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Maslakova AA, Golyshev SA, Potashnikova DM, Moisenovich AM, Orlovsky IV, Smirnova OV, Rubtsov MA. SERPINA1 long transcripts produce non-secretory alpha1-antitrypsin isoform: In vitro translation in living cells. Int J Biol Macromol 2023; 241:124433. [PMID: 37086761 DOI: 10.1016/j.ijbiomac.2023.124433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 03/24/2023] [Accepted: 03/27/2023] [Indexed: 04/24/2023]
Abstract
SERPINA1 is a well-studied serpin gene due to its dramatic impact on human health. Translation initiation at the main SERPINA1 start codon produces the only known alpha1-antitrypsin (AAT) isoform intended for secretion. AAT performs essential functions by inhibiting proteases and modulating immunity. However, SERPINA1 expression at the level of translation is not sufficiently studied. Here we hypothesize that the main SERPINA1 ORF can be alternatively translated, producing a non-secretory AAT isoform by either masking or excluding a signal peptide. We defined SERPINA1 long mRNA isoforms specific for prostate (DU145) and liver (HepG2) cell lines and studied their individual expression by in vitro assay. We found that all long transcripts produce both glycosylated secretory AAT-eGFP fusion protein and non-glycosylated intracellular AAT-eGFP (initiated from an alternative AUG-2 start codon), with the proportion regulated by the SERPINA1 5'-UTR. Both fusion proteins localize to distinct cellular compartments: in contrast to a fusion with the secretory AAT accumulating in the ER, the intracellular one exhibits nuclear-cytoplasmic shuttling. We detected putative endogenous AAT isoform enriching the nuclear speckles. CONCLUSION: Alternative translation initiation might be a mechanism through which SERPINA1 expands the biological diversity of its protein products. Our findings open up new prospects for the study of SERPINA1 gene expression.
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Affiliation(s)
- A A Maslakova
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia.
| | - S A Golyshev
- A.N. Belozersky Institute of Physical and Chemical Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, Moscow 119992, Russia
| | - D M Potashnikova
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia
| | - A M Moisenovich
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia
| | - I V Orlovsky
- Research Institute of Molecular and Cellular Medicine, Рeoples' Friendship University of Russia (RUDN University), Miklukho-Maklaya, Moscow 117198, Russia
| | - O V Smirnova
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia
| | - M A Rubtsov
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia; Center for Industrial Technologies and Entrepreneurship, I.M. Sechenov First Moscow State Medical University (Sechenov University), Trubetskaya, Moscow 119991, Russia
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2
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Xu J, Ye W, Yang TT, Yan T, Cai H, Zhou A, Yang Y. DNA accelerates the protease inhibition of a bacterial serpin chloropin. Front Mol Biosci 2023; 10:1157186. [PMID: 37065444 PMCID: PMC10090351 DOI: 10.3389/fmolb.2023.1157186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 03/20/2023] [Indexed: 03/31/2023] Open
Abstract
Serine protease inhibitors (Serpins) are the most widely distributed protease inhibitors in nature and have been identified from all kingdoms of life. Eukaryotic serpins are most abundant with their activities often subject to modulation by cofactors; however, little is known about the regulation of prokaryotic serpins. To address this, here we prepared a recombinant bacteria serpin, termed chloropin, derived from green sulfur bacteria Chlorobium limicola and solved its crystal structure at 2.2 Å resolution. This showed a canonical inhibitory serpin conformation of native chloropin with a surface-exposed reactive loop and a large central beta-sheet. Enzyme activity analysis showed that chloropin could inhibit multiple proteases, such as thrombin and KLK7 with second order inhibition rate constants at 2.5×104 M−1s−1 and 4.5×104 M−1s−1 respectively, consistent with its P1 arginine residue. Heparin could accelerate the thrombin inhibition by ∼17-fold with a bell-shaped dose-dependent curve as seen with heparin-mediated thrombin inhibition by antithrombin. Interestingly, supercoiled DNA could accelerate the inhibition of thrombin by chloropin by 74-fold, while linear DNA accelerated the reaction by 142-fold through a heparin-like template mechanism. In contrast, DNA did not affect the inhibition of thrombin by antithrombin. These results indicate that DNA is likely a natural modulator of chloropin protecting the cell from endogenous or exogenous environmental proteases, and prokaryotic serpins have diverged during evolution to use different surface subsites for activity modulation.
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Affiliation(s)
- Jiawei Xu
- Department of Bioengineering, Zunyi Medical University Zhuhai Campus, Zhuhai, Guangdong, China
| | - Wei Ye
- Department of Preventive Dentistry, The Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ting Ting Yang
- Department of Preventive Dentistry, The Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Teng Yan
- Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Haiyan Cai
- Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Haiyan Cai, ; Aiwu Zhou, ; Yufeng Yang,
| | - Aiwu Zhou
- Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Haiyan Cai, ; Aiwu Zhou, ; Yufeng Yang,
| | - Yufeng Yang
- Department of Bioengineering, Zunyi Medical University Zhuhai Campus, Zhuhai, Guangdong, China
- *Correspondence: Haiyan Cai, ; Aiwu Zhou, ; Yufeng Yang,
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3
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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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D'Acunto E, Fra A, Visentin C, Manno M, Ricagno S, Galliciotti G, Miranda E. Neuroserpin: structure, function, physiology and pathology. Cell Mol Life Sci 2021; 78:6409-6430. [PMID: 34405255 PMCID: PMC8558161 DOI: 10.1007/s00018-021-03907-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 07/23/2021] [Accepted: 07/27/2021] [Indexed: 12/24/2022]
Abstract
Neuroserpin is a serine protease inhibitor identified in a search for proteins implicated in neuronal axon growth and synapse formation. Since its discovery over 30 years ago, it has been the focus of active research. Many efforts have concentrated in elucidating its neuroprotective role in brain ischemic lesions, the structural bases of neuroserpin conformational change and the effects of neuroserpin polymers that underlie the neurodegenerative disease FENIB (familial encephalopathy with neuroserpin inclusion bodies), but the investigation of the physiological roles of neuroserpin has increased over the last years. In this review, we present an updated and critical revision of the current literature dealing with neuroserpin, covering all aspects of research including the expression and physiological roles of neuroserpin, both inside and outside the nervous system; its inhibitory and non-inhibitory mechanisms of action; the molecular structure of the monomeric and polymeric conformations of neuroserpin, including a detailed description of the polymerisation mechanism; and the involvement of neuroserpin in human disease, with particular emphasis on FENIB. Finally, we briefly discuss the identification by genome-wide screening of novel neuroserpin variants and their possible pathogenicity.
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Affiliation(s)
- Emanuela D'Acunto
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, Rome, Italy
| | - Annamaria Fra
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Cristina Visentin
- Department of Biosciences, University of Milan, Milan, Italy
- Institute of Molecular and Translational Cardiology, I.R.C.C.S. Policlinico San Donato, Milan, Italy
| | - Mauro Manno
- Institute of Biophysics, National Research Council of Italy, Palermo, Italy
| | - Stefano Ricagno
- Department of Biosciences, University of Milan, Milan, Italy
| | - Giovanna Galliciotti
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Elena Miranda
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, Rome, Italy.
- Pasteur Institute-Cenci Bolognetti Foundation, Sapienza University of Rome, Rome, Italy.
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5
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Mkaouar H, Mariaule V, Rhimi S, Hernandez J, Kriaa A, Jablaoui A, Akermi N, Maguin E, Lesner A, Korkmaz B, Rhimi M. Gut Serpinome: Emerging Evidence in IBD. Int J Mol Sci 2021; 22:ijms22116088. [PMID: 34200095 PMCID: PMC8201313 DOI: 10.3390/ijms22116088] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/01/2021] [Accepted: 06/03/2021] [Indexed: 12/11/2022] Open
Abstract
Inflammatory bowel diseases (IBD) are incurable disorders whose prevalence and global socioeconomic impact are increasing. While the role of host genetics and immunity is well documented, that of gut microbiota dysbiosis is increasingly being studied. However, the molecular basis of the dialogue between the gut microbiota and the host remains poorly understood. Increased activity of serine proteases is demonstrated in IBD patients and may contribute to the onset and the maintenance of the disease. The intestinal proteolytic balance is the result of an equilibrium between the proteases and their corresponding inhibitors. Interestingly, the serine protease inhibitors (serpins) encoded by the host are well reported; in contrast, those from the gut microbiota remain poorly studied. In this review, we provide a concise analysis of the roles of serine protease in IBD physiopathology and we focus on the serpins from the gut microbiota (gut serpinome) and their relevance as a promising therapeutic approach.
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Affiliation(s)
- Héla Mkaouar
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute, AgroParisTech, Université Paris-Saclay, INRAE, 78350 Jouy-en-Josas, France; (H.M.); (V.M.); (S.R.); (A.K.); (A.J.); (N.A.); (E.M.)
| | - Vincent Mariaule
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute, AgroParisTech, Université Paris-Saclay, INRAE, 78350 Jouy-en-Josas, France; (H.M.); (V.M.); (S.R.); (A.K.); (A.J.); (N.A.); (E.M.)
| | - Soufien Rhimi
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute, AgroParisTech, Université Paris-Saclay, INRAE, 78350 Jouy-en-Josas, France; (H.M.); (V.M.); (S.R.); (A.K.); (A.J.); (N.A.); (E.M.)
| | - Juan Hernandez
- Department of Clinical Sciences, Nantes-Atlantic College of Veterinary Medicine and Food Sciences (Oniris), University of Nantes, 101 Route de Gachet, 44300 Nantes, France;
| | - Aicha Kriaa
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute, AgroParisTech, Université Paris-Saclay, INRAE, 78350 Jouy-en-Josas, France; (H.M.); (V.M.); (S.R.); (A.K.); (A.J.); (N.A.); (E.M.)
| | - Amin Jablaoui
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute, AgroParisTech, Université Paris-Saclay, INRAE, 78350 Jouy-en-Josas, France; (H.M.); (V.M.); (S.R.); (A.K.); (A.J.); (N.A.); (E.M.)
| | - Nizar Akermi
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute, AgroParisTech, Université Paris-Saclay, INRAE, 78350 Jouy-en-Josas, France; (H.M.); (V.M.); (S.R.); (A.K.); (A.J.); (N.A.); (E.M.)
| | - Emmanuelle Maguin
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute, AgroParisTech, Université Paris-Saclay, INRAE, 78350 Jouy-en-Josas, France; (H.M.); (V.M.); (S.R.); (A.K.); (A.J.); (N.A.); (E.M.)
| | - Adam Lesner
- Faculty of Chemistry, University of Gdansk, Uniwersytet Gdanski, Chemistry, Wita Stwosza 63, PL80-308 Gdansk, Poland;
| | - Brice Korkmaz
- INSERM UMR-1100, “Research Center for Respiratory Diseases” and University of Tours, 37032 Tours, France;
| | - Moez Rhimi
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute, AgroParisTech, Université Paris-Saclay, INRAE, 78350 Jouy-en-Josas, France; (H.M.); (V.M.); (S.R.); (A.K.); (A.J.); (N.A.); (E.M.)
- Correspondence:
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6
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Spence MA, Mortimer MD, Buckle AM, Minh BQ, Jackson CJ. A Comprehensive Phylogenetic Analysis of the Serpin Superfamily. Mol Biol Evol 2021; 38:2915-2929. [PMID: 33744972 PMCID: PMC8233489 DOI: 10.1093/molbev/msab081] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Serine protease inhibitors (serpins) are found in all kingdoms of life and play essential roles in multiple physiological processes. Owing to the diversity of the superfamily, phylogenetic analysis is challenging and prokaryotic serpins have been speculated to have been acquired from Metazoa through horizontal gene transfer due to their unexpectedly high homology. Here, we have leveraged a structural alignment of diverse serpins to generate a comprehensive 6,000-sequence phylogeny that encompasses serpins from all kingdoms of life. We show that in addition to a central “hub” of highly conserved serpins, there has been extensive diversification of the superfamily into many novel functional clades. Our analysis indicates that the hub proteins are ancient and are similar because of convergent evolution, rather than the alternative hypothesis of horizontal gene transfer. This work clarifies longstanding questions in the evolution of serpins and provides new directions for research in the field of serpin biology.
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Affiliation(s)
- Matthew A Spence
- Research School of Chemistry, Australian National University, Canberra, ACT, Australia
| | - Matthew D Mortimer
- Research School of Chemistry, Australian National University, Canberra, ACT, Australia
| | - Ashley M Buckle
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Melbourne, VIC, Australia
| | - Bui Quang Minh
- Research School of Computing and Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Colin J Jackson
- Research School of Chemistry, Australian National University, Canberra, ACT, Australia.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT, Australia.,Australian Research Council Centre of Excellence in Synthetic Biology, Research School of Chemistry, Australian National University, Canberra, ACT, Australia
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7
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Mariaule V, Kriaa A, Soussou S, Rhimi S, Boudaya H, Hernandez J, Maguin E, Lesner A, Rhimi M. Digestive Inflammation: Role of Proteolytic Dysregulation. Int J Mol Sci 2021; 22:ijms22062817. [PMID: 33802197 PMCID: PMC7999743 DOI: 10.3390/ijms22062817] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/04/2021] [Accepted: 03/05/2021] [Indexed: 12/11/2022] Open
Abstract
Dysregulation of the proteolytic balance is often associated with diseases. Serine proteases and matrix metalloproteases are involved in a multitude of biological processes and notably in the inflammatory response. Within the framework of digestive inflammation, several studies have stressed the role of serine proteases and matrix metalloproteases (MMPs) as key actors in its pathogenesis and pointed to the unbalance between these proteases and their respective inhibitors. Substantial efforts have been made in developing new inhibitors, some of which have reached clinical trial phases, notwithstanding that unwanted side effects remain a major issue. However, studies on the proteolytic imbalance and inhibitors conception are directed toward host serine/MMPs proteases revealing a hitherto overlooked factor, the potential contribution of their bacterial counterpart. In this review, we highlight the role of proteolytic imbalance in human digestive inflammation focusing on serine proteases and MMPs and their respective inhibitors considering both host and bacterial origin.
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Affiliation(s)
- Vincent Mariaule
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute, AgroParisTech, Université Paris-Saclay, INRAE, F-78350 Jouy-en-Josas, France; (V.M.); (A.K.); (S.S.); (S.R.); (H.B.); (E.M.)
| | - Aicha Kriaa
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute, AgroParisTech, Université Paris-Saclay, INRAE, F-78350 Jouy-en-Josas, France; (V.M.); (A.K.); (S.S.); (S.R.); (H.B.); (E.M.)
| | - Souha Soussou
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute, AgroParisTech, Université Paris-Saclay, INRAE, F-78350 Jouy-en-Josas, France; (V.M.); (A.K.); (S.S.); (S.R.); (H.B.); (E.M.)
| | - Soufien Rhimi
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute, AgroParisTech, Université Paris-Saclay, INRAE, F-78350 Jouy-en-Josas, France; (V.M.); (A.K.); (S.S.); (S.R.); (H.B.); (E.M.)
| | - Houda Boudaya
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute, AgroParisTech, Université Paris-Saclay, INRAE, F-78350 Jouy-en-Josas, France; (V.M.); (A.K.); (S.S.); (S.R.); (H.B.); (E.M.)
| | - Juan Hernandez
- Department of Clinical Sciences, Nantes-Atlantic College of Veterinary Medicine and Food Sciences (Oniris), University of Nantes, 101 Route de Gachet, 44300 Nantes, France;
| | - Emmanuelle Maguin
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute, AgroParisTech, Université Paris-Saclay, INRAE, F-78350 Jouy-en-Josas, France; (V.M.); (A.K.); (S.S.); (S.R.); (H.B.); (E.M.)
| | - Adam Lesner
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, PL80-308 Gdansk, Poland;
| | - Moez Rhimi
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute, AgroParisTech, Université Paris-Saclay, INRAE, F-78350 Jouy-en-Josas, France; (V.M.); (A.K.); (S.S.); (S.R.); (H.B.); (E.M.)
- Correspondence:
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8
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Ghosh DK, Ranjan A. The metastable states of proteins. Protein Sci 2020; 29:1559-1568. [PMID: 32223005 PMCID: PMC7314396 DOI: 10.1002/pro.3859] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/23/2020] [Accepted: 03/24/2020] [Indexed: 12/26/2022]
Abstract
The intriguing process of protein folding comprises discrete steps that stabilize the protein molecules in different conformations. The metastable state of protein is represented by specific conformational characteristics, which place the protein in a local free energy minimum state of the energy landscape. The native-to-metastable structural transitions are governed by transient or long-lived thermodynamic and kinetic fluctuations of the intrinsic interactions of the protein molecules. Depiction of the structural and functional properties of metastable proteins is not only required to understand the complexity of folding patterns but also to comprehend the mechanisms of anomalous aggregation of different proteins. In this article, we review the properties of metastable proteins in context of their stability and capability of undergoing atypical aggregation in physiological conditions.
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Affiliation(s)
- Debasish Kumar Ghosh
- Computational and Functional Genomics Group, Centre for DNA Fingerprinting and DiagnosticsUppal, HyderabadTelanganaIndia
| | - Akash Ranjan
- Computational and Functional Genomics Group, Centre for DNA Fingerprinting and DiagnosticsUppal, HyderabadTelanganaIndia
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9
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Gershenson A, Gosavi S, Faccioli P, Wintrode PL. Successes and challenges in simulating the folding of large proteins. J Biol Chem 2020; 295:15-33. [PMID: 31712314 PMCID: PMC6952611 DOI: 10.1074/jbc.rev119.006794] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Computational simulations of protein folding can be used to interpret experimental folding results, to design new folding experiments, and to test the effects of mutations and small molecules on folding. However, whereas major experimental and computational progress has been made in understanding how small proteins fold, research on larger, multidomain proteins, which comprise the majority of proteins, is less advanced. Specifically, large proteins often fold via long-lived partially folded intermediates, whose structures, potentially toxic oligomerization, and interactions with cellular chaperones remain poorly understood. Molecular dynamics based folding simulations that rely on knowledge of the native structure can provide critical, detailed information on folding free energy landscapes, intermediates, and pathways. Further, increases in computational power and methodological advances have made folding simulations of large proteins practical and valuable. Here, using serpins that inhibit proteases as an example, we review native-centric methods for simulating the folding of large proteins. These synergistic approaches range from Gō and related structure-based models that can predict the effects of the native structure on folding to all-atom-based methods that include side-chain chemistry and can predict how disease-associated mutations may impact folding. The application of these computational approaches to serpins and other large proteins highlights the successes and limitations of current computational methods and underscores how computational results can be used to inform experiments. These powerful simulation approaches in combination with experiments can provide unique insights into how large proteins fold and misfold, expanding our ability to predict and manipulate protein folding.
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Affiliation(s)
- Anne Gershenson
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts 01003; Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts 01003.
| | - Shachi Gosavi
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore-560065, India.
| | - Pietro Faccioli
- Dipartimento di Fisica, Universitá degli Studi di Trento, 38122 Povo (Trento), Italy; Trento Institute for Fundamental Physics and Applications, 38123 Povo (Trento), Italy.
| | - Patrick L Wintrode
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201.
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10
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Mkaouar H, Akermi N, Kriaa A, Abraham AL, Jablaoui A, Soussou S, Mokdad-Gargouri R, Maguin E, Rhimi M. Serine protease inhibitors and human wellbeing interplay: new insights for old friends. PeerJ 2019; 7:e7224. [PMID: 31531264 PMCID: PMC6718151 DOI: 10.7717/peerj.7224] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 05/31/2019] [Indexed: 12/14/2022] Open
Abstract
Serine Protease Inhibitors (Serpins) control tightly regulated physiological processes and their dysfunction is associated to various diseases. Thus, increasing interest is given to these proteins as new therapeutic targets. Several studies provided functional and structural data about human serpins. By comparison, only little knowledge regarding bacterial serpins exists. Through the emergence of metagenomic studies, many bacterial serpins were identified from numerous ecological niches including the human gut microbiota. The origin, distribution and function of these proteins remain to be established. In this report, we shed light on the key role of human and bacterial serpins in health and disease. Moreover, we analyze their function, phylogeny and ecological distribution. This review highlights the potential use of bacterial serpins to set out new therapeutic approaches.
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Affiliation(s)
- Héla Mkaouar
- INRA, UMR1319 MICALIS, Jouy-en-Josas, France, AgroParisTech, UMR MICALIS, Jouy-en-Josas, France
| | - Nizar Akermi
- INRA, UMR1319 MICALIS, Jouy-en-Josas, France, AgroParisTech, UMR MICALIS, Jouy-en-Josas, France
| | - Aicha Kriaa
- INRA, UMR1319 MICALIS, Jouy-en-Josas, France, AgroParisTech, UMR MICALIS, Jouy-en-Josas, France
| | | | - Amin Jablaoui
- INRA, UMR1319 MICALIS, Jouy-en-Josas, France, AgroParisTech, UMR MICALIS, Jouy-en-Josas, France
| | - Souha Soussou
- INRA, UMR1319 MICALIS, Jouy-en-Josas, France, AgroParisTech, UMR MICALIS, Jouy-en-Josas, France
| | - Raja Mokdad-Gargouri
- Laboratory of Molecular Biology of Eukaryotes, Center of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Emmanuelle Maguin
- INRA, UMR1319 MICALIS, Jouy-en-Josas, France, AgroParisTech, UMR MICALIS, Jouy-en-Josas, France
| | - Moez Rhimi
- INRA, UMR1319 MICALIS, Jouy-en-Josas, France, AgroParisTech, UMR MICALIS, Jouy-en-Josas, France
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11
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Akermi N, Mkaouar H, Kriaa A, Jablaoui A, Soussou S, Gargouri A, Coleman AW, Perret F, Maguin E, Rhimi M. para-Sulphonato-calix[n]arene capped silver nanoparticles challenge the catalytic efficiency and the stability of a novel human gut serine protease inhibitor. Chem Commun (Camb) 2019; 55:8935-8938. [PMID: 31286126 DOI: 10.1039/c9cc03183a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The Eubacterium saburreum serine protease inhibitor from the human gut microbiota inhibits the eukaryotic pancreatic elastase associated with acute pancreatitis. Interestingly, the inhibition efficiency and stability are markedly increased by the para-sulphonato-calix[8]arene capped silver nanoparticles. Moreover, this enzyme is distinguishable by its high inhibitory effect at broad pH range between 2-10 and temperatures from 10 to 40 °C, in the presence of para-sulphonato-calix[8]arene capped silver nanoparticles the enzyme remains active even at 70 °C.
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Affiliation(s)
- Nizar Akermi
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, F-78350 Jouy-en-Josas, France.
| | - Hela Mkaouar
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, F-78350 Jouy-en-Josas, France.
| | - Aicha Kriaa
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, F-78350 Jouy-en-Josas, France.
| | - Amin Jablaoui
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, F-78350 Jouy-en-Josas, France.
| | - Souha Soussou
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, F-78350 Jouy-en-Josas, France.
| | - Ali Gargouri
- Laboratory of Molecular Biology of Eukaryotes, Center of Biotechnology of Sfax, University of Sfax, 3038, Sfax, Tunisia
| | | | - Florent Perret
- Univ Lyon, Université Lyon 1, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, UMR 5246 CNRS, F-69622, Villeurbanne, France
| | - Emmanuelle Maguin
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, F-78350 Jouy-en-Josas, France.
| | - Moez Rhimi
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, F-78350 Jouy-en-Josas, France.
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12
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Abstract
Serine proteinase inhibitors (serpins), typically fold to a metastable native state and undergo a major conformational change in order to inhibit target proteases. However, conformational lability of the native serpin fold renders them susceptible to misfolding and aggregation, and underlies misfolding diseases such as α1-antitrypsin deficiency. Serpin specificity towards its protease target is dictated by its flexible and solvent exposed reactive centre loop (RCL), which forms the initial interaction with the target protease during inhibition. Previous studies have attempted to alter the specificity by mutating the RCL to that of a target serpin, but the rules governing specificity are not understood well enough yet to enable specificity to be engineered at will. In this paper, we use conserpin, a synthetic, thermostable serpin, as a model protein with which to investigate the determinants of serpin specificity by engineering its RCL. Replacing the RCL sequence with that from α1-antitrypsin fails to restore specificity against trypsin or human neutrophil elastase. Structural determination of the RCL-engineered conserpin and molecular dynamics simulations indicate that, although the RCL sequence may partially dictate specificity, local electrostatics and RCL dynamics may dictate the rate of insertion during protease inhibition, and thus whether it behaves as an inhibitor or a substrate. Engineering serpin specificity is therefore substantially more complex than solely manipulating the RCL sequence, and will require a more thorough understanding of how conformational dynamics achieves the delicate balance between stability, folding and function required by the exquisite serpin mechanism of action.
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13
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Probing the folding pathway of a consensus serpin using single tryptophan mutants. Sci Rep 2018; 8:2121. [PMID: 29391487 PMCID: PMC5794792 DOI: 10.1038/s41598-018-19567-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 11/03/2017] [Indexed: 01/25/2023] Open
Abstract
Conserpin is an engineered protein that represents the consensus of a sequence alignment of eukaryotic serpins: protease inhibitors typified by a metastable native state and a structurally well-conserved scaffold. Previously, this protein has been found to adopt a native inhibitory conformation, possess an atypical reversible folding pathway and exhibit pronounced resistance to inactivation. Here we have designed a version of conserpin, cAT, with the inhibitory specificity of α1-antitrypsin, and generated single-tryptophan variants to probe its folding pathway in more detail. cAT exhibited similar thermal stability to the parental protein, an inactivation associated with oligomerisation rather a transition to the latent conformation, and a native state with pronounced kinetic stability. The tryptophan variants reveal the unfolding intermediate ensemble to consist of an intact helix H, a distorted helix F and ‘breach’ region structurally similar to that of a mesophilic serpin intermediate. A combination of intrinsic fluorescence, circular dichroism, and analytical gel filtration provide insight into a highly cooperative folding pathway with concerted changes in secondary and tertiary structure, which minimises the accumulation of two directly-observed aggregation-prone intermediate species. This functional conserpin variant represents a basis for further studies of the relationship between structure and stability in the serpin superfamily.
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14
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Fei R, Zhang H, Zhong S, Xue B, Gao Y, Zhou X. Anti-inflammatory activity of a thermophilic serine protease inhibitor from extremophile Pyrobaculum neutrophilum. EUR J INFLAMM 2017. [DOI: 10.1177/1721727x17739516] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Serine protease inhibitors (serpins) are a superfamily of proteins involved in many important biological processes, including inflammation. Serpins dysfunction-related diseases are mainly treated by augmentation therapy using serpins purified from human plasma. Pnserpin from hyperthermophilic archaeon Pyrobaculum neutrophilum showed protease inhibition activity and high stability. In this study, we examined the anti-inflammatory activity of Pnserpin using xylene-induced acute inflammatory model of mouse ear swelling and lipopolysaccharide (LPS)-induced murine RAW 264.7 macrophages cellular model. The inhibition of mouse ear swelling and the production of pro-inflammatory cytokines in mouse serum or in macrophages cell were used to evaluate the anti-inflammatory effect of Pnserpin. Our results showed that Pnserpin could inhibit the xylene-induced mouse ear swelling and suppress the production of pro-inflammatory cytokines in mouse serum and in LPS-induced RAW264.7 cells. This study indicated that Pnserpin might have anti-inflammatory effect in vivo and in vitro.
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Affiliation(s)
- Rui Fei
- Department of Cell Biology, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Huan Zhang
- Department of Cell Biology, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Sheng Zhong
- Department of Neurosurgery, The First Hospital of Jilin University, Changchun, China
| | - Baigong Xue
- Department of Cell Biology, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Yuanqi Gao
- Department of Cell Biology, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Xiaoli Zhou
- Department of Cell Biology, College of Basic Medical Sciences, Jilin University, Changchun, China
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15
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Microbial serine protease inhibitors and their therapeutic applications. Int J Biol Macromol 2017; 107:1373-1387. [PMID: 28970170 DOI: 10.1016/j.ijbiomac.2017.09.115] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 09/28/2017] [Indexed: 12/22/2022]
Abstract
Serine protease inhibitors, inhibit serine proteases either partially or completely after forming complexes with their respective proteases. Protease actions are significant for many physiological pathways found in living forms and any anomalies may lead to numerous physiological complications. Each cell or organism has its own mechanism for controlling these protease actions. It is often regulated by the action of inhibitors or activators. Among the proteases, serine proteases are the most common that are involved in many life and death processes. Selective inhibitors of physiologically relevant proteases can be used as a lead compound for the drug development. Therefore, it is imperative to identify small peptides and proteins that selectively inhibit serine proteases from various sources. Microbes can be considered as a major source of diverse serine protease inhibitors since they have the prominent and diverse domain in nature. Most of the microbial serine protease inhibitors are intracellular and few are extracellular. Microbes produce protease inhibitors for protection against its own proteases or against other environmental factors. The status and future prospects of microbial serine protease inhibitors and their therapeutic benefits in treating cancer, blood coagulation disorders and viral infections, are reviewed here.
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16
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Goulas T, Ksiazek M, Garcia-Ferrer I, Sochaj-Gregorczyk AM, Waligorska I, Wasylewski M, Potempa J, Gomis-Rüth FX. A structure-derived snap-trap mechanism of a multispecific serpin from the dysbiotic human oral microbiome. J Biol Chem 2017; 292:10883-10898. [PMID: 28512127 PMCID: PMC5491774 DOI: 10.1074/jbc.m117.786533] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 05/04/2017] [Indexed: 10/19/2022] Open
Abstract
Enduring host-microbiome relationships are based on adaptive strategies within a particular ecological niche. Tannerella forsythia is a dysbiotic member of the human oral microbiome that inhabits periodontal pockets and contributes to chronic periodontitis. To counteract endopeptidases from the host or microbial competitors, T. forsythia possesses a serpin-type proteinase inhibitor called miropin. Although serpins from animals, plants, and viruses have been widely studied, those from prokaryotes have received only limited attention. Here we show that miropin uses the serpin-type suicidal mechanism. We found that, similar to a snap trap, the protein transits from a metastable native form to a relaxed triggered or induced form after cleavage of a reactive-site target bond in an exposed reactive-center loop. The prey peptidase becomes covalently attached to the inhibitor, is dragged 75 Å apart, and is irreversibly inhibited. This coincides with a large conformational rearrangement of miropin, which inserts the segment upstream of the cleavage site as an extra β-strand in a central β-sheet. Standard serpins possess a single target bond and inhibit selected endopeptidases of particular specificity and class. In contrast, miropin uniquely blocked many serine and cysteine endopeptidases of disparate architecture and substrate specificity owing to several potential target bonds within the reactive-center loop and to plasticity in accommodating extra β-strands of variable length. Phylogenetic studies revealed a patchy distribution of bacterial serpins incompatible with a vertical descent model. This finding suggests that miropin was acquired from the host through horizontal gene transfer, perhaps facilitated by the long and intimate association of T. forsythia with the human gingiva.
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Affiliation(s)
- Theodoros Goulas
- From the Proteolysis Lab, Structural Biology Unit, María de Maeztu Unit of Excellence, Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas, 08028 Barcelona, Spain
| | - Miroslaw Ksiazek
- the Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology and
- the Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, Louisville, Kentucky 40202
| | - Irene Garcia-Ferrer
- From the Proteolysis Lab, Structural Biology Unit, María de Maeztu Unit of Excellence, Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas, 08028 Barcelona, Spain
| | - Alicja M Sochaj-Gregorczyk
- the Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology and
- the Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland, and
| | - Irena Waligorska
- the Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology and
| | - Marcin Wasylewski
- the Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology and
| | - Jan Potempa
- the Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology and
- the Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, Louisville, Kentucky 40202
| | - F Xavier Gomis-Rüth
- From the Proteolysis Lab, Structural Biology Unit, María de Maeztu Unit of Excellence, Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas, 08028 Barcelona, Spain,
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17
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Miranda E, Ferrarotti I, Berardelli R, Laffranchi M, Cerea M, Gangemi F, Haq I, Ottaviani S, Lomas DA, Irving JA, Fra A. The pathological Trento variant of alpha-1-antitrypsin (E75V) shows nonclassical behaviour during polymerization. FEBS J 2017; 284:2110-2126. [PMID: 28504839 PMCID: PMC5518210 DOI: 10.1111/febs.14111] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 04/26/2017] [Accepted: 05/12/2017] [Indexed: 12/11/2022]
Abstract
Severe alpha‐1‐antitrypsin deficiency (AATD) is most frequently associated with the alpha‐1‐antitrypsin (AAT) Z variant (E342K). ZZ homozygotes exhibit accumulation of AAT as polymers in the endoplasmic reticulum of hepatocytes. This protein deposition can lead to liver disease, with the resulting low circulating levels of AAT predisposing to early‐onset emphysema due to dysregulation of elastinolytic activity in the lungs. An increasing number of rare AAT alleles have been identified in patients with severe AATD, typically in combination with the Z allele. Here we report a new mutation (E75V) in a patient with severe plasma deficiency, which we designate Trento. In contrast to the Z mutant, Trento AAT was secreted efficiently when expressed in cellular models but showed compromised conformational stability. Polyacrylamide gel electrophoresis (PAGE) and ELISA‐based analyses of the secreted protein revealed the presence of oligomeric species with electrophoretic and immunorecognition profiles different from those of Z and S (E264V) AAT polymers, including reduced recognition by conformational monoclonal antibodies 2C1 and 4B12. This altered recognition was not due to direct effects on the epitope of the 2C1 monoclonal antibody which we localized between helices E and F. Structural analyses indicate the likely basis for polymer formation is the loss of a highly conserved stabilizing interaction between helix C and the posthelix I loop. These results highlight this region as important for maintaining native state stability and, when compromised, results in the formation of pathological polymers that are different from those produced by Z and S AAT.
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Affiliation(s)
- Elena Miranda
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, Italy
| | - Ilaria Ferrarotti
- Department of Internal Medicine and Therapeutics, Pneumology Unit, University of Pavia, Italy
| | - Romina Berardelli
- Department of Molecular and Translational Medicine, University of Brescia, Italy
| | - Mattia Laffranchi
- Department of Molecular and Translational Medicine, University of Brescia, Italy
| | - Marta Cerea
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, Italy.,Department of Molecular and Translational Medicine, University of Brescia, Italy
| | - Fabrizio Gangemi
- Department of Molecular and Translational Medicine, University of Brescia, Italy
| | - Imran Haq
- UCL Respiratory and the Institute of Structural and Molecular Biology, University College London, UK
| | - Stefania Ottaviani
- Center for Diagnosis of Inherited Alpha 1-Antitrypsin Deficiency, Pneumology Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - David A Lomas
- UCL Respiratory and the Institute of Structural and Molecular Biology, University College London, UK
| | - James A Irving
- UCL Respiratory and the Institute of Structural and Molecular Biology, University College London, UK
| | - Annamaria Fra
- Department of Molecular and Translational Medicine, University of Brescia, Italy
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18
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Zhang H, Fei R, Xue B, Yu S, Zhang Z, Zhong S, Gao Y, Zhou X. Pnserpin: A Novel Serine Protease Inhibitor from Extremophile Pyrobaculum neutrophilum. Int J Mol Sci 2017; 18:ijms18010113. [PMID: 28067849 PMCID: PMC5297747 DOI: 10.3390/ijms18010113] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 12/29/2016] [Accepted: 01/03/2017] [Indexed: 11/16/2022] Open
Abstract
Serine protease inhibitors (serpins) are native inhibitors of serine proteases, constituting a large protein family with members spread over eukaryotes and prokaryotes. However, only very few prokaryotic serpins, especially from extremophiles, have been characterized to date. In this study, Pnserpin, a putative serine protease inhibitor from the thermophile Pyrobaculum neutrophilum, was overexpressed in Escherichia coli for purification and characterization. It irreversibly inhibits chymotrypsin-, trypsin-, elastase-, and subtilisin-like proteases in a temperature range from 20 to 100 °C in a concentration-dependent manner. The stoichiometry of inhibition (SI) of Pnserpin for proteases decreases as the temperature increases, indicating that the inhibitory activity of Pnserpin increases with the temperature. SDS-PAGE (sodium dodecyl sulfate polyacrylamide gel electrophoresis) showed that Pnserpin inhibits proteases by forming a SDS-resistant covalent complex. Homology modeling and molecular dynamic simulations predicted that Pnserpin can form a stable common serpin fold. Results of the present work will help in understanding the structural and functional characteristics of thermophilic serpin and will broaden the current knowledge about serpins from extremophiles.
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Affiliation(s)
- Huan Zhang
- Department of Cell Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China.
| | - Rui Fei
- Department of Cell Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China.
| | - Baigong Xue
- Department of Cell Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China.
| | - Shanshan Yu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Zuoming Zhang
- Key Laboratory for Molecular Enzymology and Engineering, Ministry of Education, Jilin University, Changchun 130012, China.
| | - Sheng Zhong
- Department of Cell Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China.
| | - Yuanqi Gao
- Department of Cell Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China.
| | - Xiaoli Zhou
- Department of Cell Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China.
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19
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Meekins DA, Zhang X, Battaile KP, Lovell S, Michel K. 1.45 Å resolution structure of SRPN18 from the malaria vector Anopheles gambiae. Acta Crystallogr F Struct Biol Commun 2016; 72:853-862. [PMID: 27917832 PMCID: PMC5137461 DOI: 10.1107/s2053230x16017854] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 11/08/2016] [Indexed: 12/28/2022] Open
Abstract
Serine protease inhibitors (serpins) in insects function within development, wound healing and immunity. The genome of the African malaria vector, Anopheles gambiae, encodes 23 distinct serpin proteins, several of which are implicated in disease-relevant physiological responses. A. gambiae serpin 18 (SRPN18) was previously categorized as non-inhibitory based on the sequence of its reactive-center loop (RCL), a region responsible for targeting and initiating protease inhibition. The crystal structure of A. gambiae SRPN18 was determined to a resolution of 1.45 Å, including nearly the entire RCL in one of the two molecules in the asymmetric unit. The structure reveals that the SRPN18 RCL is extremely short and constricted, a feature associated with noncanonical inhibitors or non-inhibitory serpin superfamily members. Furthermore, the SRPN18 RCL does not contain a suitable protease target site and contains a large number of prolines. The SRPN18 structure therefore reveals a unique RCL architecture among the highly conserved serpin fold.
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Affiliation(s)
| | - Xin Zhang
- Division of Biology, Kansas State University, USA
| | - Kevin P. Battaile
- IMCA–CAT, Hauptman–Woodward Medical Research Institute, Argonne National Laboratory, USA
| | - Scott Lovell
- Protein Structure Laboratory, Del Shankel Structural Biology Center, University of Kansas, USA
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20
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Mkaouar H, Akermi N, Mariaule V, Boudebbouze S, Gaci N, Szukala F, Pons N, Marquez J, Gargouri A, Maguin E, Rhimi M. Siropins, novel serine protease inhibitors from gut microbiota acting on human proteases involved in inflammatory bowel diseases. Microb Cell Fact 2016; 15:201. [PMID: 27894344 PMCID: PMC5127057 DOI: 10.1186/s12934-016-0596-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Accepted: 11/08/2016] [Indexed: 02/05/2023] Open
Abstract
Background In eukaryotes, the serpins constitute a wide family of protease inhibitors regulating many physiological pathways. Many reports stressed the key role of serpins in several human physiopathologies including mainly the inflammatory bowel diseases. In this context, eukaryotic serpins were largely studied and their use to limit inflammation was reported. In comparison to that, bacterial serpins and mainly those from human gut microbiota remain poorly studied. Results The two genes encoding for putative serpins from the human gut bacterium Eubacterium sireaum, display low sequence identities. These genes were overexpressed and the encoded proteins, named Siropins, were purified. Activity studies demonstrated that both purified proteins inhibited serine proteases but surprisingly they preferentially inhibited two human serine proteases (Human Neutrophil Elastase and Proteinase3). The biochemical characterization of these Siropins revealed that Siropin 1 was the most active and stable at low pH values while Siropin 2 was more thermoactive and thermostable. Kinetic analysis allowed the determination of the stoichiometry of inhibition (SI) which was around 1 and of the association rate constants of 7.7 × 104 for the Human Neutrophil Elastase and 2.6 × 105 for the Proteinase3. Moreover, both Siropins displayed the ability to inhibit proteases usually present in fecal waters. Altogether our data indicate the high efficiency of Siropins and their probable involvement in the control of the overall intestine protease activity. Conclusions Here we report the purification and the biochemical characterization of two novel serpins originated from Eubacterium sireaum, a human gastro-intestinal tract commensal bacteria. These proteins that we called Siropins, efficiently inhibited two human proteases reported to be associated with inflammatory bowel diseases. The determination of the biochemical properties of these enzymes revealed different temperature and pH behaviours that may reflect adaptation of this human commensal bacterium to different ecological environments. To the best of our knowledge, it is the first bacterial serpins showing an attractive inhibition of fecal proteases recovered from a mice group with chemically induced inflammation. Altogether our data highlight the interesting potential of Siropins, and serpins from the human gut microbiota in general, to be used as new alternative to face inflammatory diseases. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0596-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Héla Mkaouar
- UMR 1319 Micalis, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.,Laboratory of Molecular Biology of Eukaryotes, Center of Biotechnology of Sfax, University of Sfax, 3038, Sfax, Tunisia
| | - Nizar Akermi
- UMR 1319 Micalis, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.,Laboratory of Molecular Biology of Eukaryotes, Center of Biotechnology of Sfax, University of Sfax, 3038, Sfax, Tunisia
| | - Vincent Mariaule
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Cedex 9, Grenoble, France
| | - Samira Boudebbouze
- UMR 1319 Micalis, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Nadia Gaci
- UMR 1319 Micalis, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Florette Szukala
- UMR 1319 Micalis, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Nicolas Pons
- INRA, Institut National de la Recherche Agronomique, US 1367 Metagenopolis, Jouy-en-Josas, France
| | - Josan Marquez
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Cedex 9, Grenoble, France
| | - Ali Gargouri
- Laboratory of Molecular Biology of Eukaryotes, Center of Biotechnology of Sfax, University of Sfax, 3038, Sfax, Tunisia
| | - Emmanuelle Maguin
- UMR 1319 Micalis, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Moez Rhimi
- UMR 1319 Micalis, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.
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21
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Porebski BT, Keleher S, Hollins JJ, Nickson AA, Marijanovic EM, Borg NA, Costa MGS, Pearce MA, Dai W, Zhu L, Irving JA, Hoke DE, Kass I, Whisstock JC, Bottomley SP, Webb GI, McGowan S, Buckle AM. Smoothing a rugged protein folding landscape by sequence-based redesign. Sci Rep 2016; 6:33958. [PMID: 27667094 PMCID: PMC5036219 DOI: 10.1038/srep33958] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 09/01/2016] [Indexed: 11/09/2022] Open
Abstract
The rugged folding landscapes of functional proteins puts them at risk of misfolding and aggregation. Serine protease inhibitors, or serpins, are paradigms for this delicate balance between function and misfolding. Serpins exist in a metastable state that undergoes a major conformational change in order to inhibit proteases. However, conformational labiality of the native serpin fold renders them susceptible to misfolding, which underlies misfolding diseases such as α1-antitrypsin deficiency. To investigate how serpins balance function and folding, we used consensus design to create conserpin, a synthetic serpin that folds reversibly, is functional, thermostable, and polymerization resistant. Characterization of its structure, folding and dynamics suggest that consensus design has remodeled the folding landscape to reconcile competing requirements for stability and function. This approach may offer general benefits for engineering functional proteins that have risky folding landscapes, including the removal of aggregation-prone intermediates, and modifying scaffolds for use as protein therapeutics.
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Affiliation(s)
- Benjamin T Porebski
- Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.,Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, United Kingdom
| | - Shani Keleher
- Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Jeffrey J Hollins
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
| | - Adrian A Nickson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
| | - Emilia M Marijanovic
- Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Natalie A Borg
- Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Mauricio G S Costa
- Programa de Computação Científica, Fundação Oswaldo Cruz, 21949900 Rio de Janeiro, Brazil
| | - Mary A Pearce
- Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Weiwen Dai
- Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Liguang Zhu
- Faculty of Information Technology, Monash University, Clayton, Victoria 3800, Australia
| | - James A Irving
- Wolfson Institute for Biomedical Research, University College London, Gower Street, London, WC1E 6BT, United Kingdom
| | - David E Hoke
- Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Itamar Kass
- Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - James C Whisstock
- Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Stephen P Bottomley
- Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Geoffrey I Webb
- Faculty of Information Technology, Monash University, Clayton, Victoria 3800, Australia
| | - Sheena McGowan
- Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.,Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Ashley M Buckle
- Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
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22
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Oliveira JPC, Salazar N, Zani MB, de Souza LR, Passos SG, Sant'Ana AM, de Andrade RA, Marcili A, Sperança MA, Puzer L. Vioserpin, a serine protease inhibitor from Gloeobacter violaceus possibly regulated by heparin. Biochimie 2016; 127:115-20. [PMID: 27157268 DOI: 10.1016/j.biochi.2016.05.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 05/03/2016] [Indexed: 10/21/2022]
Abstract
Serine peptidase inhibitor (serpin) is the name given to the superfamily of proteins with wide range of biological functions, and that the main feature is the inhibition of serine proteases. Here we describe the inhibitory characterization of a serpin from Gloeobacter violaceus that we named vioserpin. The serpin presented a high specificity to inhibit trypsin-like enzymes with a rapid inhibition rate constant (2.1 × 10(6) M(-1) s(-1)). We also demonstrated that the inhibitory activity of the vioserpin is influenced by the concentration of heparin, and this finding may throw a new light on understanding the molecular evolution of serpins.
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Affiliation(s)
- Jocélia P C Oliveira
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Rua Arcturus 3, São Bernardo do Campo, SP, Brazil
| | - Natália Salazar
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Rua Arcturus 3, São Bernardo do Campo, SP, Brazil
| | - Marcelo B Zani
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Rua Arcturus 3, São Bernardo do Campo, SP, Brazil
| | - Lucas R de Souza
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Rua Arcturus 3, São Bernardo do Campo, SP, Brazil
| | - Silvia G Passos
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Rua Arcturus 3, São Bernardo do Campo, SP, Brazil
| | - Aquiles M Sant'Ana
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Rua Arcturus 3, São Bernardo do Campo, SP, Brazil
| | - Regiane A de Andrade
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Rua Arcturus 3, São Bernardo do Campo, SP, Brazil
| | - Arlei Marcili
- Departamento de Medicina Veterinária Preventiva e Saude Animal, Universidade de São Paulo, São Paulo, SP, Brazil; Medicina Veterinária e Bem Estar Animal, Universidade de Santo Amaro, Rua Prof. Enéas de Siqueira Neto, 340, São Paulo, SP, Brazil
| | - Marcia A Sperança
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Rua Arcturus 3, São Bernardo do Campo, SP, Brazil
| | - Luciano Puzer
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Rua Arcturus 3, São Bernardo do Campo, SP, Brazil.
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23
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Navarro-Fernández J, de la Morena-Barrio ME, Padilla J, Miñano A, Bohdan N, Águila S, Martínez-Martínez I, Sevivas TS, de Cos C, Fernández-Mosteirín N, Llamas P, Asenjo S, Medina P, Souto JC, Overvad K, Kristensen SR, Corral J, Vicente V. Antithrombin Dublin (p.Val30Glu): a relatively common variant with moderate thrombosis risk of causing transient antithrombin deficiency. Thromb Haemost 2016; 116:146-54. [PMID: 27098529 DOI: 10.1160/th15-11-0871] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 03/02/2016] [Indexed: 12/24/2022]
Abstract
The key haemostatic role of antithrombin and the risk of thrombosis associated with its deficiency support that the low incidence of antithrombin deficiency among patients with thrombosis might be explained by underestimation of this disorder. It was our aim to identify mutations in SERPINC1 causing transient antithrombin deficiency. SERPINC1 was sequenced in 214 cases with a positive test for antithrombin deficiency, including 67 with no deficiency in the sample delivered to our laboratory. The p.Val30Glu mutation (Antithrombin Dublin) was identified in five out of these 67 cases, as well as in three out of 127 cases with other SERPINC1 mutations. Genotyping in 1593 patients with venous thrombosis and 2592 controls from two populations, revealed a low prevalent polymorphism (0.3 %) that moderately increased the risk of venous thrombosis (OR: 2.9; 95 % CI: 1.07-8.09; p= 0.03) and identified one homozygous patient with an early thrombotic event. Carriers had normal anti-FXa activity, and plasma antithrombin was not sensitive to heat stress or proteolytic cleavage. Analysis of one sample with transient deficit revealed a type I deficiency, without aberrant or increased latent forms. The recombinant variant, which lacked the two amino-terminal residues, had reduced secretion from HEK-EBNA cells, formed hyperstable disulphide-linked polymers, and had negligible activity. In conclusion, p.Val30Glu by affecting the cleavage of antithrombin's signal peptide, results in a mature protein lacking the N-terminal dipeptide with no functional consequences in normal conditions, but that increases the sensitivity to be folded intracellularly into polymers, facilitating transient antithrombin deficiency and the subsequent risk of thrombosis.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Javier Corral
- Dr. Javier Corral, University of Murcia, Centro Regional de Hemodonación, Calle Ronda de Garay s/n, Murcia 30003, Spain, Tel.: +34968341990, Fax: +34968261914, E-mail:
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24
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Caccia S, Ricagno S, Bolognesi M. Molecular bases of neuroserpin function and pathology. Biomol Concepts 2015; 1:117-30. [PMID: 25961991 DOI: 10.1515/bmc.2010.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Serpins build a large and evolutionary widespread protein superfamily, hosting members that are mainly Ser-protease inhibitors. Typically, serpins display a conserved core domain composed of three main β-sheets and 9-10 α-helices, for a total of approximately 350 amino acids. Neuroserpin (NS) is mostly expressed in neurons and in the central and peripheral nervous systems, where it targets tissue-type plasminogen activator. NS activity is relevant for axogenesis, synaptogenesis and synaptic plasticity. Five (single amino acid) NS mutations are associated with severe neurodegenerative disease in man, leading to early onset dementia, epilepsy and neuronal death. The functional aspects of NS protease inhibition are linked to the presence of a long exposed loop (reactive center loop, RCL) that acts as bait for the incoming partner protease. Large NS conformational changes, associated with the cleavage of the RCL, trap the protease in an acyl-enzyme complex. Contrary to other serpins, this complex has a half-life of approximately 10 min. Conformational flexibility is held to be at the bases of NS polymerization leading to Collins bodies intracellular deposition and neuronal damage in the pathological NS variants. Two main general mechanisms of serpin polymerization are currently discussed. Both models require the swapping of the RCL among neighboring serpin molecules. Specific differences in the size of swapped regions, as well as differences in the folding stage at which polymerization can occur, distinguish the two models. The results provided by recent crystallographic and biophysical studies allow rationalization of the functional and pathological roles played by NS based on the analysis of four three-dimensional structures.
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25
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Noto R, Santangelo MG, Levantino M, Cupane A, Mangione MR, Parisi D, Ricagno S, Bolognesi M, Manno M, Martorana V. Functional and dysfunctional conformers of human neuroserpin characterized by optical spectroscopies and Molecular Dynamics. BIOCHIMICA ET BIOPHYSICA ACTA 2015; 1854:110-7. [PMID: 25450507 PMCID: PMC4332418 DOI: 10.1016/j.bbapap.2014.10.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 09/04/2014] [Accepted: 10/03/2014] [Indexed: 12/12/2022]
Abstract
Neuroserpin (NS) is a serine protease inhibitor (SERPIN) involved in different neurological pathologies, including the Familial Encephalopathy with Neuroserpin Inclusion Bodies (FENIB), related to the aberrant polymerization of NS mutants. Here we present an in vitro and in silico characterization of native neuroserpin and its dysfunctional conformation isoforms: the proteolytically cleaved conformer, the inactive latent conformer, and the polymeric species. Based on circular dichroism and fluorescence spectroscopy, we present an experimental validation of the latent model and highlight the main structural features of the different conformers. In particular, emission spectra of aromatic residues yield distinct conformational fingerprints, that provide a novel and simple spectroscopic tool for selecting serpin conformers in vitro. Based on the structural relationship between cleaved and latent serpins, we propose a structural model for latent NS, for which an experimental crystallographic structure is lacking. Molecular Dynamics simulations suggest that NS conformational stability and flexibility arise from a spatial distribution of intramolecular salt-bridges and hydrogen bonds.
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Affiliation(s)
- Rosina Noto
- Institute of Biophysics, National Research Council of Italy, Palermo, Italy
| | | | - Matteo Levantino
- Department of Physics and Chemistry, University of Palermo, Palermo, Italy
| | - Antonio Cupane
- Department of Physics and Chemistry, University of Palermo, Palermo, Italy
| | | | - Daniele Parisi
- Institute of Biophysics, National Research Council of Italy, Palermo, Italy; Department of Biosciences, Institute of Biophysics CNR, Italy and CIMAINA, University of Milano, Milan, Italy
| | - Stefano Ricagno
- Department of Biosciences, Institute of Biophysics CNR, Italy and CIMAINA, University of Milano, Milan, Italy
| | - Martino Bolognesi
- Department of Biosciences, Institute of Biophysics CNR, Italy and CIMAINA, University of Milano, Milan, Italy
| | - Mauro Manno
- Institute of Biophysics, National Research Council of Italy, Palermo, Italy.
| | - Vincenzo Martorana
- Institute of Biophysics, National Research Council of Italy, Palermo, Italy
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26
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Ksiazek M, Mizgalska D, Enghild JJ, Scavenius C, Thogersen IB, Potempa J. Miropin, a novel bacterial serpin from the periodontopathogen Tannerella forsythia, inhibits a broad range of proteases by using different peptide bonds within the reactive center loop. J Biol Chem 2014; 290:658-70. [PMID: 25389290 DOI: 10.1074/jbc.m114.601716] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
All prokaryotic genes encoding putative serpins identified to date are found in environmental and commensal microorganisms, and only very few prokaryotic serpins have been investigated from a mechanistic standpoint. Herein, we characterized a novel serpin (miropin) from the human pathogen Tannerella forsythia, a bacterium implicated in initiation and progression of human periodontitis. In contrast to other serpins, miropin efficiently inhibited a broad range of proteases (neutrophil and pancreatic elastases, cathepsin G, subtilisin, and trypsin) with a stoichiometry of inhibition of around 3 and second-order association rate constants that ranged from 2.7 × 10(4) (cathepsin G) to 7.1 × 10(5) m(-1)s(-1) (subtilisin). Inhibition was associated with the formation of complexes that were stable during SDS-PAGE. The unusually broad specificity of miropin for target proteases is achieved through different active sites within the reactive center loop upstream of the P1-P1' site, which was predicted from an alignment of the primary structure of miropin with those of well studied human and prokaryotic serpins. Thus, miropin is unique among inhibitory serpins, and it has apparently evolved the ability to inhibit a multitude of proteases at the expense of a high stoichiometry of inhibition and a low association rate constant. These characteristics suggest that miropin arose as an adaptation to the highly proteolytic environment of subgingival plaque, which is exposed continually to an array of host proteases in the inflammatory exudate. In such an environment, miropin may function as an important virulence factor by protecting bacterium from the destructive activity of neutrophil serine proteases. Alternatively, it may act as a housekeeping protein that regulates the activity of endogenous T. forsythia serine proteases.
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Affiliation(s)
- Miroslaw Ksiazek
- From the Department of Microbiology, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland,
| | - Danuta Mizgalska
- From the Department of Microbiology, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Jan J Enghild
- Center for Insoluble Protein Structures (inSPIN) and Interdisciplinary Nanoscience Center (iNANO) at the Department of Molecular Biology and Genetics, Aarhus University, Aarhus DK-8000, Denmark, and
| | - Carsten Scavenius
- Center for Insoluble Protein Structures (inSPIN) and Interdisciplinary Nanoscience Center (iNANO) at the Department of Molecular Biology and Genetics, Aarhus University, Aarhus DK-8000, Denmark, and
| | - Ida B Thogersen
- Center for Insoluble Protein Structures (inSPIN) and Interdisciplinary Nanoscience Center (iNANO) at the Department of Molecular Biology and Genetics, Aarhus University, Aarhus DK-8000, Denmark, and
| | - Jan Potempa
- From the Department of Microbiology, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland, Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, Louisville, Kentucky 40202
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27
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Liu L, Werner M, Gershenson A. Collapse of a long axis: single-molecule Förster resonance energy transfer and serpin equilibrium unfolding. Biochemistry 2014; 53:2903-14. [PMID: 24749911 PMCID: PMC4020580 DOI: 10.1021/bi401622n] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 03/17/2014] [Indexed: 01/25/2023]
Abstract
The energy required for mechanical inhibition of target proteases is stored in the native structure of inhibitory serpins and accessed by serpin structural remodeling. The overall serpin fold is ellipsoidal with one long and two short axes. Most of the structural remodeling required for function occurs along the long axis, while expansion of the short axes is associated with misfolded, inactive forms. This suggests that ellipticity, as typified by the long axis, may be important for both function and folding. Placement of donor and acceptor fluorophores approximately along the long axis or one of the short axes allows single-pair Förster resonance energy transfer (spFRET) to report on both unfolding transitions and the time-averaged shape of different conformations. Equilibrium unfolding and refolding studies of the well-characterized inhibitory serpin α1-antitrypsin reveal that the long axis collapses in the folding intermediates while the monitored short axis expands. These energetically distinct intermediates are thus more spherical than the native state. Our spFRET studies agree with other equilibrium unfolding studies that found that the region around one of the β strands, s5A, which helps define the long axis and must move for functionally required loop insertion, unfolds at low denaturant concentrations. This supports a connection between functionally important structural lability and unfolding in the inhibitory serpins.
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Affiliation(s)
- Lu Liu
- Department
of Chemistry, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Michael Werner
- Department
of Chemistry, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Anne Gershenson
- Department
of Biochemistry and Molecular Biology, University
of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
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28
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Extending the cellulosome paradigm: the modular Clostridium thermocellum cellulosomal serpin PinA is a broad-spectrum inhibitor of subtilisin-like proteases. Appl Environ Microbiol 2013; 79:6173-5. [PMID: 23872568 DOI: 10.1128/aem.01912-13] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Clostridium thermocellum encodes a cellulosomal, modular, and thermostable serine protease inhibitor (serpin), PinA. PinA stability but not inhibitory activity is affected by the Fn(III) and Doc(I) domains, and PinA is a broad inhibitor of subtilisin-like proteases and may play a key role in protecting the cellulosome from protease attack.
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29
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Abstract
Acid unfolding of non-inhibited papain at pH 2 was studied by means of spectroscopic and electrophoresis techniques as well as activity assays. We found a molten globule like species (A state) similar to that previously reported for bromelain and S-carboxy-methyl-papain. We demonstrated that this A state is not thermodynamically stable but a metastable conformer which decays into an unfolded conformation in a few hours. The mechanism of acid unfolding to the A state proved to be completely irreversible, with a biphasic time evolution of spectroscopic signals characteristic of the existence of a kinetic intermediate. This latter species showed properties in-between native and A state such as secondary structure, exposition of hydrophobic area and tryptophan environment, but a native like hydrodynamic radius. Native papain seems to unfold at acid pH through at least two kinetic barriers, being its pro-region mandatory to conduct and stabilize its active structure. Computer simulations of acid unfolding, followed by ANS docking, identified three regions of cavity formation induced by acid media which might be used as regions to be fortified by protein engineering in the quest for extreme-resistant proteases or as hot-spots for protease inactivation.
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30
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Kass I, Reboul CF, Buckle AM. Computational methods for studying serpin conformational change and structural plasticity. Methods Enzymol 2011; 501:295-323. [PMID: 22078540 DOI: 10.1016/b978-0-12-385950-1.00014-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Currently, over a hundred high-resolution structures of serpins are available, exhibiting a wide range of conformations. However, our understanding of serpin dynamics and conformational change is still limited, mainly due to challenges of monitoring structural changes and characterizing transient conformations using experimental methods. Insight can be provided, however, by employing theoretical and computational approaches. In this chapter, we present an overview of such methods, focusing on molecular dynamics and simulation. As serpin conformational dynamics span a wide range of timescales, we discuss the relative merits of each method and suggest which method is suited to specific conformational phenomena.
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Affiliation(s)
- Itamar Kass
- Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria, Australia
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31
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32
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33
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Tanaka SI, Koga Y, Takano K, Kanaya S. Inhibition of chymotrypsin- and subtilisin-like serine proteases with Tk-serpin from hyperthermophilic archaeon Thermococcus kodakaraensis. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1814:299-307. [PMID: 21112419 DOI: 10.1016/j.bbapap.2010.11.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Revised: 11/05/2010] [Accepted: 11/09/2010] [Indexed: 12/16/2022]
Abstract
A serpin homologue (Tk-serpin) from the hyperthermophilic archaeon Thermococcus kodakaraensis was overproduced in E. coli, purified, and characterized. Tk-serpin irreversibly inhibits Tk-subtilisin (TKS) from the same organism with the second-order association rate constants (k(ass)) of 5.2×10³ M⁻¹ s⁻¹ at 40°C and 3.1×10⁵ M⁻¹ s⁻¹ at 80°C, indicating that Tk-serpin inhibits TKS more strongly at 80°C than at 40°C. It also irreversibly inhibits chymotrypsin, subtilisin Carlsberg, and proteinase K at 40°C with the k(ass) values comparable to that for TKS at 80°C. Casein zymography showed that Tk-serpin inhibits these proteases by forming a SDS-resistant complex, which is typical to inhibitory serpins. The ratio of moles of Tk-serpin needed to inhibit 1 mol of protease (stoichiometry of inhibition, SI) varies from 40 to 80 at 20°C, but decreases to the minimum values of 3-7 as the temperature increases. The inhibitory activities of Tk-serpin for these proteases increase as the stabilities of these proteases decrease, suggesting that a flexibility of the active-site of protease is one of the determinants for susceptibility of protease to inhibition by Tk-serpin. This report showed for the first time that Tk-serpin inhibits both chymotrypsin- and subtilisin-like serine proteases and its inhibitory activity increases as the temperature increases up to 100°C.
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Affiliation(s)
- Shun-ichi Tanaka
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
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34
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Ricagno S, Pezzullo M, Barbiroli A, Manno M, Levantino M, Santangelo MG, Bonomi F, Bolognesi M. Two latent and two hyperstable polymeric forms of human neuroserpin. Biophys J 2010; 99:3402-11. [PMID: 21081089 PMCID: PMC2980742 DOI: 10.1016/j.bpj.2010.09.021] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2010] [Revised: 09/08/2010] [Accepted: 09/09/2010] [Indexed: 02/02/2023] Open
Abstract
Human neuroserpin (hNS) is a serine protease inhibitor that belongs to the serpin superfamily and is expressed in nervous tissues. The serpin fold is generally characterized by a long exposed loop, termed the reactive center loop, that acts as bait for the target protease. Intramolecular insertion of the reactive center loop into the main serpin β-sheet leads to the serpin latent form. As with other known serpins, hNS pathological mutants have been shown to accumulate as polymers composed of quasi-native protein molecules. Although hNS polymerization has been intensely studied, a general agreement about serpin polymer organization is still lacking. Here we report a biophysical characterization of native hNS that is shown to undergo two distinct conformational transitions, at 55°C and 85°C, both leading to distinct latent and polymeric species. The latent and polymer hNS forms obtained at 45°C and 85°C differ in their chemical and thermal stabilities; furthermore, the hNS polymers also differ in size and morphology. Finally, the 85°C polymer shows a higher content of intermolecular β-sheet interactions than the 45°C polymer. Together, these results suggest a more complex conformational scenario than was previously envisioned, and, in a general context, may help reconcile the current contrasting views on serpin polymerization.
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Affiliation(s)
- Stefano Ricagno
- Dipartimento di Scienze Biomolecolari e Biotecnologie, Centro Interdisciplinare Materiali e Interfacce Nanostrutturati, Università di Milano, Milan, Italy
- Dipartimento di Biochimica, Università di Pavia, Pavia, Italy
- Laboratori di Biotecnologie, Istituto Di Ricovero e Cura a Carattere Scientifico Fondazione Policlinico San Matteo, Pavia, Italy
| | - Margherita Pezzullo
- Dipartimento di Scienze Biomolecolari e Biotecnologie, Centro Interdisciplinare Materiali e Interfacce Nanostrutturati, Università di Milano, Milan, Italy
| | - Alberto Barbiroli
- Sezione di Biochimica, Dipartimento di Scienze Molecolari Agroalimentari, Università di Milano, Milan, Italy
| | - Mauro Manno
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, CNR, Palermo, Italy
| | - Matteo Levantino
- Dipartimento di Scienze Fisiche ed Astronomiche, Università of Palermo, Palermo, Italy
| | | | - Francesco Bonomi
- Sezione di Biochimica, Dipartimento di Scienze Molecolari Agroalimentari, Università di Milano, Milan, Italy
| | - Martino Bolognesi
- Dipartimento di Scienze Biomolecolari e Biotecnologie, Centro Interdisciplinare Materiali e Interfacce Nanostrutturati, Università di Milano, Milan, Italy
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35
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Whisstock JC, Silverman GA, Bird PI, Bottomley SP, Kaiserman D, Luke CJ, Pak SC, Reichhart JM, Huntington JA. Serpins flex their muscle: II. Structural insights into target peptidase recognition, polymerization, and transport functions. J Biol Chem 2010; 285:24307-12. [PMID: 20498368 DOI: 10.1074/jbc.r110.141408] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Inhibitory serpins are metastable proteins that undergo a substantial conformational rearrangement to covalently trap target peptidases. The serpin reactive center loop contributes a majority of the interactions that serpins make during the initial binding to target peptidases. However, structural studies on serpin-peptidase complexes reveal a broader set of contacts on the scaffold of inhibitory serpins that have substantial influence on guiding peptidase recognition. Structural and biophysical studies also reveal how aberrant serpin folding can lead to the formation of domain-swapped serpin multimers rather than the monomeric metastable state. Serpin domain swapping may therefore underlie the polymerization events characteristic of the serpinopathies. Finally, recent structural studies reveal how the serpin fold has been adapted for non-inhibitory functions such as hormone binding.
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Affiliation(s)
- James C Whisstock
- From the Department of Biochemistry and Molecular Biology and ARC Centre of Excellence in Structural and Functional Microbial Genomics, Monash University, Clayton, Victoria 3800, Australia.
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36
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Characterization of the serpin-encoding gene of Bifidobacterium breve 210B. Appl Environ Microbiol 2010; 76:3206-19. [PMID: 20348296 DOI: 10.1128/aem.02938-09] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Members of the serpin (serine protease inhibitor) superfamily have been identified in higher multicellular eukaryotes, as well as in bacteria, although examination of available genome sequences has indicated that homologs of the bacterial serpin-encoding gene (ser) are not widely distributed. In members of the genus Bifidobacterium this gene appears to be present in at least 5, and perhaps up to 9, of the 30 species tested. Moreover, phylogenetic analysis using available bacterial and eukaryotic serpin sequences revealed that bifidobacteria produce serpins that form a separate clade. We characterized the ser(210B) locus of Bifidobacterium breve 210B, which encompasses a number of genes whose deduced protein products display significant similarity to proteins encoded by corresponding loci found in several other bifidobacteria. Northern hybridization, primer extension, microarray, reverse transcription-PCR (RT-PCR), and quantitative real-time PCR (qRT-PCR) analyses revealed that a 3.5-kb polycistronic mRNA encompassing the ser(210B) operon with a single transcriptional start site is strongly induced following treatment of B. breve 210B cultures with some proteases. Interestingly, transcription of other bifidobacterial ser homologs appears to be triggered by different proteases.
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37
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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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Baek JH, Yang WS, Lee C, Yu MH. Functional unfolding of alpha1-antitrypsin probed by hydrogen-deuterium exchange coupled with mass spectrometry. Mol Cell Proteomics 2009; 8:1072-81. [PMID: 19136720 PMCID: PMC2689767 DOI: 10.1074/mcp.m800365-mcp200] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2008] [Revised: 01/08/2009] [Indexed: 11/06/2022] Open
Abstract
The native state of alpha(1)-antitrypsin (alpha(1)AT), a member of the serine protease inhibitor (serpin) family, is considered a kinetically trapped folding intermediate that converts to a more stable form upon complex formation with a target protease. Although previous structural and mutational studies of alpha(1)AT revealed the structural basis of the native strain and the kinetic trap, the mechanism of how the native molecule overcomes the kinetic barrier to reach the final stable conformation during complex formation remains unknown. We hypothesized that during complex formation, a substantial portion of the molecule undergoes unfolding, which we dubbed functional unfolding. Hydrogen-deuterium exchange coupled with ESI-MS was used to analyze this serpin in three forms: native, complexing, and complexed with bovine beta-trypsin. Comparing the deuterium content at the corresponding regions of these three samples, we probed the unfolding of alpha(1)AT during complex formation. A substantial portion of the alpha(1)AT molecule unfolded transiently during complex formation, including not only the regions expected from previous structural studies, such as the reactive site loop, helix F, and the following loop, but also regions not predicted previously, such as helix A, strand 6 of beta-sheet B, and the N terminus. Such unfolding of the native interactions may elevate the free energy level of the kinetically trapped native serpin sufficiently to cross the transition state during complex formation. In the current study, we provide evidence that protein unfolding has to accompany functional execution of the protein molecule.
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Affiliation(s)
- Je-Hyun Baek
- Functional Proteomics Center and section signLife Sciences Division Korea Institute of Science and Technology, Hawolgok-dong, Seongbuk-gu, Seoul 136-791, Korea
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39
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Takehara S, Onda M, Zhang J, Nishiyama M, Yang X, Mikami B, Lomas DA. The 2.1-A crystal structure of native neuroserpin reveals unique structural elements that contribute to conformational instability. J Mol Biol 2009; 388:11-20. [PMID: 19285087 DOI: 10.1016/j.jmb.2009.03.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2008] [Revised: 03/03/2009] [Accepted: 03/04/2009] [Indexed: 11/23/2022]
Abstract
Neuroserpin is a selective inhibitor of tissue-type plasminogen activator (tPA) that plays an important role in neuronal plasticity, memory, and learning. We report here the crystal structure of native human neuroserpin at 2.1 A resolution. The structure has a helical reactive center loop and an omega loop between strands 1B and 2B. The omega loop contributes to the inhibition of tPA, as deletion of this motif reduced the association rate constant with tPA by threefold but had no effect on the kinetics of interaction with urokinase. Point mutations in neuroserpin cause the formation of ordered intracellular polymers that underlie dementia familial encephalopathy with neuroserpin inclusion bodies (FENIB). Wild-type neuroserpin is also unstable and readily forms polymers under near-physiological conditions in vitro. This is, in part, due to the substitution of a conserved alanine for serine at position 340. The replacement of Ser340 by Ala increased the melting temperature by 3 degrees C and reduced polymerization as compared to wild-type neuroserpin. Similarly, neuroserpin has Asn-Leu-Val at the end of helix F and thus differs markedly from the Gly-X-Ile consensus sequence of the serpins. Restoration of these amino acids to the consensus sequence increased thermal stability and reduced the polymerization of neuroserpin and its transition to the latent conformer. Moreover, introduction of the consensus sequence into S49P neuroserpin that causes FENIB increased the stability and inhibitory activity of the mutant, as well as blocked polymerization and increased the yield of protein during refolding. These data provide a molecular explanation for the inherent instability of neuroserpin and the effect of point mutations that underlie the dementia FENIB.
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Affiliation(s)
- Sayaka Takehara
- Division of Applied Life Sciences, The Graduate School of Agriculture, Kyoto University, Uji 611-0011, Japan
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40
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Ricagno S, Caccia S, Sorrentino G, Antonini G, Bolognesi M. Human neuroserpin: structure and time-dependent inhibition. J Mol Biol 2009; 388:109-21. [PMID: 19265707 DOI: 10.1016/j.jmb.2009.02.056] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2009] [Revised: 02/19/2009] [Accepted: 02/24/2009] [Indexed: 11/23/2022]
Abstract
Human neuroserpin (hNS) is a protein serine protease inhibitor expressed mainly in the nervous system, where it plays key roles in neural development and plasticity by primarily targeting tissue plasminogen activator (tPA). Four hNS mutations are associated to a form of autosomal dominant dementia, known as familial encephalopathy with neuroserpin inclusion bodies. The medical interest in and the lack of structural information on hNS prompted us to study the crystal structure of native and cleaved hNS, reported here at 3.15 and 1.85 A resolution, respectively. In the light of the three-dimensional structures, we focus on the hNS reactive centre loop in its intact and cleaved conformations relative to the current serpin polymerization models and discuss the protein sites hosting neurodegenerative mutations. On the basis of homologous serpin structures, we suggest the location of a protein surface site that may stabilize the hNS native (metastable) form. In parallel, we present the results of kinetic studies on hNS inhibition of tPA. Our data analysis stresses the instability of the hNS-tPA complex with a dissociation half-life of minutes compared to a half-life of weeks observed for other serpin-cognate protease complexes.
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Affiliation(s)
- Stefano Ricagno
- Department of Biomolecular Sciences and Biotechnology, CNR-INFM and CIMAINA, University of Milano, Via Celoria 26, 20133 Milan, Italy
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41
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42
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Abstract
The serpin α2-antiplasmin (SERPINF2) is the principal inhibitor of plasmin and inhibits fibrinolysis. Accordingly, α2-antiplasmin deficiency in humans results in uncontrolled fibrinolysis and a bleeding disorder. α2-antiplasmin is an unusual serpin, in that it contains extensive N- and C-terminal sequences flanking the serpin domain. The N-terminal sequence is crosslinked to fibrin by factor XIIIa, whereas the C-terminal region mediates the initial interaction with plasmin. To understand how this may happen, we have determined the 2.65Å X-ray crystal structure of an N-terminal truncated murine α2-antiplasmin. The structure reveals that part of the C-terminal sequence is tightly associated with the body of the serpin. This would be anticipated to position the flexible plasmin-binding portion of the C-terminus in close proximity to the serpin Reactive Center Loop where it may act as a template to accelerate serpin/protease interactions.
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43
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Zhang Q, Law RHP, Bottomley SP, Whisstock JC, Buckle AM. A structural basis for loop C-sheet polymerization in serpins. J Mol Biol 2008; 376:1348-59. [PMID: 18234218 DOI: 10.1016/j.jmb.2007.12.050] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2007] [Revised: 12/17/2007] [Accepted: 12/20/2007] [Indexed: 10/22/2022]
Abstract
In this study, we report the X-ray crystal structure of an N-terminally truncated variant of the bacterial serpin, tengpin (tengpinDelta42). Our data reveal that tengpinDelta42 adopts a variation of the latent conformation in which the reactive center loop is hyperinserted into the A beta-sheet and removed from the vicinity of the C-sheet. This conformational change leaves the C beta-sheet completely exposed and permits antiparallel edge-strand interactions between the exposed portion of the reactive center loop of one molecule and strand s2C of the C beta-sheet of the neighboring molecule in the crystal lattice. Our structural data thus reveal that tengpinDelta42 forms a loop C-sheet polymer in the crystal lattice. In vivo serpins have a propensity to misfold and form long-chain polymers, a process that underlies serpinopathies such as emphysema, thrombosis and dementia. Native serpins are thought to polymerize via a loop A-sheet mechanism. However, studies on plasminogen activator inhibitor 1 and the S49P variant of human neuroserpin reveal that the latent form of these molecules can also polymerize. Polymerization of latent neuroserpin may be important for the development of familial encephalopathy with neuroserpin inclusion bodies. Our structural data provide a possible mechanism for polymerization by latent serpins.
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Affiliation(s)
- Qingwei Zhang
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Melbourne, VIC 3800, Australia
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44
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Cabrita LD, Irving JA, Pearce MC, Whisstock JC, Bottomley SP. Aeropin from the extremophile Pyrobaculum aerophilum bypasses the serpin misfolding trap. J Biol Chem 2007; 282:26802-26809. [PMID: 17635906 DOI: 10.1074/jbc.m705020200] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Serpins are metastable proteinase inhibitors. Serpin metastability drives both a large conformational change that is utilized during proteinase inhibition and confers an inherent structural flexibility that renders serpins susceptible to aggregation under certain conditions. These include point mutations (the basis of a number of important human genetic diseases), small changes in pH, and an increase in temperature. Many studies of serpins from mesophilic organisms have highlighted an inverse relationship: mutations that confer a marked increase in serpin stability compromise inhibitory activity. Here we present the first biophysical characterization of a metastable serpin from a hyperthermophilic organism. Aeropin, from the archaeon Pyrobaculum aerophilum, is both highly stable and an efficient proteinase inhibitor. We also demonstrate that because of high kinetic barriers, aeropin does not readily form the partially unfolded precursor to serpin aggregation. We conclude that stability and activity are not mutually exclusive properties in the context of the serpin fold, and propose that the increased stability of aeropin is caused by an unfolding pathway that minimizes the formation of an aggregation-prone intermediate ensemble, thereby enabling aeropin to bypass the misfolding fate observed with other serpins.
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Affiliation(s)
- Lisa D Cabrita
- Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
| | - James A Irving
- Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
| | - Mary C Pearce
- Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
| | - James C Whisstock
- Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia; ARC Centre of Excellence for Structural and Function Microbial Genomics, Monash University, Clayton 3800, Australia.
| | - Stephen P Bottomley
- Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia.
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