieman MT, Kern TS, Maas C, de Maat S, Neeves KB, Neal MD, Sen Gupta A, Stavrou EX. Nanomedicine platform for targeting activated neutrophils and neutrophil-platelet complexes using an α 1-antitrypsin-derived peptide motif. NATURE NANOTECHNOLOGY 2022; 17:1004-1014. [PMID: 35851383 PMCID: PMC9909445 DOI: 10.1038/s41565-022-01161-w] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 05/24/2022] [Indexed: 05/30/2023]
Abstract
Targeted drug delivery to disease-associated activated neutrophils can provide novel therapeutic opportunities while avoiding systemic effects on immune functions. We created a nanomedicine platform that uniquely utilizes an α1-antitrypsin-derived peptide to confer binding specificity to neutrophil elastase on activated neutrophils. Surface decoration with this peptide enabled specific anchorage of nanoparticles to activated neutrophils and platelet-neutrophil aggregates, in vitro and in vivo. Nanoparticle delivery of a model drug, hydroxychloroquine, demonstrated significant reduction of neutrophil activities in vitro and a therapeutic effect on murine venous thrombosis in vivo. This innovative approach of cell-specific and activation-state-specific targeting can be applied to several neutrophil-driven pathologies.
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Affiliation(s)
- Michelle A Cruz
- Department of Pathology, Immunology Training Program, CWRU School of Medicine, Cleveland, OH, USA
| | - Dillon Bohinc
- Department of Medicine, Hematology and Oncology Division, CWRU School of Medicine, Cleveland, OH, USA
| | - Elizabeth A Andraska
- Department of Surgery, Division of Vascular Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Jurgis Alvikas
- Department of Surgery, Pittsburgh Trauma Research Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Shruti Raghunathan
- Department of Biomedical Engineering, Case Western Reserve University (CWRU), Cleveland, OH, USA
| | - Nicole A Masters
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, USA
| | - Nadine D van Kleef
- CDL Research, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Kara L Bane
- Department of Medicine, Hematology and Oncology Division, CWRU School of Medicine, Cleveland, OH, USA
| | - Kathryn Hart
- Department of Biomedical Engineering, Case Western Reserve University (CWRU), Cleveland, OH, USA
| | - Kathryn Medrow
- Department of Biomedical Engineering, Case Western Reserve University (CWRU), Cleveland, OH, USA
| | - Michael Sun
- Department of Biomedical Engineering, Case Western Reserve University (CWRU), Cleveland, OH, USA
| | - Haitao Liu
- Department of Ophthalmology, Children's Hospital of University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Shannon Haldeman
- Department of Surgery, Pittsburgh Trauma Research Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Ankush Banerjee
- Department of Biomedical Engineering, Case Western Reserve University (CWRU), Cleveland, OH, USA
| | - Emma M Lessieur
- Center for Translational Vision Research, Gavin Herbert Eye Institute, University of California Irvine, Irvine, CA, USA
| | - Kara Hageman
- Department of Biomedical Engineering, Case Western Reserve University (CWRU), Cleveland, OH, USA
| | - Agharnan Gandhi
- Department of Medicine, Hematology and Oncology Division, CWRU School of Medicine, Cleveland, OH, USA
| | | | - Marvin T Nieman
- Department of Pharmacology, CWRU School of Medicine, Cleveland, OH, USA
| | - Timothy S Kern
- Center for Translational Vision Research, Gavin Herbert Eye Institute, University of California Irvine, Irvine, CA, USA
- Veterans Administration Medical Center Research Service, Long Beach, CA, USA
| | - Coen Maas
- CDL Research, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Steven de Maat
- CDL Research, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Keith B Neeves
- Department of Bioengineering and Pediatrics, Section of Hematology, Oncology, and Bone Marrow Transplant Hemophilia and Thrombosis Center, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Matthew D Neal
- Department of Surgery, Pittsburgh Trauma Research Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Anirban Sen Gupta
- Department of Pathology, Immunology Training Program, CWRU School of Medicine, Cleveland, OH, USA.
- Department of Biomedical Engineering, Case Western Reserve University (CWRU), Cleveland, OH, USA.
- Department of Pharmacology, CWRU School of Medicine, Cleveland, OH, USA.
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA.
| | - Evi X Stavrou
- Department of Medicine, Hematology and Oncology Division, CWRU School of Medicine, Cleveland, OH, USA.
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA.
- Department of Medicine, Section of Hematology-Oncology, Louis Stokes Veterans Administration Medical Center, Cleveland, OH, USA.
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6
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Gonzalez A, Belmonte I, Nuñez A, Farago G, Barrecheguren M, Pons M, Orriols G, Gabriel-Medina P, Rodríguez-Frías F, Miravitlles M, Esquinas C. New variants of alpha-1-antitrypsin: structural simulations and clinical expression. Respir Res 2022; 23:339. [PMID: 36496391 PMCID: PMC9741788 DOI: 10.1186/s12931-022-02271-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 12/01/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Alpha-1 antitrypsin deficiency (AATD) is characterized by reduced serum levels of the AAT protein and predisposes to liver and lung disease. The characterization at structural level of novel pathogenic SERPINA1 mutants coding for circulating AAT could provide novel insights into the mechanisms of AAT misfolding. The present study aimed to provide a practical framework for the identification and analysis of new AAT mutations, combining structural simulations and clinical data. METHODS We analysed a total of five mutations (four not previously described) in a total of six subjects presenting moderate to severe AATD: Gly95Alafs*18, Val210Glu, Asn247Ser, Pi*S + Asp341His and Pi*S + Leu383Phe + Lys394Ile. Clinical data, genotyping and phenotyping assays, structural mapping, and conformational characterization through molecular dynamic (MD) simulations were developed and combined. RESULTS Newly discovered AAT missense variants were localized both on the interaction surface and the hydrophobic core of the protein. Distribution of mutations across the structure revealed Val210Glu at the solvent exposed s4C strand and close to the "Gate" region. Asn247Ser was located on the accessible surface, which is important for glycan attachment. On the other hand, Asp341His, Leu383Phe were mapped close to the "breach" and "shutter" regions. MD analysis revealed the reshaping of local interactions around the investigated substitutions that have varying effects on AAT conformational flexibility, hydrophobic packing, and electronic surface properties. The most severe structural changes were observed in the double- and triple-mutant (Pi*S + Asp341His and Pi*S + Leu383Phe + Lys394Ile) molecular models. The two carriers presented impaired lung function. CONCLUSIONS The results characterize five variants, four of them previously unknown, of the SERPINA1 gene, which define new alleles contributing to the deficiency of AAT. Rare variants might be more frequent than expected, and therefore, in discordant cases, standardized screening of the S and Z alleles needs complementation with gene sequencing and structural approaches. The utility of computational modelling for providing supporting evidence of the pathogenicity of rare single nucleotide variations is discussed.
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Affiliation(s)
- Angel Gonzalez
- grid.7080.f0000 0001 2296 0625Department of Computational Medicine, Statistic Unit, Medicine Faculty, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Irene Belmonte
- grid.411083.f0000 0001 0675 8654Department of Clinical Biochemistry, Hospital Universitari Vall d’Hebron, Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Alexa Nuñez
- grid.411083.f0000 0001 0675 8654Pneumology Department, Hospital Universitari Vall d’Hebron, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, P. Vall d’Hebron 119-129, 08035 Barcelona, Spain
| | - Georgina Farago
- grid.411083.f0000 0001 0675 8654Pneumology Department, Hospital Universitari Vall d’Hebron, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, P. Vall d’Hebron 119-129, 08035 Barcelona, Spain
| | - Miriam Barrecheguren
- grid.411083.f0000 0001 0675 8654Pneumology Department, Hospital Universitari Vall d’Hebron, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, P. Vall d’Hebron 119-129, 08035 Barcelona, Spain
| | - Mònica Pons
- grid.411083.f0000 0001 0675 8654Liver Unit, Department of Internal Medicine, Hospital Universitari Vall d’Hebron, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Gerard Orriols
- grid.411083.f0000 0001 0675 8654Department of Clinical Biochemistry, Hospital Universitari Vall d’Hebron, Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Pablo Gabriel-Medina
- grid.411083.f0000 0001 0675 8654Department of Clinical Biochemistry, Hospital Universitari Vall d’Hebron, Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Francisco Rodríguez-Frías
- grid.411083.f0000 0001 0675 8654Department of Clinical Biochemistry, Hospital Universitari Vall d’Hebron, Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain ,grid.7080.f0000 0001 2296 0625Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain ,grid.452371.60000 0004 5930 4607Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, (CIBEREHD), Barcelona, Spain ,grid.430994.30000 0004 1763 0287Clinical Biochemistry Research Group/Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Marc Miravitlles
- grid.411083.f0000 0001 0675 8654Pneumology Department, Hospital Universitari Vall d’Hebron, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, P. Vall d’Hebron 119-129, 08035 Barcelona, Spain ,grid.512891.6Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Barcelona, Spain
| | - Cristina Esquinas
- grid.411083.f0000 0001 0675 8654Pneumology Department, Hospital Universitari Vall d’Hebron, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, P. Vall d’Hebron 119-129, 08035 Barcelona, Spain ,grid.5841.80000 0004 1937 0247Public Health, Mental, Maternal and Child Health Nursing Departament, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain
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7
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Wilkinson DJ, Falconer AMD, Wright HL, Lin H, Yamamoto K, Cheung K, Charlton SH, Arques MDC, Janciauskiene S, Refaie R, Rankin KS, Young DA, Rowan AD. Matrix metalloproteinase-13 is fully activated by neutrophil elastase and inactivates its serpin inhibitor, alpha-1 antitrypsin: Implications for osteoarthritis. FEBS J 2022; 289:121-139. [PMID: 34270864 DOI: 10.1111/febs.16127] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 06/23/2021] [Accepted: 07/15/2021] [Indexed: 01/15/2023]
Abstract
Matrix metalloproteinase-13 (MMP-13) is a uniquely important collagenase that promotes the irreversible destruction of cartilage collagen in osteoarthritis (OA). Collagenase activation is a key control point for cartilage breakdown to occur, yet our understanding of the proteinases involved in this process is limited. Neutrophil elastase (NE) is a well-described proteoglycan-degrading enzyme which is historically associated with inflammatory arthritis, but more recent evidence suggests a potential role in OA. In this study, we investigated the effect of neutrophil elastase on OA cartilage collagen destruction and collagenase activation. Neutrophil elastase induced significant collagen destruction from human OA cartilage ex vivo, in an MMP-dependent manner. In vitro, neutrophil elastase directly and robustly activated pro-MMP-13, and N-terminal sequencing identified cleavage close to the cysteine switch at 72 MKKPR, ultimately resulting in the fully active form with the neo-N terminus of 85 YNVFP. Mole-per-mole, activation was more potent than by MMP-3, a classical collagenase activator. Elastase was detectable in human OA synovial fluid and OA synovia which displayed histologically graded evidence of synovitis. Bioinformatic analyses demonstrated that, compared with other tissues, control cartilage exhibited remarkably high transcript levels of the major elastase inhibitor, (AAT) alpha-1 antitrypsin (gene name SERPINA1), but these were reduced in OA. AAT was located predominantly in superficial cartilage zones, and staining enhanced in regions of cartilage damage. Finally, active MMP-13 specifically inactivated AAT by removal of the serine proteinase cleavage/inhibition site. Taken together, this study identifies elastase as a novel activator of pro-MMP-13 that has relevance for cartilage collagen destruction in OA patients with synovitis.
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Affiliation(s)
- David J Wilkinson
- Institute of Life Course and Medical Sciences, University of Liverpool, UK
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, UK
| | - Adrian M D Falconer
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, UK
| | - Helen L Wright
- Institute of Life Course and Medical Sciences, University of Liverpool, UK
| | - Hua Lin
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, UK
| | - Kazuhiro Yamamoto
- Institute of Life Course and Medical Sciences, University of Liverpool, UK
| | - Kathleen Cheung
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, UK
| | - Sarah H Charlton
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, UK
| | | | - Sabina Janciauskiene
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Department of Respiratory Medicine, Deutsches Zentrum für Lungenforschung, Hannover Medical School, Germany
| | - Ramsay Refaie
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, UK
| | - Kenneth S Rankin
- Translational and Clinical Research Institute, Newcastle Centre for Cancer, UK
| | - David A Young
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, UK
| | - Andrew D Rowan
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, UK
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8
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Padilla-Godínez FJ, Ramos-Acevedo R, Martínez-Becerril HA, Bernal-Conde LD, Garrido-Figueroa JF, Hiriart M, Hernández-López A, Argüero-Sánchez R, Callea F, Guerra-Crespo M. Protein Misfolding and Aggregation: The Relatedness between Parkinson's Disease and Hepatic Endoplasmic Reticulum Storage Disorders. Int J Mol Sci 2021; 22:ijms222212467. [PMID: 34830348 PMCID: PMC8619695 DOI: 10.3390/ijms222212467] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/18/2021] [Accepted: 10/19/2021] [Indexed: 12/21/2022] Open
Abstract
Dysfunction of cellular homeostasis can lead to misfolding of proteins thus acquiring conformations prone to polymerization into pathological aggregates. This process is associated with several disorders, including neurodegenerative diseases, such as Parkinson’s disease (PD), and endoplasmic reticulum storage disorders (ERSDs), like alpha-1-antitrypsin deficiency (AATD) and hereditary hypofibrinogenemia with hepatic storage (HHHS). Given the shared pathophysiological mechanisms involved in such conditions, it is necessary to deepen our understanding of the basic principles of misfolding and aggregation akin to these diseases which, although heterogeneous in symptomatology, present similarities that could lead to potential mutual treatments. Here, we review: (i) the pathological bases leading to misfolding and aggregation of proteins involved in PD, AATD, and HHHS: alpha-synuclein, alpha-1-antitrypsin, and fibrinogen, respectively, (ii) the evidence linking each protein aggregation to the stress mechanisms occurring in the endoplasmic reticulum (ER) of each pathology, (iii) a comparison of the mechanisms related to dysfunction of proteostasis and regulation of homeostasis between the diseases (such as the unfolded protein response and/or autophagy), (iv) and clinical perspectives regarding possible common treatments focused on improving the defensive responses to protein aggregation for diseases as different as PD, and ERSDs.
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Affiliation(s)
- Francisco J. Padilla-Godínez
- Neurosciences Division, Cell Physiology Institute, National Autonomous University of Mexico, Mexico City 04510, Mexico; (F.J.P.-G.); (R.R.-A.); (H.A.M.-B.); (L.D.B.-C.); (J.F.G.-F.); (M.H.)
- Regenerative Medicine Laboratory, Department of Surgery, Faculty of Medicine, National Autonomous University of Mexico, Mexico City 04510, Mexico; (A.H.-L.); (R.A.-S.)
| | - Rodrigo Ramos-Acevedo
- Neurosciences Division, Cell Physiology Institute, National Autonomous University of Mexico, Mexico City 04510, Mexico; (F.J.P.-G.); (R.R.-A.); (H.A.M.-B.); (L.D.B.-C.); (J.F.G.-F.); (M.H.)
- Regenerative Medicine Laboratory, Department of Surgery, Faculty of Medicine, National Autonomous University of Mexico, Mexico City 04510, Mexico; (A.H.-L.); (R.A.-S.)
| | - Hilda Angélica Martínez-Becerril
- Neurosciences Division, Cell Physiology Institute, National Autonomous University of Mexico, Mexico City 04510, Mexico; (F.J.P.-G.); (R.R.-A.); (H.A.M.-B.); (L.D.B.-C.); (J.F.G.-F.); (M.H.)
- Regenerative Medicine Laboratory, Department of Surgery, Faculty of Medicine, National Autonomous University of Mexico, Mexico City 04510, Mexico; (A.H.-L.); (R.A.-S.)
| | - Luis D. Bernal-Conde
- Neurosciences Division, Cell Physiology Institute, National Autonomous University of Mexico, Mexico City 04510, Mexico; (F.J.P.-G.); (R.R.-A.); (H.A.M.-B.); (L.D.B.-C.); (J.F.G.-F.); (M.H.)
- Regenerative Medicine Laboratory, Department of Surgery, Faculty of Medicine, National Autonomous University of Mexico, Mexico City 04510, Mexico; (A.H.-L.); (R.A.-S.)
| | - Jerónimo F. Garrido-Figueroa
- Neurosciences Division, Cell Physiology Institute, National Autonomous University of Mexico, Mexico City 04510, Mexico; (F.J.P.-G.); (R.R.-A.); (H.A.M.-B.); (L.D.B.-C.); (J.F.G.-F.); (M.H.)
- Regenerative Medicine Laboratory, Department of Surgery, Faculty of Medicine, National Autonomous University of Mexico, Mexico City 04510, Mexico; (A.H.-L.); (R.A.-S.)
| | - Marcia Hiriart
- Neurosciences Division, Cell Physiology Institute, National Autonomous University of Mexico, Mexico City 04510, Mexico; (F.J.P.-G.); (R.R.-A.); (H.A.M.-B.); (L.D.B.-C.); (J.F.G.-F.); (M.H.)
| | - Adriana Hernández-López
- Regenerative Medicine Laboratory, Department of Surgery, Faculty of Medicine, National Autonomous University of Mexico, Mexico City 04510, Mexico; (A.H.-L.); (R.A.-S.)
| | - Rubén Argüero-Sánchez
- Regenerative Medicine Laboratory, Department of Surgery, Faculty of Medicine, National Autonomous University of Mexico, Mexico City 04510, Mexico; (A.H.-L.); (R.A.-S.)
| | - Francesco Callea
- Department of Histopathology, Bugando Medical Centre, Catholic University of Healthy and Allied Sciences, Mwanza 1464, Tanzania;
| | - Magdalena Guerra-Crespo
- Neurosciences Division, Cell Physiology Institute, National Autonomous University of Mexico, Mexico City 04510, Mexico; (F.J.P.-G.); (R.R.-A.); (H.A.M.-B.); (L.D.B.-C.); (J.F.G.-F.); (M.H.)
- Regenerative Medicine Laboratory, Department of Surgery, Faculty of Medicine, National Autonomous University of Mexico, Mexico City 04510, Mexico; (A.H.-L.); (R.A.-S.)
- Correspondence:
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9
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D'Acunto E, Fra A, Visentin C, Manno M, Ricagno S, Galliciotti G, Miranda E. Neuroserpin: structure, function, physiology and pathology. Cell Mol Life Sci 2021; 78:6409-6430. [PMID: 34405255 PMCID: PMC8558161 DOI: 10.1007/s00018-021-03907-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 07/23/2021] [Accepted: 07/27/2021] [Indexed: 12/24/2022]
Abstract
Neuroserpin is a serine protease inhibitor identified in a search for proteins implicated in neuronal axon growth and synapse formation. Since its discovery over 30 years ago, it has been the focus of active research. Many efforts have concentrated in elucidating its neuroprotective role in brain ischemic lesions, the structural bases of neuroserpin conformational change and the effects of neuroserpin polymers that underlie the neurodegenerative disease FENIB (familial encephalopathy with neuroserpin inclusion bodies), but the investigation of the physiological roles of neuroserpin has increased over the last years. In this review, we present an updated and critical revision of the current literature dealing with neuroserpin, covering all aspects of research including the expression and physiological roles of neuroserpin, both inside and outside the nervous system; its inhibitory and non-inhibitory mechanisms of action; the molecular structure of the monomeric and polymeric conformations of neuroserpin, including a detailed description of the polymerisation mechanism; and the involvement of neuroserpin in human disease, with particular emphasis on FENIB. Finally, we briefly discuss the identification by genome-wide screening of novel neuroserpin variants and their possible pathogenicity.
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Affiliation(s)
- Emanuela D'Acunto
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, Rome, Italy
| | - Annamaria Fra
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Cristina Visentin
- Department of Biosciences, University of Milan, Milan, Italy
- Institute of Molecular and Translational Cardiology, I.R.C.C.S. Policlinico San Donato, Milan, Italy
| | - Mauro Manno
- Institute of Biophysics, National Research Council of Italy, Palermo, Italy
| | - Stefano Ricagno
- Department of Biosciences, University of Milan, Milan, Italy
| | - Giovanna Galliciotti
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Elena Miranda
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, Rome, Italy.
- Pasteur Institute-Cenci Bolognetti Foundation, Sapienza University of Rome, Rome, Italy.
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10
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Sanchez-Pulido L, Ponting CP. Extending the Horizon of Homology Detection with Coevolution-based Structure Prediction. J Mol Biol 2021; 433:167106. [PMID: 34139218 PMCID: PMC8527833 DOI: 10.1016/j.jmb.2021.167106] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/09/2021] [Accepted: 06/09/2021] [Indexed: 12/12/2022]
Abstract
Traditional sequence analysis algorithms fail to identify distant homologies when they lie beyond a detection horizon. In this review, we discuss how co-evolution-based contact and distance prediction methods are pushing back this homology detection horizon, thereby yielding new functional insights and experimentally testable hypotheses. Based on correlated substitutions, these methods divine three-dimensional constraints among amino acids in protein sequences that were previously devoid of all annotated domains and repeats. The new algorithms discern hidden structure in an otherwise featureless sequence landscape. Their revelatory impact promises to be as profound as the use, by archaeologists, of ground-penetrating radar to discern long-hidden, subterranean structures. As examples of this, we describe how triplicated structures reflecting longin domains in MON1A-like proteins, or UVR-like repeats in DISC1, emerge from their predicted contact and distance maps. These methods also help to resolve structures that do not conform to a "beads-on-a-string" model of protein domains. In one such example, we describe CFAP298 whose ubiquitin-like domain was previously challenging to perceive owing to a large sequence insertion within it. More generally, the new algorithms permit an easier appreciation of domain families and folds whose evolution involved structural insertion or rearrangement. As we exemplify with α1-antitrypsin, coevolution-based predicted contacts may also yield insights into protein dynamics and conformational change. This new combination of structure prediction (using innovative co-evolution based methods) and homology inference (using more traditional sequence analysis approaches) shows great promise for bringing into view a sea of evolutionary relationships that had hitherto lain far beyond the horizon of homology detection.
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Affiliation(s)
- Luis Sanchez-Pulido
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK.
| | - Chris P Ponting
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK.
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11
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Tavanti F, Menziani MC. Computational Insight on the Interaction of Common Blood Proteins with Gold Nanoparticles. Int J Mol Sci 2021; 22:ijms22168722. [PMID: 34445432 PMCID: PMC8395736 DOI: 10.3390/ijms22168722] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/06/2021] [Accepted: 08/10/2021] [Indexed: 01/23/2023] Open
Abstract
Protein interactions with engineered gold nanoparticles (AuNPs) and the consequent formation of the protein corona are very relevant and poorly understood biological phenomena. The nanoparticle coverage affects protein binding modalities, and the adsorbed protein sites influence interactions with other macromolecules and cells. Here, we studied four common blood proteins, i.e., hemoglobin, serum albumin, α1-antiproteinase, and complement C3, interacting with AuNPs covered by hydrophobic 11-mercapto-1-undecanesulfonate (MUS). We use Molecular Dynamics and the Martini coarse−grained model to gain quantitative insight into the kinetics of the interaction, the physico-chemical characteristics of the binding site, and the nanoparticle adsorption capacity. Results show that proteins bind to MUS−capped AuNPs through strong hydrophobic interactions and that they adapt to the AuNP surfaces to maximize the contact surface, but no dramatic change in the secondary structure of the proteins is observed. We suggest a new method to calculate the maximum adsorption capacity of capped AuNPs based on the effective surface covered by each protein, which better represents the realistic behavior of these systems.
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Affiliation(s)
- Francesco Tavanti
- CNR-NANO Research Center S3, Via Campi 213/a, 41125 Modena, Italy
- Correspondence:
| | - Maria Cristina Menziani
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy;
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12
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Remih K, Amzou S, Strnad P. Alpha1-antitrypsin deficiency: New therapies on the horizon. Curr Opin Pharmacol 2021; 59:149-156. [PMID: 34256305 DOI: 10.1016/j.coph.2021.06.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 06/07/2021] [Indexed: 10/20/2022]
Abstract
Alpha1-antitrypsin deficiency (AATD) is caused by mutations in the SERPINA1 gene, coding for alpha1-antitrypsin (AAT). AAT is synthesised mainly in the liver and is released into bloodstream to protect tissues (particularly lung) with its antiprotease activity. The homozygous Pi∗Z mutation (Pi∗ZZ genotype) is the predominant cause of severe AATD. It interferes with AAT secretion thereby leading to AAT accumulation in the liver and lack of AAT in the circulation and the lung. Accordingly, Pi∗ZZ individuals are strongly predisposed to lung and liver injury. The former is treated by a weekly AAT augmentation therapy, but not medicinal products exist for the liver. Our review summarises the current approaches silencing AAT production, improving protein folding and secretion or promoting AAT degradation.
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Affiliation(s)
- Katharina Remih
- Medical Clinic III, Gastroenterology, Metabolic Diseases and Intensive Care, University Hospital RWTH Aachen, Aachen, Germany
| | - Samira Amzou
- Medical Clinic III, Gastroenterology, Metabolic Diseases and Intensive Care, University Hospital RWTH Aachen, Aachen, Germany
| | - Pavel Strnad
- Medical Clinic III, Gastroenterology, Metabolic Diseases and Intensive Care, University Hospital RWTH Aachen, Aachen, Germany; Coordinating Centre for Alpha1-Antitrypsin Deficiency-related Liver Disease of the European Reference Network (ERN) "Rare Liver" and The European Association for the Study of the Liver (EASL) Registry Group "Alpha1-Liver", Germany.
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13
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Raccosta S, Librizzi F, Jagger AM, Noto R, Martorana V, Lomas DA, Irving JA, Manno M. Scaling Concepts in Serpin Polymer Physics. MATERIALS 2021; 14:ma14102577. [PMID: 34063488 PMCID: PMC8156723 DOI: 10.3390/ma14102577] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/09/2021] [Accepted: 05/10/2021] [Indexed: 01/29/2023]
Abstract
α1-Antitrypsin is a protease inhibitor belonging to the serpin family. Serpin polymerisation is at the core of a class of genetic conformational diseases called serpinopathies. These polymers are known to be unbranched, flexible, and heterogeneous in size with a beads-on-a-string appearance viewed by negative stain electron microscopy. Here, we use atomic force microscopy and time-lapse dynamic light scattering to measure polymer size and shape for wild-type (M) and Glu342→Lys (Z) α1-antitrypsin, the most common variant that leads to severe pathological deficiency. Our data for small polymers deposited onto mica and in solution reveal a power law relation between the polymer size, namely the end-to-end distance or the hydrodynamic radius, and the polymer mass, proportional to the contour length. We use the scaling concepts of polymer physics to assess that α1-antitrypsin polymers are random linear chains with a low persistence length.
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Affiliation(s)
- Samuele Raccosta
- Institute of Biophysics, National Research Council of Italy, via Ugo La Malfa 153, 90146 Palermo, Italy; (S.R.); (F.L.); (R.N.); (V.M.)
| | - Fabio Librizzi
- Institute of Biophysics, National Research Council of Italy, via Ugo La Malfa 153, 90146 Palermo, Italy; (S.R.); (F.L.); (R.N.); (V.M.)
| | - Alistair M. Jagger
- UCL Respiratory, University College London, 5 University Street, London WC1E 6JF, UK; (A.M.J.); (D.A.L.); (J.A.I.)
- Institute of Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BN, UK
| | - Rosina Noto
- Institute of Biophysics, National Research Council of Italy, via Ugo La Malfa 153, 90146 Palermo, Italy; (S.R.); (F.L.); (R.N.); (V.M.)
| | - Vincenzo Martorana
- Institute of Biophysics, National Research Council of Italy, via Ugo La Malfa 153, 90146 Palermo, Italy; (S.R.); (F.L.); (R.N.); (V.M.)
| | - David A. Lomas
- UCL Respiratory, University College London, 5 University Street, London WC1E 6JF, UK; (A.M.J.); (D.A.L.); (J.A.I.)
- Institute of Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BN, UK
| | - James A. Irving
- UCL Respiratory, University College London, 5 University Street, London WC1E 6JF, UK; (A.M.J.); (D.A.L.); (J.A.I.)
- Institute of Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BN, UK
| | - Mauro Manno
- Institute of Biophysics, National Research Council of Italy, via Ugo La Malfa 153, 90146 Palermo, Italy; (S.R.); (F.L.); (R.N.); (V.M.)
- Correspondence:
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14
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Serpins in cartilage and osteoarthritis: what do we know? Biochem Soc Trans 2021; 49:1013-1026. [PMID: 33843993 PMCID: PMC8106492 DOI: 10.1042/bst20201231] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 02/17/2021] [Accepted: 03/04/2021] [Indexed: 12/13/2022]
Abstract
Serpins (serine proteinase inhibitors) are an ancient superfamily of structurally similar proteins, the majority of which use an elegant suicide inhibition mechanism to target serine proteinases. Despite likely evolving from a single common ancestor, the 36 human serpins have established roles regulating diverse biological processes, such as blood coagulation, embryonic development and extracellular matrix (ECM) turnover. Genetic mutations in serpin genes underpin a host of monogenic disorders — collectively termed the ‘serpinopathies’ — but serpin dysregulation has also been shown to drive pathological mechanisms in many common diseases. Osteoarthritis is a degenerative joint disorder, characterised by the progressive destruction of articular cartilage. This breakdown of the cartilage is driven by the metalloproteinases, and it has long been established that an imbalance of metalloproteinases to their inhibitors is of critical importance. More recently, a role for serine proteinases in cartilage destruction is emerging; including the activation of latent matrix metalloproteinases and cell-surface receptors, or direct proteolysis of the ECM. Serpins likely regulate these processes, as well as having roles beyond serine proteinase inhibition. Indeed, serpins are routinely observed to be highly modulated in osteoarthritic tissues and fluids by ‘omic analysis, but despite this, they are largely ignored. Confusing nomenclature and an underappreciation for the role of serine proteinases in osteoarthritis (OA) being the likely causes. In this narrative review, serpin structure, biochemistry and nomenclature are introduced, and for the first time, their putative importance in maintaining joint tissues — as well as their dysregulation in OA — are explored.
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15
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Jagger AM, Waudby CA, Irving JA, Christodoulou J, Lomas DA. High-resolution ex vivo NMR spectroscopy of human Z α 1-antitrypsin. Nat Commun 2020; 11:6371. [PMID: 33311470 PMCID: PMC7732992 DOI: 10.1038/s41467-020-20147-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 11/15/2020] [Indexed: 01/18/2023] Open
Abstract
Genetic mutations predispose the serine protease inhibitor α1-antitrypsin to misfolding and polymerisation within hepatocytes, causing liver disease and chronic obstructive pulmonary disease. This misfolding occurs via a transiently populated intermediate state, but our structural understanding of this process is limited by the instability of recombinant α1-antitrypsin variants in solution. Here we apply NMR spectroscopy to patient-derived samples of α1-antitrypsin at natural isotopic abundance to investigate the consequences of disease-causing mutations, and observe widespread chemical shift perturbations for methyl groups in Z AAT (E342K). By comparison with perturbations induced by binding of a small-molecule inhibitor of misfolding we conclude that they arise from rapid exchange between the native conformation and a well-populated intermediate state. The observation that this intermediate is stabilised by inhibitor binding suggests a paradoxical approach to the targeted treatment of protein misfolding disorders, wherein the stabilisation of disease-associated states provides selectivity while inhibiting further transitions along misfolding pathways.
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Affiliation(s)
- Alistair M Jagger
- UCL Respiratory, Rayne Institute, University College London, London, WC1E 6JF, UK
- Institute of Structural and Molecular Biology, University College London and School of Crystallography, Birkbeck College, University of London, Gower Street, London, WC1E 6BT, UK
| | - Christopher A Waudby
- Institute of Structural and Molecular Biology, University College London and School of Crystallography, Birkbeck College, University of London, Gower Street, London, WC1E 6BT, UK
| | - James A Irving
- UCL Respiratory, Rayne Institute, University College London, London, WC1E 6JF, UK.
- Institute of Structural and Molecular Biology, University College London and School of Crystallography, Birkbeck College, University of London, Gower Street, London, WC1E 6BT, UK.
| | - John Christodoulou
- Institute of Structural and Molecular Biology, University College London and School of Crystallography, Birkbeck College, University of London, Gower Street, London, WC1E 6BT, UK.
| | - David A Lomas
- UCL Respiratory, Rayne Institute, University College London, London, WC1E 6JF, UK.
- Institute of Structural and Molecular Biology, University College London and School of Crystallography, Birkbeck College, University of London, Gower Street, London, WC1E 6BT, UK.
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16
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Gong GC, Song SR, Xu X, Luo Q, Han Q, He JX, Su J. Serpina3n is closely associated with fibrotic procession and knockdown ameliorates bleomycin-induced pulmonary fibrosis. Biochem Biophys Res Commun 2020; 532:598-604. [PMID: 32900484 DOI: 10.1016/j.bbrc.2020.08.094] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 08/24/2020] [Indexed: 12/14/2022]
Abstract
OBJECTIVE Pulmonary fibrosis is a fatal interstitial lung disease that is characterized by excessive accumulation of extracellular matrix (ECM) and remodeling of lung. The precise mechanisms underlying pulmonary fibrosis still remain unclear. In the current study, we aimed to investigate the alteration and function of serine (or cysteine) peptidase inhibitor, clade A, member 3 N (Serpina3n) in pulmonary fibrotic models and explore the potential mechanisms. METHODS We induced pulmonary fibrosis in mice by silica and bleomycin respectively and determined Serpina3n in lung tissues, and then verified the expression of Serpina3n and its correlation with pulmonary fibrosis at seven time points in a bleomycin longstanding model. Moreover, adeno-associated virus type 9 (AAV9)-mediated Serpina3n knockdown was used to treat pulmonary fibrosis in the bleomycin model, whose possible mechanisms would be preliminarily explored by detecting chymotrypsin C as an example. RESULTS Serpina3n was up-regulated significantly in lungs of both models at mRNA and protein levels relative to control. Notably, the expression of Serpina3n peaked during the 3rd week and then decreased until nearly normal levels during the 10th week, which was closely related to fibrotic procession in bleomycin-treated mice. AAV-mediated Serpina3n knockdown in the lung tissues alleviated bleomycin-induced fibrotic symptoms at various levels and disinhibit chymotrypsin C. CONCLUSIONS Our study revealed that Serpina3n is a critical regulator in pulmonary fibrosis and suggested Serpina3n inhibition as a potential therapeutic strategy in chronic pulmonary injuries.
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Affiliation(s)
- Gen-Cheng Gong
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510030, PR China
| | - Sheng-Ren Song
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510030, PR China; Department of Respiratory Medicine, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, 550001, PR China
| | - Xin Xu
- Department of Thoracic Surgery, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, PR China
| | - Qun Luo
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510030, PR China
| | - Qian Han
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510030, PR China
| | - Jian-Xing He
- Department of Thoracic Surgery, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, PR China
| | - Jin Su
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510030, PR China.
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17
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Harris RC, Liu R, Shen J. Predicting Reactive Cysteines with Implicit-Solvent-Based Continuous Constant pH Molecular Dynamics in Amber. J Chem Theory Comput 2020; 16:3689-3698. [PMID: 32330035 PMCID: PMC7772776 DOI: 10.1021/acs.jctc.0c00258] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Cysteines existing in the deprotonated thiolate form or having a tendency to become deprotonated are important players in enzymatic and cellular redox functions and frequently exploited in covalent drug design; however, most computational studies assume cysteines as protonated. Thus, developing an efficient tool that can make accurate and reliable predictions of cysteine protonation states is timely needed. We recently implemented a generalized Born (GB) based continuous constant pH molecular dynamics (CpHMD) method in Amber for protein pKa calculations on CPUs and GPUs. Here we benchmark the performance of GB-CpHMD for predictions of cysteine pKa's and reactivities using a data set of 24 proteins with both down- and upshifted cysteine pKa's. We found that 10 ns single-pH or 4 ns replica-exchange CpHMD titrations gave root-mean-square errors of 1.2-1.3 and correlation coefficients of 0.8-0.9 with respect to experiment. The accuracy of predicting thiolates or reactive cysteines at physiological pH with single-pH titrations is 86 or 81% with a precision of 100 or 90%, respectively. This performance well surpasses the traditional structure-based methods, particularly a widely used empirical pKa tool that gives an accuracy less than 50%. We discuss simulation convergence, dependence on starting structures, common determinants of the pKa downshifts and upshifts, and the origin of the discrepancies from the structure-based calculations. Our work suggests that CpHMD titrations can be performed on a desktop computer equipped with a single GPU card to predict cysteine protonation states for a variety of applications, from understanding biological functions to covalent drug design.
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Affiliation(s)
- Robert C Harris
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
| | - Ruibin Liu
- ComputChem LLC, Baltimore, Maryland 21202, United States
| | - Jana Shen
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
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18
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Alpha 1-Antitrypsin Deficiency: A Disorder of Proteostasis-Mediated Protein Folding and Trafficking Pathways. Int J Mol Sci 2020; 21:ijms21041493. [PMID: 32098273 PMCID: PMC7073043 DOI: 10.3390/ijms21041493] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 02/17/2020] [Accepted: 02/19/2020] [Indexed: 12/30/2022] Open
Abstract
Human cells express large amounts of different proteins continuously that must fold into well-defined structures that need to remain correctly folded and assemble in order to ensure their cellular and biological functions. The integrity of this protein balance/homeostasis, also named proteostasis, is maintained by the proteostasis network (PN). This integrated biological system, which comprises about 2000 proteins (chaperones, folding enzymes, degradation components), control and coordinate protein synthesis folding and localization, conformational maintenance, and degradation. This network is particularly challenged by mutations such as those found in genetic diseases, because of the inability of an altered peptide sequence to properly engage PN components that trigger misfolding and loss of function. Thus, deletions found in the ΔF508 variant of the Cystic Fibrosis (CF) transmembrane regulator (CFTR) triggering CF or missense mutations found in the Z variant of Alpha 1-Antitrypsin deficiency (AATD), leading to lung and liver diseases, can accelerate misfolding and/or generate aggregates. Conversely to CF variants, for which three correctors are already approved (ivacaftor, lumacaftor/ivacaftor, and most recently tezacaftor/ivacaftor), there are limited therapeutic options for AATD. Therefore, a more detailed understanding of the PN components governing AAT variant biogenesis and their manipulation by pharmacological intervention could delay, or even better, avoid the onset of AATD-related pathologies.
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19
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Gershenson A, Gosavi S, Faccioli P, Wintrode PL. Successes and challenges in simulating the folding of large proteins. J Biol Chem 2020; 295:15-33. [PMID: 31712314 PMCID: PMC6952611 DOI: 10.1074/jbc.rev119.006794] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Computational simulations of protein folding can be used to interpret experimental folding results, to design new folding experiments, and to test the effects of mutations and small molecules on folding. However, whereas major experimental and computational progress has been made in understanding how small proteins fold, research on larger, multidomain proteins, which comprise the majority of proteins, is less advanced. Specifically, large proteins often fold via long-lived partially folded intermediates, whose structures, potentially toxic oligomerization, and interactions with cellular chaperones remain poorly understood. Molecular dynamics based folding simulations that rely on knowledge of the native structure can provide critical, detailed information on folding free energy landscapes, intermediates, and pathways. Further, increases in computational power and methodological advances have made folding simulations of large proteins practical and valuable. Here, using serpins that inhibit proteases as an example, we review native-centric methods for simulating the folding of large proteins. These synergistic approaches range from Gō and related structure-based models that can predict the effects of the native structure on folding to all-atom-based methods that include side-chain chemistry and can predict how disease-associated mutations may impact folding. The application of these computational approaches to serpins and other large proteins highlights the successes and limitations of current computational methods and underscores how computational results can be used to inform experiments. These powerful simulation approaches in combination with experiments can provide unique insights into how large proteins fold and misfold, expanding our ability to predict and manipulate protein folding.
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Affiliation(s)
- Anne Gershenson
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts 01003; Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts 01003.
| | - Shachi Gosavi
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore-560065, India.
| | - Pietro Faccioli
- Dipartimento di Fisica, Universitá degli Studi di Trento, 38122 Povo (Trento), Italy; Trento Institute for Fundamental Physics and Applications, 38123 Povo (Trento), Italy.
| | - Patrick L Wintrode
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201.
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20
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Singh J, Singh B. Inhibition of post-mortem fish muscle softening and degradation using legume seed proteinase inhibitors. JOURNAL OF FOOD SCIENCE AND TECHNOLOGY 2020; 57:1-11. [PMID: 31975702 PMCID: PMC6952507 DOI: 10.1007/s13197-019-04044-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 07/29/2019] [Accepted: 08/19/2019] [Indexed: 02/07/2023]
Abstract
Inhibitors that control muscle softening are important for regulating the activities of specific proteinases in meat. Proteolytic activity of endogenous proteinases in postmortem fish leads to the deterioration of myofibres. Calpain proteolytic enzyme system in skeletal muscles is mainly responsible for the post-mortem proteolysis. Soluble sarcoplasmic serine proteinase and the insoluble myofibrillar serine proteinase fractions contribute to the modori effects in surimi gels while myosin heavy chains contribute to gel strength. Proteolytic degenerative processes negatively affect the entire quality spectrum of the fish as food. Legume seeds are a good source of proteinase inhibitors with the potential to emerge as a promising tool in fish meat quality management. Many workers have studied the potent inhibitory effect of the seed flour from various legume crops on the flesh, surimi gels and visceral proteinases of fishes. The present review provides collective information about proteolysis in fish and its control by using legume seed flour as a natural source of proteinase inhibitors. Use of legume seed flour can reduce the dependence of the meat processing industry on the non-renewable synthetic chemical agents. Moreover, the use of natural products from sustainable resources also leads to the improved economics of meat production.
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Affiliation(s)
- Jaspreet Singh
- P.G. Department of Biotechnology, Khalsa College, Amritsar, Punjab 143002 India
| | - Balwinder Singh
- P.G. Department of Biotechnology, Khalsa College, Amritsar, Punjab 143002 India
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21
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A Novel Small Molecule Inhibits Intrahepatocellular Accumulation of Z-Variant Alpha 1-Antitrypsin In Vitro and In Vivo. Cells 2019; 8:cells8121586. [PMID: 31817705 PMCID: PMC6953066 DOI: 10.3390/cells8121586] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 12/01/2019] [Accepted: 12/03/2019] [Indexed: 11/30/2022] Open
Abstract
Alpha 1-antitrypsin deficiency (AATD) is the most common genetic cause of liver disease in children and is associated with early-onset chronic liver disease in adults. AATD associated liver injury is caused by hepatotoxic retention of polymerized mutant alpha 1-antitrypsin molecules within the endoplasmic reticulum. Currently, there is no curative therapy for AATD. In this study, we selected small molecules with the potential to bind mutant alpha 1-antitrypsin (Z-variant) to inhibit its accumulation in hepatocytes. We used molecular docking to select candidate compounds that were validated in cell and animal models of disease. A crystal structure of polymerized alpha 1-antitrypsin molecule was used as the basis for docking 139,735 compounds. Effects of the top scoring compounds were investigated in a cell model that stably expresses Z-variant alpha 1-antitrypsin and in PiZ mice expressing Z-variant human alpha 1-antitrypsin (Z-hAAT), encoded by SERPINA1*E342K. 4′,′5-(Methylenedioxy)-2-nitrocinnamic acid was predicted to bind cleaved alpha 1-antitrypsin at the polymerization interface, and observed to co-localize with Z-hAAT, increase Z-hAAT degradation, inhibit intracellular accumulation of Z-hAAT, and alleviate liver fibrosis.
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22
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Wang F, Orioli S, Ianeselli A, Spagnolli G, A Beccara S, Gershenson A, Faccioli P, Wintrode PL. All-Atom Simulations Reveal How Single-Point Mutations Promote Serpin Misfolding. Biophys J 2019; 114:2083-2094. [PMID: 29742402 DOI: 10.1016/j.bpj.2018.03.027] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 03/09/2018] [Accepted: 03/13/2018] [Indexed: 10/17/2022] Open
Abstract
Protein misfolding is implicated in many diseases, including serpinopathies. For the canonical inhibitory serpin α1-antitrypsin, mutations can result in protein deficiencies leading to lung disease, and misfolded mutants can accumulate in hepatocytes, leading to liver disease. Using all-atom simulations based on the recently developed bias functional algorithm, we elucidate how wild-type α1-antitrypsin folds and how the disease-associated S (Glu264Val) and Z (Glu342Lys) mutations lead to misfolding. The deleterious Z mutation disrupts folding at an early stage, whereas the relatively benign S mutant shows late-stage minor misfolding. A number of suppressor mutations ameliorate the effects of the Z mutation, and simulations on these mutants help to elucidate the relative roles of steric clashes and electrostatic interactions in Z misfolding. These results demonstrate a striking correlation between atomistic events and disease severity and shine light on the mechanisms driving chains away from their correct folding routes.
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Affiliation(s)
- Fang Wang
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland
| | - Simone Orioli
- Dipartimento di Fisica, Università degli Studi di Trento, Povo (Trento), Italy; Trento Institute for Fundamental Physics and Applications, Povo (Trento), Italy
| | - Alan Ianeselli
- Dipartimento di Fisica, Università degli Studi di Trento, Povo (Trento), Italy; Trento Institute for Fundamental Physics and Applications, Povo (Trento), Italy
| | - Giovanni Spagnolli
- Dipartimento di Fisica, Università degli Studi di Trento, Povo (Trento), Italy; Trento Institute for Fundamental Physics and Applications, Povo (Trento), Italy
| | - Silvio A Beccara
- Dipartimento di Fisica, Università degli Studi di Trento, Povo (Trento), Italy; Trento Institute for Fundamental Physics and Applications, Povo (Trento), Italy
| | - Anne Gershenson
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts.
| | - Pietro Faccioli
- Dipartimento di Fisica, Università degli Studi di Trento, Povo (Trento), Italy; Trento Institute for Fundamental Physics and Applications, Povo (Trento), Italy.
| | - Patrick L Wintrode
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland.
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23
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Zhang X, Pham K, Li D, Schutte RJ, Brantly M, Liu C, Ostrov DA. Targeting the site encoded by SERPINA1*E342K for treating alpha-1 antitrypsin deficiency-associated liver diseases. FEBS Lett 2019; 593:1849-1862. [PMID: 31116417 DOI: 10.1002/1873-3468.13452] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 05/14/2019] [Accepted: 05/14/2019] [Indexed: 01/22/2023]
Abstract
Alpha1-antitrypsin (AAT) deficiency predisposes individuals to emphysema and liver diseases such as cirrhosis and hepatocellular carcinoma. The deficiency results from mutations in the SERPIN1A gene encoding AAT molecules that cause hepatotoxic retention within the endoplasmic reticulum. Since the E342K mutation is the basis for destabilization leading to lung and liver pathologies, we used the crystal structure of the mutated AAT as the basis for molecular docking selection of candidate compounds that may bind and stabilize the 342K structural pocket. We identified compounds that inhibited intracellular accumulation of AAT in hepatocytes in vitro. These data suggest that drug binding to a structural site encoded by a mutation associated with AAT deficiency has the potential for clinical utility by modulating conformational transitions.
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Affiliation(s)
- Xiaojuan Zhang
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida College of Medicine, Gainesville, FL, USA
| | - Kien Pham
- Department of Pathology & Laboratory Medicine, Rutgers New Jersey Medical School & Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Danmeng Li
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida College of Medicine, Gainesville, FL, USA
| | - Ryan J Schutte
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida College of Medicine, Gainesville, FL, USA
| | - Mark Brantly
- Division of Pulmonary, Critical Care, and Sleep Medicine, University of Florida College of Medicine, Gainesville, FL, USA
| | - Chen Liu
- Department of Pathology & Laboratory Medicine, Rutgers New Jersey Medical School & Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - David A Ostrov
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida College of Medicine, Gainesville, FL, USA
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24
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Kim KH, Kim JY, Yoo JS. Mass spectrometry analysis of glycoprotein biomarkers in human blood of hepatocellular carcinoma. Expert Rev Proteomics 2019; 16:553-568. [DOI: 10.1080/14789450.2019.1626235] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Kwang Hoe Kim
- Biomedical Omics Group, Korea Basic Science Institute, Cheongju, Republic of Korea
| | - Jin Young Kim
- Biomedical Omics Group, Korea Basic Science Institute, Cheongju, Republic of Korea
| | - Jong Shin Yoo
- Biomedical Omics Group, Korea Basic Science Institute, Cheongju, Republic of Korea
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, Republic of Korea
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25
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Eggenschwiler R, Patronov A, Hegermann J, Fráguas-Eggenschwiler M, Wu G, Cortnumme L, Ochs M, Antes I, Cantz T. A combined in silico and in vitro study on mouse Serpina1a antitrypsin-deficiency mutants. Sci Rep 2019; 9:7486. [PMID: 31097772 PMCID: PMC6522476 DOI: 10.1038/s41598-019-44043-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 05/07/2019] [Indexed: 01/15/2023] Open
Abstract
Certain point-mutations in the human SERPINA1-gene can cause severe α1-antitrypsin-deficiency (A1AT-D). Affected individuals can suffer from loss-of-function lung-disease and from gain-of-function liver-disease phenotypes. However, age of onset and severity of clinical appearance is heterogeneous amongst carriers, suggesting involvement of additional genetic and environmental factors. The generation of authentic A1AT-D mouse-models has been hampered by the complexity of the mouse Serpina1-gene locus and a model with concurrent lung and liver-disease is still missing. Here, we investigate point-mutations in the mouse Serpina1a antitrypsin-orthologue, which are homolog-equivalent to ones known to cause severe A1AT-D in human. We combine in silico and in vitro methods and we find that analyzed mutations do introduce potential disease-causing properties into Serpina1a. Finally, we show that introduction of the King’s-mutation causes inactivation of neutrophil elastase inhibitory-function in both, mouse and human antitrypsin, while the mouse Z-mutant retains activity. This work paves the path to generation of better A1AT-D mouse-models.
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Affiliation(s)
- Reto Eggenschwiler
- Research Group Translational Hepatology and Stem Cell Biology, Cluster of Excellence REBIRTH, Hannover Medical School, Hannover, 30625, Germany. .,Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, 30625, Germany.
| | - Atanas Patronov
- Protein Modelling Group, Department of Life Sciences, Technical University Munich, Freising, 85354, Germany.,TUM School of Life Sciences, Center for Integrated Protein Science (CIPSM), Technical University Munich, Freising, 85354, Germany
| | - Jan Hegermann
- Research Core Unit Electron Microscopy, Hannover Medical School, Hannover, 30625, Germany.,Institute of Functional and Applied Anatomy, Hannover Medical School, Hannover, 30625, Germany.,Imaging Platform of the Cluster of Excellence REBIRTH, Hannover Medical School, Hannover, 30625, Germany
| | - Mariane Fráguas-Eggenschwiler
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, 30625, Germany.,TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, 30625, Germany
| | - Guangming Wu
- Max Planck Institute for Molecular Biomedicine, Cell and Developmental Biology, Münster, 48149, Germany
| | - Leon Cortnumme
- Research Group Translational Hepatology and Stem Cell Biology, Cluster of Excellence REBIRTH, Hannover Medical School, Hannover, 30625, Germany.,Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, 30625, Germany
| | - Matthias Ochs
- Research Core Unit Electron Microscopy, Hannover Medical School, Hannover, 30625, Germany.,Institute of Functional and Applied Anatomy, Hannover Medical School, Hannover, 30625, Germany.,Imaging Platform of the Cluster of Excellence REBIRTH, Hannover Medical School, Hannover, 30625, Germany.,Institute of Vegetative Anatomy Charité - Universitaetsmedizin Berlin, Berlin, 10115, Germany
| | - Iris Antes
- Protein Modelling Group, Department of Life Sciences, Technical University Munich, Freising, 85354, Germany.,TUM School of Life Sciences, Center for Integrated Protein Science (CIPSM), Technical University Munich, Freising, 85354, Germany
| | - Tobias Cantz
- Research Group Translational Hepatology and Stem Cell Biology, Cluster of Excellence REBIRTH, Hannover Medical School, Hannover, 30625, Germany. .,Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, 30625, Germany. .,Max Planck Institute for Molecular Biomedicine, Cell and Developmental Biology, Münster, 48149, Germany.
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26
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Targeted Gene Delivery through the Respiratory System: Rationale for Intratracheal Gene Transfer. J Cardiovasc Dev Dis 2019; 6:jcdd6010008. [PMID: 30781363 PMCID: PMC6462990 DOI: 10.3390/jcdd6010008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/11/2019] [Accepted: 02/13/2019] [Indexed: 12/11/2022] Open
Abstract
Advances in DNA- and RNA-based technologies have made gene therapy suitable for many lung diseases, especially those that are hereditary. The main objective of gene therapy is to deliver an adequate amount of gene construct to the intended target cell, achieve stable transduction in target cells, and to produce a clinically therapeutic effect. This review focuses on the cellular organization in the normal lung and how gene therapy targets the specific cell types that are affected by pulmonary disorders caused by genetic mutations. Furthermore, it examines the pulmonary barriers that can compromise the absorption and transduction of viral vectors and genetic agents by the lung. Finally, it discusses the advantages and limitations of direct intra-tracheal gene delivery with different viral vectors in small and large animal models and in clinical trials.
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27
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Sanrattana W, Maas C, de Maat S. SERPINs-From Trap to Treatment. Front Med (Lausanne) 2019; 6:25. [PMID: 30809526 PMCID: PMC6379291 DOI: 10.3389/fmed.2019.00025] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 01/25/2019] [Indexed: 01/04/2023] Open
Abstract
Excessive enzyme activity often has pathological consequences. This for example is the case in thrombosis and hereditary angioedema, where serine proteases of the coagulation system and kallikrein-kinin system are excessively active. Serine proteases are controlled by SERPINs (serine protease inhibitors). We here describe the basic biochemical mechanisms behind SERPIN activity and identify key determinants that influence their function. We explore the clinical phenotypes of several SERPIN deficiencies and review studies where SERPINs are being used beyond replacement therapy. Excitingly, rare human SERPIN mutations have led us and others to believe that it is possible to refine SERPINs toward desired behavior for the treatment of enzyme-driven pathology.
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Affiliation(s)
| | | | - Steven de Maat
- Department of Clinical Chemistry and Haematology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
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28
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Lomas DA. New Therapeutic Targets for Alpha-1 Antitrypsin Deficiency. CHRONIC OBSTRUCTIVE PULMONARY DISEASES-JOURNAL OF THE COPD FOUNDATION 2018; 5:233-243. [PMID: 30723781 DOI: 10.15326/jcopdf.5.4.2017.0165] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Alpha-1antitrypsin deficiency (AATD) results from the intracellular polymerization and retention of mutant alpha-1antitrypsin (AAT) within the endoplasmic reticulum of hepatocytes. This causes cirrhosis whilst the deficiency of circulating AAT predisposes to early onset emphysema. This is an exciting time for researchers in the field with the development of novel therapies based on understanding the pathobiology of disease. I review here augmentation therapy to prevent the progression of lung disease and a range of approaches to treat the liver disease associated with the accumulation of mutant AAT: modifying proteostasis networks that are activated by Z AAT polymers, stimulating autophagy, small interfering RNA and small molecules to block intracellular polymerization, and stem cell technology to correct the genetic defect that underlies AATD.
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Affiliation(s)
- David A Lomas
- UCL Respiratory, Division of Medicine, University College London, United Kingdom
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29
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Dunlea DM, Fee LT, McEnery T, McElvaney NG, Reeves EP. The impact of alpha-1 antitrypsin augmentation therapy on neutrophil-driven respiratory disease in deficient individuals. J Inflamm Res 2018; 11:123-134. [PMID: 29618937 PMCID: PMC5875399 DOI: 10.2147/jir.s156405] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Alpha-1 antitrypsin (AAT) is the most abundant serine protease inhibitor circulating in the blood. AAT deficiency (AATD) is an autosomal codominant condition affecting an estimated 3.4 million individuals worldwide. The clinical disease associated with AATD can present in a number of ways including COPD, liver disease, panniculitis and antineutrophil cytoplasmic antibody vasculitis. AATD is the only proven genetic risk factor for the development of COPD, and deficient individuals who smoke are disposed to more aggressive disease. Principally, AAT is a serine protease inhibitor; however, over the past number of years, the assessment of AAT as simply an antiprotease has evolved, and it is now recognized that AAT has significant anti-inflammatory properties affecting a wide range of cells, including the circulating neutrophil.
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Affiliation(s)
- Danielle M Dunlea
- Irish Centre for Genetic Lung Disease, Department of Medicine, Royal College of Surgeons in Ireland, Beaumont Hospital, Dublin, Ireland
| | - Laura T Fee
- Irish Centre for Genetic Lung Disease, Department of Medicine, Royal College of Surgeons in Ireland, Beaumont Hospital, Dublin, Ireland
| | - Thomas McEnery
- Irish Centre for Genetic Lung Disease, Department of Medicine, Royal College of Surgeons in Ireland, Beaumont Hospital, Dublin, Ireland
| | - Noel G McElvaney
- Irish Centre for Genetic Lung Disease, Department of Medicine, Royal College of Surgeons in Ireland, Beaumont Hospital, Dublin, Ireland
| | - Emer P Reeves
- Irish Centre for Genetic Lung Disease, Department of Medicine, Royal College of Surgeons in Ireland, Beaumont Hospital, Dublin, Ireland
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30
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Race to the native state. Proc Natl Acad Sci U S A 2018; 115:2267-2269. [PMID: 29472450 DOI: 10.1073/pnas.1722622115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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31
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Mason S, Chen BY, Jagodzinski F. Exploring Protein Cavities through Rigidity Analysis. Molecules 2018; 23:molecules23020351. [PMID: 29414909 PMCID: PMC6017401 DOI: 10.3390/molecules23020351] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 01/25/2018] [Accepted: 01/31/2018] [Indexed: 12/23/2022] Open
Abstract
The geometry of cavities in the surfaces of proteins facilitates a variety of biochemical functions. To better understand the biochemical nature of protein cavities, the shape, size, chemical properties, and evolutionary nature of functional and nonfunctional surface cavities have been exhaustively surveyed in protein structures. The rigidity of surface cavities, however, is not immediately available as a characteristic of structure data, and is thus more difficult to examine. Using rigidity analysis for assessing and analyzing molecular rigidity, this paper performs the first survey of the relationships between cavity properties, such as size and residue content, and how they correspond to cavity rigidity. Our survey measured a variety of rigidity metrics on 120,323 cavities from 12,785 sequentially non-redundant protein chains. We used VASP-E, a volume-based algorithm for analyzing cavity geometry. Our results suggest that rigidity properties of protein cavities are dependent on cavity surface area.
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Affiliation(s)
- Stephanie Mason
- Department of Computer Science, Western Washington University, 516 High Street, Bellingham, WA 98225, USA.
| | - Brian Y Chen
- Department of Computer Science and Engineering, Lehigh University, 19 Memorial Drive West, Bethlehem, PA 18015, USA.
| | - Filip Jagodzinski
- Department of Computer Science, Western Washington University, 516 High Street, Bellingham, WA 98225, USA.
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32
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Nagahashi K, Takano K, Suzuki-Inoue K, Kanayama N, Umemura K, Urano T, Iwaki T. Mutation in a highly conserved glycine residue in strand 5B of plasminogen activator inhibitor 1 causes polymerisation. Thromb Haemost 2017; 117:860-869. [DOI: 10.1160/th16-07-0572] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 01/27/2017] [Indexed: 11/05/2022]
Abstract
SummarySerpinopathy is characterised as abnormal accumulation of serine protease inhibitors (SERPINs) in cells and results in clinical symptoms owing to lack of SERPIN function or excessive accumulation of abnormal SERPIN. We recently identified a patient with functional deficiency of plasminogen activator inhibitor-1 (PAI-1), a member of the SERPIN superfamily. The patient exhibited life-threatening bleeding tendencies, which have also been observed in patients with a complete deficiency in PAI-1. Sequence analysis revealed a homozygous singlenucleotide substitution from guanine to cytosine at exon 9, which changed amino acid residue 397 from glycine to arginine (c.1189G>C; p.Gly397Arg). This glycine was located in strand 5B and was well conserved in other serpins. The mutant PAI-1 was polymerised in the cells, interfering with PAI-1 secretion. The corresponding mutations in SERPINC1 (anti-thrombin III) at position 456 (Gly456Arg) and SERPINI1 (neuroserpin) at position 392 (Gly392Glu) caused an anti-thrombin deficiency and severe dementia due to intracellular retention of the polymers. Glycine is the smallest amino acid, and these mutated amino acids were larger and charged. To determine which factors were important, further mutagenesis of PAI-1 was performed. Although the G397A, C, I, L, S, T, and V were secreted, the G397D, E, F, H, K, M, N, P, Q, W, and Y were not secreted. The results revealed that the size was likely triggered by the polymerisation of SEPRINs at this position. Structural analyses of this mutated PAI-1 would be useful to develop a novel PAI-1 inhibitor, which may be applicable in the context of several pathological states.
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Differential overexpression of SERPINA3 in human prion diseases. Sci Rep 2017; 7:15637. [PMID: 29142239 PMCID: PMC5688139 DOI: 10.1038/s41598-017-15778-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 11/01/2017] [Indexed: 11/08/2022] Open
Abstract
Prion diseases are fatal neurodegenerative disorders with sporadic, genetic or acquired etiologies. The molecular alterations leading to the onset and the spreading of these diseases are still unknown. In a previous work we identified a five-gene signature able to distinguish intracranially BSE-infected macaques from healthy ones, with SERPINA3 showing the most prominent dysregulation. We analyzed 128 suitable frontal cortex samples, from prion-affected patients (variant Creutzfeldt-Jakob disease (vCJD) n = 20, iatrogenic CJD (iCJD) n = 11, sporadic CJD (sCJD) n = 23, familial CJD (gCJD) n = 17, fatal familial insomnia (FFI) n = 9, Gerstmann-Sträussler-Scheinker syndrome (GSS)) n = 4), patients with Alzheimer disease (AD, n = 14) and age-matched controls (n = 30). Real Time-quantitative PCR was performed for SERPINA3 transcript, and ACTB, RPL19, GAPDH and B2M were used as reference genes. We report SERPINA3 to be strongly up-regulated in the brain of all human prion diseases, with only a mild up-regulation in AD. We show that this striking up-regulation, both at the mRNA and at the protein level, is present in all types of human prion diseases analyzed, although to a different extent for each specific disorder. Our data suggest that SERPINA3 may be involved in the pathogenesis and the progression of prion diseases, representing a valid tool for distinguishing different forms of these disorders in humans.
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34
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Boerema DJ, An B, Gandhi RP, Papineau R, Regnier E, Wilder A, Molitor A, Tang AP, Kee SM. Biochemical comparison of four commercially available human α 1-proteinase inhibitors for treatment of α 1-antitrypsin deficiency. Biologicals 2017; 50:63-72. [PMID: 28882403 DOI: 10.1016/j.biologicals.2017.08.010] [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: 02/24/2017] [Revised: 07/13/2017] [Accepted: 08/15/2017] [Indexed: 12/21/2022] Open
Abstract
Intravenous therapy with purified plasma-derived alpha1-proteinase inhibitor (α1-PI) concentrates is the only specific treatment for α1-PI deficiency. For the therapy to be safe and efficacious, α1-PI concentrates should be highly pure and contain high amounts of functional protein. This study compared the four plasma-derived α1-PI products commercially available in Europe (Respreeza, Prolastin, Alfalastin, Trypsone) by biochemical methods with respect to function, purity, structure, and chemical modifications. Respreeza had the highest level of functional protein (48.8 mg/mL) and the highest specific activity (0.862 mg active α1-PI per mg total protein). By size exclusion chromatography, Respreeza was 97.4% pure, followed by Alfalastin 88.1%, Prolastin 76.9%, and Trypsone 70.8%. By reversed phase chromatography, Respreeza had an α1-PI purity of 97.7%, followed by Trypsone 88.0%, Prolastin 78.0%, and Alfalastin 69.5%. The main protein band by sodium dodecyl sulphate-polyacrylamide gel electrophoresis was found for all products at approximately 50 kDa. Additional protein bands were found for Prolastin, Alfalastin, and Trypsone. The α1-PI products differed in cysteine oxidation state and C-terminal lysine status. α1-PI products tested differ in purity, concentration, and chemical variation. Respreeza has the highest level of purity. The impact of the non-therapeutic proteins identified has not been evaluated.
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Affiliation(s)
| | - Bo An
- CSL Behring, Kankakee, IL, USA
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35
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Carpagnano GE, Santacroce R, Palmiotti GA, Leccese A, Giuffreda E, Margaglione M, Foschino Barbaro MP, Aliberti S, Lacedonia D. A New SERPINA-1 Missense Mutation Associated with Alpha-1 Antitrypsin Deficiency and Bronchiectasis. Lung 2017; 195:679-682. [PMID: 28668972 DOI: 10.1007/s00408-017-0033-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 06/19/2017] [Indexed: 10/19/2022]
Abstract
Alpha-1-antitrypsin deficiency (AATD) is a genetic condition caused by SERPINA1 mutations, which culminates into lower protease inhibitor activity in the serum and predisposes to emphysema. Clinical manifestations of AATD are often associated to ZZ (p.Glu342Lys) and SZ (p.Glu264Val) genotypes and less frequently to rare deficiency or null alleles in heterozygous and homozygous states. We report a case of a 52-year-old woman with bronchiectasis without other potential causes other than an electrophoresis that showed a decrease of alpha-1 globin band and AAT levels below the normal value (78 mg/dl; v.n. 90-200 mg/dl). No S or Z mutation was identified, but sequencing analysis found a novel missense variant Ile74Asn (c.221T > A) in heterozygous state on an M3 allele (Glu400Asp) in the exon 2 of the SERPINA-1gene, probably leading to a dysfunctional protein. This mutation has never been previously identified, and it is interesting to note the association with bronchiectasis in the absence of emphysema.
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Affiliation(s)
- G E Carpagnano
- Department of Medical and Surgical Sciences, Institute of Respiratory Diseases, University of Foggia, Foggia, Italy
| | - R Santacroce
- Medical Genetics, Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - G A Palmiotti
- Department of Medical and Surgical Sciences, Institute of Respiratory Diseases, University of Foggia, Foggia, Italy.
| | - A Leccese
- Medical Genetics, Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - E Giuffreda
- Department of Medical and Surgical Sciences, Institute of Respiratory Diseases, University of Foggia, Foggia, Italy
| | - M Margaglione
- Medical Genetics, Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - M P Foschino Barbaro
- Department of Medical and Surgical Sciences, Institute of Respiratory Diseases, University of Foggia, Foggia, Italy
| | - S Aliberti
- Department of Pathophysiology and Transplantation, Cardio-Thoracic Unit and Adult Cystic Fibrosis Center, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, University of Milan, Milan, Italy
| | - D Lacedonia
- Department of Medical and Surgical Sciences, Institute of Respiratory Diseases, University of Foggia, Foggia, Italy
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36
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Masurier N, Arama DP, El Amri C, Lisowski V. Inhibitors of kallikrein-related peptidases: An overview. Med Res Rev 2017; 38:655-683. [DOI: 10.1002/med.21451] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 04/24/2017] [Accepted: 05/16/2017] [Indexed: 12/11/2022]
Affiliation(s)
- Nicolas Masurier
- Institut des Biomolécules Max Mousseron, UMR 5247, CNRS; Université de Montpellier, ENSCM, UFR des Sciences Pharmaceutiques et Biologiques; Montpellier Cedex France
| | - Dominique P. Arama
- Institut des Biomolécules Max Mousseron, UMR 5247, CNRS; Université de Montpellier, ENSCM, UFR des Sciences Pharmaceutiques et Biologiques; Montpellier Cedex France
| | - Chahrazade El Amri
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8256; Biological Adaptation and Ageing, Integrated Cellular Ageing and Inflammation, Molecular & Functional Enzymology; Paris France
| | - Vincent Lisowski
- Institut des Biomolécules Max Mousseron, UMR 5247, CNRS; Université de Montpellier, ENSCM, UFR des Sciences Pharmaceutiques et Biologiques; Montpellier Cedex France
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37
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Inhibitory serpins. New insights into their folding, polymerization, regulation and clearance. Biochem J 2017; 473:2273-93. [PMID: 27470592 DOI: 10.1042/bcj20160014] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 03/31/2016] [Indexed: 12/20/2022]
Abstract
Serpins are a widely distributed family of high molecular mass protein proteinase inhibitors that can inhibit both serine and cysteine proteinases by a remarkable mechanism-based kinetic trapping of an acyl or thioacyl enzyme intermediate that involves massive conformational transformation. The trapping is based on distortion of the proteinase in the complex, with energy derived from the unique metastability of the active serpin. Serpins are the favoured inhibitors for regulation of proteinases in complex proteolytic cascades, such as are involved in blood coagulation, fibrinolysis and complement activation, by virtue of the ability to modulate their specificity and reactivity. Given their prominence as inhibitors, much work has been carried out to understand not only the mechanism of inhibition, but how it is fine-tuned, both spatially and temporally. The metastability of the active state raises the question of how serpins fold, whereas the misfolding of some serpin variants that leads to polymerization and pathologies of liver disease, emphysema and dementia makes it clinically important to understand how such polymerization might occur. Finally, since binding of serpins and their proteinase complexes, particularly plasminogen activator inhibitor-1 (PAI-1), to the clearance and signalling receptor LRP1 (low density lipoprotein receptor-related protein 1), may affect pathways linked to cell migration, angiogenesis, and tumour progression, it is important to understand the nature and specificity of binding. The current state of understanding of these areas is addressed here.
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Andersen OJ, Risør MW, Poulsen EC, Nielsen NC, Miao Y, Enghild JJ, Schiøtt B. Reactive Center Loop Insertion in α-1-Antitrypsin Captured by Accelerated Molecular Dynamics Simulation. Biochemistry 2017; 56:634-646. [PMID: 27995800 DOI: 10.1021/acs.biochem.6b00839] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Protease inhibition by metastable serine protease inhibitors (serpins) is mediated by one of the largest functional intradomain conformational changes known in biology. In this extensive structural rearrangement, protease-serpin complex formation triggers cleavage of the serpin reactive center loop (RCL), its subsequent insertion into central β-sheet A, and covalent trapping of the target protease. In this study, we present the first detailed accelerated molecular dynamics simulation of the insertion of the fully cleaved RCL in α-1-antitrypsin (α1AT), the archetypal member of the family of human serpins. Our results reveal internal water pathways that allow the initial incorporation of side chains of RCL residues into the protein interior. We observed structural plasticity of the helix F (hF) element that blocks the RCL path in the native state, which is in excellent agreement with previous experimental reports. Furthermore, the simulation suggested a novel role of hF and the connected turn (thFs3A) as chaperones that support the insertion process by reducing the conformational space available to the RCL. Transient electrostatic interactions of RCL residues potentially fine-tune the serpin inhibitory activity. On the basis of our simulation, we generated the α1AT mutants K168E, E346K, and K168E/E346K and analyzed their inhibitory activity along with their intrinsic stability and heat-induced polymerization. Remarkably, the E346K mutation exhibited enhanced inhibitory activity along with an increased rate of premature structural collapse (polymerization), suggesting a significant role of E346 in the gatekeeping of the strain in the metastable native state.
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Affiliation(s)
- Ole Juul Andersen
- Center for Insoluble Protein Structures (inSPIN) and Interdisciplinary Nanoscience Center (iNANO), Aarhus University , Aarhus, Denmark.,Department of Chemistry, Aarhus University , Aarhus, Denmark
| | - Michael Wulff Risør
- Center for Insoluble Protein Structures (inSPIN) and Interdisciplinary Nanoscience Center (iNANO), Aarhus University , Aarhus, Denmark.,Department of Molecular Biology and Genetics, Aarhus University , Aarhus, Denmark
| | - Emil Christian Poulsen
- Center for Insoluble Protein Structures (inSPIN) and Interdisciplinary Nanoscience Center (iNANO), Aarhus University , Aarhus, Denmark.,Department of Molecular Biology and Genetics, Aarhus University , Aarhus, Denmark
| | - Niels Chr Nielsen
- Center for Insoluble Protein Structures (inSPIN) and Interdisciplinary Nanoscience Center (iNANO), Aarhus University , Aarhus, Denmark.,Department of Chemistry, Aarhus University , Aarhus, Denmark
| | - Yinglong Miao
- Howard Hughes Medical Institute and Department of Pharmacology, University of California at San Diego , La Jolla, California 92093, United States
| | - Jan J Enghild
- Center for Insoluble Protein Structures (inSPIN) and Interdisciplinary Nanoscience Center (iNANO), Aarhus University , Aarhus, Denmark.,Department of Molecular Biology and Genetics, Aarhus University , Aarhus, Denmark
| | - Birgit Schiøtt
- Center for Insoluble Protein Structures (inSPIN) and Interdisciplinary Nanoscience Center (iNANO), Aarhus University , Aarhus, Denmark.,Department of Chemistry, Aarhus University , Aarhus, Denmark
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39
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Boudida Y, Gagaoua M, Becila S, Picard B, Boudjellal A, Herrera-Mendez CH, Sentandreu M, Ouali A. Serine Protease Inhibitors as Good Predictors of Meat Tenderness: Which Are They and What Are Their Functions? Crit Rev Food Sci Nutr 2017; 56:957-72. [PMID: 25085261 DOI: 10.1080/10408398.2012.741630] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Since years, serine proteases and their inhibitors were an enigma to meat scientists. They were indeed considered to be extracellular and to play no role in postmortem muscle proteolysis. In the 1990's, we observed that protease inhibitors levels in muscles are a better predictor of meat tenderness than their target enzymes. From a practical point of view, we therefore choose to look for serine protease inhibitors rather than their target enzymes, i.e. serine proteases and the purpose of this report was to overview the findings obtained. Fractionation of a muscle crude extract by gel filtration revealed three major trypsin inhibitory fractions designed as F1 (Mr:50-70 kDa), F2 (Mr:40-60 kDa) and F3 (Mr:10-15kD) which were analyzed separately. Besides antithrombin III, an heparin dependent thrombin inhibitor, F1 and F2 comprised a large set of closely related trypsin inhibitors encoded by at least 8 genes bovSERPINA3-1 to A3-8 and able to inhibit also strongly initiator and effector caspases. They all belong to the serpin superfamily, known to form covalent complexes with their target enzymes, were located within muscle cells and found in all tissues and fluids examined irrespective of the animal species. Potential biological functions in living and postmortem muscle were proposed for all of them. In contrast to F1 and F2 which have been more extensively investigated only preliminary findings were provided for F3. Taken together, these results tend to ascertain the onset of apoptosis in postmortem muscle. However, the exact mechanisms driving the cell towards apoptosis and how apoptosis, an energy dependent process, can be completed postmortem remain still unclear.
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Affiliation(s)
- Yasmine Boudida
- a Equipe Maquav, INATAA, Université Frères Mentouri , Constantine , Algeria
| | - Mohammed Gagaoua
- a Equipe Maquav, INATAA, Université Frères Mentouri , Constantine , Algeria
| | - Samira Becila
- a Equipe Maquav, INATAA, Université Frères Mentouri , Constantine , Algeria
| | - Brigitte Picard
- b UMR1213 Herbivores, URH - AMUVI, INRA de Clermont Ferrand Theix, St Genès Champanelle , France
| | | | - Carlos H Herrera-Mendez
- c Agroindustrial Engineering Department, Universidad De Guanajuato, Salvatierra , Guanajuato , Mexico
| | - Miguel Sentandreu
- d Instituto de Agroquímica y Tecnología de Alimentos, CSIC , Burjassot (Valencia ), Spain
| | - Ahmed Ouali
- e UR370, QuaPA, INRA de Clermont Ferrand - Theix, St Genès Champanelle , France
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40
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Awoonor-Williams E, Rowley CN. Evaluation of Methods for the Calculation of the pKa of Cysteine Residues in Proteins. J Chem Theory Comput 2016; 12:4662-73. [DOI: 10.1021/acs.jctc.6b00631] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ernest Awoonor-Williams
- Department of Chemistry, Memorial University of Newfoundland, St.
John’s, Newfoundland and Labrador A1B 3X9, Canada
| | - Christopher N. Rowley
- Department of Chemistry, Memorial University of Newfoundland, St.
John’s, Newfoundland and Labrador A1B 3X9, Canada
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41
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Lomas DA, Hurst JR, Gooptu B. Update on alpha-1 antitrypsin deficiency: New therapies. J Hepatol 2016; 65:413-24. [PMID: 27034252 DOI: 10.1016/j.jhep.2016.03.010] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Revised: 03/16/2016] [Accepted: 03/20/2016] [Indexed: 02/07/2023]
Abstract
α1-Antitrypsin deficiency is characterised by the misfolding and intracellular polymerisation of mutant α1-antitrypsin within the endoplasmic reticulum of hepatocytes. The retention of mutant protein causes hepatic damage and cirrhosis whilst the lack of an important circulating protease inhibitor predisposes the individuals with severe α1-antitrypsin deficiency to early onset emphysema. Our work over the past 25years has led to new paradigms for the liver and lung disease associated with α1-antitrypsin deficiency. We review here the molecular pathology of the cirrhosis and emphysema associated with α1-antitrypsin deficiency and show how an understanding of this condition provided the paradigm for a wider group of disorders that we have termed the serpinopathies. The detailed understanding of the pathobiology of α1-antitrypsin deficiency has identified important disease mechanisms to target. As a result, several novel parallel and complementary therapeutic approaches are in development with some now in clinical trials. We provide an overview of these new therapies for the liver and lung disease associated with α1-antitrypsin deficiency.
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Affiliation(s)
- David A Lomas
- UCL Respiratory, Division of Medicine, Rayne Building, University College London, UK; The London Alpha-1-Antitrypsin Deficiency Service, Royal Free London NHS Foundation Trust, London, UK; Institute of Structural and Molecular Biology, UCL/Birkbeck College, University of London, London WC1E 7HX, UK.
| | - John R Hurst
- UCL Respiratory, Division of Medicine, Rayne Building, University College London, UK; The London Alpha-1-Antitrypsin Deficiency Service, Royal Free London NHS Foundation Trust, London, UK
| | - Bibek Gooptu
- The London Alpha-1-Antitrypsin Deficiency Service, Royal Free London NHS Foundation Trust, London, UK; Institute of Structural and Molecular Biology, UCL/Birkbeck College, University of London, London WC1E 7HX, UK; Division of Asthma, Allergy and Lung Biology, King's College London, Guy's Hospital, 5th Floor, Tower Wing, London, UK
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42
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Huang X, Zheng Y, Zhang F, Wei Z, Wang Y, Carrell RW, Read RJ, Chen GQ, Zhou A. Molecular Mechanism of Z α1-Antitrypsin Deficiency. J Biol Chem 2016; 291:15674-86. [PMID: 27246852 PMCID: PMC4957051 DOI: 10.1074/jbc.m116.727826] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Indexed: 12/14/2022] Open
Abstract
The Z mutation (E342K) of α1-antitrypsin (α1-AT), carried by 4% of Northern Europeans, predisposes to early onset of emphysema due to decreased functional α1-AT in the lung and to liver cirrhosis due to accumulation of polymers in hepatocytes. However, it remains unclear why the Z mutation causes intracellular polymerization of nascent Z α1-AT and why 15% of the expressed Z α1-AT is secreted into circulation as functional, but polymerogenic, monomers. Here, we solve the crystal structure of the Z-monomer and have engineered replacements to assess the conformational role of residue Glu-342 in α1-AT. The results reveal that Z α1-AT has a labile strand 5 of the central β-sheet A (s5A) with a consequent equilibrium between a native inhibitory conformation, as in its crystal structure here, and an aberrant conformation with s5A only partially incorporated into the central β-sheet. This aberrant conformation, induced by the loss of interactions from the Glu-342 side chain, explains why Z α1-AT is prone to polymerization and readily binds to a 6-mer peptide, and it supports that annealing of s5A into the central β-sheet is a crucial step in the serpins' metastable conformational formation. The demonstration that the aberrant conformation can be rectified through stabilization of the labile s5A by binding of a small molecule opens a potential therapeutic approach for Z α1-AT deficiency.
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Affiliation(s)
- Xin Huang
- From the Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine and University of Chinese Academy of Sciences, Shanghai 200025, China
| | - Ying Zheng
- the Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology Division of Shanghai Universities E-Institutes, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China, and
| | - Fei Zhang
- the Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology Division of Shanghai Universities E-Institutes, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China, and
| | - Zhenquan Wei
- the Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology Division of Shanghai Universities E-Institutes, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China, and
| | - Yugang Wang
- the Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology Division of Shanghai Universities E-Institutes, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China, and
| | - Robin W Carrell
- the Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Randy J Read
- the Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Guo-Qiang Chen
- From the Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine and University of Chinese Academy of Sciences, Shanghai 200025, China, the Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology Division of Shanghai Universities E-Institutes, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China, and
| | - Aiwu Zhou
- the Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology Division of Shanghai Universities E-Institutes, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China, and
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43
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Serban KA, Petrache I. Alpha-1 Antitrypsin and Lung Cell Apoptosis. Ann Am Thorac Soc 2016; 13 Suppl 2:S146-9. [PMID: 27115949 PMCID: PMC5466181 DOI: 10.1513/annalsats.201505-312kv] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Accepted: 07/06/2015] [Indexed: 11/20/2022] Open
Abstract
Discovery of alpha-1 antitrypsin (A1AT) as the principal circulating inhibitor of neutrophil elastase was critical to the appreciation of protease/antiprotease imbalance involvement in the pathogenesis of emphysema. Additional targets of A1AT have been uncovered, along with their contribution to alveolar wall destruction induced by cigarette smoke exposure. We highlight in this report mechanisms of A1AT antiapoptotic effects on structural lung endothelial cells. This function was largely dependent on uptake of the protein from the circulation via clathrin- and, in part, caveolae-mediated endocytosis and on specific interactions with cysteine proteases such as capsase-3, -6, and -7. Exposures to cigarette smoke diminished A1AT intracellular uptake and its anticaspase action, suggesting that even in A1AT-suficient individuals, cigarette smoke may weaken the serpin's endothelial prosurvival effect. In addition, cigarette smoke exposure or genetic mutations known to induce posttranslational modifications such as oxidation or polymerization may alter A1AT bidirectional intracellular traffic in endothelial cells and thus determine its functional bioavailability in certain lung compartments. Uncovering and harnessing the A1AT canonical and noncanonical mechanisms will advance our understanding of the pathogenesis of emphysema and may provide means to improve the effectiveness of therapies in both A1AT-sufficient and A1AT-deficient individuals.
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Affiliation(s)
- Karina A Serban
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, National Jewish Health, Denver, Colorado
| | - Irina Petrache
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, National Jewish Health, Denver, Colorado
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44
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Gaczynska M, Karpowicz P, Stuart CE, Norton MG, Teckman JH, Marszal E, Osmulski PA. AFM Imaging Reveals Topographic Diversity of Wild Type and Z Variant Polymers of Human α1-Proteinase Inhibitor. PLoS One 2016; 11:e0151902. [PMID: 27008547 PMCID: PMC4805282 DOI: 10.1371/journal.pone.0151902] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 03/04/2016] [Indexed: 12/17/2022] Open
Abstract
α1-Proteinase inhibitor (antitrypsin) is a canonical example of the serpin family member that binds and inhibits serine proteases. The natural metastability of serpins is crucial to carry out structural rearrangements necessary for biological activity. However, the enhanced metastability of the mutant Z variant of antitrypsin, in addition to folding defect, may substantially contribute to its polymerization, a process leading to incurable serpinopathy. The metastability also impedes structural studies on the polymers. There are no crystal structures of Z monomer or any kind of polymers larger than engineered wild type (WT) trimer. Our understanding of polymerization mechanisms is based on biochemical data using in vitro generated WT oligomers and molecular simulations. Here we applied atomic force microscopy (AFM) to compare topography of monomers, in vitro formed WT oligomers, and Z type polymers isolated from transgenic mouse liver. We found the AFM images of monomers closely resembled an antitrypsin outer shell modeled after the crystal structure. We confirmed that the Z variant demonstrated higher spontaneous propensity to dimerize than WT monomers. We also detected an unexpectedly broad range of different types of polymers with periodicity and topography depending on the applied method of polymerization. Short linear oligomers of unit arrangement similar to the Z polymers were especially abundant in heat-treated WT preparations. Long linear polymers were a prominent and unique component of liver extracts. However, the liver preparations contained also multiple types of oligomers of topographies undistinguishable from those found in WT samples polymerized with heat, low pH or guanidine hydrochloride treatments. In conclusion, we established that AFM is an excellent technique to assess morphological diversity of antitrypsin polymers, which is important for etiology of serpinopathies. These data also support previous, but controversial models of in vivo polymerization showing a surprising diversity of polymer topography.
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Affiliation(s)
- Maria Gaczynska
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
| | - Przemyslaw Karpowicz
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
| | - Christine E. Stuart
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Malgorzata G. Norton
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Jeffrey H. Teckman
- Department of Pediatrics and Biochemistry, Saint Louis University School of Medicine, Cardinal Glennon Children’s Medical Center, St. Louis, Missouri, United States of America
| | - Ewa Marszal
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Pawel A. Osmulski
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
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45
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Quantitative mapping of protein structure by hydroxyl radical footprinting-mediated structural mass spectrometry: a protection factor analysis. Biophys J 2015; 108:107-15. [PMID: 25564857 DOI: 10.1016/j.bpj.2014.11.013] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 11/06/2014] [Accepted: 11/10/2014] [Indexed: 11/23/2022] Open
Abstract
Measurements from hydroxyl radical footprinting (HRF) provide rich information about the solvent accessibility of amino acid side chains of a protein. Traditional HRF data analyses focus on comparing the difference in the modification/footprinting rate of a specific site to infer structural changes across two protein states, e.g., between a free and ligand-bound state. However, the rate information itself is not fully used for the purpose of comparing different protein sites within a protein on an absolute scale. To provide such a cross-site comparison, we present a new, to our knowledge, data analysis algorithm to convert the measured footprinting rate constant to a protection factor (PF) by taking into account the known intrinsic reactivity of amino acid side chain. To examine the extent to which PFs can be used for structural interpretation, this PF analysis is applied to three model systems where radiolytic footprinting data are reported in the literature. By visualizing structures colored with the PF values for individual peptides, a rational view of the structural features of various protein sites regarding their solvent accessibility is revealed, where high-PF regions are buried and low-PF regions are more exposed to the solvent. Furthermore, a detailed analysis correlating solvent accessibility and local structural contacts for gelsolin shows a statistically significant agreement between PF values and various structure measures, demonstrating that the PFs derived from this PF analysis readily explain fundamental HRF rate measurements. We also tested this PF analysis on alternative, chemical-based HRF data, showing improved correlations of structural properties of a model protein barstar compared to examining HRF rate data alone. Together, this PF analysis not only permits a novel, to our knowledge, approach of mapping protein structures by using footprinting data, but also elevates the use of HRF measurements from a qualitative, cross-state comparison to a quantitative, cross-site assessment of protein structures in the context of individual conformational states of interest.
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Noto R, Randazzo L, Raccosta S, Caccia S, Moriconi C, Miranda E, Martorana V, Manno M. The stability and activity of human neuroserpin are modulated by a salt bridge that stabilises the reactive centre loop. Sci Rep 2015; 5:13666. [PMID: 26329378 PMCID: PMC4556959 DOI: 10.1038/srep13666] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Accepted: 08/03/2015] [Indexed: 11/26/2022] Open
Abstract
Neuroserpin (NS) is an inhibitory protein belonging to the serpin family and involved in several pathologies, including the dementia Familial Encephalopathy with Neuroserpin Inclusion Bodies (FENIB), a genetic neurodegenerative disease caused by accumulation of NS polymers. Our Molecular Dynamics simulations revealed the formation of a persistent salt bridge between Glu289 on strand s2C and Arg362 on the Reactive Centre Loop (RCL), a region important for the inhibitory activity of NS. Here, we validated this structural feature by simulating the Glu289Ala mutant, where the salt bridge is not present. Further, MD predictions were tested in vitro by purifying recombinant Glu289Ala NS from E. coli. The thermal and chemical stability along with the polymerisation propensity of both Wild Type and Glu289Ala NS were characterised by circular dichroism, emission spectroscopy and non-denaturant gel electrophoresis, respectively. The activity of both variants against the main target protease, tissue-type plasminogen activator (tPA), was assessed by SDS-PAGE and chromogenic kinetic assay. Our results showed that deletion of the salt bridge leads to a moderate but clear reduction of the overall protein stability and activity.
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Affiliation(s)
- Rosina Noto
- National Research Council of Italy, Institute of Biophysics, Palermo, Italy
| | - Loredana Randazzo
- National Research Council of Italy, Institute of Biophysics, Palermo, Italy
| | - Samuele Raccosta
- National Research Council of Italy, Institute of Biophysics, Palermo, Italy
| | - Sonia Caccia
- Department of Medical Biotechnologies and Translational Medicine, University of Milan, Milan, Italy
| | - Claudia Moriconi
- Department of Biology and Biotechnologies “Charles Darwin” and Pasteur Institute - Cenci Bolognetti Foundation, Sapienza University of Rome, Rome, Italy
| | - Elena Miranda
- Department of Biology and Biotechnologies “Charles Darwin” and Pasteur Institute - Cenci Bolognetti Foundation, Sapienza University of Rome, Rome, Italy
| | - Vincenzo Martorana
- National Research Council of Italy, Institute of Biophysics, Palermo, Italy
| | - Mauro Manno
- National Research Council of Italy, Institute of Biophysics, Palermo, Italy
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Gagaoua M, Hafid K, Boudida Y, Becila S, Ouali A, Picard B, Boudjellal A, Sentandreu MA. Caspases and Thrombin Activity Regulation by Specific Serpin Inhibitors in Bovine Skeletal Muscle. Appl Biochem Biotechnol 2015. [PMID: 26208691 DOI: 10.1007/s12010-015-1762-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
In living cells, after activation, protein inhibitors constitute the last step of proteases activity regulation. This review intends to provide original information about a group of bovine muscle serine proteases inhibitors belonging to the Serpin superfamily and characterized at the gene and protein level. This report is the only one and the first to provide much information on this group of proteases inhibitors of the serpin type and their potential biological functions. Amongst the eight genes identified in bovine, three serpins were purified from the muscle tissue and characterized. These are two members of the bovSERPINA3 family, i.e., bovSERPINA3-1 and A3-3, and the last one is antithrombin III (AT-III or BovSERPINC1). BovSERPINA3 family comprises at least eight protein members encoded by different genes mapped on chromosome 7q23-q26 cluster. BovSERPINA3-1 and A3-3 were shown to locate within muscle cells and are cross-class inhibitors strongly active against trypsin as well as against human initiator and effector caspases 8 and 3. They constitute a key apoptosis control in mammals. They were thus expressed in proliferating and confluent myoblasts phases where cells must be alive but not in myotubes. Antithrombin III inhibits trypsin and, in a heparin dependent manner, thrombin. AT-III and its mRNA were expressed in muscle cells and in differentiating primary myoblasts in culture.
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Affiliation(s)
- Mohammed Gagaoua
- Maquav team, Bioqual Laboratory, INATAA (Institut de la Nutrition, de l'Alimentation et des Technologies Agro-Alimentaires), Université Frères Mentouri Constantine 1, Route de Ain El-Bey, 25000, Constantine, Algeria,
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Oktaviani NA, Risør MW, Lee YH, Megens RP, de Jong DH, Otten R, Scheek RM, Enghild JJ, Nielsen NC, Ikegami T, Mulder FAA. Optimized co-solute paramagnetic relaxation enhancement for the rapid NMR analysis of a highly fibrillogenic peptide. JOURNAL OF BIOMOLECULAR NMR 2015; 62:129-42. [PMID: 25820763 DOI: 10.1007/s10858-015-9925-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Accepted: 03/20/2015] [Indexed: 05/21/2023]
Abstract
Co-solute paramagnetic relaxation enhancement (PRE) is an attractive way to speed up data acquisition in NMR spectroscopy by shortening the T 1 relaxation time of the nucleus of interest and thus the necessary recycle delay. Here, we present the rationale to utilize high-spin iron(III) as the optimal transition metal for this purpose and characterize the properties of its neutral chelate form Fe(DO3A) as a suitable PRE agent. Fe(DO3A) effectively reduces the T 1 values across the entire sequence of the intrinsically disordered protein α-synuclein with negligible impact on line width. The agent is better suited than currently used alternatives, shows no specific interaction with the polypeptide chain and, due to its high relaxivity, is effective at low concentrations and in 'proton-less' NMR experiments. By using Fe(DO3A) we were able to complete the backbone resonance assignment of a highly fibrillogenic peptide from α1-antitrypsin by acquiring the necessary suite of multidimensional NMR datasets in 3 h.
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Affiliation(s)
- Nur Alia Oktaviani
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
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Berthelier V, Harris JB, Estenson KN, Baudry J. Discovery of an inhibitor of Z-alpha1 antitrypsin polymerization. PLoS One 2015; 10:e0126256. [PMID: 25961288 PMCID: PMC4427445 DOI: 10.1371/journal.pone.0126256] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 03/31/2015] [Indexed: 11/25/2022] Open
Abstract
Polymerization of the Z variant alpha-1-antitrypsin (Z-α1AT) results in the most common and severe form of α1AT deficiency (α1ATD), a debilitating genetic disorder whose clinical manifestations range from asymptomatic to fatal liver and/or lung disease. As the altered conformation of Z-α1AT and its attendant aggregation are responsible for pathogenesis, the polymerization process per se has become a major target for the development of therapeutics. Based on the ability of Z-α1AT to aggregate by recruiting the reactive center loop (RCL) of another Z-α1AT into its s4A cavity, we developed a high-throughput screening assay that uses a modified 6-mer peptide mimicking the RCL to screen for inhibitors of Z-α1AT polymer growth. A subset of compounds from the Library of Pharmacologically Active Compounds (LOPAC) with molecular weights ranging from 300 to 700 Da, was used to evaluate the assay's capabilities. The inhibitor S-(4-nitrobenzyl)-6-thioguanosine was identified as a lead compound and its ability to prevent Z-α1AT polymerization confirmed by secondary assays. To further investigate the binding location of S-(4-nitrobenzyl)-6-thioguanosine, an in silico strategy was pursued and the intermediate α1AT M* state modeled to allow molecular docking simulations and explore various potential binding sites. Docking results predict that S-(4-nitrobenzyl)-6-thioguanosine can bind at the s4A cavity and at the edge of β-sheet A. The former binding site would directly block RCL insertion whereas the latter site would prevent β-sheet A from expanding between s3A/s5A, and thus indirectly impede RCL insertion. Altogether, our investigations have revealed a novel compound that inhibits the formation of Z-α1AT polymers, as well as in vitro and in silico strategies for identifying and characterizing additional blocking molecules of Z-α1AT polymerization.
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Affiliation(s)
- Valerie Berthelier
- Department of Medicine, University of Tennessee Health Science Center—Graduate School of Medicine, Knoxville, Tennessee, United States of America
- UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Jason Brett Harris
- UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, United States of America
- UT-ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Kasey Noel Estenson
- Department of Medicine, University of Tennessee Health Science Center—Graduate School of Medicine, Knoxville, Tennessee, United States of America
- UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Jerome Baudry
- UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, United States of America
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, United States of America
- UT-ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
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Noto R, Santangelo MG, Levantino M, Cupane A, Mangione MR, Parisi D, Ricagno S, Bolognesi M, Manno M, Martorana V. Functional and dysfunctional conformers of human neuroserpin characterized by optical spectroscopies and Molecular Dynamics. BIOCHIMICA ET BIOPHYSICA ACTA 2015; 1854:110-7. [PMID: 25450507 PMCID: PMC4332418 DOI: 10.1016/j.bbapap.2014.10.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 09/04/2014] [Accepted: 10/03/2014] [Indexed: 12/12/2022]
Abstract
Neuroserpin (NS) is a serine protease inhibitor (SERPIN) involved in different neurological pathologies, including the Familial Encephalopathy with Neuroserpin Inclusion Bodies (FENIB), related to the aberrant polymerization of NS mutants. Here we present an in vitro and in silico characterization of native neuroserpin and its dysfunctional conformation isoforms: the proteolytically cleaved conformer, the inactive latent conformer, and the polymeric species. Based on circular dichroism and fluorescence spectroscopy, we present an experimental validation of the latent model and highlight the main structural features of the different conformers. In particular, emission spectra of aromatic residues yield distinct conformational fingerprints, that provide a novel and simple spectroscopic tool for selecting serpin conformers in vitro. Based on the structural relationship between cleaved and latent serpins, we propose a structural model for latent NS, for which an experimental crystallographic structure is lacking. Molecular Dynamics simulations suggest that NS conformational stability and flexibility arise from a spatial distribution of intramolecular salt-bridges and hydrogen bonds.
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Affiliation(s)
- Rosina Noto
- Institute of Biophysics, National Research Council of Italy, Palermo, Italy
| | | | - Matteo Levantino
- Department of Physics and Chemistry, University of Palermo, Palermo, Italy
| | - Antonio Cupane
- Department of Physics and Chemistry, University of Palermo, Palermo, Italy
| | | | - Daniele Parisi
- Institute of Biophysics, National Research Council of Italy, Palermo, Italy; Department of Biosciences, Institute of Biophysics CNR, Italy and CIMAINA, University of Milano, Milan, Italy
| | - Stefano Ricagno
- Department of Biosciences, Institute of Biophysics CNR, Italy and CIMAINA, University of Milano, Milan, Italy
| | - Martino Bolognesi
- Department of Biosciences, Institute of Biophysics CNR, Italy and CIMAINA, University of Milano, Milan, Italy
| | - Mauro Manno
- Institute of Biophysics, National Research Council of Italy, Palermo, Italy.
| | - Vincenzo Martorana
- Institute of Biophysics, National Research Council of Italy, Palermo, Italy
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