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Wang Y, Xiao J. Recent advances in the molecular understanding of immunoglobulin A. FEBS J 2024; 291:3597-3603. [PMID: 38329005 DOI: 10.1111/febs.17089] [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: 11/29/2023] [Revised: 01/11/2024] [Accepted: 01/31/2024] [Indexed: 02/09/2024]
Abstract
Immunoglobulin A (IgA) plays a crucial role in the human immune system, particularly in mucosal immunity. IgA antibodies that target the mucosal surface are made up of two to five IgA monomers linked together by the joining chain, forming polymeric molecules. These IgA polymers are transported across mucosal epithelial cells by the polymeric immunoglobulin receptor pIgR, resulting in the formation of secretory IgA (SIgA). This review aims to explore recent advancements in our molecular understanding of IgA, with a specific focus on SIgA, and the interaction between IgA and pathogen molecules.
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Affiliation(s)
- Yuxin Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Junyu Xiao
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
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2
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Guo D, De Sciscio ML, Chi-Fung Ng J, Fraternali F. Modelling the assembly and flexibility of antibody structures. Curr Opin Struct Biol 2024; 84:102757. [PMID: 38118364 DOI: 10.1016/j.sbi.2023.102757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/29/2023] [Accepted: 11/30/2023] [Indexed: 12/22/2023]
Abstract
Antibodies are large protein assemblies capable of both specifically recognising antigens and engaging with other proteins and receptors to coordinate immune action. Traditionally, structural studies have been dedicated to antibody variable regions, but efforts to determine and model full-length antibody structures are emerging. Here we review the current knowledge on modelling the structures of antibody assemblies, focusing on their conformational flexibility and the challenge this poses to obtaining and evaluating structural models. Integrative modelling approaches, combining experiments (cryo-electron microscopy, mass spectrometry, etc.) and computational methods (molecular dynamics simulations, deep-learning based approaches, etc.), hold the promise to map the complex conformational landscape of full-length antibody structures.
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Affiliation(s)
- Dongjun Guo
- Institute of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London, WC1E 6BT, United Kingdom; Randall Centre for Cell & Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London, SE1 1UL, United Kingdom
| | - Maria Laura De Sciscio
- Institute of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London, WC1E 6BT, United Kingdom; Department of Chemistry, Sapienza University of Rome, P.le A. Moro 5, Rome, 00185, Italy
| | - Joseph Chi-Fung Ng
- Institute of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London, WC1E 6BT, United Kingdom
| | - Franca Fraternali
- Institute of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London, WC1E 6BT, United Kingdom.
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3
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Pathogenesis of IgA Nephropathy: Current Understanding and Implications for Development of Disease-Specific Treatment. J Clin Med 2021; 10:jcm10194501. [PMID: 34640530 PMCID: PMC8509647 DOI: 10.3390/jcm10194501] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 09/22/2021] [Indexed: 12/20/2022] Open
Abstract
IgA nephropathy, initially described in 1968 as a kidney disease with glomerular “intercapillary deposits of IgA-IgG”, has no disease-specific treatment and is a common cause of kidney failure. Clinical observations and laboratory analyses suggest that IgA nephropathy is an autoimmune disease wherein the kidneys are damaged as innocent bystanders due to deposition of IgA1-IgG immune complexes from the circulation. A multi-hit hypothesis for the pathogenesis of IgA nephropathy describes four sequential steps in disease development. Specifically, patients with IgA nephropathy have elevated circulating levels of IgA1 with some O-glycans deficient in galactose (galactose-deficient IgA1) and these IgA1 glycoforms are recognized as autoantigens by unique IgG autoantibodies, resulting in formation of circulating immune complexes, some of which deposit in glomeruli and activate mesangial cells to induce kidney injury. This proposed mechanism is supported by observations that (i) glomerular immunodeposits in patients with IgA nephropathy are enriched for galactose-deficient IgA1 glycoforms and the corresponding IgG autoantibodies; (ii) circulatory levels of galactose-deficient IgA1 and IgG autoantibodies predict disease progression; and (iii) pathogenic potential of galactose-deficient IgA1 and IgG autoantibodies was demonstrated in vivo. Thus, a better understanding of the structure–function of these immunoglobulins as autoantibodies and autoantigens will enable development of disease-specific treatments.
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Tikhonov D, Kulikova L, Kopylov AT, Rudnev V, Stepanov A, Malsagova K, Izotov A, Kulikov D, Zulkarnaev A, Enikeev D, Potoldykova N, Kaysheva AL. Proteomic and molecular dynamic investigations of PTM-induced structural fluctuations in breast and ovarian cancer. Sci Rep 2021; 11:19318. [PMID: 34588485 PMCID: PMC8481388 DOI: 10.1038/s41598-021-98201-7] [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: 05/07/2021] [Accepted: 09/06/2021] [Indexed: 11/16/2022] Open
Abstract
Post-translational processing leads to conformational changes in protein structure that modulate molecular functions and change the signature of metabolic transformations and immune responses. Some post-translational modifications (PTMs), such as phosphorylation and acetylation, are strongly related to oncogenic processes and malignancy. This study investigated a PTM pattern in patients with gender-specific ovarian or breast cancer. Proteomic profiling and analysis of cancer-specific PTM patterns were performed using high-resolution UPLC-MS/MS. Structural analysis, topology, and stability of PTMs associated with sex-specific cancers were analyzed using molecular dynamics modeling. We identified highly specific PTMs, of which 12 modified peptides from eight distinct proteins derived from patients with ovarian cancer and 6 peptides of three proteins favored patients from the group with breast cancer. We found that all defined PTMs were localized in the compact and stable structural motifs exposed outside the solvent environment. PTMs increase the solvent-accessible surface area of the modified moiety and its active environment. The observed conformational fluctuations are still inadequate to activate the structural degradation and enhance protein elimination/clearance; however, it is sufficient for the significant modulation of protein activity.
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Affiliation(s)
- Dmitry Tikhonov
- Institute of Mathematical Problems of Biology RAS-the Branch of Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, 142290, Pushchino, Moscow Region, Russia.,Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290, Pushchino, Moscow Region, Russia
| | - Liudmila Kulikova
- Institute of Mathematical Problems of Biology RAS-the Branch of Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, 142290, Pushchino, Moscow Region, Russia.,Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290, Pushchino, Moscow Region, Russia
| | - Arthur T Kopylov
- V.N. Orekhovich Institute of Biomedical Chemistry, 119121, Moscow, Russia.
| | - Vladimir Rudnev
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290, Pushchino, Moscow Region, Russia.,V.N. Orekhovich Institute of Biomedical Chemistry, 119121, Moscow, Russia
| | - Alexander Stepanov
- V.N. Orekhovich Institute of Biomedical Chemistry, 119121, Moscow, Russia
| | - Kristina Malsagova
- V.N. Orekhovich Institute of Biomedical Chemistry, 119121, Moscow, Russia
| | - Alexander Izotov
- V.N. Orekhovich Institute of Biomedical Chemistry, 119121, Moscow, Russia
| | - Dmitry Kulikov
- Moscow Regional Research and Clinical Institute, Russian Federation, 129110, Moscow, Russia
| | - Alexey Zulkarnaev
- Moscow Regional Research and Clinical Institute, Russian Federation, 129110, Moscow, Russia
| | - Dmitry Enikeev
- Institute of Urology and Reproductive Health, Sechenov University, 119121, Moscow, Russia
| | - Natalia Potoldykova
- Institute of Urology and Reproductive Health, Sechenov University, 119121, Moscow, Russia
| | - Anna L Kaysheva
- V.N. Orekhovich Institute of Biomedical Chemistry, 119121, Moscow, Russia
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Tóth CN, Baranyai E, Csípő I, Tarr T, Zeher M, Posta J, Fábián I. Elemental Analysis of Whole and Protein Separated Blood Serum of Patients with Systemic Lupus Erythematosus and Sjögren's Syndrome. Biol Trace Elem Res 2017; 179:14-22. [PMID: 28124217 DOI: 10.1007/s12011-017-0945-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 01/18/2017] [Indexed: 01/22/2023]
Abstract
Systemic lupus erythematosus (SLE) and Sjögren's syndrome (SS) are systemic autoimmune diseases with complex symptoms and pathogenesis that are still not completely understood. Several studies showed that the trace element homeostasis and also the levels of antioxidant plasma proteins are changed in autoimmune disorders; however, these results are controversial. In this study, the potassium (K), calcium (Ca), magnesium (Mg), copper (Cu), zinc (Zn), and iron (Fe) concentrations of the serum and proteins-immunoglobulin G (IgG), transferrin (Trf), albumin (Alb), and ceruloplasmin (Cp)-separated from serum samples by affinity chromatography were determined in patients with SLE and SS. Ca and K levels were found to be decreased in the case of both disorders compared to the control group, and the competitive antagonism of Cu and Zn was also observed: elevated Cu concentration together with a lower Zn concentration was measured in the sera of patients with autoimmune diseases. After fractionation, the trace element concentration of protein containing fractions altered to that of the control group. In case of the autoimmune disorders, the highest Cu concentration was determined in the Alb-containing protein fractions while the Zn level decreased in the Alb and increased in the Cp as well as in the IgG- and Trf-containing fractions compared to the healthy samples. Changes have also been found in the level and distribution of K and Ca.
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Affiliation(s)
- Csilla Noémi Tóth
- Department of Inorganic and Analitycal Chemistry, Agilent Atomic Spectroscopy Partner Laboratory, University of Debrecen, Egyetem square 1, Debrecen, 4032, Hungary
| | - Edina Baranyai
- Department of Inorganic and Analitycal Chemistry, Agilent Atomic Spectroscopy Partner Laboratory, University of Debrecen, Egyetem square 1, Debrecen, 4032, Hungary.
| | - István Csípő
- Division of Clinical Immunology, Medical Faculty, University of Debrecen, Moricz Zs. str. 22, Debrecen, 4032, Hungary
| | - Tünde Tarr
- Division of Clinical Immunology, Medical Faculty, University of Debrecen, Moricz Zs. str. 22, Debrecen, 4032, Hungary
| | - Margit Zeher
- Division of Clinical Immunology, Medical Faculty, University of Debrecen, Moricz Zs. str. 22, Debrecen, 4032, Hungary
| | - József Posta
- Department of Inorganic and Analitycal Chemistry, University of Debrecen, Egyetem square 1, Debrecen, 4032, Hungary
| | - István Fábián
- Department of Inorganic and Analitycal Chemistry, University of Debrecen, Egyetem square 1, Debrecen, 4032, Hungary
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Lambrinidis G, Vallianatou T, Tsantili-Kakoulidou A. In vitro, in silico and integrated strategies for the estimation of plasma protein binding. A review. Adv Drug Deliv Rev 2015; 86:27-45. [PMID: 25819487 DOI: 10.1016/j.addr.2015.03.011] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 02/11/2015] [Accepted: 03/20/2015] [Indexed: 12/28/2022]
Abstract
Plasma protein binding (PPB) strongly affects drug distribution and pharmacokinetic behavior with consequences in overall pharmacological action. Extended plasma protein binding may be associated with drug safety issues and several adverse effects, like low clearance, low brain penetration, drug-drug interactions, loss of efficacy, while influencing the fate of enantiomers and diastereoisomers by stereoselective binding within the body. Therefore in holistic drug design approaches, where ADME(T) properties are considered in parallel with target affinity, considerable efforts are focused in early estimation of PPB mainly in regard to human serum albumin (HSA), which is the most abundant and most important plasma protein. The second critical serum protein α1-acid glycoprotein (AGP), although often underscored, plays also an important and complicated role in clinical therapy and thus the last years it has been studied thoroughly too. In the present review, after an overview of the principles of HSA and AGP binding as well as the structure topology of the proteins, the current trends and perspectives in the field of PPB predictions are presented and discussed considering both HSA and AGP binding. Since however for the latter protein systematic studies have started only the last years, the review focuses mainly to HSA. One part of the review highlights the challenge to develop rapid techniques for HSA and AGP binding simulation and their performance in assessment of PPB. The second part focuses on in silico approaches to predict HSA and AGP binding, analyzing and evaluating structure-based and ligand-based methods, as well as combination of both methods in the aim to exploit the different information and overcome the limitations of each individual approach. Ligand-based methods use the Quantitative Structure-Activity Relationships (QSAR) methodology to establish quantitate models for the prediction of binding constants from molecular descriptors, while they provide only indirect information on binding mechanism. Efforts for the establishment of global models, automated workflows and web-based platforms for PPB predictions are presented and discussed. Structure-based methods relying on the crystal structures of drug-protein complexes provide detailed information on the underlying mechanism but are usually restricted to specific compounds. They are useful to identify the specific binding site while they may be important in investigating drug-drug interactions, related to PPB. Moreover, chemometrics or structure-based modeling may be supported by experimental data a promising integrated alternative strategy for ADME(T) properties optimization. In the case of PPB the use of molecular modeling combined with bioanalytical techniques is frequently used for the investigation of AGP binding.
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7
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Wright DW, Perkins SJ. SCT: a suite of programs for comparing atomistic models with small-angle scattering data. J Appl Crystallogr 2015; 48:953-961. [PMID: 26089768 PMCID: PMC4453981 DOI: 10.1107/s1600576715007062] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 04/08/2015] [Indexed: 12/31/2022] Open
Abstract
Small-angle X-ray and neutron scattering techniques characterize proteins in solution and complement high-resolution structural studies. They are of particular utility when large proteins cannot be crystallized or when the structure is altered by solution conditions. Atomistic models of the averaged structure can be generated through constrained modelling, a technique in which known domain or subunit structures are combined with linker models to produce candidate global conformations. By randomizing the configuration adopted by the different elements of the model, thousands of candidate structures are produced. Next, theoretical scattering curves are generated for each model for trial-and-error fits to the experimental data. From these, a small family of best-fit models is identified. In order to facilitate both the computation of theoretical scattering curves from atomistic models and their comparison with experiment, the SCT suite of tools was developed. SCT also includes programs that provide sequence-based estimates of protein volume (either incorporating hydration or not) and add a hydration layer to models for X-ray scattering modelling. The original SCT software, written in Fortran, resulted in the first atomistic scattering structures to be deposited in the Protein Data Bank, and 77 structures for antibodies, complement proteins and anionic oligosaccharides were determined between 1998 and 2014. For the first time, this software is publicly available, alongside an easier-to-use reimplementation of the same algorithms in Python. Both versions of SCT have been released as open-source software under the Apache 2 license and are available for download from https://github.com/dww100/sct.
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Affiliation(s)
- David W. Wright
- Department of Structural and Molecular Biology, Division of Biosciences, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - Stephen J. Perkins
- Department of Structural and Molecular Biology, Division of Biosciences, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
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Fujiwara SI, Amisaki T. Fatty acid binding to serum albumin: Molecular simulation approaches. Biochim Biophys Acta Gen Subj 2013; 1830:5427-34. [DOI: 10.1016/j.bbagen.2013.03.032] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 03/26/2013] [Accepted: 03/28/2013] [Indexed: 02/02/2023]
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9
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Vallianatou T, Lambrinidis G, Tsantili-Kakoulidou A. In silicoprediction of human serum albumin binding for drug leads. Expert Opin Drug Discov 2013; 8:583-95. [DOI: 10.1517/17460441.2013.777424] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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10
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Correa A, Trajtenberg F, Obal G, Pritsch O, Dighiero G, Oppezzo P, Buschiazzo A. Structure of a human IgA1 Fab fragment at 1.55 Å resolution: potential effect of the constant domains on antigen-affinity modulation. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:388-97. [PMID: 23519414 DOI: 10.1107/s0907444912048664] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Accepted: 11/27/2012] [Indexed: 11/11/2022]
Abstract
Despite being the most abundant class of immunoglobulins in humans and playing central roles in the adaptive immune response, high-resolution structural data are still lacking for the antigen-binding region of human isotype A antibodies (IgAs). The crystal structures of a human Fab fragment of IgA1 in three different crystal forms are now reported. The three-dimensional organization is similar to those of other Fab classes, but FabA1 seems to be more rigid, being constrained by a hydrophobic core in the interface between the variable and constant domains of the heavy chain (VH-CH1) as well as by a disulfide bridge that connects the light and heavy chains, influencing the relative heavy/light-chain orientation. The crystal structure of the same antibody but with a G-isotype CH1 which is reported to display different antigen affinity has also been solved. The differential structural features reveal plausible mechanisms for constant/variable-domain long-distance effects whereby antibody class switching could alter antigen affinity.
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Affiliation(s)
- Agustin Correa
- Unit of Recombinant Proteins, Institut Pasteur de Montevideo, 11400 Montevideo, Uruguay
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11
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Human serum albumin: from bench to bedside. Mol Aspects Med 2011; 33:209-90. [PMID: 22230555 DOI: 10.1016/j.mam.2011.12.002] [Citation(s) in RCA: 1189] [Impact Index Per Article: 91.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Accepted: 12/21/2011] [Indexed: 02/07/2023]
Abstract
Human serum albumin (HSA), the most abundant protein in plasma, is a monomeric multi-domain macromolecule, representing the main determinant of plasma oncotic pressure and the main modulator of fluid distribution between body compartments. HSA displays an extraordinary ligand binding capacity, providing a depot and carrier for many endogenous and exogenous compounds. Indeed, HSA represents the main carrier for fatty acids, affects pharmacokinetics of many drugs, provides the metabolic modification of some ligands, renders potential toxins harmless, accounts for most of the anti-oxidant capacity of human plasma, and displays (pseudo-)enzymatic properties. HSA is a valuable biomarker of many diseases, including cancer, rheumatoid arthritis, ischemia, post-menopausal obesity, severe acute graft-versus-host disease, and diseases that need monitoring of the glycemic control. Moreover, HSA is widely used clinically to treat several diseases, including hypovolemia, shock, burns, surgical blood loss, trauma, hemorrhage, cardiopulmonary bypass, acute respiratory distress syndrome, hemodialysis, acute liver failure, chronic liver disease, nutrition support, resuscitation, and hypoalbuminemia. Recently, biotechnological applications of HSA, including implantable biomaterials, surgical adhesives and sealants, biochromatography, ligand trapping, and fusion proteins, have been reported. Here, genetic, biochemical, biomedical, and biotechnological aspects of HSA are reviewed.
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Chen Y, Wang R, Wang S, Yang Y, Li S, Kai G. Interaction of Bilobalide and Ginkgolides B with Bovine Serum Albumin: A Fluorescence Quenching Study. B KOREAN CHEM SOC 2011. [DOI: 10.5012/bkcs.2011.32.9.3261] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Impact of albumin on drug delivery--new applications on the horizon. J Control Release 2011; 157:4-28. [PMID: 21959118 DOI: 10.1016/j.jconrel.2011.09.069] [Citation(s) in RCA: 598] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Revised: 08/11/2011] [Accepted: 09/11/2011] [Indexed: 12/17/2022]
Abstract
Over the past decades, albumin has emerged as a versatile carrier for therapeutic and diagnostic agents, primarily for diagnosing and treating diabetes, cancer, rheumatoid arthritis and infectious diseases. Market approved products include fatty acid derivatives of human insulin or the glucagon-like-1 peptide (Levemir(®) and Victoza(®)) for treating diabetes, the taxol albumin nanoparticle Abraxane(®) for treating metastatic breast cancer which is also under clinical investigation in further tumor indications, and (99m)Tc-aggregated albumin (Nanocoll(®) and Albures(®)) for diagnosing cancer and rheumatoid arthritis as well as for lymphoscintigraphy. In addition, an increasing number of albumin-based or albumin-binding drugs are in clinical trials such as antibody fusion proteins (MM-111) for treating HER2/neu positive breast cancer (phase I), a camelid albumin-binding nanobody anti-HSA-anti-TNF-α (ATN-103) in phase II studies for treating rheumatoid arthritis, an antidiabetic Exendin-4 analog bound to recombinant human albumin (phase I/II), a fluorescein-labeled albumin conjugate (AFL)-human serum albumin for visualizing the malignant borders of brain tumors for improved surgical resection, and finally an albumin-binding prodrug of doxorubicin (INNO-206) entering phase II studies against sarcoma and gastric cancer. In the preclinical setting, novel approaches include attaching peptides with high-affinity for albumin to antibody fragments, the exploitation of albumin-binding gadolinium contrast agents for magnetic resonance imaging, and physical or covalent attachment of antiviral, antibacterial, and anticancer drugs to albumin that are permanently or transiently attached to human serum albumin (HSA) or act as albumin-binding prodrugs. This review gives an overview of the expanding field of preclinical and clinical drug applications and developments that use albumin as a protein carrier to improve the pharmacokinetic profile of the drug or to target the drug to the pathogenic site addressing diseases with unmet medical needs.
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Masking of the Fc region in human IgG4 by constrained X-ray scattering modelling: implications for antibody function and therapy. Biochem J 2010; 432:101-11. [PMID: 20722630 DOI: 10.1042/bj20100641] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Of the four human IgG antibody subclasses IgG1-IgG4, IgG4 is of interest in that it does not activate complement and exhibits atypical self-association, including the formation of bispecific antibodies. The solution structures of antibodies are critical to understand function and therapeutic applications. Thus IgG4 was studied by synchrotron X-ray scattering. The Guinier X-ray radius of gyration R(G) increased from 5.0 nm to 5.1 nm with an increase of concentration. The distance distribution function P(r) revealed a single peak at 0.3 mg/ml, which resolved into two peaks that shifted to smaller r values at 1.3 mg/ml, even though the maximum dimension of IgG4 was unchanged at 17 nm. This indicated a small concentration dependence of the IgG4 solution structure. By analytical ultracentrifugation, no concentration dependence in the sedimentation coefficient of 6.4 S was observed. Constrained scattering modelling resulted in solution structural determinations that showed that IgG4 has an asymmetric solution structure in which one Fab-Fc pair is closer together than the other pair, and the accessibility of one side of the Fc region is masked by the Fab regions. The averaged distances between the two Fab-Fc pairs change by 1-2 nm with the change in IgG4 concentration. The averaged conformation of the Fab regions appear able to hinder complement C1q binding to the Fc region and the self-association of IgG4 through the Fc region. The present results clarify IgG4 function and provide a starting point to investigate antibody stability.
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15
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Perkins SJ, Okemefuna AI, Nan R, Li K, Bonner A. Constrained solution scattering modelling of human antibodies and complement proteins reveals novel biological insights. J R Soc Interface 2009; 6 Suppl 5:S679-96. [PMID: 19605402 DOI: 10.1098/rsif.2009.0164.focus] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
X-ray and neutron-scattering techniques characterize proteins in solution and complement high-resolution structural studies. They are useful when either a large protein cannot be crystallized, in which case scattering yields a solution structure, or a crystal structure has been determined and requires validation in solution. These solution structures are determined by the application of constrained modelling methods based on known subunit structures. First, an appropriate starting model is generated. Next, its conformation is randomized to generate thousands of models for trial-and-error fits. Comparison with the experimental data identifies a small family of best-fit models. Finally, their significance for biological function is assessed. We illustrate this in application to structure determinations for secretory immunoglobulin A, the most prevalent antibody in the human body and a first line of defence in mucosal immunity. We also discuss the applications to the large multi-domain proteins of the complement system, most notably its major regulator factor H, which is important in age-related macular degeneration and renal diseases. We discuss the importance of complementary data from analytical ultracentrifugation, and structural studies of protein-protein complexes. We conclude that constrained scattering modelling makes useful contributions to our understanding of antibody and complement structure and function.
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Affiliation(s)
- Stephen J Perkins
- Department of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK.
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Bonner A, Almogren A, Furtado PB, Kerr MA, Perkins SJ. Location of secretory component on the Fc edge of dimeric IgA1 reveals insight into the role of secretory IgA1 in mucosal immunity. Mucosal Immunol 2009; 2:74-84. [PMID: 19079336 DOI: 10.1038/mi.2008.68] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Secretory immunoglobulin A (SIgA) is the most prevalent antibody in the human body and a first line of defense in mucosal immunity. We located secretory component (SC) relative to dimeric IgA1 (dIgA1) within the SIgA1 structure using the constrained modeling of solution scattering and analytical ultracentrifugation data. The extended solution structure of dIgA1 is largely preserved within SIgA1. From conformational searches of SC locations, the best-fit SC models within SIgA1 show that SC is extended along the outermost convex edge of the Fc dimer in dIgA1. The topology of our SIgA1 structure reveals that it is able to bind to one FcalphaRI receptor molecule. SC binding to the Fc dimer confers protection to SIgA1 by the masking of proteolytically susceptible surface sites from bacterial proteases in the harsh environment of the mucosa. The models support a "zipper-like" unfolding of SC upon dIgA1 in the formation and transportation of SIgA1 into the mucosa.
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Affiliation(s)
- A Bonner
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, UK
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Andersen JT, Sandlie I. The Versatile MHC Class I-related FcRn Protects IgG and Albumin from Degradation: Implications for Development of New Diagnostics and Therapeutics. Drug Metab Pharmacokinet 2009; 24:318-32. [DOI: 10.2133/dmpk.24.318] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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18
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Wu LL, Chen L, Song C, Liu XW, Deng HP, Gao NY, Gao HW. Potential enzyme toxicity of perfluorooctanoic acid. Amino Acids 2008; 38:113-20. [DOI: 10.1007/s00726-008-0217-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2008] [Accepted: 11/18/2008] [Indexed: 12/26/2022]
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Bonner A, Furtado PB, Almogren A, Kerr MA, Perkins SJ. Implications of the near-planar solution structure of human myeloma dimeric IgA1 for mucosal immunity and IgA nephropathy. THE JOURNAL OF IMMUNOLOGY 2008; 180:1008-18. [PMID: 18178841 DOI: 10.4049/jimmunol.180.2.1008] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
IgA is unique in being able to form a diverse range of polymeric structures. Increases in the levels of dimeric IgA1 (dIgA1) in serum have been implicated in diseases such as IgA nephropathy. We have determined the solution structure for dIgA1 by synchrotron x-ray and neutron scattering and analytical ultracentrifugation. The Guinier radius of gyration (RG) of 7.60-8.65 nm indicated that the two monomers within dIgA1 are arranged in an extended conformation. The distance distribution curve P(r) gave an overall length (L) of 22-26 nm. These results were confirmed by the sedimentation coefficient and frictional ratio of dIgA1. Constrained scattering modeling starting from the IgA1 monomer solution structure revealed a near-planar dimer structure for dIgA1. The two Fc regions form a slightly bent arrangement in which they form end-to-end contacts, and the J chain was located at this interface. This structure was refined by optimizing the position of the four Fab regions. From this, the best-fit solution structures show that the four Fab Ag-binding sites are independent of one another, and the two Fc regions are accessible to receptor binding. This arrangement allows dIgA1 to initiate specific immune responses by binding to FcalphaRI receptors, while still retaining Ag-binding ability, and to be selectively transported to mucosal surfaces by binding to the polymeric Ig receptor to form secretory IgA. A mechanism for the involvement of dIgA1 oligomers in the pathology of IgA nephropathy is discussed in the light of this near-planar structure.
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Affiliation(s)
- Alexandra Bonner
- Department of Biochemistry and Molecular Biology, University College London, London, United Kingdom
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20
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Structure determinations of human and chimaeric antibodies by solution scattering and constrained molecular modelling. Biochem Soc Trans 2008; 36:37-42. [PMID: 18208381 DOI: 10.1042/bst0360037] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
X-ray and neutron scattering and analytical ultracentrifugation provide multiparameter structural and compositional information on proteins that complements high-resolution protein crystallography and NMR studies. They are ideal methods to use when either a large protein cannot be crystallized, when scattering provides the only means to obtain a solution structure, or the protein crystal structure has been determined and it is necessary to validate this. Once these results have been obtained, we apply automated constrained modelling methods based on known subunit crystal structures to identify the best-fit structure. Using our antibody structures as examples, we describe the generation of appropriate starting models, randomizing these for trial-and-error scattering fits, identifying the final best-fit models and interpreting these in terms of function. We discuss our structure determinations for IgA and IgD, an IgA-human serum albumin complex, the dimer of IgA and secretory component associated with this and chimaeras of mouse IgG with two complement proteins. Constrained modelling confirms the experimental data analysis and produces families of best-fit molecular models. Its usage has clarified several aspects of antibody structure and function in solution.
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Almogren A, Kerr MA. Irreversible aggregation of the Fc fragment derived from polymeric but not monomeric serum IgA1—Implications in IgA-mediated disease. Mol Immunol 2008; 45:87-94. [PMID: 17606293 DOI: 10.1016/j.molimm.2007.05.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2007] [Revised: 05/08/2007] [Accepted: 05/09/2007] [Indexed: 11/23/2022]
Abstract
IgA is by far the most abundant immunoglobulin in humans. It is found in serum and in secretions (SIgA). Unlike any other class of immunoglobulin, each form of IgA occurs naturally in different polymerisation states. In serum, the predominant form of IgA is IgA1 of which around 90% is monomeric and 10% is dimeric or polymeric. The proportion of dimeric/polymeric IgA increases in a number of important diseases, such as IgA nephropathy and in chronic liver disease. In both, there is evidence that further aggregation of dimeric/polymeric IgA is the cause of the characteristic tissue deposition. To investigate the effect of role of IgA polymerisation on the structure and function of IgA, we purified different molecular forms of IgA1 from myeloma serum (monomer, dimer and trimer) and SIgA1 from colostrum. Structural features of these different IgA1 forms were examined following proteolysis using Neisseria gonorrhoeae IgA1 type 2 protease and Streptococcus pneumoniae IgA1 protease. These IgA1 proteases cleave IgA1 at the hinge region and produce Fcalpha and Fab fragments. Western blot analysis demonstrated that the Fcalpha fragments of serum dimeric and trimeric but not monomeric IgA1 aggregated to form multimers resistant to disruption in SDS-PAGE under non-reducing conditions. Size exclusion chromatography under native conditions of cleaved serum dimeric IgA1 demonstrated that aggregation occurs because of structural changes in the IgA per se and was not an effect of the SDS-PAGE system. In the same assay, SIgA1 (dimeric) did not aggregate after digestion. The results suggest an important, previously unrecognised, property of dimeric/polymeric serum IgA1, which might explain its propensity to aggregate and deposit in tissues.
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Affiliation(s)
- Adel Almogren
- Department of Pathology, Immunology Unit, College of Medicine and King Khalid University Hospital, P.O. Box 2925, Riyadh 11461, Saudi Arabia
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Abstract
X-ray and neutron solution scattering methods provide multiparameter structural and compositional information on proteins that complements high-resolution protein crystallography and NMR studies. We describe the procedures required to (1) obtain validated X-ray and neutron scattering data, (2) perform Guinier analyses of the scattering data to extract the radius of gyration R(G) and intensity parameters, and (3) calculate the distance distribution function P(r). Constrained modeling is important because this confirms the experimental data analysis and produces families of best-fit molecular models for comparison with crystallography and NMR structures. The modeling procedures are described in terms of (4) generating appropriate starting models, (5) randomizing these for trial-and-error scattering fits, (6) identifying the final best-fit models, and (7) applying analytical ultracentrifugation (AUC) data to validate the scattering modeling. These procedures and pitfalls in them will be illustrated using work performed in the authors' laboratory on antibodies and the complement proteins of the human immune defense system. Four different types of modeling procedures are distinguished, depending on the number and type of domains in the protein. Examples when comparisons with crystallography and NMR structures are important are described. For multidomain proteins, it is often found that scattering provides essential evidence to validate or disprove a crystal structure. If a large protein cannot be crystallized, scattering provides the only means to obtain a structure.
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Sevilla P, Rivas JM, García-Blanco F, García-Ramos JV, Sánchez-Cortés S. Identification of the antitumoral drug emodin binding sites in bovine serum albumin by spectroscopic methods. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2007; 1774:1359-69. [DOI: 10.1016/j.bbapap.2007.07.022] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2007] [Revised: 07/29/2007] [Accepted: 07/30/2007] [Indexed: 10/22/2022]
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Gao HW, Xu Q, Chen L, Wang SL, Wang Y, Wu LL, Yuan Y. Potential protein toxicity of synthetic pigments: binding of poncean S to human serum albumin. Biophys J 2007; 94:906-17. [PMID: 17905844 PMCID: PMC2186231 DOI: 10.1529/biophysj.107.120865] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Using various methods, e.g., spectrophotometry, circular dichroism, and isothermal titration calorimetry, the interaction of poncean S (PS) with human serum albumin (HSA) was characterized at pH 1.81, 3.56, and 7.40 using the spectral correction technique, and Langmuir and Temkin isothermal models. The consistency among results concerning, e.g., binding number, binding energy, and type of binding, showed that ion pair electrostatic attraction fixed the position of PS in HSA and subsequently induced a combination of multiple noncovalent bonds such as H-bonds, hydrophobic interactions, and van der Waals forces. Ion pair attraction and H-bonds produced a stable PS-HSA complex and led to a marked change in the secondary structure of HSA in acidic media. The PS-HSA binding pattern and the process of change in HSA conformation were also investigated. The potentially toxic effect of PS on the transport function of HSA in a normal physiological environment was analyzed. This work provides a useful experimental strategy for studying the interaction of organic substances with biomacromolecules, helping us to understand the activity or mechanism of toxicity of an organic compound.
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Affiliation(s)
- Hong-Wen Gao
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Shanghai 200092, PR China.
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Sakai H, Sato A, Takeoka S, Tsuchida E. Rheological properties of hemoglobin vesicles (artificial oxygen carriers) suspended in a series of plasma-substitute solutions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2007; 23:8121-8. [PMID: 17567054 DOI: 10.1021/la7004503] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Hemoglobin vesicles (HbV) or liposome-encapsulated Hbs are artificial oxygen carriers that have been developed for use as transfusion alternatives. The extremely high concentration of the HbV suspension (solutes, ca. 16 g/dL; volume fraction, ca. 40 vol %) gives it an oxygen-carrying capacity that is comparable to that of blood. The HbV suspension does not possess a colloid osmotic pressure. Therefore, HbV must be suspended in or co-injected with an aqueous solution of a plasma substitute (water-soluble polymer), which might interact with HbV. This article describes our study of the rheological properties of HbV suspended in a series of plasma substitute solutions of various molecular weights: recombinant human serum albumin (rHSA), dextran (DEX), modified fluid gelatin (MFG), and hydroxylethyl starch (HES). The HbV suspended in rHSA was nearly Newtonian. Other polymers-HES, DEX, and MFG-induced HbV flocculation, possibly by depletion interaction, and rendered the suspensions as non-Newtonian with a shear-thinning profile (10(-4)-10(3) s(-1)). These HbV suspensions showed a high storage modulus (G') because of the presence of flocculated HbV. However, HbV suspended in rHSA exhibited a very low G'. The viscosities of HbV suspended in DEX, MFG, and high-molecular-weight HES solutions responded quickly to rapid step changes in shear rates of 0.1-100 s(-1) and a return to 0.1 s(-1), indicating that flocculation is both rapid and reversible. Microscopically, the flow pattern of the flocculated HbV that perfused through microchannels (4.5 microm deep, 7 microm wide, 20 cmH2O applied pressure) showed no plugging. Furthermore, the time required for passage was simply proportional to the viscosity. Collectively, the HbV suspension viscosity was influenced by the presence of plasma substitutes. The HbV suspension provides a unique opportunity to manipulate rheological properties for various clinical applications in addition to its use as a transfusion alternative.
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Affiliation(s)
- Hiromi Sakai
- Advanced Research Institute for Science and Engineering and Graduate School of Science and Engineering, Waseda University, Tokyo 169-8555, Japan
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Almogren A, Senior BW, Kerr MA. A comparison of the binding of secretory component to immunoglobulin A (IgA) in human colostral S-IgA1 and S-IgA2. Immunology 2006; 120:273-80. [PMID: 17156102 PMCID: PMC2265853 DOI: 10.1111/j.1365-2567.2006.02498.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
A detailed investigation of the binding of secretory component to immunoglobulin A (IgA) in human secretory IgA2 (S-IgA2) was made possible by the development of a new method of purifying S-IgA1, S-IgA2 and free secretory component from human colostrum using thiophilic gel chromatography and chromatography on Jacalin-agarose. Sodium dodecyl sulphate-polyacrylamide gel electrophoresis of unreduced pure S-IgA2 revealed that, unlike in S-IgA1, a significant proportion of the secretory component was bound non-covalently in S-IgA2. When S-IgA1 was incubated with a protease purified from Proteus mirabilis the secretory component, but not the alpha-chain, was cleaved. This is in contrast to serum IgA1, in which the alpha-chain was cleaved under the same conditions - direct evidence that secretory component does protect the alpha-chain from proteolytic cleavage in S-IgA. Comparisons between the products of cleavage with P. mirabilis protease of free secretory component and bound secretory component in S-IgA1 and S-IgA2 also indicated that, contrary to the general assumption, the binding of secretory component to IgA is different in S-IgA2 from that in S-IgA1.
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Affiliation(s)
- Adel Almogren
- Department of Pathology, Immunology Unit, College of Medicine and King Khalid University Hospital, Riyadh, Saudi Arabia
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