1
|
Guay KP, Ke H, Gierasch LM, Gershenson A, Hebert DN. Monitoring the Secretion and Activity of Alpha-1 Antitrypsin in Various Mammalian Cell Types. Methods Mol Biol 2024; 2750:143-163. [PMID: 38108975 PMCID: PMC10918612 DOI: 10.1007/978-1-0716-3605-3_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Overexpression of recombinant protein in mammalian cells is widely used for producing biologics, as protein maturation and post-translational modifications are similar to human cells. Some therapeutics, such as mRNA vaccines, target nonnative cells that may contain inefficient secretory machinery. For example, gene replacement therapies for alpha-1 antitrypsin (AAT), a glycoprotein normally produced in hepatocytes, are often targeted to muscle cells due to ease of delivery. In this chapter, we define methods for expressing AAT in representative cell types such as Huh-7; hepatocytes; Chinese hamster ovarian cells (CHO), a common host to produce biologics; and C2C12, a muscle progenitor cell line. Methods for metabolically labeling AAT to monitor secretion in these cell lines are described along with the use of proteostasis activators to increase the amount of AAT secreted in both C2C12 myoblasts and differentiated myotubes. Assays to assess the activity and glycan composition of overexpressed AAT are also presented. The usage of the proteostasis activator SAHA provided a 40% improvement in expression of active AAT in muscle-like cells and may be an advantageous adjuvant for recombinant production of proteins delivered by mRNA vaccines.
Collapse
Affiliation(s)
- Kevin P Guay
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, USA
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA, USA
| | - Haiping Ke
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, USA
| | - Lila M Gierasch
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, USA
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA, USA
- Department of Chemistry, University of Massachusetts, Amherst, MA, USA
| | - Anne Gershenson
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, USA
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA, USA
| | - Daniel N Hebert
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, USA.
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA, USA.
| |
Collapse
|
2
|
Guay KP, Ke H, Canniff NP, George GT, Eyles SJ, Mariappan M, Contessa JN, Gershenson A, Gierasch LM, Hebert DN. ER chaperones use a protein folding and quality control glyco-code. Mol Cell 2023; 83:4524-4537.e5. [PMID: 38052210 PMCID: PMC10790639 DOI: 10.1016/j.molcel.2023.11.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/18/2023] [Accepted: 11/07/2023] [Indexed: 12/07/2023]
Abstract
N-glycans act as quality control tags by recruiting lectin chaperones to assist protein maturation in the endoplasmic reticulum. The location and composition of N-glycans (glyco-code) are key to the chaperone-selection process. Serpins, a class of serine protease inhibitors, fold non-sequentially to achieve metastable active states. Here, the role of the glyco-code in assuring successful maturation and quality control of two human serpins, alpha-1 antitrypsin (AAT) and antithrombin III (ATIII), is described. We find that AAT, which has glycans near its N terminus, is assisted by early lectin chaperone binding. In contrast, ATIII, which has more C-terminal glycans, is initially helped by BiP and then later by lectin chaperones mediated by UGGT reglucosylation. UGGT action is increased for misfolding-prone disease variants, and these clients are preferentially glucosylated on their most C-terminal glycan. Our study illustrates how serpins utilize N-glycan presence, position, and composition to direct their proper folding, quality control, and trafficking.
Collapse
Affiliation(s)
- Kevin P Guay
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA, USA; Program in Molecular and Cellular Biology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Haiping Ke
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Nathan P Canniff
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA, USA; Program in Molecular and Cellular Biology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Gracie T George
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Stephen J Eyles
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA, USA; Program in Molecular and Cellular Biology, University of Massachusetts Amherst, Amherst, MA, USA; Institute for Applied Life Sciences, Mass Spectrometry Center, University of Massachusetts Amherst, Amherst, MA, USA
| | - Malaiyalam Mariappan
- Department of Cell Biology, Nanobiology Institute, Yale School of Medicine, West Haven, CT, USA
| | - Joseph N Contessa
- Departments of Therapeutic Radiology and Pharmacology, Yale School of Medicine, New Haven, CT, USA
| | - Anne Gershenson
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA, USA; Program in Molecular and Cellular Biology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Lila M Gierasch
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA, USA; Program in Molecular and Cellular Biology, University of Massachusetts Amherst, Amherst, MA, USA; Department of Chemistry, University of Massachusetts Amherst, Amherst, MA, USA
| | - Daniel N Hebert
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA, USA; Program in Molecular and Cellular Biology, University of Massachusetts Amherst, Amherst, MA, USA.
| |
Collapse
|
3
|
Kaur U, Kihn KC, Ke H, Kuo W, Gierasch LM, Hebert DN, Wintrode PL, Deredge D, Gershenson A. The conformational landscape of a serpin N-terminal subdomain facilitates folding and in-cell quality control. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.24.537978. [PMID: 37163105 PMCID: PMC10168285 DOI: 10.1101/2023.04.24.537978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Many multi-domain proteins including the serpin family of serine protease inhibitors contain non-sequential domains composed of regions that are far apart in sequence. Because proteins are translated vectorially from N- to C-terminus, such domains pose a particular challenge: how to balance the conformational lability necessary to form productive interactions between early and late translated regions while avoiding aggregation. This balance is mediated by the protein sequence properties and the interactions of the folding protein with the cellular quality control machinery. For serpins, particularly α 1 -antitrypsin (AAT), mutations often lead to polymer accumulation in cells and consequent disease suggesting that the lability/aggregation balance is especially precarious. Therefore, we investigated the properties of progressively longer AAT N-terminal fragments in solution and in cells. The N-terminal subdomain, residues 1-190 (AAT190), is monomeric in solution and efficiently degraded in cells. More β -rich fragments, 1-290 and 1-323, form small oligomers in solution, but are still efficiently degraded, and even the polymerization promoting Siiyama (S53F) mutation did not significantly affect fragment degradation. In vitro, the AAT190 region is among the last regions incorporated into the final structure. Hydrogen-deuterium exchange mass spectrometry and enhanced sampling molecular dynamics simulations show that AAT190 has a broad, dynamic conformational ensemble that helps protect one particularly aggregation prone β -strand from solvent. These AAT190 dynamics result in transient exposure of sequences that are buried in folded, full-length AAT, which may provide important recognition sites for the cellular quality control machinery and facilitate degradation and, under favorable conditions, reduce the likelihood of polymerization.
Collapse
Affiliation(s)
- Upneet Kaur
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA 01003
| | - Kyle C. Kihn
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201
| | - Haiping Ke
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA 01003
| | - Weiwei Kuo
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA 01003
| | - Lila M. Gierasch
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA 01003
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA 01003
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003
| | - Daniel N. Hebert
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA 01003
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA 01003
| | - Patrick L. Wintrode
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201
| | - Daniel Deredge
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201
| | - Anne Gershenson
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA 01003
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA 01003
| |
Collapse
|
4
|
Espinoza MF, Nguyen KK, Sycks MM, Lyu Z, Quanrud GM, Montoya MR, Genereux JC. Heat shock protein Hspa13 regulates endoplasmic reticulum and cytosolic proteostasis through modulation of protein translocation. J Biol Chem 2022; 298:102597. [PMID: 36244454 PMCID: PMC9691929 DOI: 10.1016/j.jbc.2022.102597] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 09/29/2022] [Accepted: 10/03/2022] [Indexed: 11/06/2022] Open
Abstract
Most eukaryotic secretory proteins are cotranslationally translocated through Sec61 into the endoplasmic reticulum (ER). Because these proteins have evolved to fold in the ER, their mistargeting is associated with toxicity. Genetic experiments have implicated the ER heat shock protein 70 (Hsp70) Hspa13/STCH as involved in processing of nascent secretory proteins. Herein, we evaluate the role of Hspa13 in protein import and the maintenance of cellular proteostasis in human cells, primarily using the human embryonic kidney 293T cell line. We find that Hspa13 interacts primarily with the Sec61 translocon and its associated factors. Hspa13 overexpression inhibits translocation of the secreted protein transthyretin, leading to accumulation and aggregation of immature transthyretin in the cytosol. ATPase-inactive mutants of Hspa13 further inhibit translocation and maturation of secretory proteins. While Hspa13 overexpression inhibits cell growth and ER quality control, we demonstrate that HSPA13 knockout destabilizes proteostasis and increases sensitivity to ER disruption. Thus, we propose that Hspa13 regulates import through the translocon to maintain both ER and cytosolic protein homeostasis. The raw mass spectrometry data associated with this article have been deposited in the PRIDE archive and can be accessed at PXD033498.
Collapse
Affiliation(s)
- Mateo F Espinoza
- Graduate Program in Microbiology, University of California, Riverside, California, USA
| | - Khanh K Nguyen
- Department of Chemistry, University of California, Riverside, California, USA
| | - Melody M Sycks
- Department of Chemistry, University of California, Riverside, California, USA
| | - Ziqi Lyu
- Department of Chemistry, University of California, Riverside, California, USA
| | - Guy M Quanrud
- Department of Chemistry, University of California, Riverside, California, USA
| | - Maureen R Montoya
- Department of Chemistry, University of California, Riverside, California, USA
| | - Joseph C Genereux
- Graduate Program in Microbiology, University of California, Riverside, California, USA; Department of Chemistry, University of California, Riverside, California, USA.
| |
Collapse
|
5
|
Finkelstein AV, Bogatyreva NS, Ivankov DN, Garbuzynskiy SO. Protein folding problem: enigma, paradox, solution. Biophys Rev 2022; 14:1255-1272. [PMID: 36659994 PMCID: PMC9842845 DOI: 10.1007/s12551-022-01000-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 09/19/2022] [Indexed: 01/22/2023] Open
Abstract
The ability of protein chains to spontaneously form their three-dimensional structures is a long-standing mystery in molecular biology. The most conceptual aspect of this mystery is how the protein chain can find its native, "working" spatial structure (which, for not too big protein chains, corresponds to the global free energy minimum) in a biologically reasonable time, without exhaustive enumeration of all possible conformations, which would take billions of years. This is the so-called "Levinthal's paradox." In this review, we discuss the key ideas and discoveries leading to the current understanding of protein folding kinetics, including folding landscapes and funnels, free energy barriers at the folding/unfolding pathways, and the solution of Levinthal's paradox. A special role here is played by the "all-or-none" phase transition occurring at protein folding and unfolding and by the point of thermodynamic (and kinetic) equilibrium between the "native" and the "unfolded" phases of the protein chain (where the theory obtains the simplest form). The modern theory provides an understanding of key features of protein folding and, in good agreement with experiments, it (i) outlines the chain length-dependent range of protein folding times, (ii) predicts the observed maximal size of "foldable" proteins and domains. Besides, it predicts the maximal size of proteins and domains that fold under solely thermodynamic (rather than kinetic) control. Complementarily, a theoretical analysis of the number of possible protein folding patterns, performed at the level of formation and assembly of secondary structures, correctly outlines the upper limit of protein folding times.
Collapse
Affiliation(s)
- Alexei V. Finkelstein
- Institute of Protein Research of the Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
- Biotechnology Department of the Lomonosov Moscow State University, 4 Institutskaya Str, 142290 Pushchino, Moscow Region, Russia
- Biology Department of the Lomonosov Moscow State University, 1-12 Leninskie Gory, 119991 Moscow, Russia
| | - Natalya S. Bogatyreva
- Institute of Protein Research of the Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
| | - Dmitry N. Ivankov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
| | - Sergiy O. Garbuzynskiy
- Institute of Protein Research of the Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
| |
Collapse
|
6
|
Liu X, Kouassi KGW, Vanbever R, Dumoulin M. Impact of the PEG length and PEGylation site on the structural, thermodynamic, thermal, and proteolytic stability of mono-PEGylated alpha-1 antitrypsin. Protein Sci 2022; 31:e4392. [PMID: 36040264 PMCID: PMC9375436 DOI: 10.1002/pro.4392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 11/11/2022]
Abstract
Conjugation to polyethylene glycol (PEG) is a widely used approach to improve the therapeutic value of proteins essentially by prolonging their body residence time. PEGylation may however induce changes in the structure and/or the stability of proteins and thus on their function(s). The effects of PEGylation on the thermodynamic stability can either be positive (stabilization), negative (destabilization), or neutral (no effect). Moreover, various factors such as the PEG length and PEGylation site can influence the consequences of PEGylation on the structure and stability of proteins. In this study, the effects of PEGylation on the structure, stability, and polymerization of alpha1-antitrypsin (AAT) were investigated, using PEGs with different lengths, different structures (linear or 2-armed) and different linking chemistries (via amine or thiol) at two distinct positions of the sequence. The results show that whatever the size, position, and structure of PEG chains, PEGylation (a) does not induce significant changes in AAT structure (either at the secondary or tertiary level); (b) does not alter the stability of the native protein upon both chemical- and heat-induced denaturation; and (c) does not prevent AAT to fully refold and recover its activity following chemical denaturation. However, the propensity of AAT to aggregate upon heat treatment was significantly decreased by PEGylation, although PEGylation did not prevent the irreversible inactivation of the enzyme. Moreover, conjugation to PEG, especially 2-armed 40 kDa PEG, greatly improved the proteolytic resistance of AAT. PEGylation of AAT could be a promising strategy to prolong its half-life after infusion in AAT-deficient patients and thereby decrease the frequency of infusions.
Collapse
Affiliation(s)
- Xiao Liu
- Advanced Drug Delivery and BiomaterialsLouvain Drug Research Institute, Université catholique de Louvain (UCLouvain)BrusselsBelgium
| | - Kobenan G. W. Kouassi
- Advanced Drug Delivery and BiomaterialsLouvain Drug Research Institute, Université catholique de Louvain (UCLouvain)BrusselsBelgium
| | - Rita Vanbever
- Advanced Drug Delivery and BiomaterialsLouvain Drug Research Institute, Université catholique de Louvain (UCLouvain)BrusselsBelgium
| | - Mireille Dumoulin
- Department of Life SciencesInBios, Center for Protein Engineering, Nanobodies to Explore Protein Structure and Functions, University of LiègeLiègeBelgium
| |
Collapse
|
7
|
Robson B. De novo protein folding on computers. Benefits and challenges. Comput Biol Med 2022; 143:105292. [PMID: 35158120 DOI: 10.1016/j.compbiomed.2022.105292] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 01/05/2023]
Abstract
There has been recent success in prediction of the three-dimensional folded native structures of proteins, most famously by the AlphaFold Algorithm running on Google's/Alphabet's DeepMind computer. However, this largely involves machine learning of protein structures and is not a de novo protein structure prediction method for predicting three-dimensional structures from amino acid residue sequences. A de novo approach would be based almost entirely on general principles of energy and entropy that govern protein folding energetics, and importantly do so without the use of the amino acid sequences and structural features of other proteins. Most consider that problem as still unsolved even though it has occupied leading scientists for decades. Many consider that it remains one of the major outstanding issues in modern science. There is crucial continuing help from experimental findings on protein unfolding and refolding in the laboratory, but only to a limited extent because many researchers consider that the speed by which real proteins folds themselves, often from milliseconds to minutes, is itself still not fully understood. This is unfortunate, because a practical solution to the problem would probably have a major effect on personalized medicine, the pharmaceutical industry, biotechnology, and nanotechnology, including for example "smaller" tasks such as better modeling of flexible "unfolded" regions of the SARS-COV-2 spike glycoprotein when interacting with its cell receptor, antibodies, and therapeutic agents. Some important ideas from earlier studies are given before moving on to lessons from periodic and aperiodic crystals, and a possible role for quantum phenomena. The conclusion is that better computation of entropy should be the priority, though that is presented guardedly.
Collapse
Affiliation(s)
- Barry Robson
- Ingine Inc.Cleveland Ohio and The Dirac Foundation, Oxfordshire, UK.
| |
Collapse
|
8
|
Plessa E, Chu LP, Chan SHS, Thomas OL, Cassaignau AME, Waudby CA, Christodoulou J, Cabrita LD. Nascent chains can form co-translational folding intermediates that promote post-translational folding outcomes in a disease-causing protein. Nat Commun 2021; 12:6447. [PMID: 34750347 PMCID: PMC8576036 DOI: 10.1038/s41467-021-26531-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 10/01/2021] [Indexed: 01/16/2023] Open
Abstract
During biosynthesis, proteins can begin folding co-translationally to acquire their biologically-active structures. Folding, however, is an imperfect process and in many cases misfolding results in disease. Less is understood of how misfolding begins during biosynthesis. The human protein, alpha-1-antitrypsin (AAT) folds under kinetic control via a folding intermediate; its pathological variants readily form self-associated polymers at the site of synthesis, leading to alpha-1-antitrypsin deficiency. We observe that AAT nascent polypeptides stall during their biosynthesis, resulting in full-length nascent chains that remain bound to ribosome, forming a persistent ribosome-nascent chain complex (RNC) prior to release. We analyse the structure of these RNCs, which reveals compacted, partially-folded co-translational folding intermediates possessing molten-globule characteristics. We find that the highly-polymerogenic mutant, Z AAT, forms a distinct co-translational folding intermediate relative to wild-type. Its very modest structural differences suggests that the ribosome uniquely tempers the impact of deleterious mutations during nascent chain emergence. Following nascent chain release however, these co-translational folding intermediates guide post-translational folding outcomes thus suggesting that Z's misfolding is initiated from co-translational structure. Our findings demonstrate that co-translational folding intermediates drive how some proteins fold under kinetic control, and may thus also serve as tractable therapeutic targets for human disease.
Collapse
Affiliation(s)
- Elena Plessa
- Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - Lien P Chu
- Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - Sammy H S Chan
- Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - Oliver L Thomas
- Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - Anaïs M E Cassaignau
- Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - Christopher A Waudby
- Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - John Christodoulou
- Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK. .,School of Crystallography, Birkbeck College, University of London, Malet Street, London, WC1E 7HX, UK.
| | - Lisa D Cabrita
- Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK.
| |
Collapse
|
9
|
Lior Y, Shtriker E, Kahremany S, Lewis EC, Gruzman A. Development of anti-inflammatory peptidomimetics based on the structure of human alpha1-antitrypsin. Eur J Med Chem 2021; 228:113969. [PMID: 34763945 DOI: 10.1016/j.ejmech.2021.113969] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 10/29/2021] [Accepted: 10/30/2021] [Indexed: 01/10/2023]
Abstract
Human α1-antitrypsin (hAAT) has two distinguishing functions: anti-protease activity and regulation of the immune system. In the present study we hypothesized that those two protein functions are mediated by different structural domains on the hAAT surface. Indeed, such biologically active immunoregulatory sites (not associated with canonical anti-protease activity) on the surface of hAAT were identified by in silico methods. Several peptides were derived from those immunoregulatory sites. Four peptides exhibited impressive biological effects in pharmacological concentration ranges. Peptidomimetic (14) was developed, based on the structure of the most druggable and active peptide. The compound exhibited a potent anti-inflammatory activity in vitro and in vivo. Such a compound could be used as a basis for developing novel anti-inflammatory drug candidates and as a research tool for better understanding hAAT functions.
Collapse
Affiliation(s)
- Yotam Lior
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Efrat Shtriker
- Department of Chemistry, Faculty of Exact Sciences, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Shirin Kahremany
- Department of Chemistry, Faculty of Exact Sciences, Bar-Ilan University, Ramat Gan, 5290002, Israel; The Skin Research Institute, The Dead Sea and Arava Science Center, 86910, Masada, Israel
| | - Eli C Lewis
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Arie Gruzman
- Department of Chemistry, Faculty of Exact Sciences, Bar-Ilan University, Ramat Gan, 5290002, Israel.
| |
Collapse
|
10
|
Britt HM, Cragnolini T, Thalassinos K. Integration of Mass Spectrometry Data for Structural Biology. Chem Rev 2021; 122:7952-7986. [PMID: 34506113 DOI: 10.1021/acs.chemrev.1c00356] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Mass spectrometry (MS) is increasingly being used to probe the structure and dynamics of proteins and the complexes they form with other macromolecules. There are now several specialized MS methods, each with unique sample preparation, data acquisition, and data processing protocols. Collectively, these methods are referred to as structural MS and include cross-linking, hydrogen-deuterium exchange, hydroxyl radical footprinting, native, ion mobility, and top-down MS. Each of these provides a unique type of structural information, ranging from composition and stoichiometry through to residue level proximity and solvent accessibility. Structural MS has proved particularly beneficial in studying protein classes for which analysis by classic structural biology techniques proves challenging such as glycosylated or intrinsically disordered proteins. To capture the structural details for a particular system, especially larger multiprotein complexes, more than one structural MS method with other structural and biophysical techniques is often required. Key to integrating these diverse data are computational strategies and software solutions to facilitate this process. We provide a background to the structural MS methods and briefly summarize other structural methods and how these are combined with MS. We then describe current state of the art approaches for the integration of structural MS data for structural biology. We quantify how often these methods are used together and provide examples where such combinations have been fruitful. To illustrate the power of integrative approaches, we discuss progress in solving the structures of the proteasome and the nuclear pore complex. We also discuss how information from structural MS, particularly pertaining to protein dynamics, is not currently utilized in integrative workflows and how such information can provide a more accurate picture of the systems studied. We conclude by discussing new developments in the MS and computational fields that will further enable in-cell structural studies.
Collapse
Affiliation(s)
- Hannah M Britt
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom
| | - Tristan Cragnolini
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom.,Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, United Kingdom
| | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom.,Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, United Kingdom
| |
Collapse
|
11
|
Bianchera A, Alomari E, Bruno S. Augmentation therapy with alpha 1-antitrypsin: present and future of production, formulation, and delivery. Curr Med Chem 2021; 29:385-410. [PMID: 34036902 DOI: 10.2174/0929867328666210525161942] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 03/24/2021] [Accepted: 04/12/2021] [Indexed: 11/22/2022]
Abstract
Alpha 1-antitrypsin is one of the first protein therapeutics introduced on the market - more than 30 years ago - and, to date, it is indicated only for the treatment of the severe forms of a genetic condition known as alpha-1 antitrypsin deficiency. The only approved preparations are derived from plasma, posing potential problems associated with its limited supply and high processing costs. Moreover, augmentation therapy with alpha 1-antitrypsin is still limited to intravenous infusions, a cumbersome regimen for patients. Here, we review the recent literature on its possible future developments, focusing on i) the recombinant alternatives to the plasma-derived protein, ii) novel formulations, and iii) novel administration routes. Regulatory issues and the still unclear noncanonical functions of alpha 1-antitrypsin - possibly associated with the glycosylation pattern found only in the plasma-derived protein - have hindered the introduction of new products. However, potentially new therapeutic indications other than the treatment of alpha-1 antitrypsin deficiency might open the way to new sources and new formulations.
Collapse
Affiliation(s)
- Annalisa Bianchera
- Dipartimento di Scienze degli Alimenti e del Farmaco, University of Parma, Parma, Italy
| | - Esraa Alomari
- Dipartimento di Scienze degli Alimenti e del Farmaco, University of Parma, Parma, Italy
| | - Stefano Bruno
- Dipartimento di Scienze degli Alimenti e del Farmaco, University of Parma, Parma, Italy
| |
Collapse
|
12
|
N-Glycosylation as a Tool to Study Antithrombin Secretion, Conformation, and Function. Int J Mol Sci 2021; 22:ijms22020516. [PMID: 33419227 PMCID: PMC7825591 DOI: 10.3390/ijms22020516] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/31/2020] [Accepted: 12/31/2020] [Indexed: 11/23/2022] Open
Abstract
N-linked glycosylation is a crucial post-translational modification involved in protein folding, function, and clearance. N-linked glycosylation is also used therapeutically to enhance the half-lives of many proteins. Antithrombin, a serpin with four potential N-glycosylation sites, plays a pivotal role in hemostasis, wherein its deficiency significantly increases thrombotic risk. In this study, we used the introduction of N-glycosylation sites as a tool to explore what effect this glycosylation has on the protein folding, secretion, and function of this key anticoagulant. To accomplish this task, we introduced an additional N-glycosylation sequence in each strand. Interestingly, all regions that likely fold rapidly or were surrounded by lysines were not glycosylated even though an N-glycosylation sequon was present. The new sequon in the strands of the A- and B-sheets reduced secretion, and the B-sheet was more sensitive to these changes. However, the mutations in the strands of the C-sheet allowed correct folding and secretion, which resulted in functional variants. Therefore, our study revealed crucial regions for antithrombin secretion and could potentially apply to all serpins. These results could also help us understand the functional effects of natural variants causing type-I deficiencies.
Collapse
|
13
|
Terse VL, Gosavi S. The Molecular Mechanism of Domain Swapping of the C-Terminal Domain of the SARS-Coronavirus Main Protease. Biophys J 2020; 120:504-516. [PMID: 33359834 PMCID: PMC7837137 DOI: 10.1016/j.bpj.2020.11.2277] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 11/09/2020] [Accepted: 11/24/2020] [Indexed: 11/25/2022] Open
Abstract
In three-dimensional domain swapping, two protein monomers exchange a part of their structures to form an intertwined homodimer, whose subunits resemble the monomer. Several viral proteins domain swap to increase their structural complexity or functional avidity. The main protease (Mpro) of the severe acute respiratory syndrome (SARS) coronavirus proteolyzes viral polyproteins and has been a target for anti-SARS drug design. Domain swapping in the α-helical C-terminal domain of Mpro (MproC) locks Mpro into a hyperactive octameric form that is hypothesized to promote the early stages of viral replication. However, in the absence of a complete molecular understanding of the mechanism of domain swapping, investigations into the biological relevance of this octameric Mpro have stalled. Isolated MproC can exist as a monomer or a domain-swapped dimer. Here, we investigate the mechanism of domain swapping of MproC using coarse-grained structure-based models and molecular dynamics simulations. Our simulations recapitulate several experimental features of MproC folding. Further, we find that a contact between a tryptophan in the MproC domain-swapping hinge and an arginine elsewhere forms early during folding, modulates the folding route, and promotes domain swapping to the native structure. An examination of the sequence and the structure of the tryptophan containing hinge loop shows that it has a propensity to form multiple secondary structures and contacts, indicating that it could be stabilized into either the monomer- or dimer-promoting conformations by mutations or ligand binding. Finally, because all residues in the tryptophan loop are identical in SARS-CoV and SARS-CoV-2, mutations that modulate domain swapping may provide insights into the role of octameric Mpro in the early-stage viral replication of both viruses.
Collapse
Affiliation(s)
- Vishram L Terse
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Shachi Gosavi
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India.
| |
Collapse
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
Lior Y, Jasevitch M, Ochayon DE, Zaretsky M, Lewis EC, Aharoni A. Application of directed evolution and back-to-consensus algorithms to human alpha1-antitrypsin leads to diminished anti-protease activity and augmented anti-inflammatory activities. Cell Immunol 2020; 355:104135. [PMID: 32703529 DOI: 10.1016/j.cellimm.2020.104135] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 05/14/2020] [Accepted: 05/18/2020] [Indexed: 12/21/2022]
Abstract
Primarily known as an elastase inhibitor, human alpha1-antitrypsin also exerts anti-inflammatory and immunomodulatory effects, both in vitro and in vivo. While the anti-protease mechanism of alpha1-antitrypsin is attributed to a particular protein domain coined the reactive center loop, anti-inflammatory and immunomodulatory loci within the molecule remain to be identified. In the present study, directed evolution and back-to-consensus algorithms were applied to human alpha1-antitrypsin. Six unique functional candidate sites were identified on the surface of the molecule; in manipulating these sites by point mutations, a recombinant mutant form of alpha1-antitrypsin was produced, depicting a requirement for sites outside the reactive center loop as essential for protease inhibition, and displaying enhanced anti-inflammatory activities. Taken together, outcomes of the present study establish a potential use for directed evolution in advancing our understanding of site-specific protein functions, offering a platform for development of context- and disease-specific alpha1-antitrypsin-based therapeutics.
Collapse
Affiliation(s)
- Yotam Lior
- Department of Clinical Biochemistry & Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel.
| | - Maria Jasevitch
- Department of Clinical Biochemistry & Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - David E Ochayon
- Department of Clinical Biochemistry & Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Mariana Zaretsky
- Department of Life Sciences, Ben-Gurion University of the Negev and National Institute for Biotechnology, Be'er Sheva, Israel
| | - Eli C Lewis
- Department of Clinical Biochemistry & Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Amir Aharoni
- Department of Life Sciences, Ben-Gurion University of the Negev and National Institute for Biotechnology, Be'er Sheva, Israel
| |
Collapse
|
16
|
Bashir A, Hazari Y, Pal D, Maity D, Bashir S, Singh LR, Shah NN, Fazili KM. Aggregation of M3 (E376D) variant of alpha1- antitrypsin. Sci Rep 2020; 10:8290. [PMID: 32427833 PMCID: PMC7237413 DOI: 10.1038/s41598-020-64860-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 04/09/2020] [Indexed: 11/22/2022] Open
Abstract
Alpha1-antitrypsin (α1AT) is an abundant serine-protease inhibitor in circulation. It has an important role in neutralizing the neutrophil elastase activity. Different pathogenic point mutations like Z(E342K)-α1AT have been implicated in the development of liver cirrhosis and Chronic Obstructive Pulmonary Disease (COPD), the latter being a cluster of progressive lung diseases including chronic bronchitis and emphysema. M3-α1AT (376Glu > Asp) is another variant of α1AT which so far is largely being considered as normal though increased frequency of the variant has been reported in many human diseases including COPD. We also observed increased frequency of M3-α1AT in COPD cases in Kashmiri population. The frequency of heterozygous (AC) genotype in cases and controls was 58.57% and 27.61% (odds-ratio 6.53 (2.27-15.21); p < 0.0001) respectively, while homozygous CC genotype was found to be 21.42% and 6.66% (odds-ratio 10.56 (3.63-18.64); p < 0.0001) respectively. Comparative in vitro investigations that include trypsin‒antitrypsin assay, Circular Dichroism spectroscopy and dynamic light scattering performed on wild-type (M-α1AT), M3-α1AT, and Z-α1AT proteins along with the molecular dynamics simulations revealed that M3-α1AT has properties similar to Z-α1AT capable of forming aggregates of varied size. Our maiden observations suggest that M3-α1AT may contribute to the pathogenesis of COPD and other disorders by mechanisms that warrant further investigations.
Collapse
Affiliation(s)
- Arif Bashir
- UPR Signalling Laboratory, Department of Biotechnology, University of Kashmir, Srinagar, 190006, Jammu and Kashmir, India.
| | - Younis Hazari
- UPR Signalling Laboratory, Department of Biotechnology, University of Kashmir, Srinagar, 190006, Jammu and Kashmir, India
- Laboratory of Proteostasis Control and Biomedicine, Faculty of Medicine, University of Chile, Av. Independencia, 1027, Santiago, Chile
| | - Debnath Pal
- Department of Computational and Data Sciences (CDS), Indian Institute of Sciences, Bengaluru, 560012, India
| | - Dibyajyoti Maity
- Department of Computational and Data Sciences (CDS), Indian Institute of Sciences, Bengaluru, 560012, India
| | - Samirul Bashir
- UPR Signalling Laboratory, Department of Biotechnology, University of Kashmir, Srinagar, 190006, Jammu and Kashmir, India
| | | | - Naveed Nazir Shah
- Department of Chest Medicine, Govt. Medical College, Srinagar, 190001, Jammu and Kashmir, India
| | - Khalid Majid Fazili
- UPR Signalling Laboratory, Department of Biotechnology, University of Kashmir, Srinagar, 190006, Jammu and Kashmir, India.
| |
Collapse
|
17
|
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.
Collapse
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.
| |
Collapse
|
18
|
Ponard D, Gaboriaud C, Charignon D, Ghannam A, Wagenaar-Bos IGA, Roem D, López-Lera A, López-Trascasa M, Tosi M, Drouet C. SERPING1 mutation update: Mutation spectrum and C1 Inhibitor phenotypes. Hum Mutat 2019; 41:38-57. [PMID: 31517426 DOI: 10.1002/humu.23917] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 08/29/2019] [Accepted: 09/04/2019] [Indexed: 12/18/2022]
Abstract
C1 inhibitor (C1Inh) deficiency is responsible for hereditary angioedema (C1-INH-HAE) and caused by variants of the SERPING1/C1INH/C1NH gene. C1Inh is the major control of kallikrein-kinin system. C1Inh deficiency leads to its uncontrolled activation, with subsequent generation of the vasoactive peptide bradykinin. This update documents 748 different SERPING1 variants, including published variants and additional 120 unpublished ones. They were identified as heterozygous variants (n = 729), as homozygous variants in 10 probands and as compound heterozygous variants (nine combinations). Six probands with heterozygous variants exhibited gonadal mosaicism. Probands with heterozygous (n = 72) and homozygous (n = 1) variants were identified as de novo cases. Overall, 58 variants were found at positions showing high residue conservation among serpins, and have been referred to as a mousetrap function of C1Inh: reactive center loop, gate, shutter, breach, and hinge. C1Inh phenotype analysis identified dysfunctional serpin variants with failed serpin-protease association and a residual 105-kDa species after incubation with target protease. Regarding this characteristic, in conditions with low antigenic C1Inh, 74 C1-INH-HAE probands presented with an additional so-called intermediate C1-INH-HAE phenotype. The present update addresses a comprehensive SERPING1 variant spectrum that facilitates genotype-phenotype correlations, highlighting residues of strategic importance for serpin function and for identification of C1Inh deficiency as serpinopathy.
Collapse
Affiliation(s)
- Denise Ponard
- Centre de Référence des Angioedèmes (CREAK), Filière MaRIH, CHU Grenoble, Grenoble, France.,Laboratoire d'Immunologie, CHU Grenoble Alpes, Grenoble, France
| | | | - Delphine Charignon
- GREPI EA7408, Université Grenoble Alpes and EFS Rhône-Alpes, Grenoble, France.,KininX SAS, Grenoble, France
| | - Arije Ghannam
- GREPI EA7408, Université Grenoble Alpes and EFS Rhône-Alpes, Grenoble, France.,KininX SAS, Grenoble, France
| | | | - Dorina Roem
- Department of Immunopathology, Sanquin Research, Amsterdam, The Netherlands
| | - Alberto López-Lera
- Biomedical Research Network on Rare Diseases (CIBERER)-U754, Instituto de Investigación Hospital Universitario La Paz (IdiPAZ), Madrid, Spain
| | | | - Mario Tosi
- Inserm U1245, University of Rouen, Rouen, France
| | - Christian Drouet
- Centre de Référence des Angioedèmes (CREAK), Filière MaRIH, CHU Grenoble, Grenoble, France.,GREPI EA7408, Université Grenoble Alpes and EFS Rhône-Alpes, Grenoble, France.,Inserm U1016, CNRS UMR8104, Institut Cochin, Université Paris-Descartes, France
| |
Collapse
|
19
|
Wang F, Orioli S, Ianeselli A, Spagnolli G, A Beccara S, Gershenson A, Faccioli P, Wintrode PL. All-Atom Simulations Reveal How Single-Point Mutations Promote Serpin Misfolding. Biophys J 2019; 114:2083-2094. [PMID: 29742402 DOI: 10.1016/j.bpj.2018.03.027] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 03/09/2018] [Accepted: 03/13/2018] [Indexed: 10/17/2022] Open
Abstract
Protein misfolding is implicated in many diseases, including serpinopathies. For the canonical inhibitory serpin α1-antitrypsin, mutations can result in protein deficiencies leading to lung disease, and misfolded mutants can accumulate in hepatocytes, leading to liver disease. Using all-atom simulations based on the recently developed bias functional algorithm, we elucidate how wild-type α1-antitrypsin folds and how the disease-associated S (Glu264Val) and Z (Glu342Lys) mutations lead to misfolding. The deleterious Z mutation disrupts folding at an early stage, whereas the relatively benign S mutant shows late-stage minor misfolding. A number of suppressor mutations ameliorate the effects of the Z mutation, and simulations on these mutants help to elucidate the relative roles of steric clashes and electrostatic interactions in Z misfolding. These results demonstrate a striking correlation between atomistic events and disease severity and shine light on the mechanisms driving chains away from their correct folding routes.
Collapse
Affiliation(s)
- Fang Wang
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland
| | - Simone Orioli
- Dipartimento di Fisica, Università degli Studi di Trento, Povo (Trento), Italy; Trento Institute for Fundamental Physics and Applications, Povo (Trento), Italy
| | - Alan Ianeselli
- Dipartimento di Fisica, Università degli Studi di Trento, Povo (Trento), Italy; Trento Institute for Fundamental Physics and Applications, Povo (Trento), Italy
| | - Giovanni Spagnolli
- Dipartimento di Fisica, Università degli Studi di Trento, Povo (Trento), Italy; Trento Institute for Fundamental Physics and Applications, Povo (Trento), Italy
| | - Silvio A Beccara
- Dipartimento di Fisica, Università degli Studi di Trento, Povo (Trento), Italy; Trento Institute for Fundamental Physics and Applications, Povo (Trento), Italy
| | - Anne Gershenson
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts.
| | - Pietro Faccioli
- Dipartimento di Fisica, Università degli Studi di Trento, Povo (Trento), Italy; Trento Institute for Fundamental Physics and Applications, Povo (Trento), Italy.
| | - Patrick L Wintrode
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland.
| |
Collapse
|
20
|
Reeves EP, Dunlea DM, McQuillan K, O'Dwyer CA, Carroll TP, Saldova R, Akepati PR, Wormald MR, McElvaney OJ, Shutchaidat V, Henry M, Meleady P, Keenan J, Liberti DC, Kotton DN, Rudd PM, Wilson AA, McElvaney NG. Circulating Truncated Alpha-1 Antitrypsin Glycoprotein in Patient Plasma Retains Anti-Inflammatory Capacity. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2019; 202:2240-2253. [PMID: 30796179 PMCID: PMC6452030 DOI: 10.4049/jimmunol.1801045] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 01/30/2019] [Indexed: 12/17/2022]
Abstract
Alpha-1 antitrypsin (AAT) is an acute phase protein that possesses immune-regulatory and anti-inflammatory functions independent of antiprotease activity. AAT deficiency (AATD) is associated with early-onset emphysema and chronic obstructive pulmonary disease. Of interest are the AATD nonsense mutations (termed null or Q0), the majority of which arise from premature termination codons in the mRNA coding region. We have recently demonstrated that plasma from an AATD patient homozygous for the Null Bolton allele (Q0bolton ) contains AAT protein of truncated size. Although the potential to alleviate the phenotypic consequences of AATD by increasing levels of truncated protein holds therapeutic promise, protein functionality is key. The goal of this study was to evaluate the structural features and anti-inflammatory capacity of Q0bolton-AAT. A low-abundance, truncated AAT protein was confirmed in plasma of a Q0bolton-AATD patient and was secreted by patient-derived induced pluripotent stem cell-hepatic cells. Functional assays confirmed the ability of purified Q0bolton-AAT protein to bind neutrophil elastase and to inhibit protease activity. Q0bolton-AAT bound IL-8 and leukotriene B4, comparable to healthy control M-AAT, and significantly decreased leukotriene B4-induced neutrophil adhesion (p = 0.04). Through a mechanism involving increased mRNA stability (p = 0.007), ataluren treatment of HEK-293 significantly increased Q0bolton-AAT mRNA expression (p = 0.03) and Q0bolton-AAT truncated protein secretion (p = 0.04). Results support the rationale for treatment with pharmacological agents that augment levels of functional Q0bolton-AAT protein, thus offering a potential therapeutic option for AATD patients with rare mutations of similar theratype.
Collapse
Affiliation(s)
- Emer P Reeves
- Irish Centre for Genetic Lung Disease, Department of Medicine, Royal College of Surgeons in Ireland, Education and Research Centre, Beaumont Hospital, Dublin 9, Ireland;
| | - Danielle M Dunlea
- Irish Centre for Genetic Lung Disease, Department of Medicine, Royal College of Surgeons in Ireland, Education and Research Centre, Beaumont Hospital, Dublin 9, Ireland
| | - Karen McQuillan
- Irish Centre for Genetic Lung Disease, Department of Medicine, Royal College of Surgeons in Ireland, Education and Research Centre, Beaumont Hospital, Dublin 9, Ireland
| | - Ciara A O'Dwyer
- Irish Centre for Genetic Lung Disease, Department of Medicine, Royal College of Surgeons in Ireland, Education and Research Centre, Beaumont Hospital, Dublin 9, Ireland
| | - Tomás P Carroll
- Alpha-1 Foundation Ireland, Royal College of Surgeons in Ireland, Beaumont Hospital, Dublin 9, Ireland
| | - Radka Saldova
- GlycoScience Group, National Institute for Bioprocessing Research and Training, Mount Merrion, Dublin, Ireland
| | - Prithvi Reddy Akepati
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118
| | - Mark R Wormald
- Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, Oxford OX1 3QU, United Kingdom; and
| | - Oliver J McElvaney
- Irish Centre for Genetic Lung Disease, Department of Medicine, Royal College of Surgeons in Ireland, Education and Research Centre, Beaumont Hospital, Dublin 9, Ireland
| | - Vipatsorn Shutchaidat
- Irish Centre for Genetic Lung Disease, Department of Medicine, Royal College of Surgeons in Ireland, Education and Research Centre, Beaumont Hospital, Dublin 9, Ireland
| | - Michael Henry
- National Institute for Cellular Biotechnology, Dublin City University, Dublin 9, Ireland
| | - Paula Meleady
- National Institute for Cellular Biotechnology, Dublin City University, Dublin 9, Ireland
| | - Joanne Keenan
- National Institute for Cellular Biotechnology, Dublin City University, Dublin 9, Ireland
| | - Derek C Liberti
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118
| | - Darrell N Kotton
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118
| | - Pauline M Rudd
- Alpha-1 Foundation Ireland, Royal College of Surgeons in Ireland, Beaumont Hospital, Dublin 9, Ireland
| | - Andrew A Wilson
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118
| | - Noel G McElvaney
- Irish Centre for Genetic Lung Disease, Department of Medicine, Royal College of Surgeons in Ireland, Education and Research Centre, Beaumont Hospital, Dublin 9, Ireland
| |
Collapse
|
21
|
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.
Collapse
|
22
|
Morifuji Y, Xu J, Karasaki N, Iiyama K, Morokuma D, Hino M, Masuda A, Yano T, Mon H, Kusakabe T, Lee JM. Expression, Purification, and Characterization of Recombinant Human α 1-Antitrypsin Produced Using Silkworm-Baculovirus Expression System. Mol Biotechnol 2018; 60:924-934. [PMID: 30302632 DOI: 10.1007/s12033-018-0127-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Human α1-antitrypsin (AAT) is the most abundant serine proteinase inhibitor (serpin) in the human plasma. Commercially available AAT for the medications of deficiency of α1-antitrypsin is mainly purified from human plasma. There is a high demand for a stable and low-cost supply of recombinant AAT (rAAT). In this study, the baculovirus expression vector system using silkworm larvae as host was employed and a large amount of highly active AAT was recovered from the silkworm serum (~ 15 mg/10 ml) with high purity. Both the enzymatic activity and stability of purified rAAT were comparable with those of commercial product. Our results provide an alternative method for mass production of the active rAAT in pharmaceutical use.
Collapse
Affiliation(s)
- Yoshiki Morifuji
- Laboratory of Insect Genome Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Science, Hakozaki 6-10-1, Higashi-ku, Fukuoka, 812-8581, Japan
| | - Jian Xu
- Laboratory of Insect Genome Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Science, Hakozaki 6-10-1, Higashi-ku, Fukuoka, 812-8581, Japan.
| | - Noriko Karasaki
- Laboratory of Insect Genome Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Science, Hakozaki 6-10-1, Higashi-ku, Fukuoka, 812-8581, Japan
| | - Kazuhiro Iiyama
- Laboratory of Plant Pathology, Kyushu University Graduate School of Bioresource and Bioenvironmental Science, Hakozaki 6-10-1, Higashi-ku, Fukuoka, 812-8581, Japan
| | - Daisuke Morokuma
- Laboratory of Insect Genome Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Science, Hakozaki 6-10-1, Higashi-ku, Fukuoka, 812-8581, Japan
| | - Masato Hino
- Laboratory of Insect Genome Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Science, Hakozaki 6-10-1, Higashi-ku, Fukuoka, 812-8581, Japan
| | - Akitsu Masuda
- Laboratory of Insect Genome Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Science, Hakozaki 6-10-1, Higashi-ku, Fukuoka, 812-8581, Japan
| | - Takumi Yano
- Laboratory of Insect Genome Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Science, Hakozaki 6-10-1, Higashi-ku, Fukuoka, 812-8581, Japan
| | - Hiroaki Mon
- Laboratory of Insect Genome Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Science, Hakozaki 6-10-1, Higashi-ku, Fukuoka, 812-8581, Japan
| | - Takahiro Kusakabe
- Laboratory of Insect Genome Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Science, Hakozaki 6-10-1, Higashi-ku, Fukuoka, 812-8581, Japan
| | - Jae Man Lee
- Laboratory of Insect Genome Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Science, Hakozaki 6-10-1, Higashi-ku, Fukuoka, 812-8581, Japan.
| |
Collapse
|
23
|
Giacopuzzi E, Laffranchi M, Berardelli R, Ravasio V, Ferrarotti I, Gooptu B, Borsani G, Fra A. Real-world clinical applicability of pathogenicity predictors assessed on SERPINA1
mutations in alpha-1-antitrypsin deficiency. Hum Mutat 2018; 39:1203-1213. [DOI: 10.1002/humu.23562] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 05/20/2018] [Accepted: 06/05/2018] [Indexed: 01/08/2023]
Affiliation(s)
- Edoardo Giacopuzzi
- Division of Biology and Genetics; Department of Molecular and Translational Medicine; University of Brescia; Brescia Italy
| | - Mattia Laffranchi
- Experimental Oncology and Immunology; Department of Molecular and Translational Medicine; University of Brescia; Brescia Italy
| | - Romina Berardelli
- Experimental Oncology and Immunology; Department of Molecular and Translational Medicine; University of Brescia; Brescia Italy
| | - Viola Ravasio
- Division of Biology and Genetics; Department of Molecular and Translational Medicine; University of Brescia; Brescia Italy
| | - Ilaria Ferrarotti
- Centre for Diagnosis of Inherited Alpha-1 Antitrypsin Deficiency; Department of Internal Medicine and Therapeutics; University of Pavia; Pavia Italy
| | - Bibek Gooptu
- Leicester Institute of Structural and Chemical Biology / NIHR Leicester BRC - Respiratory; University of Leicester; Leicester UK
| | - Giuseppe Borsani
- Division of Biology and Genetics; Department of Molecular and Translational Medicine; University of Brescia; Brescia Italy
| | - Annamaria Fra
- Experimental Oncology and Immunology; Department of Molecular and Translational Medicine; University of Brescia; Brescia Italy
| |
Collapse
|
24
|
Ramirez-Sarmiento CA, Komives EA. Hydrogen-deuterium exchange mass spectrometry reveals folding and allostery in protein-protein interactions. Methods 2018; 144:43-52. [PMID: 29627358 DOI: 10.1016/j.ymeth.2018.04.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Revised: 03/31/2018] [Accepted: 04/02/2018] [Indexed: 11/29/2022] Open
Abstract
Hydrogen-deuterium exchange mass spectrometry (HDXMS) has emerged as a powerful approach for revealing folding and allostery in protein-protein interactions. The advent of higher resolution mass spectrometers combined with ion mobility separation and ultra performance liquid chromatographic separations have allowed the complete coverage of large protein sequences and multi-protein complexes. Liquid-handling robots have improved the reproducibility and accurate temperature control of the sample preparation. Many researchers are also appreciating the power of combining biophysical approaches such as stopped-flow fluorescence, single molecule FRET, and molecular dynamics simulations with HDXMS. In this review, we focus on studies that have used a combination of approaches to reveal (re)folding of proteins as well as on long-distance allosteric changes upon interaction.
Collapse
Affiliation(s)
- Cesar A Ramirez-Sarmiento
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Catolica de Chile, Av. Vicuña Mackenna 4860, Santiago 7820436, Chile
| | - Elizabeth A Komives
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92092-0378, United States.
| |
Collapse
|
25
|
Race to the native state. Proc Natl Acad Sci U S A 2018; 115:2267-2269. [PMID: 29472450 DOI: 10.1073/pnas.1722622115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
26
|
|
27
|
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.
Collapse
|
28
|
On the folding of a structurally complex protein to its metastable active state. Proc Natl Acad Sci U S A 2018; 115:1998-2003. [PMID: 29343647 DOI: 10.1073/pnas.1708173115] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
For successful protease inhibition, the reactive center loop (RCL) of the two-domain serine protease inhibitor, α1-antitrypsin (α1-AT), needs to remain exposed in a metastable active conformation. The α1-AT RCL is sequestered in a β-sheet in the stable latent conformation. Thus, to be functional, α1-AT must always fold to a metastable conformation while avoiding folding to a stable conformation. We explore the structural basis of this choice using folding simulations of coarse-grained structure-based models of the two α1-AT conformations. Our simulations capture the key features of folding experiments performed on both conformations. The simulations also show that the free energy barrier to fold to the latent conformation is much larger than the barrier to fold to the active conformation. An entropically stabilized on-pathway intermediate lowers the barrier for folding to the active conformation. In this intermediate, the RCL is in an exposed configuration, and only one of the two α1-AT domains is folded. In contrast, early conversion of the RCL into a β-strand increases the coupling between the two α1-AT domains in the transition state and creates a larger barrier for folding to the latent conformation. Thus, unlike what happens in several proteins, where separate regions promote folding and function, the structure of the RCL, formed early during folding, determines both the conformational and the functional fate of α1-AT. Further, the short 12-residue RCL modulates the free energy barrier and the folding cooperativity of the large 370-residue α1-AT. Finally, we suggest experiments to test the predicted folding mechanism for the latent state.
Collapse
|
29
|
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.
Collapse
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
| |
Collapse
|
30
|
Inhibitory serpins. New insights into their folding, polymerization, regulation and clearance. Biochem J 2017; 473:2273-93. [PMID: 27470592 DOI: 10.1042/bcj20160014] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 03/31/2016] [Indexed: 12/20/2022]
Abstract
Serpins are a widely distributed family of high molecular mass protein proteinase inhibitors that can inhibit both serine and cysteine proteinases by a remarkable mechanism-based kinetic trapping of an acyl or thioacyl enzyme intermediate that involves massive conformational transformation. The trapping is based on distortion of the proteinase in the complex, with energy derived from the unique metastability of the active serpin. Serpins are the favoured inhibitors for regulation of proteinases in complex proteolytic cascades, such as are involved in blood coagulation, fibrinolysis and complement activation, by virtue of the ability to modulate their specificity and reactivity. Given their prominence as inhibitors, much work has been carried out to understand not only the mechanism of inhibition, but how it is fine-tuned, both spatially and temporally. The metastability of the active state raises the question of how serpins fold, whereas the misfolding of some serpin variants that leads to polymerization and pathologies of liver disease, emphysema and dementia makes it clinically important to understand how such polymerization might occur. Finally, since binding of serpins and their proteinase complexes, particularly plasminogen activator inhibitor-1 (PAI-1), to the clearance and signalling receptor LRP1 (low density lipoprotein receptor-related protein 1), may affect pathways linked to cell migration, angiogenesis, and tumour progression, it is important to understand the nature and specificity of binding. The current state of understanding of these areas is addressed here.
Collapse
|
31
|
Wang L, Chance MR. Protein Footprinting Comes of Age: Mass Spectrometry for Biophysical Structure Assessment. Mol Cell Proteomics 2017; 16:706-716. [PMID: 28275051 DOI: 10.1074/mcp.o116.064386] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 03/06/2017] [Indexed: 12/17/2022] Open
Abstract
Protein footprinting mediated by mass spectrometry has evolved over the last 30 years from proof of concept to commonplace biophysics tool, with unique capabilities for assessing structure and dynamics of purified proteins in physiological states in solution. This review outlines the history and current capabilities of two major methods of protein footprinting: reversible hydrogen-deuterium exchange (HDX) and hydroxyl radical footprinting (HRF), an irreversible covalent labeling approach. Technological advances in both approaches now permit high-resolution assessments of protein structure including secondary and tertiary structure stability mediated by backbone interactions (measured via HDX) and solvent accessibility of side chains (measured via HRF). Applications across many academic fields and in biotechnology drug development are illustrated including: detection of protein interfaces, identification of ligand/drug binding sites, and monitoring dynamics of protein conformational changes along with future prospects for advancement of protein footprinting in structural biology and biophysics research.
Collapse
Affiliation(s)
- Liwen Wang
- From the ‡Center for Proteomics and Bioinformatics, Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, Ohio
| | - Mark R Chance
- From the ‡Center for Proteomics and Bioinformatics, Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, Ohio
| |
Collapse
|
32
|
Finkelstein AV, Badretdin AJ, Galzitskaya OV, Ivankov DN, Bogatyreva NS, Garbuzynskiy SO. There and back again: Two views on the protein folding puzzle. Phys Life Rev 2017; 21:56-71. [PMID: 28190683 DOI: 10.1016/j.plrev.2017.01.025] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 01/05/2017] [Accepted: 01/19/2017] [Indexed: 02/08/2023]
Abstract
The ability of protein chains to spontaneously form their spatial structures is a long-standing puzzle in molecular biology. Experimentally measured folding times of single-domain globular proteins range from microseconds to hours: the difference (10-11 orders of magnitude) is the same as that between the life span of a mosquito and the age of the universe. This review describes physical theories of rates of overcoming the free-energy barrier separating the natively folded (N) and unfolded (U) states of protein chains in both directions: "U-to-N" and "N-to-U". In the theory of protein folding rates a special role is played by the point of thermodynamic (and kinetic) equilibrium between the native and unfolded state of the chain; here, the theory obtains the simplest form. Paradoxically, a theoretical estimate of the folding time is easier to get from consideration of protein unfolding (the "N-to-U" transition) rather than folding, because it is easier to outline a good unfolding pathway of any structure than a good folding pathway that leads to the stable fold, which is yet unknown to the folding protein chain. And since the rates of direct and reverse reactions are equal at the equilibrium point (as follows from the physical "detailed balance" principle), the estimated folding time can be derived from the estimated unfolding time. Theoretical analysis of the "N-to-U" transition outlines the range of protein folding rates in a good agreement with experiment. Theoretical analysis of folding (the "U-to-N" transition), performed at the level of formation and assembly of protein secondary structures, outlines the upper limit of protein folding times (i.e., of the time of search for the most stable fold). Both theories come to essentially the same results; this is not a surprise, because they describe overcoming one and the same free-energy barrier, although the way to the top of this barrier from the side of the unfolded state is very different from the way from the side of the native state; and both theories agree with experiment. In addition, they predict the maximal size of protein domains that fold under solely thermodynamic (rather than kinetic) control and explain the observed maximal size of the "foldable" protein domains.
Collapse
Affiliation(s)
- Alexei V Finkelstein
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russian Federation.
| | - Azat J Badretdin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Oxana V Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russian Federation
| | - Dmitry N Ivankov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russian Federation; Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Natalya S Bogatyreva
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russian Federation; Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Sergiy O Garbuzynskiy
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russian Federation
| |
Collapse
|
33
|
Andersen OJ, Risør MW, Poulsen EC, Nielsen NC, Miao Y, Enghild JJ, Schiøtt B. Reactive Center Loop Insertion in α-1-Antitrypsin Captured by Accelerated Molecular Dynamics Simulation. Biochemistry 2017; 56:634-646. [PMID: 27995800 DOI: 10.1021/acs.biochem.6b00839] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Protease inhibition by metastable serine protease inhibitors (serpins) is mediated by one of the largest functional intradomain conformational changes known in biology. In this extensive structural rearrangement, protease-serpin complex formation triggers cleavage of the serpin reactive center loop (RCL), its subsequent insertion into central β-sheet A, and covalent trapping of the target protease. In this study, we present the first detailed accelerated molecular dynamics simulation of the insertion of the fully cleaved RCL in α-1-antitrypsin (α1AT), the archetypal member of the family of human serpins. Our results reveal internal water pathways that allow the initial incorporation of side chains of RCL residues into the protein interior. We observed structural plasticity of the helix F (hF) element that blocks the RCL path in the native state, which is in excellent agreement with previous experimental reports. Furthermore, the simulation suggested a novel role of hF and the connected turn (thFs3A) as chaperones that support the insertion process by reducing the conformational space available to the RCL. Transient electrostatic interactions of RCL residues potentially fine-tune the serpin inhibitory activity. On the basis of our simulation, we generated the α1AT mutants K168E, E346K, and K168E/E346K and analyzed their inhibitory activity along with their intrinsic stability and heat-induced polymerization. Remarkably, the E346K mutation exhibited enhanced inhibitory activity along with an increased rate of premature structural collapse (polymerization), suggesting a significant role of E346 in the gatekeeping of the strain in the metastable native state.
Collapse
Affiliation(s)
- Ole Juul Andersen
- Center for Insoluble Protein Structures (inSPIN) and Interdisciplinary Nanoscience Center (iNANO), Aarhus University , Aarhus, Denmark.,Department of Chemistry, Aarhus University , Aarhus, Denmark
| | - Michael Wulff Risør
- Center for Insoluble Protein Structures (inSPIN) and Interdisciplinary Nanoscience Center (iNANO), Aarhus University , Aarhus, Denmark.,Department of Molecular Biology and Genetics, Aarhus University , Aarhus, Denmark
| | - Emil Christian Poulsen
- Center for Insoluble Protein Structures (inSPIN) and Interdisciplinary Nanoscience Center (iNANO), Aarhus University , Aarhus, Denmark.,Department of Molecular Biology and Genetics, Aarhus University , Aarhus, Denmark
| | - Niels Chr Nielsen
- Center for Insoluble Protein Structures (inSPIN) and Interdisciplinary Nanoscience Center (iNANO), Aarhus University , Aarhus, Denmark.,Department of Chemistry, Aarhus University , Aarhus, Denmark
| | - Yinglong Miao
- Howard Hughes Medical Institute and Department of Pharmacology, University of California at San Diego , La Jolla, California 92093, United States
| | - Jan J Enghild
- Center for Insoluble Protein Structures (inSPIN) and Interdisciplinary Nanoscience Center (iNANO), Aarhus University , Aarhus, Denmark.,Department of Molecular Biology and Genetics, Aarhus University , Aarhus, Denmark
| | - Birgit Schiøtt
- Center for Insoluble Protein Structures (inSPIN) and Interdisciplinary Nanoscience Center (iNANO), Aarhus University , Aarhus, Denmark.,Department of Chemistry, Aarhus University , Aarhus, Denmark
| |
Collapse
|
34
|
Faull SV, Brown AE, Haq I, Irving JA. Electrophoresis- and FRET-Based Measures of Serpin Polymerization. Methods Mol Biol 2017; 1639:235-248. [PMID: 28752464 DOI: 10.1007/978-1-4939-7163-3_24] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Many serpinopathies, including alpha-1 antitrypsin (A1AT) deficiency, are associated with the formation of unbranched polymer chains of mutant serpins. In vivo, this deficiency is the result of mutations that cause kinetic or thermodynamic destabilization of the molecule. However, polymerization can also be induced in vitro from mutant or wild-type serpins under destabilizing conditions. The characteristics of the resulting polymers are dependent upon induction conditions. Due to their relationship to disease, serpin polymers, mainly those formed from A1AT, have been widely studied. Here, we describe Förster resonance energy transfer (FRET) and gel-based approaches for their characterization.
Collapse
Affiliation(s)
- Sarah V Faull
- Division of Structural Biology, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Anwen E Brown
- UCL Respiratory, University College London, London, WC1E 6JF, UK
| | - Imran Haq
- UCL Respiratory, University College London, London, WC1E 6JF, UK
| | - James A Irving
- UCL Respiratory, University College London, London, WC1E 6JF, UK.
| |
Collapse
|
35
|
Motamedi-Shad N, Jagger AM, Liedtke M, Faull SV, Nanda AS, Salvadori E, Wort JL, Kay CW, Heyer-Chauhan N, Miranda E, Perez J, Ordóñez A, Haq I, Irving JA, Lomas DA. An antibody that prevents serpin polymerisation acts by inducing a novel allosteric behaviour. Biochem J 2016; 473:3269-90. [PMID: 27407165 PMCID: PMC5264506 DOI: 10.1042/bcj20160159] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 07/08/2016] [Accepted: 07/12/2016] [Indexed: 11/30/2022]
Abstract
Serpins are important regulators of proteolytic pathways with an antiprotease activity that involves a conformational transition from a metastable to a hyperstable state. Certain mutations permit the transition to occur in the absence of a protease; when associated with an intermolecular interaction, this yields linear polymers of hyperstable serpin molecules, which accumulate at the site of synthesis. This is the basis of many pathologies termed the serpinopathies. We have previously identified a monoclonal antibody (mAb4B12) that, in single-chain form, blocks α1-antitrypsin (α1-AT) polymerisation in cells. Here, we describe the structural basis for this activity. The mAb4B12 epitope was found to encompass residues Glu32, Glu39 and His43 on helix A and Leu306 on helix I. This is not a region typically associated with the serpin mechanism of conformational change, and correspondingly the epitope was present in all tested structural forms of the protein. Antibody binding rendered β-sheet A - on the opposite face of the molecule - more liable to adopt an 'open' state, mediated by changes distal to the breach region and proximal to helix F. The allosteric propagation of induced changes through the molecule was evidenced by an increased rate of peptide incorporation and destabilisation of a preformed serpin-enzyme complex following mAb4B12 binding. These data suggest that prematurely shifting the β-sheet A equilibrium towards the 'open' state out of sequence with other changes suppresses polymer formation. This work identifies a region potentially exploitable for a rational design of ligands that is able to dynamically influence α1-AT polymerisation.
Collapse
Affiliation(s)
- Neda Motamedi-Shad
- Centre for Respiratory Biology, UCL Respiratory, University College London, London WC1E 6JF, U.K
- Institute of Structural and Molecular Biology/Birkbeck, University of London, London WC1E 7HX, U.K
| | - Alistair M. Jagger
- Centre for Respiratory Biology, UCL Respiratory, University College London, London WC1E 6JF, U.K
- Institute of Structural and Molecular Biology/Birkbeck, University of London, London WC1E 7HX, U.K
| | - Maximilian Liedtke
- Centre for Respiratory Biology, UCL Respiratory, University College London, London WC1E 6JF, U.K
| | - Sarah V. Faull
- Centre for Respiratory Biology, UCL Respiratory, University College London, London WC1E 6JF, U.K
- Institute of Structural and Molecular Biology/Birkbeck, University of London, London WC1E 7HX, U.K
- Department of Medicine, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/Medical Research Council Building, Hills Road, Cambridge CB2 0XY, U.K
| | - Arjun Scott Nanda
- Institute of Structural and Molecular Biology/Birkbeck, University of London, London WC1E 7HX, U.K
| | - Enrico Salvadori
- Institute of Structural and Molecular Biology/Birkbeck, University of London, London WC1E 7HX, U.K
- London Centre for Nanotechnology, 17-19 Gordon Street, London WC1H 0AH, U.K
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, U.K
| | - Joshua L. Wort
- Institute of Structural and Molecular Biology/Birkbeck, University of London, London WC1E 7HX, U.K
| | - Christopher W.M. Kay
- Institute of Structural and Molecular Biology/Birkbeck, University of London, London WC1E 7HX, U.K
- London Centre for Nanotechnology, 17-19 Gordon Street, London WC1H 0AH, U.K
| | - Narinder Heyer-Chauhan
- Centre for Respiratory Biology, UCL Respiratory, University College London, London WC1E 6JF, U.K
- Institute of Structural and Molecular Biology/Birkbeck, University of London, London WC1E 7HX, U.K
| | - Elena Miranda
- Department of Biology and Biotechnologies ‘Charles Darwin’, Sapienza University of Rome, Rome 00185, Italy
| | - Juan Perez
- Departamento de Biologia Celular, Genetica y Fisiologia, Facultad de Ciencias, Campus Teatinos, Universidad de Malaga, Malaga 29071, Spain
| | - Adriana Ordóñez
- Department of Medicine, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/Medical Research Council Building, Hills Road, Cambridge CB2 0XY, U.K
| | - Imran Haq
- Centre for Respiratory Biology, UCL Respiratory, University College London, London WC1E 6JF, U.K
- Institute of Structural and Molecular Biology/Birkbeck, University of London, London WC1E 7HX, U.K
| | - James A. Irving
- Centre for Respiratory Biology, UCL Respiratory, University College London, London WC1E 6JF, U.K
- Institute of Structural and Molecular Biology/Birkbeck, University of London, London WC1E 7HX, U.K
| | - David A. Lomas
- Centre for Respiratory Biology, UCL Respiratory, University College London, London WC1E 6JF, U.K
- Institute of Structural and Molecular Biology/Birkbeck, University of London, London WC1E 7HX, U.K
| |
Collapse
|
36
|
High Resolution Mapping of Bactericidal Monoclonal Antibody Binding Epitopes on Staphylococcus aureus Antigen MntC. PLoS Pathog 2016; 12:e1005908. [PMID: 27689696 PMCID: PMC5045189 DOI: 10.1371/journal.ppat.1005908] [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: 02/05/2016] [Accepted: 08/30/2016] [Indexed: 11/19/2022] Open
Abstract
The Staphylococcus aureus manganese transporter protein MntC is under investigation as a component of a prophylactic S.aureus vaccine. Passive immunization with monoclonal antibodies mAB 305-78-7 and mAB 305-101-8 produced using MntC was shown to significantly reduce S. aureus burden in an infant rat model of infection. Earlier interference mapping suggested that a total of 23 monoclonal antibodies generated against MntC could be subdivided into three interference groups, representing three independent immunogenic regions. In the current work binding epitopes for selected representatives of each of these interference groups (mAB 305-72-5 – group 1, mAB 305-78-7 – group 2, and mAB 305-101-8 – group 3) were mapped using Hydrogen-Deuterium Exchange Mass Spectrometry (DXMS). All of the identified epitopes are discontinuous, with binding surface formed by structural elements that are separated within the primary sequence of the protein but adjacent in the context of the three-dimensional structure. The approach was validated by co-crystallizing the Fab fragment of one of the antibodies (mAB 305-78-7) with MntC and solving the three-dimensional structure of the complex. X-ray results themselves and localization of the mAB 305-78-7 epitope were further validated using antibody binding experiments with MntC variants containing substitutions of key amino acid residues. These results provided insight into the antigenic properties of MntC and how these properties may play a role in protecting the hostagainst S. aureus infection by preventing the capture and transport of Mn2+, a key element that the pathogen uses to evade host immunity. Staphylococcus aureus protein MntC is a metal-binding protein of the ABC-type transporter involved in the acquisition of an essential nutrient, Mn2+, by the pathogen. An earlier study demonstrated that use of MntC as an antigen in experimental vaccine can provide protection against staphylococcal infections in animals and identified three groups of protective monoclonal antibodies induced by the protein. In the current work we employed Deuterium-Hydrogen Exchange Mass Spectrometry (DXMS) to determine binding sites of selected representatives from each of those three groups. DXMS results were further validated using X-ray crystallography, site-directed mutagenesis and functional studies. Locations of the binding sites and results of the functional studies were used to draw conclusion on molecular mechanisms of protection afforded by MntC: antibodies belonging to two of the groups are predicted to interfere with Mn2+ transfer from the protein to the transmembrane channel pore, while the third group of the antibodies is expected to interfere with Mn2+ binding to MntC itself. The net result in both cases is impaired Mn2+ transport across the bacterial membrane and increased susceptibility of the bacterium to the oxidative stress, likely due to the reduced activity of superoxide dismutase which requires Mn2+ as an essential co-factor for activity.
Collapse
|
37
|
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.
Collapse
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
| |
Collapse
|
38
|
Lomas DA, Hurst JR, Gooptu B. Update on alpha-1 antitrypsin deficiency: New therapies. J Hepatol 2016; 65:413-24. [PMID: 27034252 DOI: 10.1016/j.jhep.2016.03.010] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Revised: 03/16/2016] [Accepted: 03/20/2016] [Indexed: 02/07/2023]
Abstract
α1-Antitrypsin deficiency is characterised by the misfolding and intracellular polymerisation of mutant α1-antitrypsin within the endoplasmic reticulum of hepatocytes. The retention of mutant protein causes hepatic damage and cirrhosis whilst the lack of an important circulating protease inhibitor predisposes the individuals with severe α1-antitrypsin deficiency to early onset emphysema. Our work over the past 25years has led to new paradigms for the liver and lung disease associated with α1-antitrypsin deficiency. We review here the molecular pathology of the cirrhosis and emphysema associated with α1-antitrypsin deficiency and show how an understanding of this condition provided the paradigm for a wider group of disorders that we have termed the serpinopathies. The detailed understanding of the pathobiology of α1-antitrypsin deficiency has identified important disease mechanisms to target. As a result, several novel parallel and complementary therapeutic approaches are in development with some now in clinical trials. We provide an overview of these new therapies for the liver and lung disease associated with α1-antitrypsin deficiency.
Collapse
Affiliation(s)
- David A Lomas
- UCL Respiratory, Division of Medicine, Rayne Building, University College London, UK; The London Alpha-1-Antitrypsin Deficiency Service, Royal Free London NHS Foundation Trust, London, UK; Institute of Structural and Molecular Biology, UCL/Birkbeck College, University of London, London WC1E 7HX, UK.
| | - John R Hurst
- UCL Respiratory, Division of Medicine, Rayne Building, University College London, UK; The London Alpha-1-Antitrypsin Deficiency Service, Royal Free London NHS Foundation Trust, London, UK
| | - Bibek Gooptu
- The London Alpha-1-Antitrypsin Deficiency Service, Royal Free London NHS Foundation Trust, London, UK; Institute of Structural and Molecular Biology, UCL/Birkbeck College, University of London, London WC1E 7HX, UK; Division of Asthma, Allergy and Lung Biology, King's College London, Guy's Hospital, 5th Floor, Tower Wing, London, UK
| |
Collapse
|
39
|
Huang X, Zheng Y, Zhang F, Wei Z, Wang Y, Carrell RW, Read RJ, Chen GQ, Zhou A. Molecular Mechanism of Z α1-Antitrypsin Deficiency. J Biol Chem 2016; 291:15674-86. [PMID: 27246852 PMCID: PMC4957051 DOI: 10.1074/jbc.m116.727826] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Indexed: 12/14/2022] Open
Abstract
The Z mutation (E342K) of α1-antitrypsin (α1-AT), carried by 4% of Northern Europeans, predisposes to early onset of emphysema due to decreased functional α1-AT in the lung and to liver cirrhosis due to accumulation of polymers in hepatocytes. However, it remains unclear why the Z mutation causes intracellular polymerization of nascent Z α1-AT and why 15% of the expressed Z α1-AT is secreted into circulation as functional, but polymerogenic, monomers. Here, we solve the crystal structure of the Z-monomer and have engineered replacements to assess the conformational role of residue Glu-342 in α1-AT. The results reveal that Z α1-AT has a labile strand 5 of the central β-sheet A (s5A) with a consequent equilibrium between a native inhibitory conformation, as in its crystal structure here, and an aberrant conformation with s5A only partially incorporated into the central β-sheet. This aberrant conformation, induced by the loss of interactions from the Glu-342 side chain, explains why Z α1-AT is prone to polymerization and readily binds to a 6-mer peptide, and it supports that annealing of s5A into the central β-sheet is a crucial step in the serpins' metastable conformational formation. The demonstration that the aberrant conformation can be rectified through stabilization of the labile s5A by binding of a small molecule opens a potential therapeutic approach for Z α1-AT deficiency.
Collapse
Affiliation(s)
- Xin Huang
- From the Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine and University of Chinese Academy of Sciences, Shanghai 200025, China
| | - Ying Zheng
- the Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology Division of Shanghai Universities E-Institutes, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China, and
| | - Fei Zhang
- the Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology Division of Shanghai Universities E-Institutes, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China, and
| | - Zhenquan Wei
- the Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology Division of Shanghai Universities E-Institutes, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China, and
| | - Yugang Wang
- the Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology Division of Shanghai Universities E-Institutes, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China, and
| | - Robin W Carrell
- the Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Randy J Read
- the Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Guo-Qiang Chen
- From the Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine and University of Chinese Academy of Sciences, Shanghai 200025, China, the Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology Division of Shanghai Universities E-Institutes, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China, and
| | - Aiwu Zhou
- the Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology Division of Shanghai Universities E-Institutes, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China, and
| |
Collapse
|
40
|
Abstract
Although proteins generally fold to their thermodynamically most stable state, some metastable proteins populate higher free energy states. Conformational changes from metastable higher free energy states to lower free energy states with greater stability can then generate the work required to perform physiologically important functions. However, how metastable proteins fold to these higher free energy states in the cell and avoid more stable but inactive conformations is poorly understood. The serpin family of metastable protease inhibitors uses large conformational changes that are downhill in free energy to inhibit target proteases by pulling apart the protease active site. The serpin antithrombin III (ATIII) targets thrombin and other proteases involved in blood coagulation, and ATIII misfolding can thus lead to thrombosis and other diseases. ATIII has three disulfide bonds, two near the N terminus and one near the C terminus. Our studies of ATIII in-cell folding reveal a surprising, biased order of disulfide bond formation, with early formation of the C-terminal disulfide, before formation of the N-terminal disulfides, critical for folding to the active, metastable state. Early folding of the predominantly β-sheet ATIII domain in this two-domain protein constrains the reactive center loop (RCL), which contains the protease-binding site, ensuring that the RCL remains accessible. N-linked glycans and carbohydrate-binding molecular chaperones contribute to the efficient folding and secretion of functional ATIII. The inability of a number of disease-associated ATIII variants to navigate the folding reaction helps to explain their disease phenotypes.
Collapse
|
41
|
Haq I, Irving JA, Saleh AD, Dron L, Regan-Mochrie GL, Motamedi-Shad N, Hurst JR, Gooptu B, Lomas DA. Deficiency Mutations of Alpha-1 Antitrypsin. Effects on Folding, Function, and Polymerization. Am J Respir Cell Mol Biol 2016; 54:71-80. [PMID: 26091018 DOI: 10.1165/rcmb.2015-0154oc] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Misfolding, polymerization, and defective secretion of functional alpha-1 antitrypsin underlies the predisposition to severe liver and lung disease in alpha-1 antitrypsin deficiency. We have identified a novel (Ala336Pro, Baghdad) deficiency variant and characterized it relative to the wild-type (M) and Glu342Lys (Z) alleles. The index case is a homozygous individual of consanguineous parentage, with levels of circulating alpha-1 antitrypsin in the moderate deficiency range, but is a biochemical phenotype that could not be classified by standard methods. The majority of the protein was present as functionally inactive polymer, and the remaining monomer was 37% active relative to the wild-type protein. These factors combined indicate an 85 to 95% functional deficiency, similar to that seen with ZZ homozygotes. Biochemical, biophysical, and computational studies further defined the molecular basis of this deficiency. These studies demonstrated that native Ala336Pro alpha-1 antitrypsin could populate the polymerogenic intermediate-and therefore polymerize-more readily than either wild-type alpha-1 antitrypsin or the Z variant. In contrast, folding was far less impaired in Ala336Pro alpha-1 antitrypsin than in the Z variant. The data are consistent with a disparate contribution by the "breach" region and "shutter" region of strand 5A to folding and polymerization mechanisms. Moreover, the findings demonstrate that, in these variants, folding efficiency does not correlate directly with the tendency to polymerize in vitro or in vivo. They therefore differentiate generalized misfolding from polymerization tendencies in missense variants of alpha-1 antitrypsin. Clinically, they further support the need to quantify loss-of-function in alpha-1 antitrypsin deficiency to individualize patient care.
Collapse
Affiliation(s)
- Imran Haq
- 1 Wolfson Institute for Biomedical Research, University College London, London, United Kingdom.,2 Institute of Structural and Molecular Biology/Birkbeck, University of London, London, United Kingdom
| | - James A Irving
- 1 Wolfson Institute for Biomedical Research, University College London, London, United Kingdom.,2 Institute of Structural and Molecular Biology/Birkbeck, University of London, London, United Kingdom
| | - Aarash D Saleh
- 3 London Alpha-1 Antitrypsin Deficiency Service, Royal Free Hospital, Pond Street, London, United Kingdom; and
| | - Louis Dron
- 3 London Alpha-1 Antitrypsin Deficiency Service, Royal Free Hospital, Pond Street, London, United Kingdom; and
| | - Gemma L Regan-Mochrie
- 1 Wolfson Institute for Biomedical Research, University College London, London, United Kingdom
| | - Neda Motamedi-Shad
- 1 Wolfson Institute for Biomedical Research, University College London, London, United Kingdom.,2 Institute of Structural and Molecular Biology/Birkbeck, University of London, London, United Kingdom
| | - John R Hurst
- 3 London Alpha-1 Antitrypsin Deficiency Service, Royal Free Hospital, Pond Street, London, United Kingdom; and
| | - Bibek Gooptu
- 2 Institute of Structural and Molecular Biology/Birkbeck, University of London, London, United Kingdom.,3 London Alpha-1 Antitrypsin Deficiency Service, Royal Free Hospital, Pond Street, London, United Kingdom; and.,4 Division of Asthma, Allergy and Lung Biology, King's College London, London, United Kingdom
| | - David A Lomas
- 1 Wolfson Institute for Biomedical Research, University College London, London, United Kingdom.,2 Institute of Structural and Molecular Biology/Birkbeck, University of London, London, United Kingdom.,3 London Alpha-1 Antitrypsin Deficiency Service, Royal Free Hospital, Pond Street, London, United Kingdom; and
| |
Collapse
|
42
|
Malhotra P, Udgaonkar JB. Secondary Structural Change Can Occur Diffusely and Not Modularly during Protein Folding and Unfolding Reactions. J Am Chem Soc 2016; 138:5866-78. [DOI: 10.1021/jacs.6b03356] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Pooja Malhotra
- National Centre for Biological
Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
| | - Jayant B. Udgaonkar
- National Centre for Biological
Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
| |
Collapse
|
43
|
Using the folding landscapes of proteins to understand protein function. Curr Opin Struct Biol 2016; 36:67-74. [PMID: 26812092 DOI: 10.1016/j.sbi.2016.01.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 12/31/2015] [Accepted: 01/06/2016] [Indexed: 11/20/2022]
Abstract
Proteins fold on a biologically-relevant timescale because of a funnel-shaped energy landscape. This landscape is sculpted through evolution by selecting amino-acid sequences that stabilize native interactions while suppressing stable non-native interactions that occur during folding. However, there is strong evolutionary selection for functional residues and these cannot be chosen to optimize folding. Their presence impacts the folding energy landscape in a variety of ways. Here, we survey the effects of functional residues on folding by providing several examples. We then review how such effects can be detected computationally and be used as assays for protein function. Overall, an understanding of how functional residues modulate folding should provide insights into the design of natural proteins and their homeostasis.
Collapse
|
44
|
Affiliation(s)
- Gregory
F. Pirrone
- Department of Chemistry and
Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, Massachusetts 02115 United States
| | - Roxana E. Iacob
- Department of Chemistry and
Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, Massachusetts 02115 United States
| | - John R. Engen
- Department of Chemistry and
Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, Massachusetts 02115 United States
| |
Collapse
|
45
|
Trelle MB, Madsen JB, Andreasen PA, Jørgensen TJD. Local Transient Unfolding of Native State PAI-1 Associated with Serpin Metastability. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201402796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
46
|
Trelle MB, Madsen JB, Andreasen PA, Jørgensen TJD. Local Transient Unfolding of Native State PAI-1 Associated with Serpin Metastability. Angew Chem Int Ed Engl 2014; 53:9751-4. [DOI: 10.1002/anie.201402796] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 05/26/2014] [Indexed: 11/08/2022]
|
47
|
Therapeutic targeting of misfolding and conformational change in α1-antitrypsin deficiency. Future Med Chem 2014; 6:1047-65. [DOI: 10.4155/fmc.14.58] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Misfolding and conformational diseases are increasing in prominence and prevalence. Both misfolding and ‘postfolding’ conformational mechanisms can contribute to pathogenesis and can coexist. The different contexts of folding and native state behavior may have implications for the development of therapeutic strategies. α1-antitrypsin deficiency illustrates how these issues can be addressed with therapeutic approaches to rescue folding, ameliorate downstream consequences of aberrant polymerization and/or maintain physiological function. Small-molecule strategies have successfully targeted structural features of the native conformer. Recent developments include the capability to follow solution behavior of α1-antitrypsin in the context of disease mutations and interactions with drug-like compounds. Moreover, preclinical studies in cells and organisms support the potential of manipulating cellular response repertoires to process misfolded and polymer states.
Collapse
|
48
|
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.
Collapse
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
| |
Collapse
|
49
|
Isolation and molecular characterization of a major hemolymph serpin from the triatomine, Panstrongylus megistus. Parasit Vectors 2014; 7:23. [PMID: 24423259 PMCID: PMC3898217 DOI: 10.1186/1756-3305-7-23] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 12/21/2013] [Indexed: 11/10/2022] Open
Abstract
Background Chagas disease kills 2.5 thousand people per year of 15 million persons infected in Latin America. The disease is caused by the protozoan, Trypanosome cruzi, and vectored by triatomine insects, including Panstrongylus megistus, an important vector in Brazil. Medicines treating Chagas disease have unpleasant side effects and may be ineffective, therefore, alternative control techniques are required. Knowledge of the T. cruzi interactions with the triatomine host needs extending and new targets/strategies for control identified. Serine and cysteine peptidases play vital roles in protozoan life cycles including invasion and entry of T. cruzi into host cells. Peptidase inhibitors are, therefore, promising targets for disease control. Methods SDS PAGE and chromatograpy detected and isolated a P. megistus serpin which was peptide sequenced by mass spectrometry. A full amino acid sequence was obtained from the cDNA and compared with other insect serpins. Reverse transcription PCR analysis measured serpin transcripts of P. megistus tissues with and without T. cruzi infection. Serpin homology modeling used the Swiss Model and Swiss-PDB viewer programmes. Results The P. megistus serpin (PMSRP1) has a ca. 40 kDa molecular mass with 404 amino acid residues. A reactive site loop contains a highly conserved hinge region but, based on sequence alignment, the normal cleavage site for serine proteases at P1-P1′ was translocated to the putative position P4′-P5′. A small peptide obtained corresponded to the C-terminal 40 amino acid region. The secondary structure of PMSRP1 indicated nine α-helices and three β-sheets, similar to other serpins. PMSRP1 transcripts occurred in all tested tissues but were highest in the fat body and hemocytes. Levels of mRNA encoding PMSRP1 were significantly modulated in the hemocytes and stomach by T. cruzi infection indicating a role for PMSRP1 in the parasite interactions with P. megistus. Conclusions For the first time, a constitutively expressed serpin has been characterized from the hemolymph of a triatomine. This opens up new research avenues into the roles of serine peptidases in the T. cruzi/P. megistus association. Initial experiments indicate a role for PMSRP1 in T. cruzi interactions with P. megistus and will lead to further functional studies of this molecule.
Collapse
|
50
|
Konermann L, Vahidi S, Sowole MA. Mass Spectrometry Methods for Studying Structure and Dynamics of Biological Macromolecules. Anal Chem 2013; 86:213-32. [DOI: 10.1021/ac4039306] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario, N6A 5B7 Canada
| | - Siavash Vahidi
- Department of Chemistry, The University of Western Ontario, London, Ontario, N6A 5B7 Canada
| | - Modupeola A. Sowole
- Department of Chemistry, The University of Western Ontario, London, Ontario, N6A 5B7 Canada
| |
Collapse
|