1
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Liu X, Kouassi KGW, Vanbever R, Dumoulin M. Impact of the PEG length and PEGylation site on the structural, thermodynamic, thermal, and proteolytic stability of mono-PEGylated alpha-1 antitrypsin. Protein Sci 2022; 31:e4392. [PMID: 36040264 PMCID: PMC9375436 DOI: 10.1002/pro.4392] [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: 03/25/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 11/11/2022]
Abstract
Conjugation to polyethylene glycol (PEG) is a widely used approach to improve the therapeutic value of proteins essentially by prolonging their body residence time. PEGylation may however induce changes in the structure and/or the stability of proteins and thus on their function(s). The effects of PEGylation on the thermodynamic stability can either be positive (stabilization), negative (destabilization), or neutral (no effect). Moreover, various factors such as the PEG length and PEGylation site can influence the consequences of PEGylation on the structure and stability of proteins. In this study, the effects of PEGylation on the structure, stability, and polymerization of alpha1-antitrypsin (AAT) were investigated, using PEGs with different lengths, different structures (linear or 2-armed) and different linking chemistries (via amine or thiol) at two distinct positions of the sequence. The results show that whatever the size, position, and structure of PEG chains, PEGylation (a) does not induce significant changes in AAT structure (either at the secondary or tertiary level); (b) does not alter the stability of the native protein upon both chemical- and heat-induced denaturation; and (c) does not prevent AAT to fully refold and recover its activity following chemical denaturation. However, the propensity of AAT to aggregate upon heat treatment was significantly decreased by PEGylation, although PEGylation did not prevent the irreversible inactivation of the enzyme. Moreover, conjugation to PEG, especially 2-armed 40 kDa PEG, greatly improved the proteolytic resistance of AAT. PEGylation of AAT could be a promising strategy to prolong its half-life after infusion in AAT-deficient patients and thereby decrease the frequency of infusions.
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Affiliation(s)
- Xiao Liu
- Advanced Drug Delivery and BiomaterialsLouvain Drug Research Institute, Université catholique de Louvain (UCLouvain)BrusselsBelgium
| | - Kobenan G. W. Kouassi
- Advanced Drug Delivery and BiomaterialsLouvain Drug Research Institute, Université catholique de Louvain (UCLouvain)BrusselsBelgium
| | - Rita Vanbever
- Advanced Drug Delivery and BiomaterialsLouvain Drug Research Institute, Université catholique de Louvain (UCLouvain)BrusselsBelgium
| | - Mireille Dumoulin
- Department of Life SciencesInBios, Center for Protein Engineering, Nanobodies to Explore Protein Structure and Functions, University of LiègeLiègeBelgium
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2
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Maas C, de Maat S. Therapeutic SERPINs: Improving on Nature. Front Cardiovasc Med 2021; 8:648349. [PMID: 33869308 PMCID: PMC8044344 DOI: 10.3389/fcvm.2021.648349] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 03/10/2021] [Indexed: 01/22/2023] Open
Abstract
Serine proteases drive important physiological processes such as coagulation, fibrinolysis, inflammation and angiogenesis. These proteases are controlled by serine protease inhibitors (SERPINs) that neutralize their activity. Currently, over 1,500 SERPINs are known in nature, but only 37 SERPINs are found in humans. Thirty of these are functional protease inhibitors. The inhibitory potential of SERPINs is in perfect balance with the proteolytic activities of its targets to enable physiological protease activity. Hence, SERPIN deficiency (either qualitative or quantitative) can lead to disease. Several SERPIN resupplementation strategies have been developed to treat SERPIN deficiencies, including concentrates derived from plasma and recombinant SERPINs. SERPINs usually inhibit multiple proteases, but only in their active state. Over the past decades, considerable insights have been acquired in the identification of SERPIN biological functions, their inhibitory mechanisms and specificity determinants. This paves the way for the development of therapeutic SERPINs. Through rational design, the inhibitory properties (selectivity and inhibitory potential) of SERPINs can be reformed and optimized. This review explores the current state of SERPIN engineering with a focus on reactive center loop modifications and backbone stabilization. We will discuss the lessons learned from these recombinant SERPINs and explore novel techniques and strategies that will be essential for the creation and application of the future generation of therapeutic SERPINs.
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Affiliation(s)
- Coen Maas
- CDL Research, University Medical Center Utrecht, Utrecht, Netherlands
| | - Steven de Maat
- CDL Research, University Medical Center Utrecht, Utrecht, Netherlands
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3
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Scott BM, Sheffield WP. Engineering the serpin α 1 -antitrypsin: A diversity of goals and techniques. Protein Sci 2019; 29:856-871. [PMID: 31774589 DOI: 10.1002/pro.3794] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 11/19/2019] [Accepted: 11/19/2019] [Indexed: 12/19/2022]
Abstract
α1 -Antitrypsin (α1 -AT) serves as an archetypal example for the serine proteinase inhibitor (serpin) protein family and has been used as a scaffold for protein engineering for >35 years. Techniques used to engineer α1 -AT include targeted mutagenesis, protein fusions, phage display, glycoengineering, and consensus protein design. The goals of engineering have also been diverse, ranging from understanding serpin structure-function relationships, to the design of more potent or more specific proteinase inhibitors with potential therapeutic relevance. Here we summarize the history of these protein engineering efforts, describing the techniques applied to engineer α1 -AT, specific mutants of interest, and providing an appended catalog of the >200 α1 -AT mutants published to date.
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Affiliation(s)
- Benjamin M Scott
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland.,Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, Maryland
| | - William P Sheffield
- Canadian Blood Services, Centre for Innovation, Hamilton, Ontario, Canada.,Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
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4
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Anelli T, Panina-Bordignon P. How to Avoid a No-Deal ER Exit. Cells 2019; 8:cells8091051. [PMID: 31500301 PMCID: PMC6769657 DOI: 10.3390/cells8091051] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 08/28/2019] [Accepted: 09/06/2019] [Indexed: 01/01/2023] Open
Abstract
Efficiency and fidelity of protein secretion are achieved thanks to the presence of different steps, located sequentially in time and space along the secretory compartment, controlling protein folding and maturation. After entering into the endoplasmic reticulum (ER), secretory proteins attain their native structure thanks to specific chaperones and enzymes. Only correctly folded molecules are allowed by quality control (QC) mechanisms to leave the ER and proceed to downstream compartments. Proteins that cannot fold properly are instead retained in the ER to be finally destined to proteasomal degradation. Exiting from the ER requires, in most cases, the use of coated vesicles, departing at the ER exit sites, which will fuse with the Golgi compartment, thus releasing their cargoes. Protein accumulation in the ER can be caused by a too stringent QC or by ineffective transport: these situations could be deleterious for the organism, due to the loss of the secreted protein, and to the cell itself, because of abnormal increase of protein concentration in the ER. In both cases, diseases can arise. In this review, we will describe the pathophysiology of protein folding and transport between the ER and the Golgi compartment.
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Affiliation(s)
- Tiziana Anelli
- Vita-Salute San Raffaele University, 20132 Milan, Italy.
- Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, 20132 Milan, Italy.
| | - Paola Panina-Bordignon
- Vita-Salute San Raffaele University, 20132 Milan, Italy.
- Division of Neuroscience, IRCCS Ospedale San Raffaele, 20132 Milan, Italy.
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5
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In Vitro Approaches for the Assessment of Serpin Polymerization. Methods Mol Biol 2018. [PMID: 30194595 DOI: 10.1007/978-1-4939-8645-3_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Serpin polymerization is the result of end-to-end ordered aggregation of serpin monomers into linear unbranched chains. This change in molecular state represents the basis of several conformational diseases with pathological gain-of-function and loss-of-function phenotypes, termed serpinopathies. Tools that enable quantification and characterization of polymer formation are therefore important to the study of serpin behavior in this pathophysiological context. Such methods rely on different manifestations of molecular change: polymerization-the generation of molecules with increasing molecular weight-is accompanied by concomitant structural rearrangements in the constituent subunits. Different approaches may be appropriate dependent on whether measurements are made on static samples, such as tissue or cell culture extracts, or in time-resolved experiments, often undertaken using polymers artificially induced under in vitro destabilizing conditions. In the former category, we describe the application of polyacrylamide electrophoresis, Western blot, ELISA, and negative-stain electron microscopy and in the latter category, Förster resonance energy transfer and fluorescence spectroscopy using environment-sensitive probes.
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6
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Yang L, Mei Y, Fang Q, Wang J, Yan Z, Song Q, Lin Z, Ye G. Identification and characterization of serine protease inhibitors in a parasitic wasp, Pteromalus puparum. Sci Rep 2017; 7:15755. [PMID: 29147019 PMCID: PMC5691223 DOI: 10.1038/s41598-017-16000-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 11/03/2017] [Indexed: 11/08/2022] Open
Abstract
Serine protease inhibitors (SPIs) regulate protease-mediated activities by inactivating their cognate proteinases, and are involved in multiple physiological processes. SPIs have been extensively studied in vertebrates and invertebrates; however, little SPI information is available in parasitoids. Herein, we identified 57 SPI genes in total through the genome of a parasitoid wasp, Pteromalus puparum. Gene structure analyses revealed that these SPIs contain 7 SPI domains. Depending on their mode of action, these SPIs can be categorized into serpins, canonical inhibitors and alpha-2-macroglobulins (A2Ms). For serpins and canonical inhibitors, we predicted their putative inhibitory activities to trypsin/chymotrypsin/elastase-like enzymes based on the amino acids in cleaved reactive sites. Sequence alignment and phylogenetic tree indicated that some serpins similar to known functional inhibitory serpins may participate in immune responses. Transcriptome analysis also showed some canonical SPI genes displayed distinct expression patterns in the venom gland and this was confirmed by quantitative real-time PCR (qPCR) analysis, suggesting their specific physiological functions as venom proteins in suppressing host immune responses. The study provides valuable information to clarify the functions of SPIs in digestion, development, reproduction and innate immunity.
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Affiliation(s)
- Lei Yang
- State Key Laboratory of Rice Biology & Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yaotian Mei
- State Key Laboratory of Rice Biology & Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Qi Fang
- State Key Laboratory of Rice Biology & Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jiale Wang
- State Key Laboratory of Rice Biology & Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zhichao Yan
- State Key Laboratory of Rice Biology & Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Qisheng Song
- Division of Plant Sciences, College of Agriculture, Food and Natural Resources, University of Missouri, Columbia, Missouri, USA
| | - Zhe Lin
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Gongyin Ye
- State Key Laboratory of Rice Biology & Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China.
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7
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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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8
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Motamedi-Shad N, Jagger AM, Liedtke M, Faull SV, Nanda AS, Salvadori E, Wort JL, Kay CW, Heyer-Chauhan N, Miranda E, Perez J, Ordóñez A, Haq I, Irving JA, Lomas DA. An antibody that prevents serpin polymerisation acts by inducing a novel allosteric behaviour. Biochem J 2016; 473:3269-90. [PMID: 27407165 PMCID: PMC5264506 DOI: 10.1042/bcj20160159] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 07/08/2016] [Accepted: 07/12/2016] [Indexed: 11/30/2022]
Abstract
Serpins are important regulators of proteolytic pathways with an antiprotease activity that involves a conformational transition from a metastable to a hyperstable state. Certain mutations permit the transition to occur in the absence of a protease; when associated with an intermolecular interaction, this yields linear polymers of hyperstable serpin molecules, which accumulate at the site of synthesis. This is the basis of many pathologies termed the serpinopathies. We have previously identified a monoclonal antibody (mAb4B12) that, in single-chain form, blocks α1-antitrypsin (α1-AT) polymerisation in cells. Here, we describe the structural basis for this activity. The mAb4B12 epitope was found to encompass residues Glu32, Glu39 and His43 on helix A and Leu306 on helix I. This is not a region typically associated with the serpin mechanism of conformational change, and correspondingly the epitope was present in all tested structural forms of the protein. Antibody binding rendered β-sheet A - on the opposite face of the molecule - more liable to adopt an 'open' state, mediated by changes distal to the breach region and proximal to helix F. The allosteric propagation of induced changes through the molecule was evidenced by an increased rate of peptide incorporation and destabilisation of a preformed serpin-enzyme complex following mAb4B12 binding. These data suggest that prematurely shifting the β-sheet A equilibrium towards the 'open' state out of sequence with other changes suppresses polymer formation. This work identifies a region potentially exploitable for a rational design of ligands that is able to dynamically influence α1-AT polymerisation.
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Affiliation(s)
- Neda Motamedi-Shad
- Centre for Respiratory Biology, UCL Respiratory, University College London, London WC1E 6JF, U.K
- Institute of Structural and Molecular Biology/Birkbeck, University of London, London WC1E 7HX, U.K
| | - Alistair M. Jagger
- Centre for Respiratory Biology, UCL Respiratory, University College London, London WC1E 6JF, U.K
- Institute of Structural and Molecular Biology/Birkbeck, University of London, London WC1E 7HX, U.K
| | - Maximilian Liedtke
- Centre for Respiratory Biology, UCL Respiratory, University College London, London WC1E 6JF, U.K
| | - Sarah V. Faull
- Centre for Respiratory Biology, UCL Respiratory, University College London, London WC1E 6JF, U.K
- Institute of Structural and Molecular Biology/Birkbeck, University of London, London WC1E 7HX, U.K
- Department of Medicine, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/Medical Research Council Building, Hills Road, Cambridge CB2 0XY, U.K
| | - Arjun Scott Nanda
- Institute of Structural and Molecular Biology/Birkbeck, University of London, London WC1E 7HX, U.K
| | - Enrico Salvadori
- Institute of Structural and Molecular Biology/Birkbeck, University of London, London WC1E 7HX, U.K
- London Centre for Nanotechnology, 17-19 Gordon Street, London WC1H 0AH, U.K
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, U.K
| | - Joshua L. Wort
- Institute of Structural and Molecular Biology/Birkbeck, University of London, London WC1E 7HX, U.K
| | - Christopher W.M. Kay
- Institute of Structural and Molecular Biology/Birkbeck, University of London, London WC1E 7HX, U.K
- London Centre for Nanotechnology, 17-19 Gordon Street, London WC1H 0AH, U.K
| | - Narinder Heyer-Chauhan
- Centre for Respiratory Biology, UCL Respiratory, University College London, London WC1E 6JF, U.K
- Institute of Structural and Molecular Biology/Birkbeck, University of London, London WC1E 7HX, U.K
| | - Elena Miranda
- Department of Biology and Biotechnologies ‘Charles Darwin’, Sapienza University of Rome, Rome 00185, Italy
| | - Juan Perez
- Departamento de Biologia Celular, Genetica y Fisiologia, Facultad de Ciencias, Campus Teatinos, Universidad de Malaga, Malaga 29071, Spain
| | - Adriana Ordóñez
- Department of Medicine, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/Medical Research Council Building, Hills Road, Cambridge CB2 0XY, U.K
| | - Imran Haq
- Centre for Respiratory Biology, UCL Respiratory, University College London, London WC1E 6JF, U.K
- Institute of Structural and Molecular Biology/Birkbeck, University of London, London WC1E 7HX, U.K
| | - James A. Irving
- Centre for Respiratory Biology, UCL Respiratory, University College London, London WC1E 6JF, U.K
- Institute of Structural and Molecular Biology/Birkbeck, University of London, London WC1E 7HX, U.K
| | - David A. Lomas
- Centre for Respiratory Biology, UCL Respiratory, University College London, London WC1E 6JF, U.K
- Institute of Structural and Molecular Biology/Birkbeck, University of London, London WC1E 7HX, U.K
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9
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Haq I, Irving JA, Saleh AD, Dron L, Regan-Mochrie GL, Motamedi-Shad N, Hurst JR, Gooptu B, Lomas DA. Deficiency Mutations of Alpha-1 Antitrypsin. Effects on Folding, Function, and Polymerization. Am J Respir Cell Mol Biol 2016; 54:71-80. [PMID: 26091018 DOI: 10.1165/rcmb.2015-0154oc] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Misfolding, polymerization, and defective secretion of functional alpha-1 antitrypsin underlies the predisposition to severe liver and lung disease in alpha-1 antitrypsin deficiency. We have identified a novel (Ala336Pro, Baghdad) deficiency variant and characterized it relative to the wild-type (M) and Glu342Lys (Z) alleles. The index case is a homozygous individual of consanguineous parentage, with levels of circulating alpha-1 antitrypsin in the moderate deficiency range, but is a biochemical phenotype that could not be classified by standard methods. The majority of the protein was present as functionally inactive polymer, and the remaining monomer was 37% active relative to the wild-type protein. These factors combined indicate an 85 to 95% functional deficiency, similar to that seen with ZZ homozygotes. Biochemical, biophysical, and computational studies further defined the molecular basis of this deficiency. These studies demonstrated that native Ala336Pro alpha-1 antitrypsin could populate the polymerogenic intermediate-and therefore polymerize-more readily than either wild-type alpha-1 antitrypsin or the Z variant. In contrast, folding was far less impaired in Ala336Pro alpha-1 antitrypsin than in the Z variant. The data are consistent with a disparate contribution by the "breach" region and "shutter" region of strand 5A to folding and polymerization mechanisms. Moreover, the findings demonstrate that, in these variants, folding efficiency does not correlate directly with the tendency to polymerize in vitro or in vivo. They therefore differentiate generalized misfolding from polymerization tendencies in missense variants of alpha-1 antitrypsin. Clinically, they further support the need to quantify loss-of-function in alpha-1 antitrypsin deficiency to individualize patient care.
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Affiliation(s)
- Imran Haq
- 1 Wolfson Institute for Biomedical Research, University College London, London, United Kingdom.,2 Institute of Structural and Molecular Biology/Birkbeck, University of London, London, United Kingdom
| | - James A Irving
- 1 Wolfson Institute for Biomedical Research, University College London, London, United Kingdom.,2 Institute of Structural and Molecular Biology/Birkbeck, University of London, London, United Kingdom
| | - Aarash D Saleh
- 3 London Alpha-1 Antitrypsin Deficiency Service, Royal Free Hospital, Pond Street, London, United Kingdom; and
| | - Louis Dron
- 3 London Alpha-1 Antitrypsin Deficiency Service, Royal Free Hospital, Pond Street, London, United Kingdom; and
| | - Gemma L Regan-Mochrie
- 1 Wolfson Institute for Biomedical Research, University College London, London, United Kingdom
| | - Neda Motamedi-Shad
- 1 Wolfson Institute for Biomedical Research, University College London, London, United Kingdom.,2 Institute of Structural and Molecular Biology/Birkbeck, University of London, London, United Kingdom
| | - John R Hurst
- 3 London Alpha-1 Antitrypsin Deficiency Service, Royal Free Hospital, Pond Street, London, United Kingdom; and
| | - Bibek Gooptu
- 2 Institute of Structural and Molecular Biology/Birkbeck, University of London, London, United Kingdom.,3 London Alpha-1 Antitrypsin Deficiency Service, Royal Free Hospital, Pond Street, London, United Kingdom; and.,4 Division of Asthma, Allergy and Lung Biology, King's College London, London, United Kingdom
| | - David A Lomas
- 1 Wolfson Institute for Biomedical Research, University College London, London, United Kingdom.,2 Institute of Structural and Molecular Biology/Birkbeck, University of London, London, United Kingdom.,3 London Alpha-1 Antitrypsin Deficiency Service, Royal Free Hospital, Pond Street, London, United Kingdom; and
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10
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Ehlers MR. Immune-modulating effects of alpha-1 antitrypsin. Biol Chem 2015; 395:1187-93. [PMID: 24854541 DOI: 10.1515/hsz-2014-0161] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Accepted: 04/09/2014] [Indexed: 01/27/2023]
Abstract
Alpha-1 antitrypsin (AAT) is a circulating serine protease inhibitor (serpin) that inhibits neutrophil elastase in the lung, and AAT deficiency is associated with early-onset emphysema. AAT is also a liver-derived acute-phase protein that, in vitro and in vivo, reduces production of pro-inflammatory cytokines, inhibits apoptosis, blocks leukocyte degranulation and migration, and modulates local and systemic inflammatory responses. In monocytes, AAT has been shown to increase intracellular cAMP, regulate expression of CD14, and suppress NFκB nuclear translocation. These effects may be mediated by AAT's serpin activity or by other protein-binding activities. In preclinical models of autoimmunity and transplantation, AAT therapy prevents or reverses autoimmune disease and graft loss, and these effects are accompanied by tolerogenic changes in cytokine and transcriptional profiles and T cell subsets. This review highlights advances in our understanding of the immune-modulating effects of AAT and their potential therapeutic utility.
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11
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Hughes VA, Meklemburg R, Bottomley SP, Wintrode PL. The Z mutation alters the global structural dynamics of α1-antitrypsin. PLoS One 2014; 9:e102617. [PMID: 25181470 PMCID: PMC4151987 DOI: 10.1371/journal.pone.0102617] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 06/12/2014] [Indexed: 11/25/2022] Open
Abstract
α1-Antitrypsin (α1AT) deficiency, the most common serpinopathy, results in both emphysema and liver disease. Over 90% of all clinical cases of α1AT deficiency are caused by the Z variant in which Glu342, located at the top of s5A, is replaced by a Lys which results in polymerization both in vivo and in vitro. The Glu342Lys mutation removes a salt bridge and a hydrogen bond but does not effect the thermodynamic stability of Z α1AT compared to the wild type protein, M α1AT, and so it is unclear why Z α1AT has an increased polymerization propensity. We speculated that the loss of these interactions would make the native state of Z α1AT more dynamic than M α1AT and that this change renders the protein more polymerization prone. We have used hydrogen/deuterium exchange combined with mass spectrometry (HXMS) to determine the structural and dynamic differences between native Z and M α1AT to reveal the molecular basis of Z α1AT polymerization. Our HXMS data shows that the Z mutation significantly perturbs the region around the site of mutation. Strikingly the Z mutation also alters the dynamics of regions distant to the mutation such as the B, D and I helices and specific regions of each β-sheet. These changes in global dynamics may lead to an increase in the likelihood of Z α1AT sampling a polymerogenic structure thereby causing disease.
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Affiliation(s)
- Victoria A. Hughes
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Robert Meklemburg
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland, United States of America
| | - Stephen P. Bottomley
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Patrick L. Wintrode
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland, United States of America
- * E-mail:
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12
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Yang L, Dinarvand P, Qureshi SH, Rezaie AR. Engineering D-helix of antithrombin in alpha-1-proteinase inhibitor confers antiinflammatory properties on the chimeric serpin. Thromb Haemost 2014; 112:164-75. [PMID: 24522239 PMCID: PMC4087087 DOI: 10.1160/th13-12-1029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 01/29/2014] [Indexed: 01/20/2023]
Abstract
Antithrombin (AT) is a heparin-binding serpin in plasma which regulates the proteolytic activity of procoagulant proteases of the clotting cascade. In addition to being an anticoagulant, AT also exhibits antiinflammatory activities when it binds to cell surface heparan sulfate proteoglycans (HSPGs) on the endothelium via its basic residues of D-helix to elicit intracellular signalling responses. By contrast to AT, α1-proteinase inhibitor (α1-PI) is a non-heparin-binding serpin that exhibits very slow reactivity with coagulation proteases and possesses no HSPG-dependent antiinflammatory properties. To determine whether the antiinflammatory signaling specificity of AT can be transferred to α1-PI, we replaced the D-helix of human α1-PI with the corresponding sequence of human AT and expressed the chimeric serpin α1-PI/D-helix) in a bacterial expression system. High molecular weight heparin bound to α1-PI/D-helix and accelerated the inhibition of thrombin by the serpin mutant by a template mechanism reminiscent of the cofactor effect of heparin on inhibition of thrombin by AT. Like AT, α1-PI/D-helix exhibited antiinflammatory properties in both cellular and animal models. Thus, α1-PI/D-helix inhibited the barrier-disruptive effect of proinflammatory cytokines and inhibited the activation of nuclear factor-κB transcription factor in lipopolysaccharide-stimulated endothelial cells by a concentration-dependent manner. Furthermore, the chimeric serpin reduced lipopolysaccharide-mediated lethality, elicited a vascular protective effect and inhibited infiltration of activated leukocytes to the peritoneal cavity of mice in an HMGB1-mediated inflammatory model. These results suggest that grafting the D-helix of AT to α1-PI confers antiinflammatory properties on the serpin and that the chimeric serpin may have therapeutic utility for treating inflammatory disorders.
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Affiliation(s)
| | | | | | - A R Rezaie
- Alireza R. Rezaie, PhD, Department of Biochemistry and Molecular Biology, St. Louis University School of Medicine, 1100 S. Grand Blvd., St. Louis, MO 63104, USA, Tel.: +1 314 977 9240, Fax: +1 314 977 9205 , E-mail:
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13
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Therapeutic targeting of misfolding and conformational change in α1-antitrypsin deficiency. Future Med Chem 2014; 6:1047-65. [DOI: 10.4155/fmc.14.58] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Misfolding and conformational diseases are increasing in prominence and prevalence. Both misfolding and ‘postfolding’ conformational mechanisms can contribute to pathogenesis and can coexist. The different contexts of folding and native state behavior may have implications for the development of therapeutic strategies. α1-antitrypsin deficiency illustrates how these issues can be addressed with therapeutic approaches to rescue folding, ameliorate downstream consequences of aberrant polymerization and/or maintain physiological function. Small-molecule strategies have successfully targeted structural features of the native conformer. Recent developments include the capability to follow solution behavior of α1-antitrypsin in the context of disease mutations and interactions with drug-like compounds. Moreover, preclinical studies in cells and organisms support the potential of manipulating cellular response repertoires to process misfolded and polymer states.
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14
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Scott BM, Matochko WL, Gierczak RF, Bhakta V, Derda R, Sheffield WP. Phage display of the serpin alpha-1 proteinase inhibitor randomized at consecutive residues in the reactive centre loop and biopanned with or without thrombin. PLoS One 2014; 9:e84491. [PMID: 24427287 PMCID: PMC3888415 DOI: 10.1371/journal.pone.0084491] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Accepted: 11/15/2013] [Indexed: 02/04/2023] Open
Abstract
In spite of the power of phage display technology to identify variant proteins with novel properties in large libraries, it has only been previously applied to one member of the serpin superfamily. Here we describe phage display of human alpha-1 proteinase inhibitor (API) in a T7 bacteriophage system. API M358R fused to the C-terminus of T7 capsid protein 10B was directly shown to form denaturation-resistant complexes with thrombin by electrophoresis and immunoblotting following exposure of intact phages to thrombin. We therefore developed a biopanning protocol in which thrombin-reactive phages were selected using biotinylated anti-thrombin antibodies and streptavidin-coated magnetic beads. A library consisting of displayed API randomized at residues 357 and 358 (P2-P1) yielded predominantly Pro-Arg at these positions after five rounds of thrombin selection; in contrast the same degree of mock selection yielded only non-functional variants. A more diverse library of API M358R randomized at residues 352-356 (P7-P3) was also probed, yielding numerous variants fitting a loose consensus of DLTVS as judged by sequencing of the inserts of plaque-purified phages. The thrombin-selected sequences were transferred en masse into bacterial expression plasmids, and lysates from individual colonies were screening for API-thrombin complexing. The most active candidates from this sixth round of screening contained DITMA and AAFVS at P7-P3 and inhibited thrombin 2.1-fold more rapidly than API M358R with no change in reaction stoichiometry. Deep sequencing using the Ion Torrent platform confirmed that over 800 sequences were significantly enriched in the thrombin-panned versus naïve phage display library, including some detected using the combined phage display/bacterial lysate screening approach. Our results show that API joins Plasminogen Activator Inhibitor-1 (PAI-1) as a serpin amenable to phage display and suggest the utility of this approach for the selection of "designer serpins" with novel reactivity and/or specificity.
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Affiliation(s)
- Benjamin M. Scott
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Wadim L. Matochko
- Department of Chemistry, Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta, Canada
| | - Richard F. Gierczak
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Varsha Bhakta
- Canadian Blood Services, Research and Development, Hamilton, Ontario, Canada
| | - Ratmir Derda
- Department of Chemistry, Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta, Canada
| | - William P. Sheffield
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
- Canadian Blood Services, Research and Development, Hamilton, Ontario, Canada
- * E-mail:
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15
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Gooptu B, Dickens JA, Lomas DA. The molecular and cellular pathology of α₁-antitrypsin deficiency. Trends Mol Med 2013; 20:116-27. [PMID: 24374162 DOI: 10.1016/j.molmed.2013.10.007] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 10/28/2013] [Accepted: 10/31/2013] [Indexed: 12/30/2022]
Abstract
Since its discovery 50 years ago, α₁-antitrypsin deficiency has represented a case study in molecular medicine, with careful clinical characterisation guiding genetic, biochemical, biophysical, structural, cellular, and in vivo studies. Here we highlight the milestones in understanding the disease mechanisms and show how they have spurred the development of novel therapeutic strategies. α₁-Antitrypsin deficiency is an archetypal conformational disease. Its pathogenesis demonstrates the interplay between protein folding and quality control mechanisms, with aberrant conformational changes causing liver and lung disease through combined loss- and toxic gain-of-function effects. Moreover, α₁-antitrypsin exemplifies the ability of diverse proteins to self-associate into a range of morphologically distinct polymers, suggesting a mechanism for protein and cell evolution.
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Affiliation(s)
- Bibek Gooptu
- Division of Asthma, Allergy, and Lung Biology, King's College London, 5th Floor, Tower Wing, Guy's Hospital, London, SE1 9RT, UK; Institute of Structural and Molecular Biology/Crystallography, Department of Biological Sciences, Birkbeck College, University of London, Malet Street, London, WC1E 7HX, UK
| | - Jennifer A Dickens
- Department of Medicine, University of Cambridge, Cambridge Institute for Medical Research, Cambridge, CB2 0XY, UK
| | - David A Lomas
- Institute of Structural and Molecular Biology/Crystallography, Department of Biological Sciences, Birkbeck College, University of London, Malet Street, London, WC1E 7HX, UK; Division of Medicine, University College London, 1st Floor, Maple House, 149, Tottenham Court Road, London, W1T 7NF, UK.
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16
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Bhakta V, Gierczak RF, Sheffield WP. Expression screening of bacterial libraries of recombinant alpha-1 proteinase inhibitor variants for candidates with thrombin inhibitory capacity. J Biotechnol 2013; 168:373-81. [DOI: 10.1016/j.jbiotec.2013.10.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Revised: 10/03/2013] [Accepted: 10/07/2013] [Indexed: 11/30/2022]
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17
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Roddick LA, Bhakta V, Sheffield WP. Fusion of the C-terminal triskaidecapeptide of hirudin variant 3 to alpha1-proteinase inhibitor M358R increases the serpin-mediated rate of thrombin inhibition. BMC BIOCHEMISTRY 2013; 14:31. [PMID: 24215622 PMCID: PMC3830444 DOI: 10.1186/1471-2091-14-31] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 11/05/2013] [Indexed: 11/10/2022]
Abstract
BACKGROUND Alpha-1 proteinase inhibitor (API) is a plasma serpin superfamily member that inhibits neutrophil elastase; variant API M358R inhibits thrombin and activated protein C (APC). Fusing residues 1-75 of another serpin, heparin cofactor II (HCII), to API M358R (in HAPI M358R) was previously shown to accelerate thrombin inhibition over API M358R by conferring thrombin exosite 1 binding properties. We hypothesized that replacing HCII 1-75 region with the 13 C-terminal residues (triskaidecapeptide) of hirudin variant 3 (HV354-66) would further enhance the inhibitory potency of API M358R fusion proteins. We therefore expressed HV3API M358R (HV354-66 fused to API M358R) and HV3API RCL5 (HV354-66 fused to API F352A/L353V/E354V/A355I/I356A/I460L/M358R) API M358R) as N-terminally hexahistidine-tagged polypeptides in E. coli. RESULTS HV3API M358R inhibited thrombin 3.3-fold more rapidly than API M358R; for HV3API RCL5 the rate enhancement was 1.9-fold versus API RCL5; neither protein inhibited thrombin as rapidly as HAPI M358R. While the thrombin/Activated Protein C rate constant ratio was 77-fold higher for HV3API RCL5 than for HV3API M358R, most of the increased specificity derived from the API F352A/L353V/E354V/A355I/I356A/I460L API RCL 5 mutations, since API RCL5 remained 3-fold more specific than HV3API RCL5. An HV3 54-66 peptide doubled the Thrombin Clotting Time (TCT) and halved the binding of thrombin to immobilized HCII 1-75 at lower concentrations than free HCII 1-75. HV3API RCL5 bound active site-inhibited FPR-chloromethyl ketone-thrombin more effectively than HAPI RCL5. Transferring the position of the fused HV3 triskaidecapeptide to the C-terminus of API M358R decreased the rate of thrombin inhibition relative to that mediated by HV3API M358R by 11-to 14-fold. CONCLUSIONS Fusing the C-terminal triskaidecapeptide of HV3 to API M358R-containing serpins significantly increased their effectiveness as thrombin inhibitors, but the enhancement was less than that seen in HCII 1-75-API M358R fusion proteins. HCII 1-75 was a superior fusion partner, in spite of the greater affinity of the HV3 triskaidecapeptide, manifested both in isolated and API-fused form, for thrombin exosite 1. Our results suggest that HCII 1-75 binds thrombin exosite 1 and orients the attached serpin scaffold for more efficient interaction with the active site of thrombin than the HV3 triskaidecapeptide.
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Affiliation(s)
| | | | - William P Sheffield
- Pathology and Molecular Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4 K1, Canada.
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18
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Jha S, Sanyal I, Amla DV. Single amino acid substitutions in recombinant plant-derived human α1-proteinase inhibitor confer enhanced stability and functional efficacy. Biochim Biophys Acta Gen Subj 2013; 1840:416-27. [PMID: 24090883 DOI: 10.1016/j.bbagen.2013.09.034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Revised: 09/22/2013] [Accepted: 09/23/2013] [Indexed: 11/26/2022]
Abstract
BACKGROUND Human α1-proteinase inhibitor (α1-PI) is the most abundant serine protease inhibitor in the blood and the heterologous expression of recombinant α1-PI has great potential for possible therapeutic applications. However, stability and functional efficacy of the recombinant protein expressed in alternate hosts are of major concern. METHODS Five variants of plant-expressed recombinant α1-PI protein were developed by incorporating single amino acid substitutions at specific sites, namely F51C, F51L, A70G, M358V and M374I. Purified recombinant α1-PI variants were analyzed for their expression, biological activity, oxidation-resistance, conformational and thermal stability by DAC-ELISA, porcine pancreatic elastase (PPE) inhibition assays, transverse urea gradient (TUG) gel electrophoresis, fluorescence spectroscopy and far-UV CD spectroscopy. RESULTS Urea-induced unfolding of recombinant α1-PI variants revealed that the F51C mutation shifted the mid-point of transition from 1.4M to 4.3M, thus increasing the conformational stability close to the human plasma form, followed by F51L, A70G and M374I variants. The variants also exhibited enhanced stability for heat denaturation, and the size-reducing substitution at Phe51 slowed down the deactivation rate ~5-fold at 54°C. The M358V mutation at the active site of the protein did not significantly affect the conformational or thermal stability of the recombinant α1-PI but provided enhanced resistance to oxidative inactivation. CONCLUSIONS Our results suggest that single amino acid substitutions resulted in improved stability and oxidation-resistance of the plant-derived recombinant α1-PI protein, without inflicting the inhibitory activity of the protein. GENERAL SIGNIFICANCE Our results demonstrate the significance of engineered modifications in plant-derived recombinant α1-PI protein molecule for further therapeutic development.
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Affiliation(s)
- Shweta Jha
- Plant Transgenic Lab, MB and GE Division, CSIR-National Botanical Research Institute, P.O. Box 436, Rana Pratap Marg, Lucknow 226 001, India.
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19
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Haq I, Irving J, Faull S, Dickens J, Ordóñez A, Belorgey D, Gooptu B, Lomas D. Reactive centre loop mutants of α-1-antitrypsin reveal position-specific effects on intermediate formation along the polymerization pathway. Biosci Rep 2013; 33:e00046. [PMID: 23659468 PMCID: PMC3691886 DOI: 10.1042/bsr20130038] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 04/22/2013] [Accepted: 04/25/2013] [Indexed: 11/29/2022] Open
Abstract
The common severe Z mutation (E342K) of α1-antitrypsin forms intracellular polymers that are associated with liver cirrhosis. The native fold of this protein is well-established and models have been proposed from crystallographic and biophysical data for the stable inter-molecular configuration that terminates the polymerization pathway. Despite these molecular 'snapshots', the details of the transition between monomer and polymer remain only partially understood. We surveyed the RCL (reactive centre loop) of α1-antitrypsin to identify sites important for progression, through intermediate states, to polymer. Mutations at P14P12 and P4, but not P10P8 or P2P1', resulted in a decrease in detectable polymer in a cell model that recapitulates the intracellular polymerization of the Z variant, consistent with polymerization from a near-native conformation. We have developed a FRET (Förster resonance energy transfer)-based assay to monitor polymerization in small sample volumes. An in vitro assessment revealed the position-specific effects on the unimolecular and multimolecular phases of polymerization: the P14P12 region self-inserts early during activation, while the interaction between P6P4 and β-sheet A presents a kinetic barrier late in the polymerization pathway. Correspondingly, mutations at P6P4, but not P14P12, yield an increase in the overall apparent activation energy of association from ~360 to 550 kJ mol(-1).
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Key Words
- cirrhosis
- emphysema
- fret
- intermediate
- polymerization
- serpin
- ans, 8-anilinonaphthalene-1-sulfonic acid
- bis-ans, 4,4′-dianilino-1,1′-binaphthyl-5,5′-disulfonic acid
- fret, förster resonance energy transfer
- nta, nitrilotriacetic acid
- rcl, reactive centre loop
- si, stoichiometry of inhibition
- tm,midpoint of thermal denaturation
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Affiliation(s)
- Imran Haq
- *Department of Medicine, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, U.K
| | - James A. Irving
- *Department of Medicine, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, U.K
| | - Sarah V. Faull
- *Department of Medicine, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, U.K
| | - Jennifer A. Dickens
- *Department of Medicine, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, U.K
| | - Adriana Ordóñez
- *Department of Medicine, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, U.K
| | - Didier Belorgey
- *Department of Medicine, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, U.K
| | - Bibek Gooptu
- †Institute of Structural and Molecular Biology, Birkbeck, University of London, London, U.K
| | - David A. Lomas
- *Department of Medicine, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, U.K
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20
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Lomas DA. Twenty Years of Polymers: A Personal Perspective on Alpha-1 Antitrypsin Deficiency. COPD 2013; 10 Suppl 1:17-25. [DOI: 10.3109/15412555.2013.764401] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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21
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Abdul-Wahab MF, Homma T, Wright M, Olerenshaw D, Dafforn TR, Nagata K, Miller AD. The pH sensitivity of murine heat shock protein 47 (HSP47) binding to collagen is affected by mutations in the breach histidine cluster. J Biol Chem 2012; 288:4452-61. [PMID: 23212911 DOI: 10.1074/jbc.m112.409029] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Heat shock protein 47 (HSP47) is a single-substrate molecular chaperone crucial for collagen biosynthesis. Although its function is well established, the molecular mechanisms that govern binding to procollagen peptides and triple helices in the endoplasmic reticulum (followed by controlled release in the Golgi) are unclear. HSP47 binds procollagen at a neutral pH but releases at a pH similar to the pK(a) of the imidazole side chain of histidine residues. It thus seems likely that these residues are involved in this pH-dependent mechanism. Murine HSP47 has 14 histidine residues grouped into three clusters, known as the breach, gate, and shutter. Here, we report the use of histidine mutagenesis to demonstrate the relative contribution of these three clusters to HSP47 structure and the "pH switch." Many of the tested mutants are silent; however, breach mutants H197A and H198A show binding but no apparent pH switch and are unable to control release. Another breach mutant, H191A, shows perturbed collagen release characteristics, consistent with observed perturbations in pH-driven trans-conformational changes. Thus, His-198, His-197 and His-191 are important (if not central) to HSP47 mechanism of binding/release to collagen. This is consistent with the breach cluster residues being well conserved across the HSP47 family.
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Affiliation(s)
- Mohd Firdaus Abdul-Wahab
- Imperial College Genetic Therapies Centre, Department of Chemistry, Flowers Building, Armstrong Road, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom
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22
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Blanchet X, Péré-Brissaud A, Duprat N, Pinault E, Delourme D, Ouali A, Combet C, Maftah A, Pélissier P, Brémaud L. Mutagenesis of the bovSERPINA3-3 demonstrates the requirement of aspartate-371 for intermolecular interaction and formation of dimers. Protein Sci 2012; 21:977-86. [PMID: 22505318 DOI: 10.1002/pro.2078] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Revised: 03/30/2012] [Accepted: 04/02/2012] [Indexed: 11/10/2022]
Abstract
The family of serpins is known to fold into a metastable state that is required for the proteinase inhibition mechanism. One of the consequences of this conformational flexibility is the tendency of some mutated serpins to form polymers, which occur through the insertion of the reactive center loop of one serpin molecule into the A-sheet of another. This "A-sheet polymerization" has remained an attractive explanation for the molecular mechanism of serpinopathies. Polymerization of serpins can also take place in vitro under certain conditions (e.g., pH or temperature). Surprisingly, on sodium dodecyl sulfate/polyacrylamide gel electrophoresis, bovSERPINA3-3 extracted from skeletal muscle or expressed in Escherichia coli was mainly observed as a homodimer. Here, in this report, by site-directed mutagenesis of recombinant bovSERPINA3-3, with substitution D371A, we demonstrate the importance of D371 for the intermolecular linkage observed in denaturing and reducing conditions. This residue influences the electrophoretic and conformational properties of bovSERPINA3-3. By structural modeling of mature bovSERPINA3-3, we propose a new "non-A-sheet swap" model of serpin homodimer in which D371 is involved at the molecular interface.
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Affiliation(s)
- X Blanchet
- Faculté des Sciences et Techniques, INRA, UMR1061 Unité de génétique Moléculaire Animale, Université de Limoges, FR 3503 GEIST, 87060 Limoges, France
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23
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Dolmer K, Gettins PGW. How the serpin α1-proteinase inhibitor folds. J Biol Chem 2012; 287:12425-32. [PMID: 22334651 PMCID: PMC3320992 DOI: 10.1074/jbc.m111.315465] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Revised: 01/27/2012] [Indexed: 11/06/2022] Open
Abstract
Serpins are remarkable and unique proteins in being able to spontaneously fold into a metastable conformation without the aid of a chaperone or prodomain. This metastable conformation is essential for inhibition of proteinases, so that massive serpin conformational change, driven by the favorable energetics of relaxation of the metastable conformation to the more stable one, can kinetically trap the proteinase-serpin acylenzyme intermediate. Failure to direct folding to the metastable conformation would lead to inactive, latent serpin. How serpins fold into such a metastable state is unknown. Using the ability of component peptides from the serpin α(1)PI to associate, we have now elucidated the pathway by which this serpin efficiently folds into its metastable state. In addition we have established the likely structure of the polymerogenic intermediate of the Z variant of α(1)PI.
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Affiliation(s)
- Klavs Dolmer
- From the Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois 60607
| | - Peter G. W. Gettins
- From the Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois 60607
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24
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Knaupp AS, Bottomley SP. Structural change in β-sheet A of Z α(1)-antitrypsin is responsible for accelerated polymerization and disease. J Mol Biol 2011; 413:888-98. [PMID: 21945526 DOI: 10.1016/j.jmb.2011.09.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Revised: 09/07/2011] [Accepted: 09/11/2011] [Indexed: 11/26/2022]
Abstract
The presence of the Z mutation (Glu342Lys) is responsible for more than 95% of α(1)-antitrypsin (α(1)AT) deficiency cases. It leads to increased polymerization of the serpin α(1)AT during its synthesis and in circulation. It has been proposed that the Z mutation results in a conformational change within the folded state of antitrypsin that enhances its polymerization. In order to localize the conformational change, we have created two single tryptophan mutants of Z α(1)AT and analyzed their fluorescence properties. α(1)AT contains two tryptophan residues that are located in distinct regions of the molecule: Trp194 at the top of β-sheet A and Trp238 on β-sheet B. We have replaced each tryptophan residue individually with a phenylalanine in order to study the local environment of the remaining tryptophan residue in both M and Z α(1)AT. A detailed fluorescence spectroscopic analysis of each mutant was carried out, and we detected differences in the emission spectrum, the Stern-Volmer constant for potassium iodide quenching and the anisotropy of only Trp194 in Z α(1)AT compared to M α(1)AT. Our data reveal that the Z mutation results in a conformational change at the top of β-sheet A but does not affect the structural integrity of β-sheet B.
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Affiliation(s)
- Anja S Knaupp
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800, Australia
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25
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26
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Kelly E, Greene CM, Carroll TP, McElvaney NG, O’Neill SJ. Alpha-1 antitrypsin deficiency. ACTA ACUST UNITED AC 2011. [DOI: 10.1016/j.rmedc.2011.04.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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27
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Characterization of the serpin-encoding gene of Bifidobacterium breve 210B. Appl Environ Microbiol 2010; 76:3206-19. [PMID: 20348296 DOI: 10.1128/aem.02938-09] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Members of the serpin (serine protease inhibitor) superfamily have been identified in higher multicellular eukaryotes, as well as in bacteria, although examination of available genome sequences has indicated that homologs of the bacterial serpin-encoding gene (ser) are not widely distributed. In members of the genus Bifidobacterium this gene appears to be present in at least 5, and perhaps up to 9, of the 30 species tested. Moreover, phylogenetic analysis using available bacterial and eukaryotic serpin sequences revealed that bifidobacteria produce serpins that form a separate clade. We characterized the ser(210B) locus of Bifidobacterium breve 210B, which encompasses a number of genes whose deduced protein products display significant similarity to proteins encoded by corresponding loci found in several other bifidobacteria. Northern hybridization, primer extension, microarray, reverse transcription-PCR (RT-PCR), and quantitative real-time PCR (qRT-PCR) analyses revealed that a 3.5-kb polycistronic mRNA encompassing the ser(210B) operon with a single transcriptional start site is strongly induced following treatment of B. breve 210B cultures with some proteases. Interestingly, transcription of other bifidobacterial ser homologs appears to be triggered by different proteases.
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28
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Kelly E, Greene CM, Carroll TP, McElvaney NG, O'Neill SJ. Alpha-1 antitrypsin deficiency. Respir Med 2010; 104:763-72. [PMID: 20303723 DOI: 10.1016/j.rmed.2010.01.016] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2009] [Revised: 01/22/2010] [Accepted: 01/24/2010] [Indexed: 02/06/2023]
Abstract
OBJECTIVE To review the topic of alpha-1 antitrypsin (AAT) deficiency. METHOD Narrative literature review. RESULTS Much work has been carried out on this condition with many questions being answered but still further questions remain. DISCUSSION AND CONCLUSIONS AAT deficiency is an autosomal co-dominantly inherited disease which affects the lungs and liver predominantly. The clinical manifestations, prevalence, genetics, molecular pathophysiology, screening and treatment recommendations are summarised in this review.
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Affiliation(s)
- Emer Kelly
- Department of Respiratory Research, Royal College of Surgeons in Ireland, Beaumont Hospital, Education Research Building, Beaumont Road, Dublin, Ireland.
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29
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α1-Antitrypsin deficiency, chronic obstructive pulmonary disease and the serpinopathies. Clin Sci (Lond) 2009; 116:837-50. [DOI: 10.1042/cs20080484] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
α1-Antitrypsin is the prototypical member of the serine proteinase inhibitor or serpin superfamily of proteins. The family includes α1-antichymotrypsin, C1 inhibitor, antithrombin and neuroserpin, which are all linked by a common molecular structure and the same suicidal mechanism for inhibiting their target enzymes. Point mutations result in an aberrant conformational transition and the formation of polymers that are retained within the cell of synthesis. The intracellular accumulation of polymers of mutant α1-antitrypsin and neuroserpin results in a toxic gain-of-function phenotype associated with cirrhosis and dementia respectively. The lack of important inhibitors results in overactivity of proteolytic cascades and diseases such as COPD (chronic obstructive pulmonary disease) (α1-antitrypsin and α1-antichymotrypsin), thrombosis (antithrombin) and angio-oedema (C1 inhibitor). We have grouped these conditions that share the same underlying disease mechanism together as the serpinopathies. In the present review, the molecular and pathophysiological basis of α1-antitrypsin deficiency and other serpinopathies are considered, and we show how understanding this unusual mechanism of disease has resulted in the development of novel therapeutic strategies.
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30
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The serpin gene family in Anopheles gambiae. Gene 2009; 442:47-54. [PMID: 19394412 DOI: 10.1016/j.gene.2009.04.013] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2009] [Revised: 04/10/2009] [Accepted: 04/17/2009] [Indexed: 12/16/2022]
Abstract
Serpins (serine protease inhibitors) regulate some innate immune responses of insects by inhibiting endogenous proteases. In this study, we characterized the serpin (SRPN) gene family in the mosquito Anopheles gambiae, the major malaria vector in Sub-Saharan Africa. We identified 18 A. gambiae SRPN genes, all on chromosomes 2 and 3, through searches of genomic DNA and EST databases. In addition to SRPN10, previously documented to exhibit alternative splicing, we found three splicing isoforms of SRPN4. We completed sequencing of cDNAs for the A. gambiae serpins to obtain complete coding sequence information and to verify or improve gene predictions. The predicted SRPN9 and 15 in the initial genome annotation were determined to be a single gene (SRPN9). Sixteen of the serpins contained putative secretion signal sequences. Multiple sequence alignments showing conserved residues important in structural conformation, including the consensus pattern within the hinge region, indicated that most of the A. gambiae serpins may be inhibitory. Phylogenetic analyses confirmed that SRPN1, 2, 3, 8, 9 and 10 formed phylogenetic clusters with known inhibitory serpins from Drosophila melanogaster and Manduca sexta. Many of the A. gambiae serpins were expressed during all life stages. However, SRPN7, 8, 12, and 19 were expressed at very low levels in the adult stage. SRPN13 was expressed mostly in eggs and young larvae, whereas SRPN5 and 14 were expressed mostly in adults. Such differences in expression pattern suggest that the serpins are involved in multiple physiological processes. Determining the biological functions of the mosquito serpins will require future work to identify the proteases they inhibit in vivo.
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31
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Gooptu B, Miranda E, Nobeli I, Mallya M, Purkiss A, Brown SCL, Summers C, Phillips RL, Lomas DA, Barrett TE. Crystallographic and cellular characterisation of two mechanisms stabilising the native fold of alpha1-antitrypsin: implications for disease and drug design. J Mol Biol 2009; 387:857-68. [PMID: 19232354 PMCID: PMC2723994 DOI: 10.1016/j.jmb.2009.01.069] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2009] [Accepted: 01/31/2009] [Indexed: 11/28/2022]
Abstract
The common Z mutant (Glu342Lys) of alpha(1)-antitrypsin results in the formation of polymers that are retained within hepatocytes. This causes liver disease whilst the plasma deficiency of an important proteinase inhibitor predisposes to emphysema. The Thr114Phe and Gly117Phe mutations border a surface cavity identified as a target for rational drug design. These mutations preserve inhibitory activity but reduce the polymerisation of wild-type native alpha(1)-antitrypsin in vitro and increase secretion in a Xenopus oocyte model of disease. To understand these effects, we have crystallised both mutants and solved their structures. The 2.2 A structure of Thr114Phe alpha(1)-antitrypsin demonstrates that the effects of the mutation are mediated entirely by well-defined partial cavity blockade and allows in silico screening of fragments capable of mimicking the effects of the mutation. The Gly117Phe mutation operates differently, repacking aromatic side chains in the helix F-beta-sheet A interface to induce a half-turn downward shift of the adjacent F helix. We have further characterised the effects of these two mutations in combination with the Z mutation in a eukaryotic cell model of disease. Both mutations increase the secretion of Z alpha(1)-antitrypsin in the native conformation, but the double mutants remain more polymerogenic than the wild-type (M) protein. Taken together, these data support different mechanisms by which the Thr114Phe and Gly117Phe mutations stabilise the native fold of alpha(1)-antitrypsin and increase secretion of monomeric protein in cell models of disease.
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Affiliation(s)
- Bibek Gooptu
- School of Crystallography, Birkbeck College, University of London, London, UK.
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32
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Knaupp AS, Bottomley SP. Serpin polymerization and its role in disease--the molecular basis of alpha1-antitrypsin deficiency. IUBMB Life 2009; 61:1-5. [PMID: 18785256 DOI: 10.1002/iub.127] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Protein aggregation is the cause of several human diseases. Understanding the molecular mechanisms involved in protein aggregation requires knowledge of the kinetics and structures populated during the reaction. Arguably, the best structurally characterized misfolding reaction is that of alpha(1)-antitrypsin. Alpha(1)-antitrypsin misfolding leads to both liver disease and emphysema and affect approximately 1 in 2000 of the population. This review will focus on the mechanism of alpha(1)-antitrypsin misfolding and the development of potential therapeutic strategies.
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Affiliation(s)
- Anja S Knaupp
- Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria, Australia
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33
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Klieber MA, Underhill C, Hammond GL, Muller YA. Corticosteroid-binding globulin, a structural basis for steroid transport and proteinase-triggered release. J Biol Chem 2007; 282:29594-603. [PMID: 17644521 DOI: 10.1074/jbc.m705014200] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Corticosteroid-binding globulin (CBG) is a serine proteinase inhibitor (serpin) family member that transports glucocorticoids in blood and regulates their access to target cells. The 1.9A crystal structure of rat CBG shows that its steroid-binding site resembles the thyroxin-binding site in the related serpin, thyroxin-binding globulin, and mutagenesis studies have confirmed the contributions of key residues that constitute the steroid-binding pocket. Unlike thyroxin-bound thyroxin-binding globulin, the cortisol-bound CBG displays an "active" serpin conformation with the proteinase-sensitive, reactive center loop (RCL) fully expelled from the regulatory beta-sheet A. Moreover, the CBG structure allows us to predict that complete insertion of the proteolytically cleaved RCL into the serpin fold occurs in concert with a displacement and unwinding of helix D that would disrupt the steroid-binding site. This allosteric coupling between RCL positioning and occupancy of the CBG steroid-binding site, which resembles the ligand (glycosamino-glycan)-dependent activation of the thrombin inhibitory serpins heparin cofactor II and anti-thrombin RCLs, ensures both optimal recognition of CBG by target proteinases and efficient release of steroid to sites of action.
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Affiliation(s)
- Michael A Klieber
- Lehrstuhl für Biotechnik, Department of Biology, Friedrich-Alexander-University Erlangen-Nuremberg, D-91052 Erlangen, Germany
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34
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Pearce MC, Cabrita LD, Ellisdon AM, Bottomley SP. The loss of tryptophan 194 in antichymotrypsin lowers the kinetic barrier to misfolding. FEBS J 2007; 274:3622-3632. [PMID: 17608807 DOI: 10.1111/j.1742-4658.2007.05897.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Antichymotrypsin, a member of the serpin superfamily, has been shown to form inactive polymers in vivo, leading to chronic obstructive pulmonary disease. At present, however, the molecular determinants underlying the polymerization transition are unclear. Within a serpin, the breach position is implicated in conformational change, as it is the first point of contact for the reactive center loop and the body of the molecule. W194, situated within the breach, represents one of the most highly conserved residues within the serpin architecture. Using a range of equilibrium and kinetic experiments, the contribution of W194 to proteinase inhibition, stability and polymerization was studied for antichymotrypsin. Replacement of W194 with phenylalanine resulted in a fully active inhibitor that was destabilized relative to the wild-type protein. The aggregation kinetics were significantly altered; wild-type antichymotrypsin exhibits a lag phase followed by chain elongation. The loss of W194 almost entirely removed the lag phase and accelerated the elongation phase. On the basis of our data, we propose that one of the main roles of W194 in antichymotrypsin is in preventing polymerization.
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Affiliation(s)
- Mary C Pearce
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Lisa D Cabrita
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Andrew M Ellisdon
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Stephen P Bottomley
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
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35
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Li W, Adams TE, Kjellberg M, Stenflo J, Huntington JA. Structure of native protein C inhibitor provides insight into its multiple functions. J Biol Chem 2007; 282:13759-68. [PMID: 17337440 DOI: 10.1074/jbc.m701074200] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Protein C inhibitor (PCI) is a multifunctional serpin with wide ranging protease inhibitory functions, unique cofactor binding activities, and potential non-inhibitory functions akin to the hormone-transporting serpins. To gain insight into the molecular mechanisms utilized by PCI we developed a robust expression system in Escherichia coli and solved the crystal structure of PCI in its native state. The five monomers obtained from our two crystal forms provide an NMR-like ensemble revealing regions of inherent flexibility. The reactive center loop (RCL) of PCI is long and highly flexible with no evidence of hinge region incorporation into beta-sheet A, as seen for other heparin-binding serpins. We adapted an extrinsic fluorescence method for determining dissociation constants for heparin and find that the N-terminal tail of PCI and residues adjacent to helix H are not involved in heparin binding. The minimal heparin length capable of tight binding to PCI was determined to be chains of eight monosaccharide units. A large hydrophobic pocket occupied by hydrophobic crystal contacts was found in an analogous position to the hormone-binding site in thyroxine-binding globulin. In conclusion, the data presented here provide important insights into the mechanisms by which PCI exercises its multiple inhibitory and non-inhibitory functions.
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Affiliation(s)
- Wei Li
- Department of Haematology, Division of Structural Medicine, Thrombosis Research Unit, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 2XY, United Kingdom
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36
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Belorgey D, Hägglöf P, Karlsson-Li S, Lomas DA. Protein misfolding and the serpinopathies. Prion 2007; 1:15-20. [PMID: 19164889 DOI: 10.4161/pri.1.1.3974] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The serpins are the largest superfamily of protease inhibitors. They are found in almost all branches of life including viruses, prokaryotes and eukaryotes. They inhibit their target protease by a unique mechanism that involves a large conformational transition and the translocation of the enzyme from the upper to the lower pole of the protein. This complex mechanism, and the involvement of serpins in important biological regulatory processes, makes them prone to mutation-related diseases. For example the polymerization of mutant alpha(1)-antitrypsin leads to the accumulation of ordered polymers within the endoplasmic reticulum of hepatocytes in association with cirrhosis. An identical process in the neuron specific serpin, neuroserpin, results in the accumulation of polymers in neurons and the dementia FENIB. In both cases there is a clear correlation between the molecular instability, the rate of polymer formation and the severity of disease. A similar process underlies the hepatic retention and plasma deficiency of antithrombin, C1 inhibitor, alpha(1)-antichymotrypsin and heparin co-factor II. The common mechanism of polymerization has allowed us to group these conditions together as a novel class of disease, the serpinopathies.
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Affiliation(s)
- Didier Belorgey
- Department of Medicine, University of Cambridge, Cambridge Institute for Medical Research, Cambridge, United Kingdom
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37
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Abstract
C1-INH belongs to the family of serpins. Structural studies have yielded a clear understanding of the biochemical principle underlying the functional activities of these proteins. Although the crystal structure of C1-INH has yet to be revealed, homology modeling has provided a three-dimensional model of the serpin part of C1-INH. This model has helped us understand the biochemical consequences of mutations of the C1-INH gene as they occur in patients who have HAE. The structure of the N-terminal domain of C1-INH remains unknown; however, this part of the molecule is unlikely to be important in the inhibitory activity of C1-INH toward its target proteases. Mutations in this part have not been described in patients who have HAE, except for a deletion containing two cysteine residues involved in the stabilization of the serpin domain. Recent studies suggest some anti-inflammatory functions for this N-terminal part, possibly explaining the effects of C1-INH in diseases other than HAE.
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Affiliation(s)
- Ineke G A Wagenaar-Bos
- Department of Immunopathology, Sanquin Research at CLB and Landsteiner Laboratory, Academical Medical Center, University of Amsterdam, Plesmanlaan 125, 1066 CX Amsterdam, the Netherlands.
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38
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Huntington JA. Shape-shifting serpins – advantages of a mobile mechanism. Trends Biochem Sci 2006; 31:427-35. [PMID: 16820297 DOI: 10.1016/j.tibs.2006.06.005] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2006] [Revised: 05/24/2006] [Accepted: 06/21/2006] [Indexed: 11/30/2022]
Abstract
Serpins use an extraordinary mechanism of protease inhibition that depends on a rapid and marked conformational change and causes destruction of the covalently linked protease. Serpins thus provide stoichiometric, irreversible inhibition, and their dependence on conformational change is exploited for signalling and clearance. The regulatory advantages provided by structural mobility are best illustrated by the heparin activation mechanisms of the plasma serpins antithrombin and heparin cofactor II. This mechanistic complexity, however, renders serpins highly susceptible to disease-causing mutations. Recent crystal structures reveal the intricate conformational rearrangements involved in protease inhibition, activity modulation and the unique molecular pathology of the remarkable shape-shifting serpins.
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Affiliation(s)
- James A Huntington
- University of Cambridge, Department of Haematology, Cambridge Institute for Medical Research, Division of Structural Medicine, Thrombosis Research Unit, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 2XY, UK.
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39
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Kim MJ, Jung CH, Im H. Characterization and suppression of dysfunctional human alpha1-antitrypsin variants. Biochem Biophys Res Commun 2006; 343:295-302. [PMID: 16540089 DOI: 10.1016/j.bbrc.2006.02.151] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2006] [Accepted: 02/22/2006] [Indexed: 10/24/2022]
Abstract
Human alpha1-antitrypsin-deficient variants may aggregate in the liver, with subsequent deficiency in the plasma, which can lead to emphysema. The structural and functional characteristics of 10 dysfunctional alpha1-antitrypsin variants (R39C, S53F, V55P, I92N, G115S, N158K, E264V, A336T, P369S, and P369L) were analyzed in detail. Most of them were unstable, as compared to the wild-type molecule, and many of the variants folded into an intermediate form. When five thermostable mutations (T68A, A70G, M374I, S381A, and K387R) were introduced into dysfunctional alpha1-antitrypsin variants, the stabilities and inhibitory activities of most of the variants were restored to levels comparable to those of the wild-type molecule. However, the extremely unstable S53F variant was not stabilized sufficiently by these mutations so as to exhibit function. N158K variant, which carries a mutation in the region critical for the reactive site loop insertion into beta-sheet A, exhibited a reduced level of inhibitory activity, despite conformational stabilization. These results show that aberrant folding caused by conformational destabilization due to mutations can be compensated for by increasing the overall stability of the alpha1-antitrypsin molecule, with exception of a mutation in the highly localized region critical for functional execution.
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Affiliation(s)
- Min-Jung Kim
- Department of Molecular Biology, Conformational Disease Research Center, Sejong University, 98 Gunja-dong, Kwangjin-gu, Seoul 143-747, Republic of Korea
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40
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Horvath AJ, Irving JA, Rossjohn J, Law RH, Bottomley SP, Quinsey NS, Pike RN, Coughlin PB, Whisstock JC. The murine orthologue of human antichymotrypsin: a structural paradigm for clade A3 serpins. J Biol Chem 2005; 280:43168-78. [PMID: 16141197 DOI: 10.1074/jbc.m505598200] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Antichymotrypsin (SERPINA3) is a widely expressed member of the serpin superfamily, required for the regulation of leukocyte proteases released during an inflammatory response and with a permissive role in the development of amyloid encephalopathy. Despite its biological significance, there is at present no available structure of this serpin in its native, inhibitory state. We present here the first fully refined structure of a murine antichymotrypsin orthologue to 2.1 A, which we propose as a template for other antichymotrypsin-like serpins. A most unexpected feature of the structure of murine serpina3n is that it reveals the reactive center loop (RCL) to be partially inserted into the A beta-sheet, a structural motif associated with ligand-dependent activation in other serpins. The RCL is, in addition, stabilized by salt bridges, and its plane is oriented at 90 degrees to the RCL of antitrypsin. A biochemical and biophysical analysis of this serpin demonstrates that it is a fast and efficient inhibitor of human leukocyte elastase (ka: 4 +/- 0.9 x 10(6) m(-1) s(-)1) and cathepsin G (ka: 7.9 +/- 0.9 x 10(5) m(-1) s(-)1) giving a spectrum of activity intermediate between that of human antichymotrypsin and human antitrypsin. An evolutionary analysis reveals that residues subject to positive selection and that have contributed to the diversity of sequences in this sub-branch (A3) of the serpin superfamily are essentially restricted to the P4-P6' region of the RCL, the distal hinge, and the loop between strands 4B and 5B.
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Affiliation(s)
- Anita J Horvath
- Australian Centre for Blood Diseases, Monash University, Commercial Road, 6th Floor, MacFarlane Burnet Building, Alfred Medical Research Precinct, Prahran, Victoria, 3181
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41
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Marushchak D, Johansson LBA. On the Quantitative Treatment of Donor–Donor Energy Migration in Regularly Aggregated Proteins. J Fluoresc 2005; 15:797-803. [PMID: 16341799 DOI: 10.1007/s10895-005-2989-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2005] [Accepted: 07/26/2005] [Indexed: 11/29/2022]
Abstract
An algorithm is presented that quantitatively accounts for donor-donor energy migration (DDEM) among fluorophore-labeled proteins forming regular aggregates. The DDEM algorithm is based on Monte Carlo and Brownian dynamics simulations and applies to calculation of fluorescence depolarisation data, such as the fluorescence anisotropy. Thereby local orientations, as well as reorienting motions of the fluorescent group are considered in the absence and presence of DDEM and among, in principle, infinitely many proteins as they form regular aggregates. Here we apply the algorithm for calculating and illustrating the DDEM and the time-resolved fluorescence anisotropy under static as well as dynamic conditions within helical, linear and circular aggregate structures. A principal approach of the DDEM algorithm for analysing protein aggregates is also outlined.
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Affiliation(s)
- Denys Marushchak
- Department of Chemistry, University of Umeå, S-901 87, Umeå, Sweden
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42
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Dufour EK, Désilets A, Longpré JM, Leduc R. Stability of mutant serpin/furin complexes: dependence on pH and regulation at the deacylation step. Protein Sci 2005; 14:303-15. [PMID: 15659365 PMCID: PMC2253415 DOI: 10.1110/ps.04843305] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Furin proteolytically cleaves a wide variety of proprotein substrates mainly within the trans-Golgi network (TGN) but also at the cell membrane and in endosomal compartments where pH is more acidic. Incorporation of furin recognition sequences within the reactive site loop (RSL) of alpha(1)-antitrypsin (AT) leads to the production of furin inhibitors. In an attempt to design more stable, potent, and specific serpin-based inhibitors, we constructed a series of AT and alpha(1)-antichymotrypsin (ACT) mutants by modifying the P(7)-P(1) region of their RSLs. The biochemical properties of these variants were assessed by evaluating their propensity to establish SDS-resistant complexes with furin in a variety of conditions (pH 6.0-9.0) and by measuring their association rate constants. The effect of pH during the initial steps of complex formation was minimal, suggesting that the acylation step is not rate-limiting. The decrease in stoichiometry of inhibition (SI) values observed in AT variants at high pHs was a result of the reduced pH-dependent deacylation rate, which is rate-limiting in this mechanism and which suggests increased complex stability. Conversely, the SI values for ACT mutants had a tendency to be lower at acidic pH. Transiently transfecting HEK293 cells with these mutants abolished processing of the pro-von Willebrand factor precursor but, interestingly, only the ACT variants were secreted in the media as uncleaved forms. Our results suggest that reengineering the reactive site loops of serpins to accommodate and target furin or other serine proteases must take into account the intrinsic physicochemical properties of the serpin.
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Affiliation(s)
- Erick K Dufour
- Department of Pharmacology, Faculty of Medicine, Université de Sherbrooke, Sherbrooke, Québec, Canada
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43
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Buck MJ, Atchley WR. Networks of coevolving sites in structural and functional domains of serpin proteins. Mol Biol Evol 2005; 22:1627-34. [PMID: 15858204 DOI: 10.1093/molbev/msi157] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Amino acids do not occur randomly in proteins; rather, their occurrence at any given site is strongly influenced by the amino acid composition at other sites, the structural and functional aspects of the region of the protein in which they occur, and the evolutionary history of the protein. The goal of our research study is to identify networks of coevolving sites within the serpin proteins (serine protease inhibitors) and classify them as being caused by structural-functional constraints or by evolutionary history. To address this, a matrix of pairwise normalized mutual information (NMI) values was computed among amino acid sites for the serpin proteins. The NMI matrix was partitioned into orthogonal patterns of amino acid variability by factor analysis. Each common factor pattern was interpreted as having phylogenetic and/or structural-functional explanations. In addition, we used a bootstrap factor analysis technique to limit the effects of phylogenetic history on our factor patterns. Our results show an extensive network of correlations among amino acid sites in key functional regions (reactive center loop, shutter, and breach). Additionally, we have discovered long-range coevolution for packed amino acids within the serpin protein core. Lastly, we have discovered a group of serpin sites which coevolve in the hydrophobic core region (s5B and s4B) and appear to represent sites important for formation of the "native" instead of the "latent" serpin structure. This research provides a better understanding on how protein structure evolves; in particular, it elucidates the selective forces creating coevolution among protein sites.
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Affiliation(s)
- Michael J Buck
- Department of Genetics and The Center for Computational Biology, North Carolina State University, USA.
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44
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Lomas DA, Belorgey D, Mallya M, Miranda E, Kinghorn KJ, Sharp LK, Phillips RL, Page R, Robertson AS, Crowther DC. Molecular mousetraps and the serpinopathies1. Biochem Soc Trans 2005; 33:321-30. [PMID: 15787598 DOI: 10.1042/bst0330321] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Members of the serine proteinase inhibitor or serpin superfamily inhibit their target proteinases by a remarkable conformational transition that involves the enzyme being translocated more than 70 Å (1 Å=10−10 m) from the upper to the lower pole of the inhibitor. This elegant mechanism is subverted by point mutations to form ordered polymers that are retained within the endoplasmic reticulum of secretory cells. The accumulation of polymers underlies the retention of mutants of α1-antitrypsin and neuroserpin within hepatocytes and neurons to cause cirrhosis and dementia respectively. The formation of polymers results in the failure to secrete mutants of other members of the serpin superfamily: antithrombin, C1 inhibitor and α1-antichymotrypsin, to cause a plasma deficiency that results in the clinical syndromes of thrombosis, angio-oedema and emphysema respectively. Understanding the common mechanism underlying the retention and deficiency of mutants of the serpins has allowed us to group these conditions as the serpinopathies. We review in this paper the molecular and structural basis of the serpinopathies and show how this has allowed the development of specific agents to block the polymerization that underlies disease.
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Affiliation(s)
- D A Lomas
- Department of Medicine, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 2XY, UK.
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45
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Roberts TH, Hejgaard J, Saunders NFW, Cavicchioli R, Curmi PMG. Serpins in unicellular Eukarya, Archaea, and Bacteria: sequence analysis and evolution. J Mol Evol 2005; 59:437-47. [PMID: 15638455 DOI: 10.1007/s00239-004-2635-6] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Most serpins irreversibly inactivate specific serine proteinases of the chymotrypsin family. Inhibitory serpins are unusual proteins in that their native structure is metastable, and rapid conversion to a relaxed state is required to trap target enzymes in a covalent complex. The evolutionary origin of the serpin fold is unresolved, and while serpins in animals are known to be involved in the regulation of a remarkable diversity of metabolic processes, the physiological functions of homologues from other phyla are unknown. Addressing these questions, here we analyze serpin genes identified in unicellular eukaryotes: the green alga Chlamydomonas reinhardtii, the dinoflagellate Alexandrium tamarense, and the human pathogens Entamoeba spp., Eimera tenella, Toxoplasma gondii, and Giardia lamblia. We compare these sequences to others, particularly those in the complete genome sequences of Archaea, where serpins were found in only 4 of 13 genera, and Bacteria, in only 9 of 56 genera. The serpins from unicellular organisms appear to be phylogenetically distinct from all of the clades of higher eukaryotic serpins. Most of the sequences from unicellular organisms have the characteristics of inhibitory serpins, and where multiple serpin genes are found in one genome, variability is displayed in the region of the reactive-center loop important for specificity. All the unicellular eukaryotic serpins have large hydrophobic or positively charged residues at the putative PI position. In contrast, none of the prokaryotic serpins has a residue of these types at the predicted P1 position, but many have smaller, neutral residues. Serpin evolution is discussed.
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Affiliation(s)
- Thomas H Roberts
- Department of Biological Sciences, Macquarie University, NSW 2109, Australia.
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Al-Ayyoubi M, Gettins PGW, Volz K. Crystal Structure of Human Maspin, a Serpin with Antitumor Properties. J Biol Chem 2004; 279:55540-4. [PMID: 15501821 DOI: 10.1074/jbc.m409957200] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Maspin, a member of the serpin superfamily, has tumor suppressing activity against breast and prostate cancer. Maspin inhibits tumor growth by blocking cell invasion, and its reactive center loop (RCL) is thought to mediate this activity. To understand this function on the molecular level, we have solved the three-dimensional structure of Maspin to 3.1 A resolution. The molecular structure shows the characteristic features of the serpin fold, but the RCL of Maspin is unique in length, composition, and placement. Although the RCL of Maspin is accessible and cleavable by some proteinases, it functions in the uncleaved, constrained conformation observed here. These structural results will contribute to our understanding of the mechanism by which Maspin suppresses tumors.
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Affiliation(s)
- Maher Al-Ayyoubi
- Department of Biochemistry and Molecular Biology, University of Illinois at Chicago, 835 S. Wolcott Avenue, Chicago, IL 60612-7334
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Kang UB, Baek JH, Ryu SH, Kim J, Yu MH, Lee C. Kinetic mechanism of protease inhibition by alpha1-antitrypsin. Biochem Biophys Res Commun 2004; 323:409-15. [PMID: 15369767 DOI: 10.1016/j.bbrc.2004.08.105] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2004] [Indexed: 11/20/2022]
Abstract
The native form of serine protease inhibitor (serpin) is kinetically trapped in a metastable state. Metastability in these proteins is critical to inhibit target protease by forming a stable covalent complex. Despite recent determination of the crystal structures of a Michaelis protease-serpin complex as well as a stable covalent complex, details on the kinetic mechanism remain unsolved. In this report, we examined the reaction mechanism of alpha1-antitrypsin toward elastase by a combination of stopped-flow experiments via fluorescence resonance energy transfer and rapid-quench studies. The results suggest a non-covalent complex intermediate other than Michaelis complex as an intermediate before the cleavage of P1-P1' scissile bond, whose formation is the rate-determining step of the overall reaction. This rate-limiting step represents rearrangement of the reactive site loop, and is regulated by a salt bridge between E354 and R196. The ionic interaction is unique to alpha1-antitrypsin, which suggests that protease inhibition mechanisms are varied among serpins.
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Affiliation(s)
- Un-Beom Kang
- Biomedical Research Center, Korea Institute of Science and Technology, P.O. Box 131, Cheongryang, Seoul 130-650, Republic of Korea
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Abstract
Alpha-1-antitrypsin (AT) deficiency was first described in the late 1960s in patients with severe pulmonary emphysema. The recognition of AT deficiency as a cause of emphysema then led to what is still the prevailing theory for the pathogenesis of emphysema, the protease-antiprotease theory. Soon it was found that AT deficiency accounted for a significant number of cases of neonatal liver disease that were previously categorized as idiopathic. We now know that AT deficiency is the most common genetic cause of neonatal liver disease and the most frequent diagnosis necessitating liver transplantation. It has also been shown to cause chronic liver disease, cryptogenic cirrhosis, and hepatocellular carcinoma in adults never previously known to have liver disease in infancy or childhood. Observations indicate that genetic traits unlinked to the AT gene or environmental factors predispose to or protect AT-deficient individuals from liver disease.
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Cabrita LD, Dai W, Bottomley SP. Different Conformational Changes within the F-Helix Occur during Serpin Folding, Polymerization, and Proteinase Inhibition†. Biochemistry 2004; 43:9834-9. [PMID: 15274637 DOI: 10.1021/bi0491346] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The intrinsic metastability of the serpin native state is the thermodynamic driving force for both proteinase inhibition and the formation of inactive polymers. A number of mechanisms has been proposed to explain how both these conformational changes are achieved. However, one aspect that has received little attention is the movement of the F-helix, which physically impedes both these events. We have applied a protein engineering approach to investigate the conformational changes of this helix during proteinase inhibition, serpin folding, and polymerization. We systematically mutated two highly conserved hydrophobic residues on the F-helix, V161 and I157, and in addition, removed a hydrogen bond between D149 and the first turn of the helix. Our data demonstrate that while all three interactions are important for the stability and folding of the molecule, their contribution during inhibition and polymerization differ. The presence of I157 is crucial to all conformational changes as its loss results in inactivation of the serpin and rapid polymerization. The replacement of D149 does not affect activity but significantly increases the polymerization rate. The interactions formed by V161 play an important role only in maintaining the native conformation. Taken together, these data suggest that the F-helix undergoes a reversible conformational change in both its N- and C-termini during proteinase inhibition only the C-terminus undergoes changes during polymerization, but there is a global change required for folding.
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Affiliation(s)
- Lisa D Cabrita
- Department of Biochemistry and Molecular Biology, P.O. Box 13D, Monash University, Melbourne, Australia 3800
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50
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Abstract
The molecular basis of alpha(1)-antitrypsin deficiency is reviewed and is shown to be due to the accumulation of mutant protein as ordered polymers within the endoplasmic reticulum of hepatocytes. The current goals are to determine the cellular response to polymeric alpha(1)-antitrypsin and to develop therapeutic strategies to block polymerisation in vivo.
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Affiliation(s)
- D A Lomas
- Respiratory Medicine Unit, Department of Medicine, University of Cambridge, Cambridge Institute for Medical Research, Cambridge CB2 2XY, UK.
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