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Arriaza RH, Kapingidza AB, Dolamore C, Khatri K, O’Malley A, Glesner J, Wuenschmann S, Hyduke NP, Easley W, Chhiv C, Pomés A, Chruszcz M. Structural, Biophysical, and Computational Studies of a Murine Light Chain Dimer. Molecules 2024; 29:2885. [PMID: 38930950 PMCID: PMC11206851 DOI: 10.3390/molecules29122885] [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: 05/03/2024] [Revised: 06/05/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024] Open
Abstract
Antibodies are widely used in medicinal and scientific research due to their ability to bind to a specific antigen. Most often, antibodies are composed of heavy and light chain domains. Under physiological conditions, light chains are produced in excess, as compared to the heavy chain. It is now known that light chains are not silent partners of the heavy chain and can modulate the immune response independently. In this work, the first crystal structure of a light chain dimer originating from mice is described. It represents the light chain dimer of 6A8, a monoclonal antibody specific to the allergen Der f 1. Building on the unexpected occurrence of this kind of dimer, we have demonstrated that this light chain is stable in solution alone. Moreover, enzyme-linked immunosorbent assays (ELISA) have revealed that, when the light chain is not partnered to its corresponding heavy chain, it interacts non-specifically with a wide range of proteins. Computational studies were used to provide insight on the role of the 6A8 heavy chain domain in the specific binding to Der f 1. Overall, this work demonstrates and supports the ongoing notion that light chains can function by themselves and are not silent partners of heavy chains.
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Affiliation(s)
- Ricardo H. Arriaza
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48864, USA; (R.H.A.); (K.K.); (A.O.)
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA; (A.B.K.); (C.D.); (N.P.H.); (W.E.); (C.C.)
| | - A. Brenda Kapingidza
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA; (A.B.K.); (C.D.); (N.P.H.); (W.E.); (C.C.)
| | - Coleman Dolamore
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA; (A.B.K.); (C.D.); (N.P.H.); (W.E.); (C.C.)
| | - Kriti Khatri
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48864, USA; (R.H.A.); (K.K.); (A.O.)
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA; (A.B.K.); (C.D.); (N.P.H.); (W.E.); (C.C.)
| | - Andrea O’Malley
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48864, USA; (R.H.A.); (K.K.); (A.O.)
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA; (A.B.K.); (C.D.); (N.P.H.); (W.E.); (C.C.)
| | - Jill Glesner
- InBio, Charlottesville, VA 22903, USA; (J.G.); (S.W.); (A.P.)
| | | | - Noah P. Hyduke
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA; (A.B.K.); (C.D.); (N.P.H.); (W.E.); (C.C.)
| | - William Easley
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA; (A.B.K.); (C.D.); (N.P.H.); (W.E.); (C.C.)
| | - Charline Chhiv
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA; (A.B.K.); (C.D.); (N.P.H.); (W.E.); (C.C.)
| | - Anna Pomés
- InBio, Charlottesville, VA 22903, USA; (J.G.); (S.W.); (A.P.)
| | - Maksymilian Chruszcz
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48864, USA; (R.H.A.); (K.K.); (A.O.)
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA; (A.B.K.); (C.D.); (N.P.H.); (W.E.); (C.C.)
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Klimtchuk ES, Peterle D, Bullitt EA, Connors LH, Engen JR, Gursky O. Role of complementarity-determining regions 1 and 3 in pathologic amyloid formation by human immunoglobulin κ1 light chains. Amyloid 2023; 30:364-378. [PMID: 37216473 PMCID: PMC10663386 DOI: 10.1080/13506129.2023.2212397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/24/2023] [Accepted: 05/04/2023] [Indexed: 05/24/2023]
Abstract
BACKGROUND Immunoglobulin light chain (LC) amyloidosis is a life-threatening disease complicated by vast numbers of patient-specific mutations. We explored 14 patient-derived and engineered proteins related to κ1-family germline genes IGKVLD-33*01 and IGKVLD-39*01. METHODS Hydrogen-deuterium exchange mass spectrometry analysis of conformational dynamics in recombinant LCs and their fragments was integrated with studies of thermal stability, proteolytic susceptibility, amyloid formation and amyloidogenic sequence propensity. The results were mapped on the structures of native and fibrillary proteins. RESULTS Proteins from two κ1 subfamilies showed unexpected differences. Compared to their germline counterparts, amyloid LC related to IGKVLD-33*01 was less stable and formed amyloid faster, whereas amyloid LC related to IGKVLD-39*01 had similar stability and formed amyloid slower, suggesting different major factors influencing amyloidogenesis. In 33*01-related amyloid LC, these factors involved destabilization of the native structure and probable stabilization of amyloid. The atypical behavior of 39*01-related amyloid LC stemmed from increased dynamics/exposure of amyloidogenic segments in βC'V and βEV that could initiate aggregation and decreased dynamics/exposure near the Cys23-Cys88 disulfide. CONCLUSIONS The results suggest distinct amyloidogenic pathways for closely related LCs and point to the complementarity-defining regions CDR1 and CDR3, linked via the conserved internal disulfide, as key factors in amyloid formation.
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Affiliation(s)
- Elena S. Klimtchuk
- Amyloidosis Center, Boston University Chobanian and Avedisian School of Medicine, Boston MA 02118, United States
| | - Daniele Peterle
- Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, MA, 02115, United States
| | - Esther A. Bullitt
- Department of Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, W302, 700 Albany Street, Boston, MA, 02118, United States
| | - Lawreen H. Connors
- Amyloidosis Center, Boston University Chobanian and Avedisian School of Medicine, Boston MA 02118, United States
| | - John R. Engen
- Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, MA, 02115, United States
| | - Olga Gursky
- Amyloidosis Center, Boston University Chobanian and Avedisian School of Medicine, Boston MA 02118, United States
- Department of Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, W302, 700 Albany Street, Boston, MA, 02118, United States
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3
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An N-glycosylation hotspot in immunoglobulin κ light chains is associated with AL amyloidosis. Leukemia 2022; 36:2076-2085. [PMID: 35610346 DOI: 10.1038/s41375-022-01599-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 05/05/2022] [Accepted: 05/11/2022] [Indexed: 12/24/2022]
Abstract
Immunoglobulin light chain (AL) amyloidosis is caused by a small, minimally proliferating B-cell/plasma-cell clone secreting a patient-unique, aggregation-prone, toxic light chain (LC). The pathogenicity of LCs is encrypted in their sequence, yet molecular determinants of amyloidogenesis are poorly understood. Higher rates of N-glycosylation among clonal κ LCs from patients with AL amyloidosis compared to other monoclonal gammopathies indicate that this post-translational modification is associated with a higher risk of developing AL amyloidosis. Here, we exploited LC sequence information from previously published amyloidogenic and control clonal LCs and from a series of 220 patients with AL amyloidosis or multiple myeloma followed at our Institutions to define sequence and spatial features of N-glycosylation, combining bioinformatics, biochemical, proteomics, structural and genetic analyses. We found peculiar sequence and spatial pattern of N-glycosylation in amyloidogenic κ LCs, with most of the N-glycosylation sites laying in the framework region 3, particularly within the E strand, and consisting mainly of the NFT sequon, setting them apart with respect to non-amyloidogenic clonal LCs. Our data further support a potential role of N-glycosylation in determining the pathogenic behavior of a subset of amyloidogenic LCs and may help refine current N-glycosylation-based prognostic assessments for patients with monoclonal gammopathies.
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Yan NL, Santos-Martins D, Nair R, Chu A, Wilson IA, Johnson KA, Forli S, Morgan GJ, Petrassi HM, Kelly JW. Discovery of Potent Coumarin-Based Kinetic Stabilizers of Amyloidogenic Immunoglobulin Light Chains Using Structure-Based Design. J Med Chem 2021; 64:6273-6299. [PMID: 33939422 DOI: 10.1021/acs.jmedchem.1c00339] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In immunoglobulin light-chain (LC) amyloidosis, transient unfolding or unfolding and proteolysis enable aggregation of LC proteins, causing potentially fatal organ damage. A drug that kinetically stabilizes LCs could suppress aggregation; however, LC sequences are variable and have no natural ligands, hindering drug development efforts. We previously identified high-throughput screening hits that bind to a site at the interface between the two variable domains of the LC homodimer. We hypothesized that extending the stabilizers beyond this initially characterized binding site would improve affinity. Here, using protease sensitivity assays, we identified stabilizers that can be divided into four substructures. Some stabilizers exhibit nanomolar EC50 values, a 3000-fold enhancement over the screening hits. Crystal structures reveal a key π-π stacking interaction with a conserved tyrosine residue that was not utilized by the screening hits. These data provide a foundation for developing LC stabilizers with improved binding selectivity and enhanced physicochemical properties.
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Affiliation(s)
- Nicholas L Yan
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Diogo Santos-Martins
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Reji Nair
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Alan Chu
- California Institute for Biomedical Research, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Kristen A Johnson
- California Institute for Biomedical Research, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Stefano Forli
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Gareth J Morgan
- Section of Hematology and Medical Oncology, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts 02118, United States.,The Amyloidosis Center, Boston University School of Medicine, Boston, Massachusetts 02118, United States
| | - H Michael Petrassi
- California Institute for Biomedical Research, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Jeffery W Kelly
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States.,The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, United States
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5
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Timchenko M, Abdullatypov A, Kihara H, Timchenko A. Effect of Single Amino Acid Substitutions by Asn and Gln on Aggregation Properties of Bence-Jones Protein BIF. Int J Mol Sci 2019; 20:ijms20205197. [PMID: 31635169 PMCID: PMC6834151 DOI: 10.3390/ijms20205197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 10/17/2019] [Accepted: 10/19/2019] [Indexed: 11/24/2022] Open
Abstract
The nature of renal amyloidosis involving Bence-Jones proteins in multiple myeloma is still unclear. The development of amyloidosis in neurodegenerative diseases is often associated with a high content of asparagine and glutamine residues in proteins forming amyloid deposits. To estimate the influence of Asn and Gln residues on the aggregation of Bence-Jones protein BIF, we obtained recombinant BIF and its mutants with the substitution of Tyr187→Asn (Y187N) in α-helix of CL domain, Lys170→Asn (K170N) and Ser157→Gln (S157Q) in CL domain loops, Arg109→Asn in VL-CL linker (R109N) and Asp29→Gln in VL domain loop (D29Q). The morphology of protein aggregates was studied at pH corresponding to the conditions in bloodstream (pH 7.2), distal (pH 6.5) and proximal renal tubules (pH 4.5) by atomic force microscopy (AFM) and small-angle X-ray scattering (SAXS). The Lys170→Asn replacement almost completely inhibits amyloidogenic activity. The Y187N forms fibril-like aggregates at all pH values. The Arg109→Asn replacement resulted in formation of fibril-like structures at pH 7.2 and 6.5 while the substitutions by Gln provoked formation of those structures only at pH 7.2. Therefore, the amyloidogenic properties are highly dependent on the location of Asn or Gln.
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Affiliation(s)
- Maria Timchenko
- Laboratory of NMR of Biosystems, Institute of Theoretical and Experimental Biophysics RAS, Pushchino 142290, Russia.
| | - Azat Abdullatypov
- Laboratory of Biotechnology and Physiology of Phototrophic Organisms, Institute of Basic Biological Problems RAS-a separate subdivision of PSCBR RAS (IBBP RAS), Pushchino 142290, Russia.
| | - Hiroshi Kihara
- Himeji-Hinomoto College, 890 Koro, Kodera-cho, Himeji 679-2151, Russia.
| | - Alexander Timchenko
- Laboratory of Protein Physics, Institute of Protein Research RAS, Pushchino 142290, Russia.
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Blancas-Mejia LM, Misra P, Dick CJ, Cooper SA, Redhage KR, Bergman MR, Jordan TL, Maar K, Ramirez-Alvarado M. Immunoglobulin light chain amyloid aggregation. Chem Commun (Camb) 2018; 54:10664-10674. [PMID: 30087961 DOI: 10.1039/c8cc04396e] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Light chain (AL) amyloidosis is a devastating, complex, and incurable protein misfolding disease. It is characterized by an abnormal proliferation of plasma cells (fully differentiated B cells) producing an excess of monoclonal immunoglobulin light chains that are secreted into circulation, where the light chains misfold, aggregate as amyloid fibrils in target organs, and cause organ dysfunction, organ failure, and death. In this article, we will review the factors that contribute to AL amyloidosis complexity, the findings by our laboratory from the last 16 years and the work from other laboratories on understanding the structural, kinetics, and thermodynamic contributions that drive immunoglobulin light chain-associated amyloidosis. We will discuss the role of cofactors and the mechanism of cellular damage. Last, we will review our recent findings on the high resolution structure of AL amyloid fibrils. AL amyloidosis is the best example of protein sequence diversity in misfolding diseases, as each patient has a unique combination of germline donor sequences and multiple amino acid mutations in the protein that forms the amyloid fibril.
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Affiliation(s)
- Luis M Blancas-Mejia
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA.
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Morgan GJ, Usher GA, Kelly JW. Incomplete Refolding of Antibody Light Chains to Non-Native, Protease-Sensitive Conformations Leads to Aggregation: A Mechanism of Amyloidogenesis in Patients? Biochemistry 2017; 56:6597-6614. [PMID: 29200282 DOI: 10.1021/acs.biochem.7b00579] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Genetic, biochemical, and pharmacologic evidence supports the hypothesis that conformationally altered or misfolded protein states enable aggregation and cytotoxicity in the systemic amyloid diseases. Reversible structural fluctuations of natively folded proteins are involved in the aggregation of many degenerative disease associated proteins. Herein, we use antibody light chains (LCs) that form amyloid fibrils in AL amyloidosis to consider an alternative hypothesis of amyloidogenesis: that transient unfolding and incomplete extracellular refolding of secreted proteins can lead to metastable, alternatively folded states that are more susceptible to aggregation or to endoproteolysis that can release aggregation-prone fragments. Refolding of full-length λ6a LC dimers comprising an interchain disulfide bond from heat- or chaotrope-denatured ensembles in buffers yields the native dimeric state as well as alternatively folded dimers and aggregates. LC variants lacking an interchain disulfide bond appear to refold fully reversibly to the native state. The conformation of a backbone peptidyl-proline amide in the LC constant domain, which is cis in the native state, may determine whether the LC refolds back to the native state. A proline to alanine (P147A) LC variant, which cannot form the native cis-amide conformation, forms amyloid fibrils from the alternatively folded ensemble, whereas all the full-length λ6a LCs we have studied to date do not form amyloid under analogous conditions. P147A LC variants are susceptible to endoproteolysis by thrombin, enabling amyloidogenesis of the fragments released. Thus, non-native LC structural ensembles containing a tyrosine 146-proline 147 trans-amide bond can initiate and propagate amyloid formation, either directly or after aberrant endoproteolysis.
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Affiliation(s)
- Gareth J Morgan
- Departments of Chemistry and Molecular Medicine, and ‡The Skaggs Institute for Chemical Biology, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Grace A Usher
- Departments of Chemistry and Molecular Medicine, and ‡The Skaggs Institute for Chemical Biology, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Jeffery W Kelly
- Departments of Chemistry and Molecular Medicine, and ‡The Skaggs Institute for Chemical Biology, The Scripps Research Institute , La Jolla, California 92037, United States
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Free immunoglobulin light chain (FLC) promotes murine colitis and colitis-associated colon carcinogenesis by activating the inflammasome. Sci Rep 2017; 7:5165. [PMID: 28701727 PMCID: PMC5507933 DOI: 10.1038/s41598-017-05468-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 05/31/2017] [Indexed: 01/10/2023] Open
Abstract
Numerous studies have demonstrated that free Ig light chain (FLC), a novel inflammation mediator, participates in many inflammatory diseases by activating mast cells and extending the survival of neutrophils. However, it remains unclear whether FLC is involved in colitis and colitis-associated colon carcinogenesis (CAC). In this study, we found a significant increase in FLC in murine models of DSS (Dextran Sulfate Sodium Salt)-induced colitis and CAC compared to controls. Peptide F991, a functional blocker of FLC, significantly attenuated colitis progression, which included abrogating the development of diarrhea and tumor burden, elevating survival rate, greatly reducing the infiltration of inflammatory cells (such as ROS+ active neutrophils), especially reducing tumorigenesis in CAC. Furthermore, we demonstrated that F991 inhibited the activation of the inflammasome by reducing the expression of cleaved caspase-1 and the maturation of IL-1β and IL-18. Altogether, our findings demonstrate that FLC can promote the pathogenesis of colitis and CAC and may be used as novel biomarker for the diagnosis of inflammatory bowel disease. Additionally, F991 may become a potential therapeutic option for colitis or colorectal cancer.
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9
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Hereditary systemic immunoglobulin light-chain amyloidosis. Blood 2015; 125:3281-6. [DOI: 10.1182/blood-2014-12-618108] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 03/29/2015] [Indexed: 01/01/2023] Open
Abstract
Key Points
Protein and DNA analyses reveal that mutation in the immunoglobulin κ light-chain constant region gene may cause hereditary amyloidosis. Sequencing of immunoglobulin light-chain constant region genes is indicated for patients with AL amyloidosis and no evidence of a plasma cell dyscrasia.
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Kaneko K, Seta K, Soma J, Kuwahara T, Koizumi M, Kikuchi Y, Sugawara A, Yahata K. Gamma 1-heavy chain deposition disease accompanied by IgG kappa in serum, urine, and bone marrow. CEN Case Rep 2014; 3:44-48. [PMID: 28509245 DOI: 10.1007/s13730-013-0083-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 04/30/2013] [Indexed: 11/24/2022] Open
Abstract
A 32-year-old Japanese woman presented with hypertension, nephrotic syndrome, microhematuria, and severe hypocomplementemia. Her serum creatinine concentration increased from 1.46 mg/dL (129.0 μmol/L) to 3.46 mg/dL (305.8 μmol/L) over 1 month. Renal biopsy revealed Congo red-negative nodular glomerulosclerosis accompanied by mesangial proliferation. There was extensive staining of immunoglobulin (Ig) G in the glomerular and tubular basement membranes and expanded mesangial regions. Staining was negative for IgA, IgM, and kappa and lambda light chains and positive for the gamma 1 IgG subclass. Staining for constant domains of the gamma heavy chains showed a deletion of the first constant domain (CH1). Electron microscopy revealed electron-dense deposits in the glomerular and tubular basement membranes and mesangium. These findings indicated gamma 1-heavy chain deposition disease (HCDD). Serum and urine immunoelectrophoresis revealed an IgG kappa monoclonal band, whereas bone marrow biopsy revealed monoclonal plasmacytosis with positive staining for kappa chains. HCDD associated with kappa light chain is extremely rare. We report the first case of HCDD with IgG kappa detected in the serum, urine, and bone marrow.
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Affiliation(s)
- Keiichi Kaneko
- Department of Nephrology, National Hospital Organization Kyoto Medical Center, 1-1 Fukakusa Mukaihata-cho, Fushimi-ku, Kyoto, 612-8555, Japan
| | - Koichi Seta
- Department of Nephrology, National Hospital Organization Kyoto Medical Center, 1-1 Fukakusa Mukaihata-cho, Fushimi-ku, Kyoto, 612-8555, Japan.
| | - Jun Soma
- Department of Nephrology, Iwate Prefectural Central Hospital, 1-4-1 Ueda, Morioka-shi, Iwate, 020-0066, Japan
| | - Takashi Kuwahara
- Department of Nephrology, Saiseikai Ibaraki Hospital, 2-1-45 Mitsukeyama, Ibaraki-shi, Osaka, 567-0035, Japan
| | - Mitsuteru Koizumi
- Department of Nephrology, National Hospital Organization Kyoto Medical Center, 1-1 Fukakusa Mukaihata-cho, Fushimi-ku, Kyoto, 612-8555, Japan
| | - Yuko Kikuchi
- Department of Nephrology, National Hospital Organization Kyoto Medical Center, 1-1 Fukakusa Mukaihata-cho, Fushimi-ku, Kyoto, 612-8555, Japan
| | - Akira Sugawara
- Department of Nephrology, Osaka Red Cross Hospital, 5-30 Hudegasaki, Ten-noji, Osaka, 543-8555, Japan
| | - Kensei Yahata
- Department of Nephrology, National Hospital Organization Kyoto Medical Center, 1-1 Fukakusa Mukaihata-cho, Fushimi-ku, Kyoto, 612-8555, Japan
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11
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Tischenko VM. Effects of interdomain interactions on amyloidogenic properties of bence jones proteins. Mol Biol 2011. [DOI: 10.1134/s002689331105013x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Lewus RA, Darcy PA, Lenhoff AM, Sandler SI. Interactions and phase behavior of a monoclonal antibody. Biotechnol Prog 2011; 27:280-9. [DOI: 10.1002/btpr.536] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2010] [Revised: 07/30/2010] [Indexed: 11/11/2022]
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13
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Peterson FC, Baden EM, Owen BAL, Volkman BF, Ramirez-Alvarado M. A single mutation promotes amyloidogenicity through a highly promiscuous dimer interface. Structure 2010; 18:563-70. [PMID: 20462490 DOI: 10.1016/j.str.2010.02.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2009] [Revised: 02/05/2010] [Accepted: 02/17/2010] [Indexed: 10/19/2022]
Abstract
Light chain amyloidosis is a devastating protein misfolding disease characterized by the accumulation of amyloid fibrils that causes tissue damage and organ failure. These fibrils are composed of monoclonal light chain protein secreted from an abnormal proliferation of bone marrow plasma cells. We previously reported that amyloidogenic light chain protein AL-09 adopts an altered dimer while its germline protein (kappaI O18/O8) forms a canonical dimer observed in other light chain crystal structures. In solution, conformational heterogeneity obscures all NMR signals at the AL-09 and kappaI O18/O8 dimer interfaces, so we solved the nuclear magnetic resonance structure of two related mutants. AL-09 H87Y adopts the normal dimer interface, but the kappaI Y87H solution structure presents an altered interface rotated 180 degrees relative to the canonical dimer interface and 90 degrees from the AL-09 arrangement. Our results suggest that promiscuity in the light chain dimer interface may promote new intermolecular contacts that may contribute to amyloid fibril structure.
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Affiliation(s)
- Francis C Peterson
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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14
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Hutchinson AT, Ramsland PA, Jones DR, Agostino M, Lund ME, Jennings CV, Bockhorni V, Yuriev E, Edmundson AB, Raison RL. Free Ig Light Chains Interact with Sphingomyelin and Are Found on the Surface of Myeloma Plasma Cells in an Aggregated Form. THE JOURNAL OF IMMUNOLOGY 2010; 185:4179-88. [DOI: 10.4049/jimmunol.1001956] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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15
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Randles EG, Thompson JR, Martin DJ, Ramirez-Alvarado M. Structural alterations within native amyloidogenic immunoglobulin light chains. J Mol Biol 2009; 389:199-210. [PMID: 19361523 PMCID: PMC2840394 DOI: 10.1016/j.jmb.2009.04.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2008] [Revised: 03/20/2009] [Accepted: 04/05/2009] [Indexed: 10/20/2022]
Abstract
Amyloid diseases are characterized by the misfolding of a precursor protein that leads to amyloid fibril formation. Despite the fact that there are different precursors, some commonalities in the misfolding mechanism are thought to exist. In light chain amyloidosis (AL), the immunoglobulin light chain forms amyloid fibrils that deposit in the extracellular space of vital organs. AL proteins are thermodynamically destabilized compared to non-amyloidogenic proteins and some studies have linked this instability to increased fibril formation rates. Here we present the crystal structures of two highly homologous AL proteins, AL-12 and AL-103. This structural study shows that these proteins retain the canonical germ line dimer interface. We highlight important structural alterations in two loops flanking the dimer interface and correlate these results with the somatic mutations present in AL-12 and AL-103. We suggest that these alterations are informative structural features that are likely contributing to protein instability that leads to conformational changes involved in the initial events of amyloid formation.
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Affiliation(s)
- Edward G. Randles
- Department of Biochemistry and Molecular Biology, College of Medicine, Mayo Clinic, 200 First Street SW, Rochester, Minnesota 55905
| | - James R. Thompson
- Department of Physiology and Biomedical Engineering, College of Medicine, Mayo Clinic, 200 First Street SW, Rochester, Minnesota 55905
| | - Douglas J. Martin
- Department of Biochemistry and Molecular Biology, College of Medicine, Mayo Clinic, 200 First Street SW, Rochester, Minnesota 55905
| | - Marina Ramirez-Alvarado
- Department of Biochemistry and Molecular Biology, College of Medicine, Mayo Clinic, 200 First Street SW, Rochester, Minnesota 55905
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Tishchenko VM, Khristoforov VS, Bliznyukov OP. Thermodynamic and hydrodynamic study of Bence-Jones proteins. Mol Biol 2009. [DOI: 10.1134/s002689330901018x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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Baden EM, Owen BAL, Peterson FC, Volkman BF, Ramirez-Alvarado M, Thompson JR. Altered dimer interface decreases stability in an amyloidogenic protein. J Biol Chem 2008; 283:15853-60. [PMID: 18400753 DOI: 10.1074/jbc.m705347200] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Amyloidoses are devastating and currently incurable diseases in which the process of amyloid formation causes fatal cellular and organ damage. The molecular mechanisms underlying amyloidoses are not well known. In this study, we address the structural basis of immunoglobulin light chain amyloidosis, which results from deposition of light chains produced by clonal plasma cells. We compare light chain amyloidosis protein AL-09 to its wild-type counterpart, the kappaI O18/O8 light chain germline. Crystallographic studies indicate that both proteins form dimers. However, AL-09 has an altered dimer interface that is rotated 90 degrees from the kappaI O18/O8 dimer interface. The three non-conservative mutations in AL-09 are located within the dimer interface, consistent with their role in the decreased stability of this amyloidogenic protein. Moreover, AL-09 forms amyloid fibrils more quickly than kappaI O18/O8 in vitro. These results support the notion that the increased stability of the monomer and delayed fibril formation, together with a properly formed dimer, may be protective against amyloidogenesis. This could open a new direction into rational drug design for amyloidogenic proteins.
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Affiliation(s)
- Elizabeth M Baden
- Department of Biochemistry and Molecular Biology, College of Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
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18
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Abstract
Deposition of immunoglobulin light chains is a result of clonal proliferation of monoclonal plasma cells that secrete free immunoglobulin light chains, also called Bence Jones proteins (BJP). These BJP are present in circulation in large amounts and excreted in urine in various light chain diseases such as light chain amyloidosis (AL), light chain deposition disease (LCDD) and multiple myeloma (MM). BJP from patients with AL, LCDD and MM were purified from their urine and studies were performed to determine their secondary structure, thermodynamic stability and aggregate formation kinetics. Our results show that LCDD and MM proteins have the lowest free energy of folding while all proteins show similar melting temperatures. Incubation of the BJP at their melting temperature produced morphologically different aggregates: amyloid fibrils from the AL proteins, amorphous aggregates from the LCDD proteins and large spherical species from the MM proteins. The aggregates formed under in vitro conditions suggested that the various proteins derived from patients with different light chain diseases might follow different aggregation pathways.
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Affiliation(s)
- Laura A Sikkink
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, Minnesota 55905, USA
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19
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Svensson HG, Wedemeyer WJ, Ekstrom JL, Callender DR, Kortemme T, Kim DE, Sjöbring U, Baker D. Contributions of amino acid side chains to the kinetics and thermodynamics of the bivalent binding of protein L to Ig kappa light chain. Biochemistry 2004; 43:2445-57. [PMID: 14992582 DOI: 10.1021/bi034873s] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein L is a bacterial surface protein with 4-5 immunoglobulin (Ig)-binding domains (B1-B5), each of which appears to have two binding sites for Ig, corresponding to the two edges of its beta-sheet. To verify these sites biochemically and to probe their relative contributions to the protein L-Ig kappa light chain (kappa) interaction, we compared the binding of PLW (the Y47W mutant of the B1 domain) to that of mutants designed to disrupt binding to sites 1 and 2, using gel filtration, BIAcore surface plasmon resonance, fluorescence titration, and solid-phase radioimmunoassays. Gel filtration experiments show that PLW binds kappa both in 1:1 complexes and multivalently, consistent with two binding sites. Covalent dimers of the A20C and V51C mutants of PLW were prepared to eliminate site 1 and site 2 binding, respectively; both the A20C and V51C dimers bind kappa in 1:1 complexes and multivalently, indicating that neither site 1 nor site 2 is solely responsible for kappa binding. The A20R mutant was designed computationally to eliminate site 1 binding while preserving site 2 binding; consistent with this design, the A20R mutant binds kappa in 1:1 complexes but not multivalently. To probe the contributions of amino acid side chains to binding, we prepared 75 point mutants spanning nearly every residue of PLW; BIAcore studies of these mutants revealed two binding-energy "hot spots" consistent with sites 1 and 2. These data indicate that PLW binds kappa at both sites with similar affinities (high nanomolar), with the strongest contributions to the binding energy from Tyr34 (site 2) and Tyr36 (site 1). Compared to other protein-protein complexes, the binding is insensitive to amino acid substitutions at these sites, consistent with the large number of main chain interactions relative to side chain interactions. The strong binding of protein L to Ig kappa light chains of various species may result from the ambidextrous binding of the B1-B5 domains and the unimportance of specific side chain interactions.
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20
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Spinelli S, Desmyter A, Frenken L, Verrips T, Tegoni M, Cambillau C. Domain swapping of a llama VHH domain builds a crystal-wide beta-sheet structure. FEBS Lett 2004; 564:35-40. [PMID: 15094039 DOI: 10.1016/s0014-5793(04)00304-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2004] [Revised: 03/12/2004] [Accepted: 03/12/2004] [Indexed: 11/21/2022]
Abstract
Among mammals, camelids have a unique immunological system since they produce functional antibodies devoid of light chains and CH1 domains. To bind antigens, whether they are proteins or haptens, camelids use the single domain VH from their heavy chain (VHH). We report here on such a llama VHH domain (VHH-R9) which was raised against a hapten, the RR6 red dye. This VHH possesses the shortest complementarity determining region 3 (CDR3) among all the known VHH sequences and nevertheless binds RR6 efficiently with a K(d) value of 83 nM. However, the crystal structure of VHH-R9 exhibits a striking feature: its CDR3 and its last beta-strand (beta9) do not follow the immunoglobulin VH domain fold, but instead extend out of the VHH molecular boundary and associate with a symmetry-related molecule. The two monomers thus form a domain-swapped dimer which establishes further contacts with symmetry-related molecules and build a crystal-wide beta-sheet structure. The driving force of the dimer formation is probably the strain induced by the short CDR3 together with the cleavage of the first seven residues.
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Affiliation(s)
- Silvia Spinelli
- Architecture et Fonction des Macromolécules Biologiques, UMR-6098, CNRS and Universités d'Aix-Marseille I and II, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
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21
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Watkins NA, Dafforn TR, Kuijpers M, Brown C, Javid B, Lehner PJ, Navarrete C, Ouwehand WH. Molecular studies of anti-HLA-A2 using light-chain shuffling: a structural model for HLA antibody binding. ACTA ACUST UNITED AC 2004; 63:345-54. [PMID: 15009806 DOI: 10.1111/j.0001-2815.2004.00194.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Human leukocyte antigen (HLA) A2 is one of the most immunodominant HLA antigens. Through a process of light-chain variable domain (VL) shuffling, we analyzed the VL domains' role in anti-HLA-A2/A28-binding site diversity. This was achieved by combining a VH3-30-encoded HLA-A2/A28-specific heavy-chain variable domain with 10(4) non-immune VL domains. Twelve HLA-A2/A28-specific antibodies were subsequently identified. VL gene analysis demonstrated an absence of Vlambda domains and that all have VkappaI-encoded light chains. The affinities correlated with the VkappaI gene present, with the seven highest affinity antibodies using Vkappa domains encoded by the O18 gene segment. A 300-fold difference in affinity was observed between the 12 antibodies, and homology modeling demonstrated a correlation between electrostatic surface potential of the antigen-binding site and affinity for HLA. Overlap between the T-cell receptor-binding site and that of the antibodies was indicated by inhibition of cytotoxic T-lymphocyte killing of peptide-pulsed target cells. A model of antibody binding to HLA-A2 suggested contact with both alpha helices of the HLA molecule, such that the antigen-binding site spans the peptide-binding groove. These data increase the understanding of antibody recognition of HLA and may facilitate the production of clonotypic antibodies with peptide-specific binding.
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Affiliation(s)
- N A Watkins
- Department of Hematology, Division of Transfusion Medicine, University of Cambridge, Long Road, Cambridge CB2 2PT, UK.
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22
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Otto M, Hansen T, Bertz S, Strøm EH, Brorson SH, Mihatsch MJ, Kriegsmann J. [Lupus nephritis with crystal structures in glomerulopathy ]. DER PATHOLOGE 2003; 24:433-8. [PMID: 14605847 DOI: 10.1007/s00292-003-0658-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Lupus nephritis is a common phenomenon in Systemic Lupus Erythematosus (SLE). We analyzed a renal biopsy of a 30-year-old woman with SLE. The clinical history showed a typical SLE with generalized symptoms without demonstrable lupus coagulant, positive for anti-nuclear antibodies and anti-ds-DNA antibodies but negative for rheumatoid factor, cryoglobulins and antiphospholipid antibodies. A paraproteinemia for IgA, IgG and IgM was not detectable. Using light, electron and immunoelectron microscopy electron-dense deposits were noted in subepithelial, subendothelial and mesangial position. Most remarkably, the electron-dense deposits and mesangial areas in the vicinity of deposits contained an electron-dense crystalline material. The crystalline structures were composed of IgG and kappa light chains, while they were negative for IgM, IgA and lambda light chains, as demonstrated by immunoelectron microscopy. As far as we know, this is the first case of lupus nephritis with crystalline structures. Since we could not detect cryoglobulinemia or paraproteinemia, other mechanisms possibly favor organization of macromolecular structures.
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Affiliation(s)
- M Otto
- Gemeinschaftspraxis für Pathologie, Trier.
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23
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Cross SSJ, Brady K, Stevenson JD, Sackin JR, Kenward N, Dietel A, Thomas NR. New variation on a theme: structure and mechanism of action of hydrolytic antibody 7F11, an aspartate rich relation of catalytic antibodies 17E8 and 29G11. J Immunol Methods 2002; 269:173-95. [PMID: 12379361 DOI: 10.1016/s0022-1759(02)00232-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
A computer model, based on homology, of the catalytic antibody 7F11 that catalyses the decomposition of the benzoate ester of a dioxetane resulting in chemiluminescence is reported. Antibody 7F11 has 89% identity in the V(L) domain, and 72% identity in the V(H) domain with hydrolytic antibodies 17E8 and 29G11 previously reported by Scanlan et al. These were also raised against a phosphonate containing hapten. The antigen-binding site of antibody 7F11 whilst similar to that of 17E8 has aspartic acids at positions 33H and 35H, reminiscent in position of the catalytic residues found in aspartate proteinases such as pepsin. AutoDock 3.0 has been used to identify the best binding mode for the hapten. Molecular dynamic simulations have also been undertaken to examine any major conformational changes induced by hapten binding. A mechanism for benzoate ester hydrolysis involving the aspartic acid side-chains is proposed. Construction of a single-chain variable fragment (scFv) of 7F11 is also reported.
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Affiliation(s)
- Simon S J Cross
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK
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24
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Generalized crystal-storing histiocytosis associated with monoclonal gammopathy: molecular analysis of a disorder with rapid clinical course and review of the literature. Blood 2002. [DOI: 10.1182/blood.v100.5.1817.h81702001817_1817_1827] [Citation(s) in RCA: 113] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Crystal-storing histiocytosis (CSH) is a rare event in disorders associated with monoclonal gammopathy. The intracellular crystal formation is almost always accompanied by the expression of κ light chains. However, the exact mechanism for the storage has not been clarified until now. We report a case of generalized CSH in a 73-year-old man who presented with IgA κ paraproteinemia and paraproteinuria. The initially observed CSH in the bone marrow biopsy was associated with the clinical and pathomorphologic features of a monoclonal gammopathy of undetermined significance. The progression of disease could not be affected by steroid therapy and the patient died of septic shock 7 months after detection of CSH. At the time of autopsy there was evidence for multiple myeloma and generalized CSH. Two-dimensional gel electrophoresis of liver tissue combined with immunoblotting revealed the massive storage of heavy chains of α type and light chains of κ type, each in a monoclonal pattern. Analysis of the stored κ light chain by nanoelectrospray-ionization mass spectrometry indicated that it belongs to the variable κI variability subgroup. We identified some unusual amino acid substitutions including Leu59, usually important for hydrophobic interactions within a protein, at a position where it has never been previously described in plasma cell disorders. In conclusion, we present the first case of CSH with molecular identification of the stored κ subgroup and detection of unusual amino acid substitutions. Our results suggest that conformational alterations induced by amino acid exchanges represent a crucial pathogenic factor in CSH.
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Abstract
Antibody light chains (LCs) comprise the most structurally diverse family of proteins involved in amyloidosis. Many antibody LCs incorporate structural features that impair their stability and solubility, leading to their assembly into fibrils and to their subsequent pathological deposition when produced in excess during multiple myeloma and primary amyloidosis. The particular amino acid variations in antibody LCs that account for fibril formation and amyloidogenesis have not been identified. This study focuses on amyloidogenesis within the kappa1 family of human LCs. Reanalysis of the current database of primary structures of proteins from more than 100 patients who produced kappa1 LCs, 37 of which were amyloidogenic, reveals apparent structural features that may contribute to amyloidosis. These features include loss of conserved residues or the gain of particular residues through mutation at sites involving a repertoire of approximately 20% of the amino acid positions in the light chain variable domain (V(L)). Moreover 80% of all kappa1 amyloidogenic V(L)s are identifiable by the presence of at least one of three single-site substitutions or the acquisition of an N-linked glycosylation site through mutations. These findings suggest that it is feasible to predict fibril propensity by analysis of primary structure.
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Affiliation(s)
- F J Stevens
- Biosciences Division, Argonne National Laboratory, IL 60439-3883 USA.
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26
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Bellotti V, Mangione P, Merlini G. Review: immunoglobulin light chain amyloidosis--the archetype of structural and pathogenic variability. J Struct Biol 2000; 130:280-9. [PMID: 10940232 DOI: 10.1006/jsbi.2000.4248] [Citation(s) in RCA: 138] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
AL amyloidosis is caused by deposition in target tissue of amyloid fibrils constituted by monoclonal immunoglobulin light chains. The amyloidogenic plasma cells derive from a transformed memory B cell that can be identified by anti-idiotype monoclonal antibodies. Comparison of the primary structures of amyloidogenic and nonamyloidogenic light chains does not show any common structural motif in the amyloidogenic variants but reveals peculiar replacements which can destabilize the folding state. Reduced folding stability now appears to be a unifying property of amyloidogenic light chains. The tendency of these proteins to populate a partially unfolded intermediate state is a key event in the self-association that progresses to the formation of oligomers and fibrils. The mechanism of organ damage caused by AL amyloid deposition is not known, but clinical findings suggest that the process of amyloid fibril formation itself exerts tissue toxic effects independently of the amount of amyloid deposited. Since the disease is caused by the neoplastic expansion of the plasma cell population synthesizing the amyloidogenic light chains, the clone represents the prime therapeutic target of conventional chemotherapy and experimental immunotherapy. In common with other types of amyloidosis the therapeutic strategy can take advantage of drugs able to improve the reabsorption of the amyloid deposits or able to bind and stabilize the light chain in the native-like folded state.
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Affiliation(s)
- V Bellotti
- Department of Biochemistry, University of Pavia, Pavia, Italy
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