1
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Damen LAA, Bui TP, van Wessel T, Li Y, Straten BF, Pampiermole R, Daamen WF, Fernig DG, van Kuppevelt TH. Identification of heparin-binding amino acid residues in antibody HS4C3 with the potential to design antibodies against heparan sulfate domains. Glycobiology 2024; 34:cwae046. [PMID: 38963938 PMCID: PMC11231949 DOI: 10.1093/glycob/cwae046] [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: 01/02/2024] [Revised: 06/06/2024] [Indexed: 07/06/2024] Open
Abstract
Heparan sulfate (HS) is a linear polysaccharide with high structural and functional diversity. Detection and localization of HS in tissues can be performed using single chain variable fragment (scFv) antibodies. Although several anti-HS antibodies recognizing different sulfation motifs have been identified, little is known about their interaction with HS. In this study the interaction between the scFv antibody HS4C3 and heparin was investigated. Heparin-binding lysine and arginine residues were identified using a protect and label methodology. Site-directed mutagenesis was applied to further identify critical heparin-binding lysine/arginine residues using immunohistochemical and biochemical assays. In addition, computational docking of a heparin tetrasaccharide towards a 3-D homology model of HS4C3 was applied to identify potential heparin-binding sites. Of the 12 lysine and 15 arginine residues within the HS4C3 antibody, 6 and 9, respectively, were identified as heparin-binding. Most of these residues are located within one of the complementarity determining regions (CDR) or in their proximity. All basic amino acid residues in the CDR3 region of the heavy chain were involved in binding. Computational docking showed a heparin tetrasaccharide close to these regions. Mutagenesis of heparin-binding residues reduced or altered reactivity towards HS and heparin. Identification of heparin-binding arginine and lysine residues in HS4C3 allows for better understanding of the interaction with HS and creates a framework to rationally design antibodies targeting specific HS motifs.
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Affiliation(s)
- Lars A A Damen
- Department of Medical BioSciences, Radboud Institute for Medical Innovation, Radboud University Medical Center, PO Box 9101, Nijmegen 6500 HB, the Netherlands
| | - Thao P Bui
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrated Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
| | - Thierry van Wessel
- Department of Medical BioSciences, Radboud Institute for Medical Innovation, Radboud University Medical Center, PO Box 9101, Nijmegen 6500 HB, the Netherlands
| | - Yong Li
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrated Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
| | - Bart F Straten
- Department of Medical BioSciences, Radboud Institute for Medical Innovation, Radboud University Medical Center, PO Box 9101, Nijmegen 6500 HB, the Netherlands
| | - Robin Pampiermole
- Department of Medical BioSciences, Radboud Institute for Medical Innovation, Radboud University Medical Center, PO Box 9101, Nijmegen 6500 HB, the Netherlands
| | - Willeke F Daamen
- Department of Medical BioSciences, Radboud Institute for Medical Innovation, Radboud University Medical Center, PO Box 9101, Nijmegen 6500 HB, the Netherlands
| | - David G Fernig
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrated Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
| | - Toin H van Kuppevelt
- Department of Medical BioSciences, Radboud Institute for Medical Innovation, Radboud University Medical Center, PO Box 9101, Nijmegen 6500 HB, the Netherlands
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2
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Guo C, Feng Q, Xie X, Li Y, Hu H, Hu J, Fang S, Shang L. Cross-reaction mediated by distinct key amino acid combinations in the complementary-determining region (CDR) of a monoclonal antibody. J Med Virol 2024; 96:e29430. [PMID: 38285507 DOI: 10.1002/jmv.29430] [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: 11/03/2023] [Revised: 12/27/2023] [Accepted: 01/16/2024] [Indexed: 01/31/2024]
Abstract
In immunology, cross-reaction between antigens and antibodies are commonly observed. Prior research has shown that various monoclonal antibodies (mAbs) can recognize a broad spectrum of epitopes related to influenza viruses. However, existing theories on cross-reactions fall short in explaining the phenomena observed. This study explored the interaction characteristics of H1-74 mAb with three peptides: two natural peptides, LVLWGIHHP and LPFQNI, derived from the hemagglutinin (HA) antigen of the H1N1 influenza virus, and one synthetic peptide, WPFQNY. Our findings indicate that the complementarity-determining region (CDR) of H1-74 mAb comprised five antigen-binding sites, containing eight key amino acid residues from the light chain variable region and 16 from the heavy chain variable region. These critical residues formed distinct hydrophobic or hydrophilic clusters and functional groups within the binding sites, facilitating interaction with antigen epitopes through hydrogen bonding, salt bridge formation, and π-π stacking. The study revealed that the formation of the antibody molecule led to the creation of binding groups and small units in the CDR, allowing the antibody to attach to a variety of antigen epitopes through diverse combinations of these small units and functional groups. This unique ability of the antibody to bind with antigen epitopes provides a new molecular basis for explaining the phenomenon of antibody cross-reaction.
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Affiliation(s)
- Chunyan Guo
- Central Laboratory of Shaanxi Provincial People's Hospital, Xi'an, Shaanxi, China
- Research Center of Cell Immunological Engineering and Technology of Shaanxi Province, Xi'an, Shaanxi, China
- Shaanxi Provincial Key Laboratory of Infection and Immune Diseases, Xi'an, Shaanxi, China
| | - Qing Feng
- Central Laboratory of Shaanxi Provincial People's Hospital, Xi'an, Shaanxi, China
- Research Center of Cell Immunological Engineering and Technology of Shaanxi Province, Xi'an, Shaanxi, China
- Shaanxi Provincial Key Laboratory of Infection and Immune Diseases, Xi'an, Shaanxi, China
| | - Xin Xie
- Central Laboratory of Shaanxi Provincial People's Hospital, Xi'an, Shaanxi, China
| | - Yan Li
- Central Laboratory of Shaanxi Provincial People's Hospital, Xi'an, Shaanxi, China
- Research Center of Cell Immunological Engineering and Technology of Shaanxi Province, Xi'an, Shaanxi, China
- Shaanxi Provincial Key Laboratory of Infection and Immune Diseases, Xi'an, Shaanxi, China
| | - Hanyu Hu
- Shaanxi Ruiqi Biology Sci-Tech Co., Ltd., Xi'an, Shaanxi, China
| | - Jun Hu
- Central Laboratory of Shaanxi Provincial People's Hospital, Xi'an, Shaanxi, China
- Research Center of Cell Immunological Engineering and Technology of Shaanxi Province, Xi'an, Shaanxi, China
| | - Senbiao Fang
- Department of Molecular Pharmacology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Lijun Shang
- School of Human Sciences, London Metropolitan University, London, UK
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3
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Jiang J, Boughter CT, Ahmad J, Natarajan K, Boyd LF, Meier-Schellersheim M, Margulies DH. SARS-CoV-2 antibodies recognize 23 distinct epitopic sites on the receptor binding domain. Commun Biol 2023; 6:953. [PMID: 37726484 PMCID: PMC10509263 DOI: 10.1038/s42003-023-05332-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 09/07/2023] [Indexed: 09/21/2023] Open
Abstract
The COVID-19 pandemic and SARS-CoV-2 variants have dramatically illustrated the need for a better understanding of antigen (epitope)-antibody (paratope) interactions. To gain insight into the immunogenic characteristics of epitopic sites (ES), we systematically investigated the structures of 340 Abs and 83 nanobodies (Nbs) complexed with the Receptor Binding Domain (RBD) of the SARS-CoV-2 spike protein. We identified 23 distinct ES on the RBD surface and determined the frequencies of amino acid usage in the corresponding CDR paratopes. We describe a clustering method for analysis of ES similarities that reveals binding motifs of the paratopes and that provides insights for vaccine design and therapies for SARS-CoV-2, as well as a broader understanding of the structural basis of Ab-protein antigen (Ag) interactions.
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Affiliation(s)
- Jiansheng Jiang
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892, USA.
| | - Christopher T Boughter
- Computational Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892, USA
| | - Javeed Ahmad
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892, USA
| | - Kannan Natarajan
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892, USA
| | - Lisa F Boyd
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892, USA
| | - Martin Meier-Schellersheim
- Computational Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892, USA
| | - David H Margulies
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892, USA.
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4
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Zeng X, Bai G, Sun C, Ma B. Recent Progress in Antibody Epitope Prediction. Antibodies (Basel) 2023; 12:52. [PMID: 37606436 PMCID: PMC10443277 DOI: 10.3390/antib12030052] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 07/31/2023] [Accepted: 08/03/2023] [Indexed: 08/23/2023] Open
Abstract
Recent progress in epitope prediction has shown promising results in the development of vaccines and therapeutics against various diseases. However, the overall accuracy and success rate need to be improved greatly to gain practical application significance, especially conformational epitope prediction. In this review, we examined the general features of antibody-antigen recognition, highlighting the conformation selection mechanism in flexible antibody-antigen binding. We recently highlighted the success and warning signs of antibody epitope predictions, including linear and conformation epitope predictions. While deep learning-based models gradually outperform traditional feature-based machine learning, sequence and structure features still provide insight into antibody-antigen recognition problems.
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Affiliation(s)
- Xincheng Zeng
- Engineering Research Center of Cell & Therapeutic Antibody (MOE), School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China; (X.Z.); (C.S.)
| | - Ganggang Bai
- Engineering Research Center of Cell & Therapeutic Antibody (MOE), School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China; (X.Z.); (C.S.)
| | - Chuance Sun
- Engineering Research Center of Cell & Therapeutic Antibody (MOE), School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China; (X.Z.); (C.S.)
| | - Buyong Ma
- Engineering Research Center of Cell & Therapeutic Antibody (MOE), School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China; (X.Z.); (C.S.)
- Shanghai Digiwiser Biological, Inc., Shanghai 200131, China
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5
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Del Pozo-Yauner L, Herrera GA, Perez Carreon JI, Turbat-Herrera EA, Rodriguez-Alvarez FJ, Ruiz Zamora RA. Role of the mechanisms for antibody repertoire diversification in monoclonal light chain deposition disorders: when a friend becomes foe. Front Immunol 2023; 14:1203425. [PMID: 37520549 PMCID: PMC10374031 DOI: 10.3389/fimmu.2023.1203425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 06/20/2023] [Indexed: 08/01/2023] Open
Abstract
The adaptive immune system of jawed vertebrates generates a highly diverse repertoire of antibodies to meet the antigenic challenges of a constantly evolving biological ecosystem. Most of the diversity is generated by two mechanisms: V(D)J gene recombination and somatic hypermutation (SHM). SHM introduces changes in the variable domain of antibodies, mostly in the regions that form the paratope, yielding antibodies with higher antigen binding affinity. However, antigen recognition is only possible if the antibody folds into a stable functional conformation. Therefore, a key force determining the survival of B cell clones undergoing somatic hypermutation is the ability of the mutated heavy and light chains to efficiently fold and assemble into a functional antibody. The antibody is the structural context where the selection of the somatic mutations occurs, and where both the heavy and light chains benefit from protective mechanisms that counteract the potentially deleterious impact of the changes. However, in patients with monoclonal gammopathies, the proliferating plasma cell clone may overproduce the light chain, which is then secreted into the bloodstream. This places the light chain out of the protective context provided by the quaternary structure of the antibody, increasing the risk of misfolding and aggregation due to destabilizing somatic mutations. Light chain-derived (AL) amyloidosis, light chain deposition disease (LCDD), Fanconi syndrome, and myeloma (cast) nephropathy are a diverse group of diseases derived from the pathologic aggregation of light chains, in which somatic mutations are recognized to play a role. In this review, we address the mechanisms by which somatic mutations promote the misfolding and pathological aggregation of the light chains, with an emphasis on AL amyloidosis. We also analyze the contribution of the variable domain (VL) gene segments and somatic mutations on light chain cytotoxicity, organ tropism, and structure of the AL fibrils. Finally, we analyze the most recent advances in the development of computational algorithms to predict the role of somatic mutations in the cardiotoxicity of amyloidogenic light chains and discuss the challenges and perspectives that this approach faces.
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Affiliation(s)
- Luis Del Pozo-Yauner
- Department of Pathology, University of South Alabama-College of Medicine, Mobile, AL, United States
| | - Guillermo A. Herrera
- Department of Pathology, University of South Alabama-College of Medicine, Mobile, AL, United States
| | | | - Elba A. Turbat-Herrera
- Department of Pathology, University of South Alabama-College of Medicine, Mobile, AL, United States
- Mitchell Cancer Institute, University of South Alabama-College of Medicine, Mobile, AL, United States
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6
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Banerjee S, Hemmat MA, Shubham S, Gosai A, Devarakonda S, Jiang N, Geekiyanage C, Dillard JA, Maury W, Shrotriya P, Lamm MH, Nilsen-Hamilton M. Structurally Different Yet Functionally Similar: Aptamers Specific for the Ebola Virus Soluble Glycoprotein and GP1,2 and Their Application in Electrochemical Sensing. Int J Mol Sci 2023; 24:4627. [PMID: 36902059 PMCID: PMC10003157 DOI: 10.3390/ijms24054627] [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: 12/31/2022] [Revised: 02/20/2023] [Accepted: 02/21/2023] [Indexed: 03/04/2023] Open
Abstract
The Ebola virus glycoprotein (GP) gene templates several mRNAs that produce either the virion-associated transmembrane protein or one of two secreted glycoproteins. Soluble glycoprotein (sGP) is the predominant product. GP1 and sGP share an amino terminal sequence of 295 amino acids but differ in quaternary structure, with GP1 being a heterohexamer with GP2 and sGP a homodimer. Two structurally different DNA aptamers were selected against sGP that also bound GP1,2. These DNA aptamers were compared with a 2'FY-RNA aptamer for their interactions with the Ebola GP gene products. The three aptamers have almost identical binding isotherms for sGP and GP1,2 in solution and on the virion. They demonstrated high affinity and selectivity for sGP and GP1,2. Furthermore, one aptamer, used as a sensing element in an electrochemical format, detected GP1,2 on pseudotyped virions and sGP with high sensitivity in the presence of serum, including from an Ebola-virus-infected monkey. Our results suggest that the aptamers interact with sGP across the interface between the monomers, which is different from the sites on the protein bound by most antibodies. The remarkable similarity in functional features of three structurally distinct aptamers suggests that aptamers, like antibodies, have preferred binding sites on proteins.
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Affiliation(s)
- Soma Banerjee
- Ames Laboratory, U.S. Department of Energy, Ames, IA 50011, USA
| | - Mahsa Askary Hemmat
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Shambhavi Shubham
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Agnivo Gosai
- Department of Mechanical Engineering, Iowa State University, Ames, IA 50011, USA
| | | | - Nianyu Jiang
- Department of Mechanical Engineering, Iowa State University, Ames, IA 50011, USA
| | | | - Jacob A. Dillard
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 50011, USA
| | - Wendy Maury
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 50011, USA
| | - Pranav Shrotriya
- Department of Mechanical Engineering, Iowa State University, Ames, IA 50011, USA
| | - Monica H. Lamm
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA 50011, USA
| | - Marit Nilsen-Hamilton
- Ames Laboratory, U.S. Department of Energy, Ames, IA 50011, USA
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
- Aptalogic Inc., Ames, IA 50014, USA
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7
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Chauhan VM, Pantazes RJ. Analysis of conformational stability of interacting residues in protein binding interfaces. Protein Eng Des Sel 2023; 36:gzad016. [PMID: 37889566 PMCID: PMC10681001 DOI: 10.1093/protein/gzad016] [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: 05/14/2023] [Revised: 10/17/2023] [Accepted: 10/18/2023] [Indexed: 10/28/2023] Open
Abstract
After approximately 60 years of work, the protein folding problem has recently seen rapid advancement thanks to the inventions of AlphaFold and RoseTTAFold, which are machine-learning algorithms capable of reliably predicting protein structures from their sequences. A key component in their success was the inclusion of pairwise interaction information between residues. As research focus shifts towards developing algorithms to design and engineer binding proteins, it is likely that knowledge of interaction features at protein interfaces can improve predictions. Here, 574 protein complexes were analyzed to identify the stability features of their pairwise interactions, revealing that interactions between pre-stabilized residues are a selected feature in protein binding interfaces. In a retrospective analysis of 475 de novo designed binding proteins with an experimental success rate of 19%, inclusion of pairwise interaction pre-stabilization parameters increased the frequency of identifying experimentally successful binders to 40%.
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Affiliation(s)
- Varun M Chauhan
- Department of Chemical Engineering, Auburn University, Auburn, AL 36849, USA
| | - Robert J Pantazes
- Department of Chemical Engineering, Auburn University, Auburn, AL 36849, USA
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8
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Mollica L, Giachin G. Recognition Mechanisms between a Nanobody and Disordered Epitopes of the Human Prion Protein: An Integrative Molecular Dynamics Study. J Chem Inf Model 2022; 63:531-545. [PMID: 36580661 PMCID: PMC9875307 DOI: 10.1021/acs.jcim.2c01062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Immunotherapy using antibodies to target the aggregation of flexible proteins holds promise for therapeutic interventions in neurodegenerative diseases caused by protein misfolding. Prions or PrPSc, the causal agents of transmissible spongiform encephalopathies (TSE), represent a model target for immunotherapies as TSE are prototypical protein misfolding diseases. The X-ray crystal structure of the wild-type (WT) human prion protein (HuPrP) bound to a camelid antibody fragment, denoted as Nanobody 484 (Nb484), has been previously solved. Nb484 was found to inhibit prion aggregation in vitro through a unique mechanism of structural stabilization of two disordered epitopes, that is, the palindromic motif (residues 113-120) and the β2-α2 loop region (residues 164-185). The study of the structural basis for antibody recognition of flexible proteins requires appropriate sampling techniques for the identification of conformational states occurring in disordered epitopes. To elucidate the Nb484-HuPrP recognition mechanisms, here we applied molecular dynamics (MD) simulations complemented with available NMR and X-ray crystallography data collected on the WT HuPrP to describe the conformational spaces occurring on HuPrP prior to Nb484 binding. We observe the experimentally determined binding competent conformations within the ensembles of pre-existing conformational states in solution before binding. We also described the Nb484 recognition mechanisms in two HuPrP carrying a polymorphism (E219K) and a TSE-causing mutation (V210I). Our hybrid approaches allow the identification of dynamic conformational landscapes existing on HuPrP and highly characterized by molecular disorder to identify physiologically relevant and druggable transitions.
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Affiliation(s)
- Luca Mollica
- Department
of Medical Biotechnology and Translational Medicine, University of Milan, Segrate, 20090 Milan, Italy,
| | - Gabriele Giachin
- Department
of Chemical Sciences (DiSC), University
of Padua, 35131 Padova, Italy,
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9
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Caoili SEC. Comprehending B-Cell Epitope Prediction to Develop Vaccines and Immunodiagnostics. Front Immunol 2022; 13:908459. [PMID: 35874755 PMCID: PMC9300992 DOI: 10.3389/fimmu.2022.908459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 06/13/2022] [Indexed: 11/18/2022] Open
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10
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Yokoo T, Tanabe A, Yoshida Y, Caaveiro JMM, Nakakido M, Ikeda Y, Fujimura Y, Matsumoto M, Entzminger K, Maruyama T, Okumura CJ, Nangaku M, Tsumoto K. Antibody recognition of complement Factor H reveals a flexible loop involved in Atypical Hemolytic Uremic Syndrome pathogenesis. J Biol Chem 2022; 298:101962. [PMID: 35452676 PMCID: PMC9127587 DOI: 10.1016/j.jbc.2022.101962] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 04/15/2022] [Accepted: 04/16/2022] [Indexed: 11/28/2022] Open
Abstract
Atypical hemolytic uremic syndrome (aHUS) is a disease associated with dysregulation of the immune complement system, especially of the alternative pathway (AP). Complement factor H (CFH), consisting of 20 domains called CCP1-20, downregulates the AP as a cofactor for mediating C3 inactivation by complement factor I (CFI). However, anomalies related to CFH are known to cause excessive complement activation and cytotoxicity. In aHUS, mutations and the presence of anti-CFH autoantibodies (AAbs) have been reported as plausible causes of CFH dysfunction, and it is known that CFH-related aHUS carries a high probability of end-stage renal disease. Elucidating the detailed functions of CFH at the molecular level will help to understand aHUS pathogenesis. Herein, we used biophysical data to reveal that a heavy-chain antibody fragment, termed VHH4, recognized CFH with high affinity. Hemolytic assays also indicated that VHH4 disrupted the protective function of CFH on sheep erythrocytes. Furthermore, X-ray crystallography revealed that VHH4 recognized the Leu1181-Leu1189CCP20 loop, a known anti-CFH AAbs epitope. We next analyzed the dynamics of the C-terminal region of CFH, and showed that the epitopes recognized by anti-CFH AAbs and VHH4 were the most flexible regions in CCP18-20. Finally, we conducted mutation analyses to elucidate the mechanism of VHH4 recognition of CFH, and revealed that VHH4 inserts Trp1183CCP20 residue of CFH into the pocket formed by the complementary determining region 3 loop. These results suggested that anti-CFH AAbs may adopt a similar molecular mechanism to recognize the flexible loop of Leu1181-Leu1189CCP20, leading to aHUS pathogenesis.
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Affiliation(s)
- Takanori Yokoo
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Aki Tanabe
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Yoko Yoshida
- Division of Nephrology and Endocrinology, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Jose M M Caaveiro
- Department of Global Healthcare, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Makoto Nakakido
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan; Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.
| | - Yoichiro Ikeda
- Division of Nephrology and Endocrinology, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Yoshihiro Fujimura
- Department of Blood Transfusion Medicine, Nara Medical University, 840, Shijo-Cho, Kashihara, Nara, 634-8521, Japan
| | - Masanori Matsumoto
- Department of Blood Transfusion Medicine, Nara Medical University, 840, Shijo-Cho, Kashihara, Nara, 634-8521, Japan
| | - Kevin Entzminger
- Abwiz Bio Inc, 9823 Pacific Heights Blvd, Ste J, San Diego, California, 92121, USA
| | - Toshiaki Maruyama
- Abwiz Bio Inc, 9823 Pacific Heights Blvd, Ste J, San Diego, California, 92121, USA
| | - C J Okumura
- Abwiz Bio Inc, 9823 Pacific Heights Blvd, Ste J, San Diego, California, 92121, USA
| | - Masaomi Nangaku
- Division of Nephrology and Endocrinology, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Kouhei Tsumoto
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan; Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan; The institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan.
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11
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Qiao X, Qu L, Guo Y, Hoshino T. Secondary Structure and Conformational Stability of the Antigen Residues Making Contact with Antibodies. J Phys Chem B 2021; 125:11374-11385. [PMID: 34615354 DOI: 10.1021/acs.jpcb.1c05997] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Antibodies are crucial biomolecules that bring high therapeutic efficacy in medicine and accurate molecular detection in diagnosis. Many studies have been devoted to analyzing the antigen-antibody interaction from the importance of understanding the antibody recognition mechanism. However, most of the previous studies examined the characteristic of the antibody for interaction. It is also informative to clarify the significant antigen residues contributing to the binding. To characterize the molecular interaction of antigens, we computationally analyzed 350 antigen-antibody complex structures by molecular mechanics (MM) calculations and molecular dynamics (MD) simulations. Based on the MM calculations, the antigen residues contributing to the binding were extracted from all the 350 complexes. The extracted residues are located at the antigen-antibody interface and are responsible for making contact with the antibody. The appearances of the charged polar residues, Asp, Glu, Arg, and Lys, were noticeably large. In contrast, the populations of the hydrophobic residues, Leu, Val, and Ala, were relatively low. The appearance frequencies of the other amino acid residues were almost close to the abundance of general proteins of eukaryotes. The binding score indicated that the hydrophilic interaction was dominant at the antigen-antibody contact instead of the hydrophobic one. The positively charged residues, Arg and Lys, remarkably contributed to the binding compared to the negatively charged ones, Asp and Glu. Considerable contributions were also observed for the noncharged polar residues, Asn and Gln. The analysis of the secondary structures of the extracted antigen residues suggested that there was no marked difference in recognition by antibodies among helix, sheet, turn, and coil. A long helix of the antigen sometimes made contact with antibody complementarity-determining regions, and a large sheet also frequently covered the antibody heavy and light chains. The turn structure was the most popularly observed at the contact with antibody among 350 complexes. Three typical complexes were picked up for each of the four secondary structures. MD simulations were performed to examine the stability of the interfacial structures of the antigens for these 12 complex models. The alterations of secondary structures were monitored through the simulations. The structural fluctuations of the contact residues were low compared with the other domains of antigen molecules. No drastic conversion was observed for every model during the 100 ns simulation. The motions of the interfacial antigen residues were small compared to the other residues on the protein surface. Therefore, diverse molecular conformations are possible for antibody recognition as long as the target areas are polar, nonflexible, and protruding on the protein surface.
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Affiliation(s)
- Xinyue Qiao
- Graduate School of Pharmaceutical Sciences, Chiba University, Inohana 1-8-1, Chuo-ku, Chiba 260-8675, Japan
| | - Liang Qu
- Graduate School of Pharmaceutical Sciences, Chiba University, Inohana 1-8-1, Chuo-ku, Chiba 260-8675, Japan
| | - Yan Guo
- Graduate School of Pharmaceutical Sciences, Chiba University, Inohana 1-8-1, Chuo-ku, Chiba 260-8675, Japan
| | - Tyuji Hoshino
- Graduate School of Pharmaceutical Sciences, Chiba University, Inohana 1-8-1, Chuo-ku, Chiba 260-8675, Japan
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12
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Štambuk N, Konjevoda P, Pavan J. Antisense Peptide Technology for Diagnostic Tests and Bioengineering Research. Int J Mol Sci 2021; 22:9106. [PMID: 34502016 PMCID: PMC8431130 DOI: 10.3390/ijms22179106] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 08/10/2021] [Accepted: 08/13/2021] [Indexed: 01/01/2023] Open
Abstract
Antisense peptide technology (APT) is based on a useful heuristic algorithm for rational peptide design. It was deduced from empirical observations that peptides consisting of complementary (sense and antisense) amino acids interact with higher probability and affinity than the randomly selected ones. This phenomenon is closely related to the structure of the standard genetic code table, and at the same time, is unrelated to the direction of its codon sequence translation. The concept of complementary peptide interaction is discussed, and its possible applications to diagnostic tests and bioengineering research are summarized. Problems and difficulties that may arise using APT are discussed, and possible solutions are proposed. The methodology was tested on the example of SARS-CoV-2. It is shown that the CABS-dock server accurately predicts the binding of antisense peptides to the SARS-CoV-2 receptor binding domain without requiring predefinition of the binding site. It is concluded that the benefits of APT outweigh the costs of random peptide screening and could lead to considerable savings in time and resources, especially if combined with other computational and immunochemical methods.
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Affiliation(s)
- Nikola Štambuk
- Center for Nuclear Magnetic Resonance, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia
| | - Paško Konjevoda
- Laboratory for Epigenomics, Division of Molecular Medicine, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia
| | - Josip Pavan
- Department of Ophthalmology, University Hospital Dubrava, Avenija Gojka Šuška 6, HR-10000 Zagreb, Croatia
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A Novel Nanobody Precisely Visualizes Phosphorylated Histone H2AX in Living Cancer Cells under Drug-Induced Replication Stress. Cancers (Basel) 2021; 13:cancers13133317. [PMID: 34282773 PMCID: PMC8267817 DOI: 10.3390/cancers13133317] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 12/21/2022] Open
Abstract
Simple Summary γ-H2AX, a phosphorylated variant of histone H2A, is a widely used biomarker of DNA replication stress. To develop an immunological probe able to detect and track γ-H2AX in live cancer cells, we have isolated single domain antibodies (called nanobodies) that are easily expressed as functional recombinant proteins and here we report the extensive characterization of a novel nanobody that specifically recognizes γ-H2AX. The interaction of this nanobody with the C-terminal end of γ-H2AX was determined by X-ray crystallography. Moreover, the generation of a bivalent nanobody allowed us to precisely detect γ-H2AX foci in drug-treated cells as efficiently as with commercially available conventional antibodies. Furthermore, we tracked γ-H2AX foci in live cells upon intracellular delivery of the bivalent nanobody fused to the red fluorescent protein dTomato, making, consequently, this new cost-effective reagent useful for studying drug-induced replication stress in both fixed and living cancer cells. Abstract Histone H2AX phosphorylated at serine 139 (γ-H2AX) is a hallmark of DNA damage, signaling the presence of DNA double-strand breaks and global replication stress in mammalian cells. While γ-H2AX can be visualized with antibodies in fixed cells, its detection in living cells was so far not possible. Here, we used immune libraries and phage display to isolate nanobodies that specifically bind to γ-H2AX. We solved the crystal structure of the most soluble nanobody in complex with the phosphopeptide corresponding to the C-terminus of γ-H2AX and show the atomic constituents behind its specificity. We engineered a bivalent version of this nanobody and show that bivalency is essential to quantitatively visualize γ-H2AX in fixed drug-treated cells. After labelling with a chemical fluorophore, we were able to detect γ-H2AX in a single-step assay with the same sensitivity as with validated antibodies. Moreover, we produced fluorescent nanobody-dTomato fusion proteins and applied a transduction strategy to visualize with precision γ-H2AX foci present in intact living cells following drug treatment. Together, this novel tool allows performing fast screenings of genotoxic drugs and enables to study the dynamics of this particular chromatin modification in individual cancer cells under a variety of conditions.
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