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Nady A, Reichheld SE, Sharpe S. Structural studies of a serum amyloid A octamer that is primed to scaffold lipid nanodiscs. Protein Sci 2024; 33:e4983. [PMID: 38659173 PMCID: PMC11043621 DOI: 10.1002/pro.4983] [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: 02/06/2024] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/26/2024]
Abstract
Serum amyloid A (SAA) is a highly conserved acute-phase protein that plays roles in activating multiple pro-inflammatory pathways during the acute inflammatory response and is commonly used as a biomarker of inflammation. It has been linked to beneficial roles in tissue repair through improved clearance of lipids and cholesterol from sites of damage. In patients with chronic inflammatory diseases, elevated levels of SAA may contribute to increased severity of the underlying condition. The majority of circulating SAA is bound to lipoproteins, primarily high-density lipoprotein (HDL). Interaction with HDL not only stabilizes SAA but also alters its functional properties, likely through altered accessibility of protein-protein interaction sites on SAA. While high-resolution structures for lipid-free, or apo-, forms of SAA have been reported, their relationship with the HDL-bound form of the protein, and with other possible mechanisms of SAA binding to lipids, has not been established. Here, we have used multiple biophysical techniques, including SAXS, TEM, SEC-MALS, native gel electrophoresis, glutaraldehyde crosslinking, and trypsin digestion to characterize the lipid-free and lipid-bound forms of SAA. The SAXS and TEM data show the presence of soluble octamers of SAA with structural similarity to the ring-like structures reported for lipid-free ApoA-I. These SAA octamers represent a previously uncharacterized structure for lipid-free SAA and are capable of scaffolding lipid nanodiscs with similar morphology to those formed by ApoA-I. The SAA-lipid nanodiscs contain four SAA molecules and have similar exterior dimensions as the lipid-free SAA octamer, suggesting that relatively few conformational rearrangements may be required to allow SAA interactions with lipid-containing particles such as HDL. This study suggests a new model for SAA-lipid interactions and provides new insight into how SAA might stabilize protein-lipid nanodiscs or even replace ApoA-I as a scaffold for HDL particles during inflammation.
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Affiliation(s)
- Asal Nady
- Molecular Medicine ProgramThe Hospital for Sick ChildrenTorontoCanada
- Department of BiochemistryUniversity of TorontoTorontoCanada
| | - Sean E. Reichheld
- Molecular Medicine ProgramThe Hospital for Sick ChildrenTorontoCanada
| | - Simon Sharpe
- Molecular Medicine ProgramThe Hospital for Sick ChildrenTorontoCanada
- Department of BiochemistryUniversity of TorontoTorontoCanada
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2
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Chen R, Chen Q, Zheng J, Zeng Z, Chen M, Li L, Zhang S. Serum amyloid protein A in inflammatory bowel disease: from bench to bedside. Cell Death Discov 2023; 9:154. [PMID: 37164984 PMCID: PMC10172326 DOI: 10.1038/s41420-023-01455-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/18/2023] [Accepted: 04/27/2023] [Indexed: 05/12/2023] Open
Abstract
Inflammatory bowel diseases (IBD) is featured by gastrointestinal inflammation and a disease course with alternating recurrence and remission. The global burden caused by IBD has significantly boosted in recent years, necessitating treatment optimization. Serum amyloid A (SAA) is a class of 104 amino acid conservative acute-phase proteins, which is essential in immune-mediated inflammatory processes, like IBD. The SAA monomeric structure is composed of four α-helical regions and a C-terminal amorphous tail. Its disordered structure enables multiple bindings to different ligands and permits multiple functions. It has been proven that SAA has dual roles in the inflammatory process. SAA stimulates the pro-inflammatory cytokine expression and promotes the pathogenic differentiation of TH17 cells. In addition, SAA can remove toxic lipids produced during inflammatory responses and membrane debris from dead cells, redirect HDL, and recycle cholesterol for tissue repair. In IBD, SAA acts on gut epithelium barriers, induces T-cell differentiation, and promotes phagocytosis of Gram-negative bacteria. Owing to the tight connection between SAA and IBD, several clinical studies have taken SAA for a biomarker for diagnosis, assessing disease activity, and predicting prognosis in IBD. Furthermore, 5-MER peptide, a drug specifically targeting SAA, has shown anti-inflammatory effects in some SAA-dependent animal models, providing novel insights into the therapeutic targets of IBD.
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Affiliation(s)
- Rirong Chen
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Qia Chen
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Jieqi Zheng
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Zhirong Zeng
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Minhu Chen
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Li Li
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
| | - Shenghong Zhang
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
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3
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Schönfelder J, Pfeiffer PB, Pradhan T, Bijzet J, Hazenberg BPC, Schönland SO, Hegenbart U, Reif B, Haupt C, Fändrich M. Protease resistance of ex vivo amyloid fibrils implies the proteolytic selection of disease-associated fibril morphologies. Amyloid 2021; 28:243-251. [PMID: 34338090 DOI: 10.1080/13506129.2021.1960501] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Several studies recently showed that ex vivo fibrils from patient or animal tissue were structurally different from in vitro formed fibrils from the same polypeptide chain. Analysis of serum amyloid A (SAA) and Aβ-derived amyloid fibrils additionally revealed that ex vivo fibrils were more protease stable than in vitro fibrils. These observations gave rise to the proteolytic selection hypothesis that suggested that disease-associated amyloid fibrils were selected inside the body by their ability to resist endogenous clearance mechanisms. We here show, for more than twenty different fibril samples, that ex vivo fibrils are more protease stable than in vitro fibrils. These data support the idea of a proteolytic selection of pathogenic amyloid fibril morphologies and help to explain why only few amino acid sequences lead to amyloid diseases, although many, if not all, polypeptide chains can form amyloid fibrils in vitro.
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Affiliation(s)
| | | | - Tejaswini Pradhan
- Bayerisches NMR Zentrum at the Department Chemie, Technische Universität München, Garching, Germany
| | - Johan Bijzet
- Department of Rheumatology & Clinical Immunology, AA21, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Bouke P C Hazenberg
- Department of Rheumatology & Clinical Immunology, AA21, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Stefan O Schönland
- Department of Internal Medicine V (Hematology, Oncology and Rheumatology), Amyloidosis Center, University Hospital Heidelberg, Heidelberg, Germany
| | - Ute Hegenbart
- Department of Internal Medicine V (Hematology, Oncology and Rheumatology), Amyloidosis Center, University Hospital Heidelberg, Heidelberg, Germany
| | - Bernd Reif
- Bayerisches NMR Zentrum at the Department Chemie, Technische Universität München, Garching, Germany
| | - Christian Haupt
- Institute of Protein Biochemistry, Ulm University, Ulm, Germany
| | - Marcus Fändrich
- Institute of Protein Biochemistry, Ulm University, Ulm, Germany
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Structural Basis for Vital Function and Malfunction of Serum Amyloid A: an Acute-Phase Protein that Wears Hydrophobicity on Its Sleeve. Curr Atheroscler Rep 2020; 22:69. [PMID: 32968930 PMCID: PMC7511256 DOI: 10.1007/s11883-020-00888-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/10/2020] [Indexed: 12/13/2022]
Abstract
PURPOSE OF REVIEW This review addresses normal and pathologic functions of serum amyloid A (SAA), an enigmatic biomarker of inflammation and protein precursor of AA amyloidosis, a life-threatening complication of chronic inflammation. SAA is a small, highly evolutionarily conserved acute-phase protein whose plasma levels increase up to one thousand-fold in inflammation, infection, or after trauma. The advantage of this dramatic but transient increase is unclear, and the complex role of SAA in immune response is intensely investigated. This review summarizes recent advances in our understanding of the structure-function relationship of this intrinsically disordered protein, outlines its newly emerging beneficial roles in lipid transport and inflammation control, and discusses factors that critically influence its misfolding in AA amyloidosis. RECENT FINDINGS High-resolution structures of lipid-free SAA in crystals and fibrils have been determined by x-ray crystallography and electron cryo-microscopy. Low-resolution structural studies of SAA-lipid complexes, together with biochemical, cell-based, animal model, genetic, and clinical studies, have provided surprising new insights into a wide range of SAA functions. An emerging vital role of SAA is lipid encapsulation to remove cell membrane debris from sites of injury. The structural basis for this role has been proposed. The lysosomal origin of AA amyloidosis has solidified, and its molecular and cellular mechanisms have emerged. Recent studies have revealed molecular underpinnings for understanding complex functions of this Cambrian protein in lipid transport, immune response, and amyloid formation. These findings help guide the search for much-needed targeted therapies to block the protein deposition in AA amyloidosis.
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Frame NM, Kumanan M, Wales TE, Bandara A, Fändrich M, Straub JE, Engen JR, Gursky O. Structural Basis for Lipid Binding and Function by an Evolutionarily Conserved Protein, Serum Amyloid A. J Mol Biol 2020; 432:1978-1995. [PMID: 32035904 PMCID: PMC7225066 DOI: 10.1016/j.jmb.2020.01.029] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/21/2020] [Accepted: 01/21/2020] [Indexed: 01/28/2023]
Abstract
Serum amyloid A (SAA) is a plasma protein that transports lipids during inflammation. To explore SAA solution conformations and lipid-binding mechanism, we used hydrogen-deuterium exchange mass spectrometry, lipoprotein reconstitution, amino acid sequence analysis, and molecular dynamics simulations. Solution conformations of lipid-bound and lipid-free mSAA1 at pH~7.4 agreed in details with the crystal structures but also showed important differences. The results revealed that amphipathic α-helices h1 and h3 comprise a lipid-binding site that is partially pre-formed in solution, is stabilized upon binding lipids, and shows lipid-induced folding of h3. This site sequesters apolar ligands via a concave hydrophobic surface in SAA oligomers. The largely disordered/dynamic C-terminal region is conjectured to mediate the promiscuous binding of other ligands. The h1-h2 linker region is predicted to form an unexpected β-hairpin that may represent an early amyloidogenic intermediate. The results help establish structural underpinnings for understanding SAA interactions with its key functional ligands, its evolutional conservation, and its transition to amyloid.
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Affiliation(s)
- Nicholas M Frame
- Department of Physiology & Biophysics, Boston University School of Medicine, 700 Albany Street, Boston, MA, 02118, United States
| | - Meera Kumanan
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, MA, 02215, United States
| | - Thomas E Wales
- Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, MA, 02115, United States
| | - Asanga Bandara
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, MA, 02215, United States
| | - Marcus Fändrich
- Institute of Protein Biochemistry, Ulm University, Ulm, 89081, Germany
| | - John E Straub
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, MA, 02215, United States.
| | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, MA, 02115, United States.
| | - Olga Gursky
- Department of Physiology & Biophysics, Boston University School of Medicine, 700 Albany Street, Boston, MA, 02118, United States; Amyloidosis Treatment and Research Center, Boston University School of Medicine, Boston, MA, 02118, United States.
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Kurvits L, Reimann E, Kadastik-Eerme L, Truu L, Kingo K, Erm T, Kõks S, Taba P, Planken A. Serum Amyloid Alpha Is Downregulated in Peripheral Tissues of Parkinson's Disease Patients. Front Neurosci 2019; 13:13. [PMID: 30760975 PMCID: PMC6361740 DOI: 10.3389/fnins.2019.00013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Accepted: 01/08/2019] [Indexed: 11/13/2022] Open
Abstract
We report the changed levels of serum amyloid alpha, an immunologically active protein, in Parkinson’s disease (PD) patients’ peripheral tissues. We have previously shown that Saa-1 and -2 (serum amyloid alpha-1,-2, genes) were among the top downregulated genes in PD patients’ skin, using whole-genome RNA sequencing. In the current study, we characterized the gene and protein expression profiles of skin and blood samples from patients with confirmed PD diagnosis and age/sex matched controls. qRT-PCR analysis of PD skin demonstrated downregulation of Saa-1 and -2 genes in PD patients. However, the lowered amount of protein could not be visualized using immunohistochemistry, due to low quantity of SAA (Serum Amyloid Alpha, protein) in skin. Saa-1 and -2 expression levels in whole blood were below detection threshold based on RNA sequencing, however significantly lowered protein levels of SAA1/2 in PD patients’ serum were shown with ELISA, implying that SAA is secreted into the blood. These results show that SAA is differentially expressed in the peripheral tissues of PD patients.
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Affiliation(s)
- Lille Kurvits
- Department of Neurology and Neurosurgery, University of Tartu, Tartu, Estonia.,Department of Neurology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Ene Reimann
- Institute of Pathophysiology, University of Tartu, Tartu, Estonia
| | - Liis Kadastik-Eerme
- Department of Neurology and Neurosurgery, University of Tartu, Tartu, Estonia
| | - Laura Truu
- Laboratory of Bioenergetics, National Institute of Chemical Physics and Biophysics, Tallinn, Estonia
| | - Külli Kingo
- Department of Dermatology, University of Tartu, Tartu, Estonia.,Dermatology Clinic, Tartu University Hospital, Tartu, Estonia
| | - Triin Erm
- Department of Pathology, Tartu University Hospital, Tartu, Estonia
| | - Sulev Kõks
- Centre for Comparative Genomics, Murdoch University, Perth, WA, Australia.,Perron Institute for Neurological and Translational Science, University of Western Australia, Perth, WA, Australia
| | - Pille Taba
- Department of Neurology and Neurosurgery, University of Tartu, Tartu, Estonia
| | - Anu Planken
- Oncology and Haematology Clinic, North-Estonian Medical Centre, Tallinn, Estonia
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Serum amyloid A forms stable oligomers that disrupt vesicles at lysosomal pH and contribute to the pathogenesis of reactive amyloidosis. Proc Natl Acad Sci U S A 2017; 114:E6507-E6515. [PMID: 28743750 DOI: 10.1073/pnas.1707120114] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Serum amyloid A (SAA) is an acute-phase plasma protein that functions in innate immunity and lipid homeostasis. SAA is a protein precursor of reactive AA amyloidosis, the major complication of chronic inflammation and one of the most common human systemic amyloid diseases worldwide. Most circulating SAA is protected from proteolysis and misfolding by binding to plasma high-density lipoproteins. However, unbound soluble SAA is intrinsically disordered and is either rapidly degraded or forms amyloid in a lysosome-initiated process. Although acidic pH promotes amyloid fibril formation by this and many other proteins, the molecular underpinnings are unclear. We used an array of spectroscopic, biochemical, and structural methods to uncover that at pH 3.5-4.5, murine SAA1 forms stable soluble oligomers that are maximally folded at pH 4.3 with ∼35% α-helix and are unusually resistant to proteolysis. In solution, these oligomers neither readily convert into mature fibrils nor bind lipid surfaces via their amphipathic α-helices in a manner typical of apolipoproteins. Rather, these oligomers undergo an α-helix to β-sheet conversion catalyzed by lipid vesicles and disrupt these vesicles, suggesting a membranolytic potential. Our results provide an explanation for the lysosomal origin of AA amyloidosis. They suggest that high structural stability and resistance to proteolysis of SAA oligomers at pH 3.5-4.5 help them escape lysosomal degradation, promote SAA accumulation in lysosomes, and ultimately damage cellular membranes and liberate intracellular amyloid. We posit that these soluble prefibrillar oligomers provide a missing link in our understanding of the development of AA amyloidosis.
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Frame NM, Jayaraman S, Gantz DL, Gursky O. Serum amyloid A self-assembles with phospholipids to form stable protein-rich nanoparticles with a distinct structure: A hypothetical function of SAA as a "molecular mop" in immune response. J Struct Biol 2017. [PMID: 28645735 DOI: 10.1016/j.jsb.2017.06.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Serum amyloid A (SAA) is an acute-phase protein whose action in innate immunity and lipid homeostasis is unclear. Most circulating SAA binds plasma high-density lipoproteins (HDL) and reroutes lipid transport. In vivo SAA binds existing lipoproteins or generates them de novo upon lipid uptake from cells. We explored the products of SAA-lipid interactions and lipoprotein remodeling in vitro. SAA complexes with palmitoyl-oleoyl phosphocholine (POPC) were analyzed for structure and stability using circular dichroism and fluorescence spectroscopy, electron microscopy, gel electrophoresis and gel filtration. The results revealed the formation of 8-11nm lipoproteins that were∼50% α-helical and stable at near-physiological conditions but were irreversibly remodeled at Tm∼52°C. Similar HDL-size nanoparticles formed spontaneously at ambient conditions or upon thermal remodeling of parent lipoproteins containing various amounts of proteins and lipids, including POPC and cholesterol. Therefore, such HDL-size particles formed stable kinetically accessible structures in a wide range of conditions. Based on their size and stoichiometry, each particle contained about 12 SAA and 72 POPC molecules, with a protein:lipid weight ratio circa 2.5:1, suggesting a structure distinct from HDL. High stability of these nanoparticles and their HDL-like size suggest that similar lipoproteins may form in vivo during inflammation or injury when SAA concentration is high and membranes from dead cells require rapid removal. We speculate that solubilization of membranes by SAA to generate lipoproteins in a spontaneous energy-independent process constitutes the primordial function of this ancient protein, providing the first line of defense in clearing cell debris from the injured sites.
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Affiliation(s)
- Nicholas M Frame
- Department of Physiology & Biophysics, Boston University School of Medicine, 700 Albany St., Boston, MA 02118, USA.
| | - Shobini Jayaraman
- Department of Physiology & Biophysics, Boston University School of Medicine, 700 Albany St., Boston, MA 02118, USA.
| | - Donald L Gantz
- Department of Physiology & Biophysics, Boston University School of Medicine, 700 Albany St., Boston, MA 02118, USA.
| | - Olga Gursky
- Department of Physiology & Biophysics, Boston University School of Medicine, 700 Albany St., Boston, MA 02118, USA.
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Frame NM, Gursky O. Structure of serum amyloid A suggests a mechanism for selective lipoprotein binding and functions: SAA as a hub in macromolecular interaction networks. FEBS Lett 2016; 590:866-79. [PMID: 26918388 DOI: 10.1002/1873-3468.12116] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 02/19/2016] [Accepted: 02/19/2016] [Indexed: 01/19/2023]
Abstract
Serum amyloid A is a major acute-phase plasma protein that modulates innate immunity and cholesterol homeostasis. We combine sequence analysis with x-ray crystal structures to postulate that SAA acts as an intrinsically disordered hub mediating interactions among proteins, lipids and proteoglycans. A structural model of lipoprotein-bound SAA monomer is proposed wherein two α-helices from the N-domain form a concave hydrophobic surface that binds lipoproteins. A C-domain, connected to the N-domain via a flexible linker, binds polar/charged ligands including cell receptors, bridging them with lipoproteins and rerouting cholesterol transport. Our model is supported by the SAA cleavage in the interdomain linker to generate the 1-76 fragment deposited in reactive amyloidosis. This model sheds new light on functions of this enigmatic protein.
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Affiliation(s)
- Nicholas M Frame
- Department of Physiology & Biophysics, Boston University School of Medicine, Boston, MA, USA
| | - Olga Gursky
- Department of Physiology & Biophysics, Boston University School of Medicine, Boston, MA, USA
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