1
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Strand 1A variant in neuroserpin shows increased aggregation and no loss of inhibition: implication in ameliorating polymerization to retain activity. Biosci Rep 2022; 42:232125. [PMID: 36408789 PMCID: PMC9760604 DOI: 10.1042/bsr20221825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 10/31/2022] [Accepted: 11/18/2022] [Indexed: 11/22/2022] Open
Abstract
Neuroserpin (NS) is predominantly expressed in the brain and is the primary inhibitor of tissue plasminogen activator (tPA). NS variants are associated with the neurogenerative disease termed familial encephalopathy with neuroserpin inclusion bodies (FENIB). The disease is characterized by variable age of onset and severity. The reactive center loop (RCL) insertion-based inhibitory mechanism of NS requires a coordinated conformational change leading to a shift in the strands of the β-sheet A and movement of helix F. Strand 1A is connected to the helix F at its C terminal end and with the strand 2A at its N terminal, both these domain move for accommodating the inserting loop; therefore, a variant that influences their movement may alter the inhibition rates. A molecular dynamic simulation analysis of a H138C NS variant from strand 1A showed a large decrease in conformational fluctuations as compared with wild-type NS. H138 was mutated, expressed, purified and a native-PAGE and transmission electron microscopy (TEM) analysis showed that this variant forms large molecular weight aggregates on a slight increase in temperature. However, a circular dichroism analysis showed its secondary structure to be largely conserved. Surprisingly, its tPA inhibition activity and complex formation remain unhindered even after the site-specific labeling of H138C with Alexa fluor C5 maleimide. Further, a helix F-strand 1A (W154C-H138C) double variant still shows appreciable inhibitory activity. Increasingly, it appears that aggregation and not loss of inhibition is the more likely cause of shutter region-based variants phenotypes, indicating that hindering polymer formation using small molecules may retain inhibitory activity in pathological variants of NS.
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2
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Reactive Centre Loop Mutagenesis of SerpinB3 to Target TMPRSS2 and Furin: Inhibition of SARS-CoV-2 Cell Entry and Replication. Int J Mol Sci 2022; 23:ijms232012522. [PMID: 36293378 PMCID: PMC9604144 DOI: 10.3390/ijms232012522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/14/2022] [Accepted: 10/16/2022] [Indexed: 11/16/2022] Open
Abstract
The SARS-CoV-2 virus can utilize host cell proteases to facilitate cell entry, whereby the Spike (S) protein is cleaved at two specific sites to enable membrane fusion. Furin, transmembrane protease serine 2 (TMPRSS2), and cathepsin L (CatL) are the major proteases implicated, and are thus targets for anti-viral therapy. The human serpin (serine protease inhibitor) alpha-1 antitrypsin (A1AT) shows inhibitory activity for TMPRSS2, and has previously been found to suppress cell infection with SARS-CoV-2. Here, we have generated modified serpin inhibitors with increased specificity for these cellular proteases. Using SerpinB3 (SCCA-1), a cross-class inhibitor of CatL, as a scaffold, we have designed and produced reactive centre loop (RCL) variants to more specifically target both furin and TMPRSS2. Two further variants were generated by substituting the RCL P7–P1 with the spike protein S1/S2 cleavage site from either SARS-CoV-2 alpha or delta (P681R) sequences. Altered inhibitory specificity of purified recombinant proteins was verified in protease assays, with attenuated CatL inhibition and gain of furin or TMPRSS2 inhibition, as predicted, and modified serpins were shown to block S protein cleavage in vitro. Furthermore, the serpin variants were able to inhibit S-pseudoparticle entry into A549-ACE2-TMPRSS2 cells and suppress SARS-CoV-2 replication in Vero E6 cells expressing TMPRSS2. The construct designed to inhibit TMPRSS2 (B3-TMP) was most potent. It was more effective than A1AT for TMPRSS2 enzyme inhibition (with an eighteen-fold improvement in the second order inhibition rate constant) and for blocking SARS-CoV-2 viral replication. These findings advance the potential for serpin RCL mutagenesis to generate new inhibitors, and may lead to novel anti-viral biological molecules.
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3
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Ronzoni R, Ferrarotti I, D’Acunto E, Balderacchi AM, Ottaviani S, Lomas DA, Irving JA, Miranda E, Fra A. The Importance of N186 in the Alpha-1-Antitrypsin Shutter Region Is Revealed by the Novel Bologna Deficiency Variant. Int J Mol Sci 2021; 22:5668. [PMID: 34073489 PMCID: PMC8198886 DOI: 10.3390/ijms22115668] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/18/2021] [Accepted: 05/20/2021] [Indexed: 11/17/2022] Open
Abstract
Alpha-1-antitrypsin (AAT) deficiency causes pulmonary disease due to decreased levels of circulating AAT and consequently unbalanced protease activity in the lungs. Deposition of specific AAT variants, such as the common Z AAT, within hepatocytes may also result in liver disease. These deposits are comprised of ordered polymers of AAT formed by an inter-molecular domain swap. The discovery and characterization of rare variants of AAT and other serpins have historically played a crucial role in the dissection of the structural mechanisms leading to AAT polymer formation. Here, we report a severely deficient shutter region variant, Bologna AAT (N186Y), which was identified in five unrelated subjects with different geographical origins. We characterized the new variant by expression in cellular models in comparison with known polymerogenic AAT variants. Bologna AAT showed secretion deficiency and intracellular accumulation as detergent-insoluble polymers. Extracellular polymers were detected in both the culture media of cells expressing Bologna AAT and in the plasma of a patient homozygous for this variant. Structural modelling revealed that the mutation disrupts the hydrogen bonding network in the AAT shutter region. These data support a crucial coordinating role for asparagine 186 and the importance of this network in promoting formation of the native structure.
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Affiliation(s)
- Riccardo Ronzoni
- UCL Respiratory and the Institute of Structural and Molecular Biology, University College London, London WC1E 6JF, UK; (D.A.L.); (J.A.I.)
| | - Ilaria Ferrarotti
- Pneumology Unit, Centre for Diagnosis of Inherited Alpha-1 Antitrypsin Deficiency, Department of Internal Medicine and Therapeutics, IRCCS San Matteo Hospital Foundation, University of Pavia, 27100 Pavia, Italy; (I.F.); (A.M.B.); (S.O.)
| | - Emanuela D’Acunto
- Department of Biology and Biotechnologies ‘Charles Darwin’, Sapienza University of Rome, 00185 Rome, Italy; (E.D.); (E.M.)
| | - Alice M. Balderacchi
- Pneumology Unit, Centre for Diagnosis of Inherited Alpha-1 Antitrypsin Deficiency, Department of Internal Medicine and Therapeutics, IRCCS San Matteo Hospital Foundation, University of Pavia, 27100 Pavia, Italy; (I.F.); (A.M.B.); (S.O.)
| | - Stefania Ottaviani
- Pneumology Unit, Centre for Diagnosis of Inherited Alpha-1 Antitrypsin Deficiency, Department of Internal Medicine and Therapeutics, IRCCS San Matteo Hospital Foundation, University of Pavia, 27100 Pavia, Italy; (I.F.); (A.M.B.); (S.O.)
| | - David A. Lomas
- UCL Respiratory and the Institute of Structural and Molecular Biology, University College London, London WC1E 6JF, UK; (D.A.L.); (J.A.I.)
| | - James A. Irving
- UCL Respiratory and the Institute of Structural and Molecular Biology, University College London, London WC1E 6JF, UK; (D.A.L.); (J.A.I.)
| | - Elena Miranda
- Department of Biology and Biotechnologies ‘Charles Darwin’, Sapienza University of Rome, 00185 Rome, Italy; (E.D.); (E.M.)
- Italian Pasteur Institute—Cenci Bolognetti Foundation, Sapienza University of Rome, 00185 Rome, Italy
| | - Annamaria Fra
- Department of Molecular and Translational Medicine, University of Brescia, viale Europa 11, 25123 Brescia, Italy
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4
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Trehalose: is it a potential inhibitor of antithrombin polymerization? Biosci Rep 2019; 39:BSR20190567. [PMID: 31147454 PMCID: PMC6579975 DOI: 10.1042/bsr20190567] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 05/08/2019] [Accepted: 05/09/2019] [Indexed: 11/29/2022] Open
Abstract
SERine Protease INhibitorS (Serpins) are a superfamily of proteins that are characterized by having a similar three-dimensional structure. The native conformation is not most thermodynamically stable, so polymerization is the main consequence when its stability is altered as a result of certain mutations. The polymerization of serpins has been a research topic for many years. Different mechanisms have been proposed and in the same way different compounds or strategies have been studied to prevent polymerization. A recent paper published in Bioscience Reports by Naseem et al. [Biosci. Rep. (2019) 5, 39] studies the role of trehalose in the prevention of the polymerization of antithrombin, which belongs to the serpin superfamily. The main consequence of the antithrombin polymerization is the increased thrombotic risk, since antithrombin is the main inhibitor of the coagulation cascade. The authors demonstrate that trehalose is able to prevent the in vitro polymerization of antithrombin, under conditions in which it usually tends to polymerize, and demonstrate it by using different techniques. However, the binding site of trehalose in antithrombin should be defined by site-directed mutagenesis. On the other hand, it is not clear if all serpins polymerize in vivo through the same mechanism and it is also not clear if the same serpin can even polymerize through different mechanisms. Therefore, there are still doubts about the potential of trehalose or its derivatives to prevent in vivo antithrombin polymerization and, therefore, reduce thrombotic risk, as well as whether trehalose would be able to reduce polymerization in other serpins.
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Deciphering the role of trehalose in hindering antithrombin polymerization. Biosci Rep 2019; 39:BSR20182259. [PMID: 30886063 PMCID: PMC6449516 DOI: 10.1042/bsr20182259] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 03/06/2019] [Accepted: 03/07/2019] [Indexed: 11/17/2022] Open
Abstract
Serine protease inhibitors (serpins) family have a complex mechanism of inhibition that requires a large scale conformational change. Antithrombin (AT), a member of serpin superfamily serves as a key regulator of the blood coagulation cascade, deficiency of which leads to thrombosis. In recent years, a handful of studies have identified small compounds that retard serpin polymerization but abrogated the normal activity. Here, we screened small molecules to find potential leads that can reduce AT polymer formation. We identified simple sugar molecules that successfully blocked polymer formation without a significant loss of normal activity of AT under specific buffer and temperature conditions. Of these, trehalose proved to be most promising as it showed a marked decrease in the bead like polymeric structures of AT shown by electron microscopic analysis. A circular dichroism (CD) analysis indicated alteration in the secondary structure profile and an increased thermal stability of AT in the presence of trehalose. Guanidine hydrochloride (GdnHCl)-based unfolding studies of AT show the formation of a different intermediate in the presence of trehalose. A time-dependent fluorescence study using 1,1′-bi(4-anilino)naphthalene-5,5′-disulfonic acid (Bis-ANS) shows that trehalose affects the initial conformational change step in transition from native to polymer state through its binding to exposed hydrophobic residues on AT thus making AT less polymerogenic. In conclusion, trehalose holds promise by acting as an initial scaffold that can be modified to design similar compounds with polymer retarding propensity.
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6
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Huang X, Zheng Y, Zhang F, Wei Z, Wang Y, Carrell RW, Read RJ, Chen GQ, Zhou A. Molecular Mechanism of Z α1-Antitrypsin Deficiency. J Biol Chem 2016; 291:15674-86. [PMID: 27246852 PMCID: PMC4957051 DOI: 10.1074/jbc.m116.727826] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Indexed: 12/14/2022] Open
Abstract
The Z mutation (E342K) of α1-antitrypsin (α1-AT), carried by 4% of Northern Europeans, predisposes to early onset of emphysema due to decreased functional α1-AT in the lung and to liver cirrhosis due to accumulation of polymers in hepatocytes. However, it remains unclear why the Z mutation causes intracellular polymerization of nascent Z α1-AT and why 15% of the expressed Z α1-AT is secreted into circulation as functional, but polymerogenic, monomers. Here, we solve the crystal structure of the Z-monomer and have engineered replacements to assess the conformational role of residue Glu-342 in α1-AT. The results reveal that Z α1-AT has a labile strand 5 of the central β-sheet A (s5A) with a consequent equilibrium between a native inhibitory conformation, as in its crystal structure here, and an aberrant conformation with s5A only partially incorporated into the central β-sheet. This aberrant conformation, induced by the loss of interactions from the Glu-342 side chain, explains why Z α1-AT is prone to polymerization and readily binds to a 6-mer peptide, and it supports that annealing of s5A into the central β-sheet is a crucial step in the serpins' metastable conformational formation. The demonstration that the aberrant conformation can be rectified through stabilization of the labile s5A by binding of a small molecule opens a potential therapeutic approach for Z α1-AT deficiency.
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Affiliation(s)
- Xin Huang
- From the Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine and University of Chinese Academy of Sciences, Shanghai 200025, China
| | - Ying Zheng
- the Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology Division of Shanghai Universities E-Institutes, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China, and
| | - Fei Zhang
- the Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology Division of Shanghai Universities E-Institutes, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China, and
| | - Zhenquan Wei
- the Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology Division of Shanghai Universities E-Institutes, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China, and
| | - Yugang Wang
- the Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology Division of Shanghai Universities E-Institutes, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China, and
| | - Robin W Carrell
- the Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Randy J Read
- the Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Guo-Qiang Chen
- From the Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine and University of Chinese Academy of Sciences, Shanghai 200025, China, the Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology Division of Shanghai Universities E-Institutes, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China, and
| | - Aiwu Zhou
- the Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology Division of Shanghai Universities E-Institutes, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China, and
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7
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Azhar A, Khan MS, Swaminathan A, Naseem A, Chatterjee S, Jairajpuri MA. Oxidized antithrombin is a dual inhibitor of coagulation and angiogenesis: Importance of low heparin affinity. Int J Biol Macromol 2016; 82:541-50. [DOI: 10.1016/j.ijbiomac.2015.10.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 10/01/2015] [Accepted: 10/05/2015] [Indexed: 01/09/2023]
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8
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Chang YP, Chu YH. Mixture-based combinatorial libraries from small individual peptide libraries: a case study on α1-antitrypsin deficiency. Molecules 2014; 19:6330-48. [PMID: 24840902 PMCID: PMC6271437 DOI: 10.3390/molecules19056330] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 05/12/2014] [Accepted: 05/13/2014] [Indexed: 12/12/2022] Open
Abstract
The design, synthesis and screening of diversity-oriented peptide libraries using a "libraries from libraries" strategy for the development of inhibitors of α1-antitrypsin deficiency are described. The major buttress of the biochemical approach presented here is the use of well-established solid-phase split-and-mix method for the generation of mixture-based libraries. The combinatorial technique iterative deconvolution was employed for library screening. While molecular diversity is the general consideration of combinatorial libraries, exquisite design through systematic screening of small individual libraries is a prerequisite for effective library screening and can avoid potential problems in some cases. This review will also illustrate how large peptide libraries were designed, as well as how a conformation-sensitive assay was developed based on the mechanism of the conformational disease. Finally, the combinatorially selected peptide inhibitor capable of blocking abnormal protein aggregation will be characterized by biophysical, cellular and computational methods.
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Affiliation(s)
- Yi-Pin Chang
- The Forsyth Institute, 245 First Street, Cambridge, MA 02142, USA
| | - Yen-Ho Chu
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Road, Minhsiung, Chiayi 62102, Taiwan.
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9
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Minsky BB, Zheng B, Dubin PL. Inhibition of antithrombin and bovine serum albumin native state aggregation by heparin. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:278-287. [PMID: 24313340 DOI: 10.1021/la4039232] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Protein native state aggregation, a major problem in pharmaceutical and biological processes, has been addressed pharmacologically by the addition of protein-binding excipients. Heparin (Hp), a highly sulfated polysaccharide, interacts with numerous proteins with moderate to high affinity, but reports about its effect on protein aggregation are contradictory. We studied the pH dependence of the aggregation of antithrombin (AT) and bovine serum albumin (BSA) in the presence and absence of heparin. High-precision turbidimetry showed strong aggregation for both AT and BSA in I = 10 mM NaCl, conditions at which electrostatically driven Hp binding and aggregation both occur, with more obvious aggregation of heparin-free AT appearing as larger aggregate size. Aggregation of AT was dramatically inhibited at Hp: protein 6:1 (mole ratio); however, the effect at 0.5:1 Hp:protein was greater for BSA. Frontal analysis capillary electrophoresis showed a much larger equilibrium association constant Kobs between Hp and AT, in accord with the onset of Hp binding at a higher pH; both effects are explained by the higher charge density of the positive domain for AT as revealed by modeling with DelPhi. The corresponding modeling images showed that these domains persist at high salt only for AT, consistent with the 160-fold drop in Kobs at 100 mM salt for BSA-Hp binding. The smaller inhibition effect for AT arises from the tendency of its uncomplexed monomer to form larger aggregates more rapidly, but the stronger binding of Hp to AT does not facilitate Hp-induced aggregate dissolution which occurs more readily for BSA. This can be attributed to the higher density of AT aggregates evidenced by higher fractal dimensions. Differences between inhibition and reversal by Hp arise because the former may depend on the stage at which Hp enters the aggregation process and the latter on aggregate size and morphology.
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Affiliation(s)
- Burcu Baykal Minsky
- Department of Chemistry, University of Massachusetts , Amherst, Massachusetts, 01003, United States
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10
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The roles of helix I and strand 5A in the folding, function and misfolding of α1-antitrypsin. PLoS One 2013; 8:e54766. [PMID: 23382962 PMCID: PMC3558512 DOI: 10.1371/journal.pone.0054766] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 12/14/2012] [Indexed: 11/19/2022] Open
Abstract
α1-Antitrypsin, the archetypal member of the serpin superfamily, is a metastable protein prone to polymerization when exposed to stressors such as elevated temperature, low denaturant concentrations or through the presence of deleterious mutations which, in a physiological context, are often associated with disease. Experimental evidence suggests that α1-Antitrypsin can polymerize via several alternative mechanisms in vitro. In these polymerization mechanisms different parts of the molecule are proposed to undergo conformational change. Both strand 5 and helix I are proposed to adopt different conformations when forming the various polymers, and possess a number of highly conserved residues however their role in the folding and misfolding of α1-Antitrypsin has never been examined. We have therefore created a range of α1Antitypsin variants in order to explore the role of these conserved residues in serpin folding, misfolding, stability and function. Our data suggest that key residues in helix I mediate efficient folding from the folding intermediate and residues in strand 5A ensure native state stability in order to prevent misfolding. Additionally, our data indicate that helix I is involved in the inhibitory process and that both structural elements undergo differing conformational rearrangements during unfolding and misfolding. These findings suggest that the ability of α1-Antitrypsin to adopt different types of polymers under different denaturing conditions may be due to subtle conformational differences in the transiently populated structures adopted prior to the I and M* states.
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11
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Chang YP, Chu YH. Blocking formation of large protein aggregates by small peptides. Chem Commun (Camb) 2013; 49:4591-600. [DOI: 10.1039/c3cc37518h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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12
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Gavrin LK, Denny RA, Saiah E. Small Molecules That Target Protein Misfolding. J Med Chem 2012; 55:10823-43. [DOI: 10.1021/jm301182j] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Lori Krim Gavrin
- BioTherapeutics
Chemistry, Pfizer Worldwide Medicinal Chemistry, 200 CambridgePark Drive, Cambridge,
Massachusetts 02140, United States
| | - Rajiah Aldrin Denny
- BioTherapeutics
Chemistry, Pfizer Worldwide Medicinal Chemistry, 200 CambridgePark Drive, Cambridge,
Massachusetts 02140, United States
| | - Eddine Saiah
- BioTherapeutics
Chemistry, Pfizer Worldwide Medicinal Chemistry, 200 CambridgePark Drive, Cambridge,
Massachusetts 02140, United States
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13
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Nyon M, Segu L, Cabrita L, Lévy G, Kirkpatrick J, Roussel B, Patschull A, Barrett T, Ekeowa U, Kerr R, Waudby C, Kalsheker N, Hill M, Thalassinos K, Lomas D, Christodoulou J, Gooptu B. Structural dynamics associated with intermediate formation in an archetypal conformational disease. Structure 2012; 20:504-12. [PMID: 22405009 PMCID: PMC3314904 DOI: 10.1016/j.str.2012.01.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Revised: 12/02/2011] [Accepted: 01/03/2012] [Indexed: 11/21/2022]
Abstract
In conformational diseases, native protein conformers convert to pathological intermediates that polymerize. Structural characterization of these key intermediates is challenging. They are unstable and minimally populated in dynamic equilibria that may be perturbed by many analytical techniques. We have characterized a forme fruste deficiency variant of α1-antitrypsin (Lys154Asn) that forms polymers recapitulating the conformer-specific neo-epitope observed in polymers that form in vivo. Lys154Asn α1-antitrypsin populates an intermediate ensemble along the polymerization pathway at physiological temperatures. Nuclear magnetic resonance spectroscopy was used to report the structural and dynamic changes associated with this. Our data highlight an interaction network likely to regulate conformational change and do not support the recent contention that the disease-relevant intermediate is substantially unfolded. Conformational disease intermediates may best be defined using powerful but minimally perturbing techniques, mild disease mutants, and physiological conditions.
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Affiliation(s)
- Mun Peak Nyon
- Institute of Structural and Molecular Biology (ISMB), Department of Biological Sciences, Birkbeck College, London, WC1E 7HX, UK
| | - Lakshmi Segu
- Institute of Structural and Molecular Biology (ISMB), Department of Biological Sciences, Birkbeck College, London, WC1E 7HX, UK
| | - Lisa D. Cabrita
- Institute of Structural and Molecular Biology (ISMB), Department of Biological Sciences, Birkbeck College, London, WC1E 7HX, UK
- ISMB, Division of Biosciences, University College London, London, WC1E 6BT, UK
| | - Géraldine R. Lévy
- Institute of Structural and Molecular Biology (ISMB), Department of Biological Sciences, Birkbeck College, London, WC1E 7HX, UK
- ISMB, Division of Biosciences, University College London, London, WC1E 6BT, UK
| | - John Kirkpatrick
- ISMB, Division of Biosciences, University College London, London, WC1E 6BT, UK
| | - Benoit D. Roussel
- Department of Medicine, University of Cambridge, Cambridge Institute for Medical Research, Cambridge, CB2 0XY, UK
| | - Anathe O.M. Patschull
- Institute of Structural and Molecular Biology (ISMB), Department of Biological Sciences, Birkbeck College, London, WC1E 7HX, UK
- ISMB, Division of Biosciences, University College London, London, WC1E 6BT, UK
| | - Tracey E. Barrett
- Institute of Structural and Molecular Biology (ISMB), Department of Biological Sciences, Birkbeck College, London, WC1E 7HX, UK
| | - Ugo I. Ekeowa
- Department of Medicine, University of Cambridge, Cambridge Institute for Medical Research, Cambridge, CB2 0XY, UK
| | - Richard Kerr
- ISMB, Division of Biosciences, University College London, London, WC1E 6BT, UK
| | - Christopher A. Waudby
- Institute of Structural and Molecular Biology (ISMB), Department of Biological Sciences, Birkbeck College, London, WC1E 7HX, UK
- ISMB, Division of Biosciences, University College London, London, WC1E 6BT, UK
| | - Noor Kalsheker
- Division of Clinical Chemistry, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - Marian Hill
- Division of Clinical Chemistry, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology (ISMB), Department of Biological Sciences, Birkbeck College, London, WC1E 7HX, UK
- ISMB, Division of Biosciences, University College London, London, WC1E 6BT, UK
| | - David A. Lomas
- Department of Medicine, University of Cambridge, Cambridge Institute for Medical Research, Cambridge, CB2 0XY, UK
- Corresponding author
| | - John Christodoulou
- Institute of Structural and Molecular Biology (ISMB), Department of Biological Sciences, Birkbeck College, London, WC1E 7HX, UK
- ISMB, Division of Biosciences, University College London, London, WC1E 6BT, UK
- Corresponding author
| | - Bibek Gooptu
- Institute of Structural and Molecular Biology (ISMB), Department of Biological Sciences, Birkbeck College, London, WC1E 7HX, UK
- Corresponding author
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14
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Granzin J, Huang Y, Topbas C, Huang W, Wu Z, Misra S, Hazen SL, Blanton RE, Lee X, Weiergräber OH. Three-dimensional structure of a schistosome serpin revealing an unusual configuration of the helical subdomain. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:686-94. [PMID: 22683791 PMCID: PMC3370883 DOI: 10.1107/s0907444912008372] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Accepted: 02/24/2012] [Indexed: 11/10/2022]
Abstract
Parasitic organisms are constantly challenged by the defence mechanisms of their respective hosts, which often depend on serine protease activities. Consequently, protease inhibitors such as those belonging to the serpin superfamily have emerged as protective elements that support the survival of the parasites. This report describes the crystal structure of ShSPI, a serpin from the trematode Schistosoma haematobium. The protein is exposed on the surface of invading cercaria as well as of adult worms, suggesting its involvement in the parasite-host interaction. While generally conforming to the well established serpin fold, the structure reveals several distinctive features, mostly concerning the helical subdomain of the protein. It is proposed that these peculiarities are related to the unique biological properties of a small serpin subfamily which is conserved among pathogenic schistosomes.
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Affiliation(s)
- Joachim Granzin
- Institute of Complex Systems, ICS-6: Structural Biochemistry, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Ying Huang
- Department of Cell Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Celalettin Topbas
- Department of Cell Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Wenying Huang
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Zhiping Wu
- Department of Cell Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Saurav Misra
- Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Stanley L. Hazen
- Department of Cell Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Ronald E. Blanton
- Department of Infectious Diseases, Case Western Reserve University, Cleveland, OH 44190, USA
| | - Xavier Lee
- Department of Cell Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Oliver H. Weiergräber
- Institute of Complex Systems, ICS-6: Structural Biochemistry, Forschungszentrum Jülich, 52425 Jülich, Germany
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15
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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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16
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Singh P, Khan MS, Naseem A, Jairajpuri MA. Analysis of surface cavity in serpin family reveals potential binding sites for chemical chaperone to reduce polymerization. J Mol Model 2011; 18:1143-51. [PMID: 21681443 DOI: 10.1007/s00894-011-1110-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Accepted: 04/26/2011] [Indexed: 10/18/2022]
Abstract
Serpin constitute about 10% of blood protein and are associated with mutations that results in aberrant intermolecular linkages which leads to polymer formation. Studies with short peptides have shown promise in depolymerization of serpins however a reactive center loop based peptide also makes the serpin inactive. A chemical chaperone based approach is a better option in terms of maintaining activity and retarding polymerization but not much is known about its binding and mechanism. Specific target for chemical chaperones and its effectiveness across many serpin is not known. We did an analysis of serpin cavity using CASTp and show that cavities are distributed throughout the molecule where the largest cavities are generally present in areas of major conformational change like shutter region, helix D and helix F. An analysis of different conformational states of serpins showed that this large cavity undergoes increase in size in latent and cleaved states as compared to native state. We targeted serpins with a variety of carbohydrate, methylamine and amino acid based chemical chaperones and selected those that have highest binding energy across different serpins to assess their ability to bind large cavities. The results show that carbohydrate based chemical chaperone like sorbitol, sucrose, arabitol and trehalose and amino acid based chaperones like dopamine, phenylalanine, arginine and glutamic acid are the most effective in binding serpins. Most of these chemical chaperone interacted with residues in the shutter region and the helix D arm at the C-terminal which are part of the largest cavities. We selected the carbohydrate based chemical chaperone with best binding energies and did experimental study under the condition that induce polymerization and show that indeed they were able to retard polymer formation with moderate effect on inhibition rates. However a fluorometric study with native antithrombin showed that chemical chaperone may effect the conformation of the proteins. Our study shows that chemical chaperones have the best binding affinities for the cavities around shutter region and helix D and that a cavity targeting based approach seems to be a better option for retarding polymerization in serpins, but a thorough analysis of its effect on folding, inhibition and cofactor binding is required.
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Affiliation(s)
- Poonam Singh
- Protein Conformation and Enzymology Lab, Department of Biosciences, Jamia Millia Islamia University, New-Delhi 110025, India
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17
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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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18
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Olson ST, Gettins PGW. Regulation of proteases by protein inhibitors of the serpin superfamily. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2011; 99:185-240. [PMID: 21238937 DOI: 10.1016/b978-0-12-385504-6.00005-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The serpins comprise an ancient superfamily of proteins, found abundantly in eukaryotes and even in some bacteria and archea, that have evolved to regulate proteases of both serine and cysteine mechanistic classes. Unlike the thermodynamically determined lock-and-key type inhibitors, such as those of the Kunitz and Kazal families, serpins use conformational change and consequent kinetic trapping of an enzyme intermediate to effect inhibition. By combining interactions of both an exposed reactive center loop and exosites outside this loop with the active site and complementary exosites on the target protease, serpins can achieve remarkable specificity. Together with the frequent use of regulatory cofactors, this permits a sophisticated time- and location-dependent mode of protease regulation. An understanding of the structure and function of serpins has suggested that they may provide novel scaffolds for engineering protease inhibitors of desired specificity for therapeutic use.
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Affiliation(s)
- Steven T Olson
- Center for Molecular Biology of Oral Diseases, University of Illinois at Chicago, Chicago, Illinois, USA
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19
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20
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21
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Miranda E, Pérez J, Ekeowa UI, Hadzic N, Kalsheker N, Gooptu B, Portmann B, Belorgey D, Hill M, Chambers S, Teckman J, Alexander GJ, Marciniak SJ, Lomas DA. A novel monoclonal antibody to characterize pathogenic polymers in liver disease associated with alpha1-antitrypsin deficiency. Hepatology 2010; 52:1078-88. [PMID: 20583215 DOI: 10.1002/hep.23760] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Abstract
UNLABELLED Alpha(1)-antitrypsin is the most abundant circulating protease inhibitor. The severe Z deficiency allele (Glu342Lys) causes the protein to undergo a conformational transition and form ordered polymers that are retained within hepatocytes. This causes neonatal hepatitis, cirrhosis, and hepatocellular carcinoma. We have developed a conformation-specific monoclonal antibody (2C1) that recognizes the pathological polymers formed by alpha(1)-antitrypsin. This antibody was used to characterize the Z variant and a novel shutter domain mutant (His334Asp; alpha(1)-antitrypsin King's) identified in a 6-week-old boy who presented with prolonged jaundice. His334Asp alpha(1)-antitrypsin rapidly forms polymers that accumulate within the endoplasmic reticulum and show delayed secretion when compared to the wild-type M alpha(1)-antitrypsin. The 2C1 antibody recognizes polymers formed by Z and His334Asp alpha(1)-antitrypsin despite the mutations directing their effects on different parts of the protein. This antibody also recognized polymers formed by the Siiyama (Ser53Phe) and Brescia (Gly225Arg) mutants, which also mediate their effects on the shutter region of alpha(1)-antitrypsin. CONCLUSION Z and shutter domain mutants of alpha(1)-antitrypsin form polymers with a shared epitope and so are likely to have a similar structure.
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Affiliation(s)
- Elena Miranda
- Department of Medicine, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/Medical Research Council Building, Cambridge, UK.
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22
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Belorgey D, Hägglöf P, Onda M, Lomas DA. pH-dependent stability of neuroserpin is mediated by histidines 119 and 138; implications for the control of beta-sheet A and polymerization. Protein Sci 2010; 19:220-8. [PMID: 19953505 PMCID: PMC2865726 DOI: 10.1002/pro.299] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2009] [Revised: 09/24/2009] [Accepted: 11/16/2009] [Indexed: 11/09/2022]
Abstract
Neuroserpin is a member of the serpin superfamily. Point mutations in the neuroserpin gene underlie the autosomal dominant dementia, familial encephalopathy with neuroserpin inclusion bodies. This is characterized by the retention of ordered polymers of neuroserpin within the endoplasmic reticulum of neurons. pH has been shown to affect the propensity of several serpins to form polymers. In particular, low pH favors the formation of polymers of both alpha(1)-antitrypsin and antithrombin. We report here opposite effects in neuroserpin, with a striking resistance to polymer formation at acidic pH. Mutation of specific histidine residues showed that this effect is not attributable to the shutter domain histidine as would be predicted by analogy with other serpins. Indeed, mutation of the shutter domain His338 decreased neuroserpin stability but had no effect on the pH dependence of polymerization when compared with the wild-type protein. In contrast, mutation of His119 or His138 reduced the polymerization of neuroserpin at both acidic and neutral pH. These residues are at the lower pole of neuroserpin and provide a novel mechanism to control the opening of beta-sheet A and hence polymerization. This mechanism is likely to have evolved to protect neuroserpin from the acidic environment of the secretory granules.
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Affiliation(s)
- Didier Belorgey
- Department of Medicine, University of Cambridge, Cambridge Institute for Medical Research, Cambridge CB2 0XY, United Kingdom.
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23
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Herrera-Mendez CH, Becila S, Coulis G, Sentandreu MA, Aubry L, Ouali A. Purification and partial characterization of antithrombin III from bovine skeletal muscle and possible role of thrombin in postmortem apoptosis development and in efficiency of low voltage electrical stimulation. Food Res Int 2010. [DOI: 10.1016/j.foodres.2009.10.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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24
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Gooptu B, Lomas DA. Conformational pathology of the serpins: themes, variations, and therapeutic strategies. Annu Rev Biochem 2009; 78:147-76. [PMID: 19245336 DOI: 10.1146/annurev.biochem.78.082107.133320] [Citation(s) in RCA: 193] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Point mutations cause members of the serine protease inhibitor (serpin) superfamily to undergo a novel conformational transition, forming ordered polymers. These polymers characterize a group of diseases termed the serpinopathies. The formation of polymers underlies the retention of alpha(1)-antitrypsin within hepatocytes and of neuroserpin within neurons to cause cirrhosis and dementia, respectively. Point mutations of antithrombin, C1 inhibitor, alpha(1)-antichymotrypsin, and heparin cofactor II cause a similar conformational transition, resulting in a plasma deficiency that is associated with thrombosis, angioedema, and emphysema. Polymers of serpins can also form in extracellular tissues where they activate inflammatory cascades. This is best described for the Z variant of alpha(1)-antitrypsin in which the proinflammatory properties of polymers provide an explanation for both progressive emphysema and the selective advantage of this mutant allele. Therapeutic strategies are now being developed to block the aberrant conformational transitions and so treat the serpinopathies.
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Affiliation(s)
- Bibek Gooptu
- School of Crystallography, Birkbeck College, University of London, London, UK.
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25
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Crystal structure of protein Z-dependent inhibitor complex shows how protein Z functions as a cofactor in the membrane inhibition of factor X. Blood 2009; 114:3662-7. [PMID: 19528533 DOI: 10.1182/blood-2009-04-210021] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Protein Z (PZ) binds to PZ-dependent inhibitor (ZPI) and accelerates the inhibition of the coagulation protease, activated factor X (FXa), in the presence of phospholipids and Ca2+. A 2.3A resolution crystal structure of PZ complexed with ZPI shows that ZPI is a typical serine protease inhibitor and that PZ has a serine protease fold with distorted oxyanion hole and S1 pocket. The 2 molecules bind with fully complementary surfaces spanning over 2400A(2) and involving extensive ionic and hydrophobic interactions. ZPI has an unusual shutter region with a negatively charged residue buried within the hydrophobic core of the molecule. This unique Asp(213) is critical in maintaining the balanced metastability required for optimal protease inhibition, especially when PZ is bound, with its replacement with Asn resulting in increased thermal stability, but decreased efficiency of protease inhibition. The structure of ZPI shows negatively and positively charged surfaces on top of the molecule, in keeping with mutagenesis studies in this work indicating exosite interactions with FXa when it docks on top of ZPI. As modeled in this study, the gamma-carboxy-glutamic acid-containing domains of PZ and FXa enable them to bind to the same phospholipid surfaces on platelet and other membranes, with optimal proximity for the inhibition of FXa by the complexed ZPI.
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26
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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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27
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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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28
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Tsutsui Y, Kuri B, Sengupta T, Wintrode PL. The structural basis of serpin polymerization studied by hydrogen/deuterium exchange and mass spectrometry. J Biol Chem 2008; 283:30804-11. [PMID: 18794298 DOI: 10.1074/jbc.m804048200] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The serpinopathies are a group of inherited disorders that share as their molecular basis the misfolding and polymerization of serpins, an important class of protease inhibitors. Depending on the identity of the serpin, conditions arising from polymerization include emphysema, thrombosis, and dementia. The structure of serpin polymers is thus of considerable medical interest. Wild-type alpha(1)-antitrypsin will form polymers upon incubation at moderate temperatures and has been widely used as a model system for studying serpin polymerization. Using hydrogen/deuterium exchange and mass spectrometry, we have obtained molecular level structural information on the alpha(1)-antitrypsin polymer. We found that the flexible reactive center loop becomes strongly protected upon polymerization. We also found significant increases in protection in the center of beta-sheet A and in helix F. These results support a model in which linkage between serpins is achieved through insertion of the reactive center loop of one serpin into beta-sheet A of another. We have also examined the heat-induced conformational changes preceding polymerization. We found that polymerization is preceded by significant destabilization of beta-sheet C. On the basis of our results, we propose a mechanism for polymerization in which beta-strand 1C is displaced from the rest of beta-sheet C through a binary serpin/serpin interaction. Displacement of strand 1C triggers further conformational changes, including the opening of beta-sheet A, and allows for subsequent polymerization.
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Affiliation(s)
- Yuko Tsutsui
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH 44106, USA
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29
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Li SH, Gorlatova NV, Lawrence DA, Schwartz BS. Structural differences between active forms of plasminogen activator inhibitor type 1 revealed by conformationally sensitive ligands. J Biol Chem 2008; 283:18147-57. [PMID: 18436534 DOI: 10.1074/jbc.m709455200] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Plasminogen activator inhibitor type 1 (PAI-1) is a serine protease inhibitor (serpin) in which the reactive center loop (RCL) spontaneously inserts into a central beta-sheet, beta-sheet A, resulting in inactive inhibitor. Available x-ray crystallographic studies of PAI-1 in an active conformation relied on the use of stabilizing mutations. Recently it has become evident that these structural models do not adequately explain the behavior of wild-type PAI-1 (wtPAI-1) in solution. To probe the structure of native wtPAI-1, we used three conformationally sensitive ligands: the physiologic cofactor, vitronectin; a monoclonal antibody, 33B8, that binds preferentially to RCL-inserted forms of PAI-1; and RCL-mimicking peptides that insert into beta-sheet A. From patterns of interaction with wtPAI-1 and the stable mutant, 14-1B, we propose a model of the native conformation of wtPAI-1 in which the bottom of the central sheet is closed, whereas the top of the beta-sheet A is open to allow partial insertion of the RCL. Because the incorporation of RCL-mimicking peptides into wtPAI-1 is accelerated by vitronectin, we further propose that vitronectin alters the conformation of the RCL to allow increased accessibility to beta-sheet A, yielding a structural hypothesis that is contradictory to the current structural model of PAI-1 in solution and its interaction with vitronectin.
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Affiliation(s)
- Shih-Hon Li
- Department of Biochemistry, University of Illinois, Urbana, IL 61801, USA
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30
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Dimers initiate and propagate serine protease inhibitor polymerisation. J Mol Biol 2007; 375:36-42. [PMID: 18005992 DOI: 10.1016/j.jmb.2007.10.055] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2007] [Revised: 10/18/2007] [Accepted: 10/19/2007] [Indexed: 02/06/2023]
Abstract
The serine protease inhibitor (serpin) family can readily form long-chain polymers by a process that underlies a variety of diseases. We show here that monomers of plasma serpins alpha(1)-antitrypsin and antithrombin are stable on incubation with the rate-limiting step in their polymerisation being the formation of the initial dimer. Once formed, the dimers readily interlink to form tetramers and can bind monomers to form trimers and longer oligomers. Cleavage of the only exposed reactive loop, in unit I of the dimers, prevents their interlinkage, but these cleaved dimers can still link to monomers. The rapid binding by the cleaved dimers of a peptide specific to the lower half of beta-sheet A of the molecule indicates the ready opening of this beta-sheet in unit II of the dimers. The failure of the cleaved dimers to bind peptide-complexed monomers, together with the relative inaccessibility of the P14 hinge residue in the oligomers, is evidence that partial insertion of the reactive loop into its own A-sheet is required for polymer formation. We propose that serpin dimers initiate and propagate polymerisation by having one exposed loop with an optimal conformation as a beta-strand donor and a readily opened beta-sheet as an acceptor. The sequential reformation of these activated beta-interfaces as the oligomer extends, molecule by molecule, provides a model for the fibril and amyloid formation of conformational diseases in general as well as for the infectivity of prion encephalopathies.
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31
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Hernández-Espinosa D, Mota R, Miñano A, Ordóñez A, Yélamos J, Vicente V, Corral J. In vivo effects of hyperthermia on the functional and conformational characteristics of antithrombin. J Thromb Haemost 2007; 5:963-70. [PMID: 17472584 DOI: 10.1111/j.1538-7836.2007.02479.x] [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] [Indexed: 11/26/2022]
Abstract
BACKGROUND High temperatures produce in vitro transitions of antithrombin to its inactive latent and polymeric forms. Accordingly, high body temperatures might contribute in vivo to conformational changes in antithrombin associated with increased thrombotic risk. METHODS We assessed the in vivo effects of different hyperthermic stimuli on antithrombin. We studied two mouse models of hyperthermia. (i) Febrile syndrome induced by turpentine. (ii) Heat stroke generated by exposure to 42 degrees C. Body temperatures were measured. Antigen, anti-factor Xa activity and conformational features of plasma antithrombin were studied. Furthermore, structural and ultrastructural features from livers were analyzed. Intracellular retention of serpins (antithrombin and alpha1-antitrypsin) was studied by western-blotting, immunohistochemistry, and immunogold-labeling-electron microscopy. RESULTS Hyperthermic stimuli caused a moderate deficiency of circulating antithrombin and a slight increase in its latent form. Moreover, hyperthermia caused intracellular retention of antithrombin into aggregates within the lumen of the endoplasmic reticulum of hepatocytes. This effect was similar for alpha1-antitrypsin. CONCLUSION Hyperthermia causes minor conformational changes on circulating antithrombin in vivo, although it has severe consequences for intracellular antithrombin and other hepatic serpins, inducing the intracellular retention of the nascent protein. These effects may contribute to the moderate plasma deficiency of antithrombin and the increased thrombotic risk detected in hyperthermic conditions.
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Affiliation(s)
- D Hernández-Espinosa
- Department of Medicine, Centro Regional de Hemodonación, Hospital 'Vigen de la Arrixaca', Univeristy of Murcia, Murcia, Spain
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32
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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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33
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Johnson DJD, Langdown J, Li W, Luis SA, Baglin TP, Huntington JA. Crystal structure of monomeric native antithrombin reveals a novel reactive center loop conformation. J Biol Chem 2006; 281:35478-86. [PMID: 16973611 PMCID: PMC2679979 DOI: 10.1074/jbc.m607204200] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The poor inhibitory activity of circulating antithrombin (AT) is critical to the formation of blood clots at sites of vascular damage. AT becomes an efficient inhibitor of the coagulation proteases only after binding to a specific heparin pentasaccharide, which alters the conformation of the reactive center loop (RCL). The molecular basis of this activation event lies at the heart of the regulation of hemostasis and accounts for the anticoagulant properties of the low molecular weight heparins. Although several structures of AT have been solved, the conformation of the RCL in native AT remains unknown because of the obligate crystal contact between the RCL of native AT and its latent counterpart. Here we report the crystallographic structure of a variant of AT in its monomeric native state. The RCL shifted approximately 20 A, and a salt bridge was observed between the P1 residue (Arg-393) and Glu-237. This contact explains the effect of mutations at the P1 position on the affinity of AT for heparin and also the properties of AT-Truro (E237K). The relevance of the observed conformation was verified through mutagenesis studies and by solving structures of the same variant in different crystal forms. We conclude that the poor inhibitory activity of the circulating form of AT is partially conferred by intramolecular contacts that restrain the RCL, orient the P1 residue away from attacking proteases, and additionally block the exosite utilized in protease recognition.
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Affiliation(s)
| | | | | | | | | | - James A. Huntington
- To whom correspondence should be addressed. Tel.: 44-1223-763230; Fax: 44-1223-336827; E-mail:
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Zhou A, Wei Z, Read RJ, Carrell RW. Structural mechanism for the carriage and release of thyroxine in the blood. Proc Natl Acad Sci U S A 2006; 103:13321-6. [PMID: 16938877 PMCID: PMC1557382 DOI: 10.1073/pnas.0604080103] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The hormones that most directly control tissue activities in health and disease are delivered by two noninhibitory members of the serpin family of protease inhibitors, thyroxine-binding globulin (TBG) and corticosteroid-binding globulin. The structure of TBG bound to tetra-iodo thyroxine, solved here at 2.8 A, shows how the thyroxine is carried in a surface pocket on the molecule. This unexpected binding site is confirmed by mutations associated with a loss of hormone binding in both TBG and also homologously in corticosteroid-binding globulin. TBG strikingly differs from other serpins in having the upper half of its main beta-sheet fully opened, so its reactive center peptide loop can readily move in and out of the sheet to give an equilibrated binding and release of thyroxine. The entry of the loop triggers a conformational change, with a linked contraction of the binding pocket and release of the bound thyroxine. The ready reversibility of this change is due to the unique presence in the reactive loop of TBG of a proline that impedes the full and irreversible entry of the loop that occurs in other serpins. Thus, TBG has adapted the serpin inhibitory mechanism to give a reversible flip-flop transition, from a high-affinity to a low-affinity form. The complexity and ready triggering of this conformational mechanism strongly indicates that TBG has evolved to allow a modulated and targeted delivery of thyroxine to the tissues.
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Affiliation(s)
- Aiwu Zhou
- Departments of Haematology and Medicine, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 2XY, United Kingdom
- *To whom correspondence may be addressed. E-mail:
or
| | - Zhenquan Wei
- Departments of Haematology and Medicine, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 2XY, United Kingdom
| | - Randy J. Read
- Departments of Haematology and Medicine, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 2XY, United Kingdom
| | - Robin W. Carrell
- Departments of Haematology and Medicine, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 2XY, United Kingdom
- *To whom correspondence may be addressed. E-mail:
or
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Hernández-Espinosa D, Miñano A, Martínez C, Pérez-Ceballos E, Heras I, Fuster JL, Vicente V, Corral J. L-asparaginase-induced antithrombin type I deficiency: implications for conformational diseases. THE AMERICAN JOURNAL OF PATHOLOGY 2006; 169:142-53. [PMID: 16816368 PMCID: PMC1698772 DOI: 10.2353/ajpath.2006.051238] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Serpinopathies, a group of diseases caused by mutations that disrupt the structurally sensitive serpins, have no known acquired cause. Interestingly, l-asparaginase treatment of acute lymphoblastic leukemia patients causes severe deficiency in the serpin antithrombin. We studied the consequences of this drug on antithrombin levels, activity, conformation, and immunohistological and ultrastructural features in plasma from acute lymphoblastic leukemia patients, HepG2 cells, and plasma and livers from mice treated with this drug. Additionally, we evaluated intracellular deposition of alpha1-antitrypsin. l-Asparaginase did not affect functional or conformational parameters of mature antithrombin; however, patients and mice displayed severe type I deficiency with no abnormal conformations of circulating antithrombin. Moreover, l-asparaginase impaired secretion of antithrombin by HepG2 cells. These effects were explained by the intracellular retention of antithrombin, forming aggregates within dilated endoplasmic reticulum cisterns. Similar effects were observed for alpha1-antitrypsin in plasma, cells, and livers, and intracellular aggregates of additional proteins were observed in frontal cortex and pancreas. This is the first report of a conformational drug-associated effect on serpins without genetic factors involved. l-Asparaginase treatment induces severe, acquired, and transient type I deficiency of antithrombin (and alpha1-antitrypsin) with intracellular accumulation of the nascent molecule, increasing the risk of thrombosis.
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Hernández-Espinosa D, Ayala I, Castells MT, García-Pérez B, Martín-Castillo A, Miñano A, Arcas I, Vicente V, Corral J. Intracellular retention of hepatic serpins caused by severe hyperlipidemia. Liver Int 2006; 26:708-15. [PMID: 16842328 DOI: 10.1111/j.1478-3231.2006.01274.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
BACKGROUND High levels of circulating lipids contribute to both the development of non-alcoholic liver steatosis (NALS) and peripheral arterial disease, leading to increased thrombotic risk. However, the effects of hyperlipidemia on hepatic proteins have barely been studied. Antithrombin is a hepatic serpin with anticoagulant and anti-inflammatory roles. The conformational flexibility of antithrombin renders it susceptible to both, genetic and posttranslational modifications. Thus, mutations and environmental factors have been shown to alter this molecule. METHODS We used a chick model to assess the effects of hyperlipidemic diets (HD) on this conformationally sensitive molecule. We determined antithrombin activity in plasma and evaluated the histological and immunohistological features of livers from these animals. RESULTS A HD for 6 months led to a significant intrahepatic retention and aggregation of antithrombin, which correlated with hepatic steatosis, as revealed by immunohistological analysis. Accordingly, a decrease in circulating antithrombin activity (48.71 +/- 6.35%) was observed. Other hepatic proteins, including heparin cofactor II, another anticoagulant serpin, also accumulated intracellularly. Atorvastatin and reversion to a normal diet after 3 months partially protected livers from these deleterious effects. CONCLUSIONS Our results support that hyperlipidemia-induced NALS causes a significant intracellular aggregation of hemostatic serpins in liver, which determines a decrease in their circulating levels.
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Sharp LK, Mallya M, Kinghorn KJ, Wang Z, Crowther DC, Huntington JA, Belorgey D, Lomas DA. Sugar and alcohol molecules provide a therapeutic strategy for the serpinopathies that cause dementia and cirrhosis. FEBS J 2006; 273:2540-52. [PMID: 16704419 DOI: 10.1111/j.1742-4658.2006.05262.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Mutations in neuroserpin and alpha1-antitrypsin cause these proteins to form ordered polymers that are retained within the endoplasmic reticulum of neurones and hepatocytes, respectively. The resulting inclusions underlie the dementia familial encephalopathy with neuroserpin inclusion bodies (FENIB) and Z alpha1-antitrypsin-associated cirrhosis. Polymers form by a sequential linkage between the reactive centre loop of one molecule and beta-sheet A of another, and strategies that block polymer formation are likely to be successful in treating the associated disease. We show here that glycerol, the sugar alcohol erythritol, the disaccharide trehalose and its breakdown product glucose reduce the rate of polymerization of wild-type neuroserpin and the Ser49Pro mutant that causes dementia. They also attenuate the polymerization of the Z variant of alpha1-antitrypsin. The effect on polymerization was apparent even when these agents had been removed from the buffer. None of these agents had any detectable effect on the structure or inhibitory activity of neuroserpin or alpha1-antitrypsin. These data demonstrate that sugar and alcohol molecules can reduce the polymerization of serpin mutants that cause disease, possibly by binding to and stabilizing beta-sheet A.
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38
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Wang H, Pap S, Wiman B. Structures of importance for the stability of antiplasmin as studied by site-directed mutagenesis. Thromb Res 2006; 117:315-22. [PMID: 16378834 DOI: 10.1016/j.thromres.2005.02.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2004] [Revised: 02/25/2005] [Accepted: 02/25/2005] [Indexed: 11/28/2022]
Abstract
Human antiplasmin, a fast-acting inhibitor of plasmin in plasma, belongs to the serpin super-family of proteins. Like other members of this family, antiplasmin has a scissile peptide bond exposed within a reactive centre loop, typically present at the surface of the molecule. Antiplasmin is stable at neutral pH, but at acidic pH or at elevated temperatures it rapidly becomes inactivated. Data regarding "native" antiplasmin have demonstrated that both polymerization processes and formation of latent molecules are important in this respect. In this work we used site-directed mutagenesis to produce 11 single-site mutants (mainly within Abeta-sheet, Bbeta-sheet and reactive centre loop), which were expressed in Drosophila S2 cells, purified and characterized. Five of the 11 mutants were found to have a deviating stability at decreased pH. Glu346Thr was the only mutant with a lesser stability as compared to wt-antiplasmin, but the other 4 were more stable. The most stable mutant, His341Thr, was 7-fold more stable at pH 4.9 as compared to wt-antiplasmin. The wt-antiplasmin had a much more pronounced tendency to polymerize at decreased pH, as compared to "native" antiplasmin. However, many of the mutants clearly rather formed latent molecules, as judged both from PAGE-analysis at non-denaturing condition and reactivation experiments.
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Affiliation(s)
- Haiyao Wang
- Department of Clinical Chemistry and Blood Coagulation, Karolinska University Hospital, Karolinska Institute, SE-171 76 Stockholm, Sweden
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39
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Di Giusto DA, Sutherland APR, Jankova L, Harrop SJ, Curmi PMG, King GC. Plasminogen activator inhibitor-2 is highly tolerant to P8 residue substitution--implications for serpin mechanistic model and prediction of nsSNP activities. J Mol Biol 2005; 353:1069-80. [PMID: 16214170 DOI: 10.1016/j.jmb.2005.09.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2005] [Revised: 09/02/2005] [Accepted: 09/06/2005] [Indexed: 11/18/2022]
Abstract
The serine protease inhibitor (serpin) superfamily is involved in a wide range of cellular processes including fibrinolysis, angiogenesis, apoptosis, inflammation, metastasis and viral pathogenesis. Here, we investigate the unique mousetrap inhibition mechanism of serpins through saturation mutagenesis of the P8 residue for a typical family member, plasminogen activator inhibitor-2 (PAI-2). A number of studies have proposed an important role for the P8 residue in the efficient insertion and stabilisation of the cleaved reactive centre loop (RCL), which is a key event in the serpin inhibitory mechanism. The importance of this residue for inhibition of the PAI-2 protease target urinary plasminogen activator (urokinase, uPA) is confirmed, although a high degree of tolerance to P8 substitution is observed. Out of 19 possible PAI-2 P8 mutants, 16 display inhibitory activities within an order of magnitude of the wild-type P8 Thr species. Crystal structures of complexes between PAI-2 and RCL-mimicking peptides with P8 Met or Asp mutations are determined, and structural comparison with the wild-type complex substantiates the ability of the S8 pocket to accommodate disparate side-chains. These data indicate that the identity of the P8 residue is not a determinant of efficient RCL insertion, and provide further evidence for functional plasticity of key residues within enzyme structures. Poor correlation of observed PAI-2 P8 mutant activities with a range of physicochemical, evolutionary and thermodynamic predictive indices highlights the practical limitations of existing approaches to predicting the molecular phenotype of protein variants.
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Affiliation(s)
- Daniel A Di Giusto
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
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40
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Abstract
Serpins are the largest family of protease inhibitors and are fundamental for the control of proteolysis in multicellular eukaryotes. Most eukaryote serpins inhibit serine or cysteine proteases, however, noninhibitory members have been identified that perform diverse functions in processes such as hormone delivery and tumour metastasis. More recently inhibitory serpins have been identified in prokaryotes and unicellular eukaryotes, nevertheless, the precise molecular targets of these molecules remains to be identified. The serpin mechanism of protease inhibition is unusual and involves a major conformational rearrangement of the molecule concomitant with a distortion of the target protease. As a result of this requirement, serpins are susceptible to mutations that result in polymerization and conformational diseases such as the human serpinopathies. This review reports on recent major discoveries in the serpin field, based upon presentations made at the 4th International Symposium on Serpin Structure, Function and Biology (Cairns, Australia).
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Affiliation(s)
- James C Whisstock
- The Department of Biochemistry and Molecular Biology, Monash University Clayton Campus, Melbourne, Victoria, Australia.
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41
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Benarafa C, Remold-O'Donnell E. The ovalbumin serpins revisited: perspective from the chicken genome of clade B serpin evolution in vertebrates. Proc Natl Acad Sci U S A 2005; 102:11367-72. [PMID: 16055559 PMCID: PMC1183561 DOI: 10.1073/pnas.0502934102] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Serpin superfamily proteins, most of which are serine protease inhibitors, share an unusual mechanism rooted in their conserved metastable tertiary structure. Although serpins have been identified in isolated members of archea, bacteria, and plants, a remarkable expansion is found in vertebrates. The chicken protein ovalbumin, a storage protein from egg white, lacking protease inhibitory activity, is an historical member of the superfamily and the founding member of the subgroup known as ov-serpins (ovalbumin-related serpins) or clade B serpins. In the human, ov-serpins include 13 proteins involved in the regulation of inflammation, apoptosis, angiogenesis, and embryogenesis. Here, a detailed analysis of the chicken (Gallus gallus) genome identified 10 clade B serpin genes that map to a single approximately 150-kb locus and contain the signature protein sequence of serpins and the gene structure of ov-serpins, with either seven or eight exons. Orthologues of PAI-2 (SERPINB2), MNEI (SERPINB1), PI-6 (SERPINB6), and maspin (SERPINB5) are highly conserved. Comparison with human ov-serpins identified avian-specific and mammal-specific genes. Importantly, a unique model of mammalian ov-serpin evolution is revealed from the comparative analysis of the chicken and human loci. The presence of a subset of ov-serpin genes in zebrafish (Danio rerio) gives insight into the ancestral locus. This comparative genomic study provides a valuable perspective on the evolutionary pathway for the clade B serpins, allowing the identification of genes with functions that may have been conserved since the origin of vertebrates. In addition, it suggests that "newer" serpins, such as ovalbumin, have contributed to vertebrate adaptation.
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Affiliation(s)
- Charaf Benarafa
- CBR Institute for Biomedical Research and Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.
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42
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Wang H, Pap S, Wiman B. Inactivation of antiplasmin at low pH: evidence for the formation of latent molecules. Thromb Res 2005; 114:301-6. [PMID: 15381394 DOI: 10.1016/j.thromres.2004.06.014] [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: 04/08/2004] [Revised: 06/11/2004] [Accepted: 06/15/2004] [Indexed: 10/26/2022]
Abstract
Several serine proteinase inhibitors (serpins) are metastable proteins which under certain conditions may undergo conformational changes resulting in the insertion of the reactive centre loop into the so-called Abeta-sheet and hence forming latent molecules. Here we have studied the inactivation of antiplasmin as a function of pH and temperature with time. At decreased pH (4.9-5.8) and at room temperature, antiplasmin activity decreased following first-order kinetics. Analysis by polyacrylamide gel electrophoresis under non-denaturing conditions demonstrated that only minor amounts of polymerized material formed after extensive incubation (4 days) at room temperature. However, on incubation at elevated temperatures (45 or 55 degrees C), a rapid formation of polymerized material was observed. We also demonstrated that antiplasmin inactivated by treatment at pH approximately 5 at room temperature spontaneously slowly regained some activity if incubated in a buffer of neutral pH. Furthermore, by treatment with 4 M guanidinium chloride for about 30 min, followed by dialysis against a neutral phosphate buffer, considerable activity (almost 40%) was regained. Thus, we conclude that antiplasmin, at least partially, at lower temperatures is transformed into a latent form, which could be reactivated, in a similar manner as PAI-1. At increased temperature, however, polymerization seems to be the predominant reason for inactivation.
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Affiliation(s)
- Haiyao Wang
- Department of Clinical Chemistry and Blood Coagulation, Karolinska hospital, Karolinska Institute, Stockholm SE-17176, Sweden
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43
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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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44
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Takahashi N, Terakado K, Nakamura G, Soekmadji C, Masuoka T, Yamasaki M, Hirose M. Dynamic Mechanism for the Serpin Loop Insertion as Revealed by Quantitative Kinetics. J Mol Biol 2005; 348:409-18. [PMID: 15811377 DOI: 10.1016/j.jmb.2005.02.054] [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: 11/25/2004] [Revised: 02/09/2005] [Accepted: 02/25/2005] [Indexed: 11/28/2022]
Abstract
The serpin conformational change by insertion of the reactive center loop into beta-sheet A plays a central role in multiple physiological consequences such as serine proteinase inhibition, latency and serpinopathic polymerization. To study the dynamic mechanism for the loop insertion, a novel kinetic method was established utilizing the ovalbumin mutant R339T/A352R; the loop insertion progressed after the cleavage of P1-P1' (Arg352-Ser353) by trypsin was quenched at pH 8 and 0.5 degrees C, and different conformers were quantified by separation using ion-exchange HPLC. The apparent first-order rate constant k(app) determined for various R339T/A352R derivatives differing in conformational stability was greatly increased by lowering the pH. The pH-dependence of k(app) indicated that the protonation of side-chain(s) with a pK(a) value of around 4.6 is a pre-requisite for the loop insertion. The theoretical rate constant k for the protonated form calculated from k(app) was highly variable, depending on the ovalbumin derivative; structural modifications that give increased mobility to helix F and the sheet-A half (s3A/s2A/s1A) resulted in a striking increase in the loop insertion rate constant k. The k values were determined at different temperatures for all the ovalbumin derivatives, and DeltaH(double dagger) and DeltaS(double dagger) values for the loop insertion reaction were determined according to the transition theory. The formation of the transition state was highly endothermic with minor entropy gain, requiring a DeltaG(double dagger) larger than 18 kcal/mol, which can offset the hydrogen-bond cleavages between s3A and s5A. These results are consistent with the transition state with an opened sheet A and altered orientation of helix F.
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Affiliation(s)
- Nobuyuki Takahashi
- Division of Applied Life Sciences, The Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
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45
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Mushunje A, Evans G, Brennan SO, Carrell RW, Zhou A. Latent antithrombin and its detection, formation and turnover in the circulation. J Thromb Haemost 2004; 2:2170-7. [PMID: 15613023 DOI: 10.1111/j.1538-7836.2004.01047.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
It is now apparent that the inactivated latent and cleaved conformers of antithrombin (AT) are of pathological significance. Using a single-run electrophoretic technique that allows the quantitative assessment of these conformers in 2 microL plasma, we show that near 3% of the total AT in the circulations of normal individuals is in latent conformation. Only trace amounts of cleaved AT were observed. The slow decline in AT activity on incubation of plasma at 37 degrees C was shown to be almost wholly due to a transition of native AT to its inactive latent form. Also initial studies in the rabbit indicate that the latent form, like the cleaved, has an identical circulatory half-life to that of native AT. We deduce that the steady concentration of latent AT in the circulation is due to the transition of some 10(12) molecules of AT per second balanced by an equivalent clearance of the latent form. Examples of clinical applications of the new technique include its use as a comprehensive single-step screen for genetic variants associated with AT deficiency, and notably the potential it provides to monitor the changes responsible for the loss of AT in the shock syndromes.
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Affiliation(s)
- A Mushunje
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Cambridge, UK
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46
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Van de Water N, Tan T, Ashton F, O'Grady A, Day T, Browett P, Ockelford P, Harper P. Mutations within the protein Z-dependent protease inhibitor gene are associated with venous thromboembolic disease: a new form of thrombophilia. Br J Haematol 2004; 127:190-4. [PMID: 15461625 DOI: 10.1111/j.1365-2141.2004.05189.x] [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
Protein Z-dependent protease inhibitor (ZPI) is a serpin that inhibits the activated coagulation factors X and XI. The precise physiological significance of ZPI in the control of haemostasis is unknown although a deficiency of ZPI may be predicted to alter this balance. The coding region of the ZPI gene was screened for mutations using denaturing high-performance liquid chromatography. 16 mutations/polymorphisms within the coding region of ZPI were identified including two mutations, which generated stop codons at residues R67 and W303. We observed nonsense mutations within the ZPI gene in 4.4% of thrombosis patients (n = 250) compared with 0.8% of controls (n = 250). The difference in distribution of stop codon mutations between thrombosis patients and controls was significant (P = 0.02) with an odds ratio of 5.7 (95% confidence interval, 1.25-26.0). Our results suggest an association between ZPI deficiency and venous thrombosis and we propose that ZPI deficiency is potentially a new form of thrombophilia.
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47
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Differential detection of PAS-positive inclusions formed by the Z, Siiyama, and Mmalton variants of alpha1-antitrypsin. Hepatology 2004; 40:1203-10. [PMID: 15486938 DOI: 10.1002/hep.20451] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Several point mutations of alpha(1)-antitrypsin cause a perturbation in protein structure with consequent polymerization and intracellular accumulation. The retention of polymers of alpha(1)-antitrypsin within hepatocytes results in protein overload that in turn is associated with juvenile hepatitis, cirrhosis, and hepatocellular carcinoma. The detection of alpha(1)-antitrypsin polymers and understanding the molecular basis of polymer formation is of considerable clinical importance. We have used a monoclonal antibody (ATZ11) that specifically recognizes a conformation-dependent neoepitope on polymerized alpha(1)-antitrypsin to detect polymers within hepatocytes of individuals with alpha(1)-antitrypsin deficiency. Paraffin-embedded liver tissue specimens were obtained from individuals who were homozygous for the Z (Glu342Lys), Mmalton (52Phe del), and Siiyama (Ser53Phe) alleles of alpha(1)-antitrypsin that result in hepatic inclusions and profound plasma deficiency. Immunohistological staining with a polyclonal anti-human alpha(1)-antitrypsin antibody showed hepatic inclusions in all 3 cases, while ATZ11 reacted with hepatic inclusions formed by only Z alpha(1)-antitrypsin. Polymers of plasma M and Z alpha(1)-antitrypsin prepared under different conditions in vitro and polymers of recombinant mutants of alpha(1)-antitrypsin demonstrated that the monoclonal antibody detected a neoepitope on the polymerized protein. It did not detect polymers formed by a recombinant shutter domain mutant (that mirrors the effects of the Siiyama and Mmalton variants), polymers formed by cleaving alpha(1)-antitrypsin at the reactive loop, or C-sheet polymers formed by heating alpha(1)-antitrypsin in citrate. In conclusion, the ATZ11 monoclonal antibody detects Z alpha(1)-antitrypsin in hepatic inclusions by detecting a neoepitope that is specific to the polymeric conformer and that is localized close to residue 342.
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48
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Zhou A, Stein PE, Huntington JA, Sivasothy P, Lomas DA, Carrell RW. How Small Peptides Block and Reverse Serpin Polymerisation. J Mol Biol 2004; 342:931-41. [PMID: 15342247 DOI: 10.1016/j.jmb.2004.07.078] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2004] [Revised: 07/20/2004] [Accepted: 07/22/2004] [Indexed: 11/25/2022]
Abstract
Many of the late-onset dementias, including Alzheimer's disease and the prion encephalopathies, arise from the aberrant aggregation of individual proteins. The serpin family of serine protease inhibitors provides a well-defined structural example of such pathological aggregation, as its mutant variants readily form long-chain polymers, resulting in diseases ranging from thrombosis to dementia. The intermolecular linkages result from the insertion of the reactive site loop of one serpin molecule into the middle strand (s4A) position of the A beta-sheet of another molecule. We define here the structural requirements for small peptides to competitively bind to and block the s4A position to prevent this intermolecular linkage and polymerisation. The entry and anchoring of blocking-peptides is facilitated by the presence of a threonine which inserts into the site equivalent to P8 of s4A. But the critical requirement for small blocking-peptides is demonstrated in crystallographic structures of the complexes formed with selected tri- and tetrapeptides. These structures indicate that the binding is primarily due to the insertion of peptide hydrophobic side-chains into the P4 and P6 sites of s4A. The findings allow the rational design of synthetic blocking-peptides small enough to be suitable for mimetic design. This is demonstrated here with a tetrapeptide that preferentially blocks the polymerisation of a pathologically unstable serpin commonly present in people of European descent.
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Affiliation(s)
- Aiwu Zhou
- Departments of Haematology and Medicine, University of Cambridge, Cambridge Institute for Medical Research, Hills Road, Cambridge CB2 2XY, UK
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Miranda E, Römisch K, Lomas DA. Mutants of neuroserpin that cause dementia accumulate as polymers within the endoplasmic reticulum. J Biol Chem 2004; 279:28283-91. [PMID: 15090543 DOI: 10.1074/jbc.m313166200] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The dementia familial encephalopathy with neuroserpin inclusion bodies (FENIB) is caused by the accumulation of mutant neuroserpin within neurons (Davis, R. L., Shrimpton, A. E., Holohan, P. D., Bradshaw, C., Feiglin, D., Sonderegger, P., Kinter, J., Becker, L. M., Lacbawan, F., Krasnewich, D., Muenke, M., Lawrence, D. A., Yerby, M. S., Shaw, C.-M., Gooptu, B., Elliott, P. R., Finch, J. T., Carrell, R. W., and Lomas, D. A. (1999) Nature 401, 376-379), but little is known about the trafficking of wild type and mutant neuroserpins. We have established a cell model to study the processing of wild type neuroserpin and the Syracuse (S49P) and Portland (S52R) mutants that cause FENIB. Here we show that Syracuse and Portland neuroserpin are retained soon after their synthesis in the endoplasmic reticulum and that the limiting step in their processing is the transport to the Golgi complex. This is in contrast to the wild type protein, which is secreted into the culture medium. Mutant neuroserpin is retained within the endoplasmic reticulum as polymers, similar to those isolated from the intraneuronal inclusions in the brains of individuals with FENIB. Remarkably, the Portland mutant showed faster accumulation and slower secretion compared with the Syracuse mutant, in keeping with the more severe clinical phenotype found in patients with the Portland variant of neuroserpin. Both mutant and wild type neuroserpin were partially degraded by proteasomes. Taken together, our results provide further understanding of how cells handle defective but ordered mutant proteins and provide strong support for a common mechanism of disease caused by mutants of the serine protease inhibitor superfamily.
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Affiliation(s)
- Elena Miranda
- Departments of Medicine and Clinical Biochemistry, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/Medical Research Council Building, Hills Road, Cambridge CB2 2XY, United Kingdom.
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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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