1
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Kaur U, Kihn KC, Ke H, Kuo W, Gierasch LM, Hebert DN, Wintrode PL, Deredge D, Gershenson A. The conformational landscape of a serpin N-terminal subdomain facilitates folding and in-cell quality control. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.24.537978. [PMID: 37163105 PMCID: PMC10168285 DOI: 10.1101/2023.04.24.537978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Many multi-domain proteins including the serpin family of serine protease inhibitors contain non-sequential domains composed of regions that are far apart in sequence. Because proteins are translated vectorially from N- to C-terminus, such domains pose a particular challenge: how to balance the conformational lability necessary to form productive interactions between early and late translated regions while avoiding aggregation. This balance is mediated by the protein sequence properties and the interactions of the folding protein with the cellular quality control machinery. For serpins, particularly α 1 -antitrypsin (AAT), mutations often lead to polymer accumulation in cells and consequent disease suggesting that the lability/aggregation balance is especially precarious. Therefore, we investigated the properties of progressively longer AAT N-terminal fragments in solution and in cells. The N-terminal subdomain, residues 1-190 (AAT190), is monomeric in solution and efficiently degraded in cells. More β -rich fragments, 1-290 and 1-323, form small oligomers in solution, but are still efficiently degraded, and even the polymerization promoting Siiyama (S53F) mutation did not significantly affect fragment degradation. In vitro, the AAT190 region is among the last regions incorporated into the final structure. Hydrogen-deuterium exchange mass spectrometry and enhanced sampling molecular dynamics simulations show that AAT190 has a broad, dynamic conformational ensemble that helps protect one particularly aggregation prone β -strand from solvent. These AAT190 dynamics result in transient exposure of sequences that are buried in folded, full-length AAT, which may provide important recognition sites for the cellular quality control machinery and facilitate degradation and, under favorable conditions, reduce the likelihood of polymerization.
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Affiliation(s)
- Upneet Kaur
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA 01003
| | - Kyle C. Kihn
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201
| | - Haiping Ke
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA 01003
| | - Weiwei Kuo
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA 01003
| | - Lila M. Gierasch
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA 01003
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA 01003
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003
| | - Daniel N. Hebert
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA 01003
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA 01003
| | - Patrick L. Wintrode
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201
| | - Daniel Deredge
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201
| | - Anne Gershenson
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA 01003
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA 01003
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2
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N-Glycosylation as a Tool to Study Antithrombin Secretion, Conformation, and Function. Int J Mol Sci 2021; 22:ijms22020516. [PMID: 33419227 PMCID: PMC7825591 DOI: 10.3390/ijms22020516] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/31/2020] [Accepted: 12/31/2020] [Indexed: 11/23/2022] Open
Abstract
N-linked glycosylation is a crucial post-translational modification involved in protein folding, function, and clearance. N-linked glycosylation is also used therapeutically to enhance the half-lives of many proteins. Antithrombin, a serpin with four potential N-glycosylation sites, plays a pivotal role in hemostasis, wherein its deficiency significantly increases thrombotic risk. In this study, we used the introduction of N-glycosylation sites as a tool to explore what effect this glycosylation has on the protein folding, secretion, and function of this key anticoagulant. To accomplish this task, we introduced an additional N-glycosylation sequence in each strand. Interestingly, all regions that likely fold rapidly or were surrounded by lysines were not glycosylated even though an N-glycosylation sequon was present. The new sequon in the strands of the A- and B-sheets reduced secretion, and the B-sheet was more sensitive to these changes. However, the mutations in the strands of the C-sheet allowed correct folding and secretion, which resulted in functional variants. Therefore, our study revealed crucial regions for antithrombin secretion and could potentially apply to all serpins. These results could also help us understand the functional effects of natural variants causing type-I deficiencies.
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3
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Pongprayoon P, Niramitranon J, Kaewhom P, Kaewmongkol S, Suwan E, Stich RW, Jittapalapong S. Dynamic and structural insights into tick serpin from Ixodes ricinus. J Biomol Struct Dyn 2019; 38:2296-2303. [PMID: 31215334 DOI: 10.1080/07391102.2019.1630003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Ixodid ticks have a crucial impact on people and domestic animals worldwide. These parasites also pose a serious threat to livestock. To date, vaccination of hosts against ticks is a safer, more sustainable alternative to chemical control of ticks and the disease agents they transmit. Because of their roles in tick physiology, serpins (serine protease inhibitors) from tick saliva are among the candidates for anti-tick vaccines. Inhibitory serpins employ a suicide inhibition mechanism to inhibit proteases, where the serpin reactive centre loop (RCL) is cleaved, by the targeted protease, and then inserted into the main β-sheet of the serpin. This causes a massive conformational change called the 'stressed to relaxed' (S→R) transition, leading to the breakdown of serpin into two regions (core domain and cleaved polypeptide). Recently, the first tick serpin crystal structure from Ixodes ricinus in R-state was reported. We thus employed molecular dynamics simulations to better understand serpin structure and dynamics in atomic detail. Overall, R-state serpin showed high rigidity, especially the core domain. The most flexible region is the terminal of the cleaved polypeptide, due to its high-water exposure, while the rest of the cleaved polypeptide is stably trapped behind the core domain. T363, D367 and N375 are found to play a vital role in protein-protein attachment. This finding can be used to explain the high stability of the R-state serpin at the atomic level and provides insight into this tick serpin which will be useful for rational anti-tick vaccine development. AbbreviationsMDMolecular DynamicsRCLReactive centre loopCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Prapasiri Pongprayoon
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, Thailand.,Center for Advanced Studies in Nanotechnology for Chemical, Food and Agricultural Industries, KU Institute for Advanced Studies, Kasetsart University, Bangkok, Thailand
| | - Jitti Niramitranon
- Department of Computer Engineering, Faculty of Engineering, Kasetsart University, Chatuchak, Bangkok, Thailand
| | - Phaitoon Kaewhom
- Faculty of Agricultural Technology, Burapha University, Sakaeo Campus, Sakaeo, Thailand
| | | | - Eukote Suwan
- Faculty of Veterinary Technology, Kasetsart University, Bangkok, Thailand
| | - Roger W Stich
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO, USA
| | - Sathaporn Jittapalapong
- Faculty of Veterinary Technology, Kasetsart University, Bangkok, Thailand.,Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand
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4
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Laffranchi M, Elliston ELK, Gangemi F, Berardelli R, Lomas DA, Irving JA, Fra A. Characterisation of a type II functionally-deficient variant of alpha-1-antitrypsin discovered in the general population. PLoS One 2019; 14:e0206955. [PMID: 30633749 PMCID: PMC6329500 DOI: 10.1371/journal.pone.0206955] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 01/02/2019] [Indexed: 11/23/2022] Open
Abstract
Lung disease in alpha-1-antitrypsin deficiency (AATD) results from dysregulated proteolytic activity, mainly by neutrophil elastase (HNE), in the lung parenchyma. This is the result of a substantial reduction of circulating alpha-1-antitrypsin (AAT) and the presence in the plasma of inactive polymers of AAT. Moreover, some AAT mutants have reduced intrinsic activity toward HNE, as demonstrated for the common Z mutant, as well as for other rarer variants. Here we report the identification and characterisation of the novel AAT reactive centre loop variant Gly349Arg (p.G373R) present in the ExAC database. This AAT variant is secreted at normal levels in cellular models of AATD but shows a severe reduction in anti-HNE activity. Biochemical and molecular dynamics studies suggest it exhibits unfavourable RCL presentation to cognate proteases and compromised insertion of the RCL into β-sheet A. Identification of a fully dysfunctional AAT mutant that does not show a secretory defect underlines the importance of accurate genotyping of patients with pulmonary AATD manifestations regardless of the presence of normal levels of AAT in the circulation. This subtype of disease is reminiscent of dysfunctional phenotypes in anti-thrombin and C1-inibitor deficiencies so, accordingly, we classify this variant as the first pure functionally-deficient (type II) AATD mutant.
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Affiliation(s)
- Mattia Laffranchi
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Emma L K Elliston
- UCL Respiratory and the Institute of Structural and Molecular Biology, University College London, London, United Kingdom
| | - Fabrizio Gangemi
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Romina Berardelli
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - David A Lomas
- UCL Respiratory and the Institute of Structural and Molecular Biology, University College London, London, United Kingdom
| | - James A Irving
- UCL Respiratory and the Institute of Structural and Molecular Biology, University College London, London, United Kingdom
| | - Annamaria Fra
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
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5
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Yu HM, Zhu BJ, Sun Y, Wei GQ, Wang L, Qian C, Nadeem Abbas M, Liu CL. Characterization and functional analysis of serpin-1 like gene from oak silkworm Antheraea pernyi. BULLETIN OF ENTOMOLOGICAL RESEARCH 2017; 107:620-626. [PMID: 28228181 DOI: 10.1017/s000748531700013x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Serpins are a broadly distributed family of proteases found in various organisms that play an important role in regulating the immune response. Here, we identified a serpin-1 gene from Antheraea pernyi that encodes a 279 amino acid protein with a molecular weight of 30.8 kDa. We expressed the recombinant Ap-serpin-1 protein in Escherichia coli and used the purified protein to prepare rabbit anti-Ap-serpin-1 polyclonal antibodies. We calculated the enzyme-linked immunosorbent assay titer of the antibody as 1:128000. Quantitative real-time polymerase chain reaction analysis revealed that Ap-serpin-1 was expressed in all examined tissues, including hemolymph, malpighian tubules, midgut, silk gland, integument and the fat body; the highest Ap-serpin-1 expression levels was detected in the fat body. We next investigated the expression patterns of Ap-serpin-1 in both fat body and hemolymph samples, following treatment with E. coli, Beauveria bassiana, Micrococcus luteus and nuclear polyhedrosis virus (NPV). We reported that NPV and M. luteus significantly enhanced Ap-serpin-1 expression in the fat body. While, in the hemolymph samples, treatment with B. bassiana and M. luteus was shown to upregulate Ap-serpin-1 expression at 24 h induction. Altogether, our results suggest that Ap-serpin-1 is involved in the innate immunity of A. pernyi.
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Affiliation(s)
- H M Yu
- College of Life Sciences,Anhui Agricultural University,Hefei,230036,China
| | - B J Zhu
- College of Life Sciences,Anhui Agricultural University,Hefei,230036,China
| | - Y Sun
- College of Life Sciences,Anhui Agricultural University,Hefei,230036,China
| | - G Q Wei
- College of Life Sciences,Anhui Agricultural University,Hefei,230036,China
| | - L Wang
- College of Life Sciences,Anhui Agricultural University,Hefei,230036,China
| | - C Qian
- College of Life Sciences,Anhui Agricultural University,Hefei,230036,China
| | - M Nadeem Abbas
- College of Life Sciences,Anhui Agricultural University,Hefei,230036,China
| | - C L Liu
- College of Life Sciences,Anhui Agricultural University,Hefei,230036,China
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6
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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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7
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Gaczynska M, Karpowicz P, Stuart CE, Norton MG, Teckman JH, Marszal E, Osmulski PA. AFM Imaging Reveals Topographic Diversity of Wild Type and Z Variant Polymers of Human α1-Proteinase Inhibitor. PLoS One 2016; 11:e0151902. [PMID: 27008547 PMCID: PMC4805282 DOI: 10.1371/journal.pone.0151902] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 03/04/2016] [Indexed: 12/17/2022] Open
Abstract
α1-Proteinase inhibitor (antitrypsin) is a canonical example of the serpin family member that binds and inhibits serine proteases. The natural metastability of serpins is crucial to carry out structural rearrangements necessary for biological activity. However, the enhanced metastability of the mutant Z variant of antitrypsin, in addition to folding defect, may substantially contribute to its polymerization, a process leading to incurable serpinopathy. The metastability also impedes structural studies on the polymers. There are no crystal structures of Z monomer or any kind of polymers larger than engineered wild type (WT) trimer. Our understanding of polymerization mechanisms is based on biochemical data using in vitro generated WT oligomers and molecular simulations. Here we applied atomic force microscopy (AFM) to compare topography of monomers, in vitro formed WT oligomers, and Z type polymers isolated from transgenic mouse liver. We found the AFM images of monomers closely resembled an antitrypsin outer shell modeled after the crystal structure. We confirmed that the Z variant demonstrated higher spontaneous propensity to dimerize than WT monomers. We also detected an unexpectedly broad range of different types of polymers with periodicity and topography depending on the applied method of polymerization. Short linear oligomers of unit arrangement similar to the Z polymers were especially abundant in heat-treated WT preparations. Long linear polymers were a prominent and unique component of liver extracts. However, the liver preparations contained also multiple types of oligomers of topographies undistinguishable from those found in WT samples polymerized with heat, low pH or guanidine hydrochloride treatments. In conclusion, we established that AFM is an excellent technique to assess morphological diversity of antitrypsin polymers, which is important for etiology of serpinopathies. These data also support previous, but controversial models of in vivo polymerization showing a surprising diversity of polymer topography.
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Affiliation(s)
- Maria Gaczynska
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
| | - Przemyslaw Karpowicz
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
| | - Christine E. Stuart
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Malgorzata G. Norton
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Jeffrey H. Teckman
- Department of Pediatrics and Biochemistry, Saint Louis University School of Medicine, Cardinal Glennon Children’s Medical Center, St. Louis, Missouri, United States of America
| | - Ewa Marszal
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Pawel A. Osmulski
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
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8
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Cloning, expression and characterization of Ostrinia furnacalis serpin1, a regulator of the prophenoloxidase activation system. Comp Biochem Physiol B Biochem Mol Biol 2016; 192:9-20. [DOI: 10.1016/j.cbpb.2015.11.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 11/10/2015] [Accepted: 11/11/2015] [Indexed: 01/29/2023]
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9
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Gospodarek AM, Sun W, O’Connell JP, Fernandez EJ. Structures of multidomain proteins adsorbed on hydrophobic interaction chromatography surfaces. J Chromatogr A 2014; 1371:204-19. [DOI: 10.1016/j.chroma.2014.10.080] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 10/08/2014] [Accepted: 10/25/2014] [Indexed: 11/17/2022]
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10
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Functional analysis of novel alpha-1 antitrypsin variants G320R and V321F. Mol Biol Rep 2014; 41:6133-41. [PMID: 24969485 DOI: 10.1007/s11033-014-3492-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 06/17/2014] [Indexed: 12/12/2022]
Abstract
Alpha-1 antitrypsin (AAT) gene is highly polymorphic, with a large number of rare variants whose phenotypic consequences often remain inconclusive. Studies addressing functional characteristics of AAT variants are of significant biomedical importance since deficiency and dysfunctionality of AAT are associated with liver and lung diseases. We report the results of the functional analysis of two naturally occurring AAT variants, G320R and V321F, previously identified in patients with lung disease. Neither of variants has been fully functionally characterized. In order to perform their functional analysis both variants were expressed in prokaryotic and eukaryotic systems and their intracellular localization, activity, stability, and polymerization were determined. The results of this study demonstrated that variants G320R and V321F have neither impaired activity against porcine pancreatic elastase nor propensity to form polymers. However, both variants had altered electrophoretic mobility and reduced thermostability when compared to M variant of the protein, indicating a slightly impaired secondary or tertiary structure.
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11
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Xin D, Holzenburg A, Burgess K. Small Molecule Probes That Perturb A Protein-protein Interface In Antithrombin. Chem Sci 2014; 5:4914-4921. [PMID: 25396040 DOI: 10.1039/c4sc01295j] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Small molecule probes for perturbing protein-protein interactions (PPIs) in vitro can be useful if they cause the target proteins to undergo biomedically relevant changes to their tertiary and quaternary structures. Application of the Exploring Key Orientations (EKO) strategy (J. Am. Chem. Soc., 2013, 135, 167 - 173) to a piperidinone-piperidine chemotype 1 indicated specific derivatives were candidates to perturb a protein-protein interface in the α-antithrombin dimer; those particular derivatives of 1 were prepared and tested. In the event, most of them significantly accelerated oligomerization of monomeric α-antithrombin, which is metastable in its oligomeric state. This assertion is supported by data from gel electrophoresis (non-denaturing PAGE; throughout) and probe-induced loss of α-antithrombin's inhibitor activity in a reaction catalyzed by thrombin. Kinetics of α-antithrombin oligomerization induced by the target compounds were examined. It was found that probes with O-benzyl-protected serine side-chains are the most active catalysts in the series, and reasons for this, based on modeling experiments, are proposed. Overall, this study reveals one of the first examples of small molecules designed to act at a protein-protein interface relevant to oligomerization of a serpin (ie α-antithrombin). The relevance of this to formation of oligomeric serpin fibrils, associated with the disease states known as "serpinopathies", is discussed.
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Affiliation(s)
- Dongyue Xin
- Department of Chemistry, Texas A & M University, Box 30012, College Station, TX 77842
| | - Andreas Holzenburg
- Microscopy and Imaging Center, Department of Biology, and Department of Biochemistry & Biophysics TAMU, College Station, TX 77843-2257
| | - Kevin Burgess
- Department of Chemistry, Texas A & M University, Box 30012, College Station, TX 77842
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12
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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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13
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Maruyama K, Morishita E, Karato M, Kadono T, Sekiya A, Goto Y, Sato T, Nomoto H, Omi W, Tsuzura S, Imai H, Asakura H, Ohtake S, Nakao S. Antithrombin deficiency in three Japanese families: one novel and two reported point mutations in the antithrombin gene. Thromb Res 2013; 132:e118-23. [PMID: 23809926 DOI: 10.1016/j.thromres.2013.06.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Revised: 05/25/2013] [Accepted: 06/02/2013] [Indexed: 11/18/2022]
Abstract
INTRODUCTION Inherited antithrombin (AT) deficiency is associated with a predisposition to familial venous thromboembolic disease. We analyzed the AT gene in three unrelated patients with an AT deficiency who developed thrombosis. MATERIALS AND METHODS We analyzed the SERPINC1 gene in three patients. Additionally, we expressed the three mutants in the COS-1 cells and compared their secretion rates and levels of AT activity with those of the wild-type (WT). RESULTS We identified three distinct heterozygous mutations of c.2534C>T: p.56Arginine → Cysteine (R56C), c.13398C>A: p.459Alanine → Aspartic acid (A459D) and c.2703C>G: p.112 Proline → Arginine (P112R). In the in vitro expression experiments, the AT antigen levels in the conditioned media (CM) of the R56C mutant were nearly equal to those of WT. In contrast, the AT antigen levels in the CM of the A459D and P112R mutants were significantly decreased. The AT activity of R56C was decreased in association with a shorter incubation time in a FXa inhibition assay and a thrombin inhibition-based activity test. However, the AT activity of R56C was comparable to that of WT when the incubation time was increased. CONCLUSIONS We concluded that the R56C mutant is responsible for type II HBS deficiency. We considered that the A459D and P112R mutants can be classified as belonging to the type I AT deficiency.
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Affiliation(s)
- Keiko Maruyama
- Department of Clinical Laboratory Science, Kanazawa University Graduate School of Medical Science, Kanazawa, Japan
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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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15
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A peptide mimicking the C-terminal part of the reactive center loop induces the transition to the latent form of plasminogen activator inhibitor type-1. FEBS Lett 2012; 586:686-92. [DOI: 10.1016/j.febslet.2012.02.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Revised: 02/02/2012] [Accepted: 02/08/2012] [Indexed: 11/21/2022]
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16
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Patschull AOM, Segu L, Nyon MP, Lomas DA, Nobeli I, Barrett TE, Gooptu B. Therapeutic target-site variability in α1-antitrypsin characterized at high resolution. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1492-7. [PMID: 22139150 PMCID: PMC3232123 DOI: 10.1107/s1744309111040267] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Accepted: 09/29/2011] [Indexed: 11/17/2022]
Abstract
The intrinsic propensity of α(1)-antitrypsin to undergo conformational transitions from its metastable native state to hyperstable forms provides a motive force for its antiprotease function. However, aberrant conformational change can also occur via an intermolecular linkage that results in polymerization. This has both loss-of-function and gain-of-function effects that lead to deficiency of the protein in human circulation, emphysema and hepatic cirrhosis. One of the most promising therapeutic strategies being developed to treat this disease targets small molecules to an allosteric site in the α(1)-antitrypsin molecule. Partial filling of this site impedes polymerization without abolishing function. Drug development can be improved by optimizing data on the structure and dynamics of this site. A new 1.8 Å resolution structure of α(1)-antitrypsin demonstrates structural variability within this site, with associated fluctuations in its upper and lower entrance grooves and ligand-binding characteristics around the innermost stable enclosed hydrophobic recess. These data will allow a broader selection of chemotypes and derivatives to be tested in silico and in vitro when screening and developing compounds to modulate conformational change to block the pathological mechanism while preserving function.
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Affiliation(s)
- Anathe O. M. Patschull
- Institute of Structural and Molecular Biology, Crystallography, Department of Biological Sciences, Birkbeck College, Malet Street, London WC1E 7HX, England
| | - Lakshmi Segu
- Institute of Structural and Molecular Biology, Crystallography, Department of Biological Sciences, Birkbeck College, Malet Street, London WC1E 7HX, England
| | - Mun Peak Nyon
- Institute of Structural and Molecular Biology, Crystallography, Department of Biological Sciences, Birkbeck College, Malet Street, London WC1E 7HX, England
| | - David A. Lomas
- Cambridge Institute for Medical Research, Department of Medicine, University of Cambridge, Hills Road, Cambridge CB2 0XY, England
| | - Irene Nobeli
- Institute of Structural and Molecular Biology, Crystallography, Department of Biological Sciences, Birkbeck College, Malet Street, London WC1E 7HX, England
| | - Tracey E. Barrett
- Institute of Structural and Molecular Biology, Crystallography, Department of Biological Sciences, Birkbeck College, Malet Street, London WC1E 7HX, England
| | - Bibek Gooptu
- Institute of Structural and Molecular Biology, Crystallography, Department of Biological Sciences, Birkbeck College, Malet Street, London WC1E 7HX, England
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Yamasaki M, Sendall TJ, Pearce MC, Whisstock JC, Huntington JA. Molecular basis of α1-antitrypsin deficiency revealed by the structure of a domain-swapped trimer. EMBO Rep 2011; 12:1011-7. [PMID: 21909074 DOI: 10.1038/embor.2011.171] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Revised: 07/20/2011] [Accepted: 07/22/2011] [Indexed: 11/09/2022] Open
Abstract
α(1)-Antitrypsin (α1AT) deficiency is a disease with multiple manifestations, including cirrhosis and emphysema, caused by the accumulation of stable polymers of mutant protein in the endoplasmic reticulum of hepatocytes. However, the molecular basis of misfolding and polymerization remain unknown. We produced and crystallized a trimeric form of α1AT that is recognized by an antibody specific for the pathological polymer. Unexpectedly, this structure reveals a polymeric linkage mediated by domain swapping the carboxy-terminal 34 residues. Disulphide-trapping and antibody-binding studies further demonstrate that runaway C-terminal domain swapping, rather than the s4A/s5A domain swap previously proposed, underlies polymerization of the common Z-mutant of α1AT in vivo.
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Affiliation(s)
- Masayuki Yamasaki
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, UK
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18
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Abstract
Serpins have been studied as a distinct protein superfamily since the early 80s. In spite of the poor sequence homology between family members, serpins share a highly conserved core structure that is critical for their functioning as serine protease inhibitors. Therefore, discoveries made about one serpin can be related to the others. In this short review, I introduce the serpin structure and general mechanism of protease inhibition, and illustrate, using recent crystallographic and biochemical data on antithrombin (AT), how serpin activity can be modulated by cofactors. The ability of the serpins to undergo conformational change is critical for their function, but it also renders them uniquely susceptible to mutations that perturb their folding, leading to deficiency and disease. A recent crystal structure of an AT dimer revealed that serpins can participate in large-scale domain-swaps to form stable polymers, and that such a mechanism may explain the accumulation of misfolded serpins within secretory cells. Serpins play important roles in haemostasis and fibrinolysis, and although each will have some elements specifically tailored for its individual function, the mechanisms described here provide a general conceptual framework.
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Affiliation(s)
- J A Huntington
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK.
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Dynamic local unfolding in the serpin α-1 antitrypsin provides a mechanism for loop insertion and polymerization. Nat Struct Mol Biol 2011; 18:222-6. [PMID: 21258324 PMCID: PMC3074950 DOI: 10.1038/nsmb.1976] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Accepted: 11/12/2010] [Indexed: 01/22/2023]
Abstract
The conformational plasticity of serine protease inhibitors (serpins) underlies both their activities as protease inhibitors and their susceptibility to pathogenic misfolding and aggregation. Here, we structurally characterize a sheet-opened state of the serpin α-1 antitrypsin (α₁AT) and show how local unfolding allows functionally essential strand insertion. Mutations in α₁AT that cause polymerization-induced serpinopathies map to the labile region, suggesting that the evolution of serpin function required sampling of high risk conformations on a dynamic energy landscape.
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22
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Tanaka N, Morimoto Y, Noguchi Y, Tada T, Waku T, Kunugi S, Morii T, Lee YF, Konno T, Takahashi N. The mechanism of fibril formation of a non-inhibitory serpin ovalbumin revealed by the identification of amyloidogenic core regions. J Biol Chem 2010; 286:5884-94. [PMID: 21156792 DOI: 10.1074/jbc.m110.176396] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Ovalbumin (OVA), a non-inhibitory member of the serpin superfamily, forms fibrillar aggregates upon heat-induced denaturation. Recent studies suggested that OVA fibrils are generated by a mechanism similar to that of amyloid fibril formation, which is distinct from polymerization mechanisms proposed for other serpins. In this study, we provide new insights into the mechanism of OVA fibril formation through identification of amyloidogenic core regions using synthetic peptide fragments, site-directed mutagenesis, and limited proteolysis. OVA possesses a single disulfide bond between Cys(73) and Cys(120) in the N-terminal helical region of the protein. Heat treatment of disulfide-reduced OVA resulted in the formation of long straight fibrils that are distinct from the semiflexible fibrils formed from OVA with an intact disulfide. Computer predictions suggest that helix B (hB) of the N-terminal region, strand 3A, and strands 4-5B are highly β-aggregation-prone regions. These predictions were confirmed by the fact that synthetic peptides corresponding to these regions formed amyloid fibrils. Site-directed mutagenesis of OVA indicated that V41A substitution in hB interfered with the formation of fibrils. Co-incubation of a soluble peptide fragment of hB with the disulfide-intact full-length OVA consistently promoted formation of long straight fibrils. In addition, the N-terminal helical region of the heat-induced fibril of OVA was protected from limited proteolysis. These results indicate that the heat-induced fibril formation of OVA occurs by a mechanism involving transformation of the N-terminal helical region of the protein to β-strands, thereby forming sequential intermolecular linkages.
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Affiliation(s)
- Naoki Tanaka
- Department of Biomolecular Engineering, Kyoto Institute of Technology, Matsugasaki, Sakyo, Kyoto 606-8585, Japan.
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