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Musunuri S, Weidenbacher PAB, Kim PS. Bringing immunofocusing into focus. NPJ Vaccines 2024; 9:11. [PMID: 38195562 PMCID: PMC10776678 DOI: 10.1038/s41541-023-00792-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 12/07/2023] [Indexed: 01/11/2024] Open
Abstract
Immunofocusing is a strategy to create immunogens that redirect humoral immune responses towards a targeted epitope and away from non-desirable epitopes. Immunofocusing methods often aim to develop "universal" vaccines that provide broad protection against highly variant viruses such as influenza virus, human immunodeficiency virus (HIV-1), and most recently, severe acute respiratory syndrome coronavirus (SARS-CoV-2). We use existing examples to illustrate five main immunofocusing strategies-cross-strain boosting, mosaic display, protein dissection, epitope scaffolding, and epitope masking. We also discuss obstacles for immunofocusing like immune imprinting. A thorough understanding, advancement, and application of the methods we outline here will enable the design of high-resolution vaccines that protect against future viral outbreaks.
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Affiliation(s)
- Sriharshita Musunuri
- Stanford ChEM-H, Stanford University, Stanford, CA, 94305, USA
- Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA
| | - Payton A B Weidenbacher
- Stanford ChEM-H, Stanford University, Stanford, CA, 94305, USA
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Peter S Kim
- Stanford ChEM-H, Stanford University, Stanford, CA, 94305, USA.
- Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
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2
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Fernández-Quintero ML, Pomarici ND, Fischer ALM, Hoerschinger VJ, Kroell KB, Riccabona JR, Kamenik AS, Loeffler JR, Ferguson JA, Perrett HR, Liedl KR, Han J, Ward AB. Structure and Dynamics Guiding Design of Antibody Therapeutics and Vaccines. Antibodies (Basel) 2023; 12:67. [PMID: 37873864 PMCID: PMC10594513 DOI: 10.3390/antib12040067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/10/2023] [Accepted: 10/13/2023] [Indexed: 10/25/2023] Open
Abstract
Antibodies and other new antibody-like formats have emerged as one of the most rapidly growing classes of biotherapeutic proteins. Understanding the structural features that drive antibody function and, consequently, their molecular recognition is critical for engineering antibodies. Here, we present the structural architecture of conventional IgG antibodies alongside other formats. We emphasize the importance of considering antibodies as conformational ensembles in solution instead of focusing on single-static structures because their functions and properties are strongly governed by their dynamic nature. Thus, in this review, we provide an overview of the unique structural and dynamic characteristics of antibodies with respect to their antigen recognition, biophysical properties, and effector functions. We highlight the numerous technical advances in antibody structure prediction and design, enabled by the vast number of experimentally determined high-quality structures recorded with cryo-EM, NMR, and X-ray crystallography. Lastly, we assess antibody and vaccine design strategies in the context of structure and dynamics.
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Affiliation(s)
- Monica L. Fernández-Quintero
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nancy D. Pomarici
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Anna-Lena M. Fischer
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Valentin J. Hoerschinger
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Katharina B. Kroell
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Jakob R. Riccabona
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Anna S. Kamenik
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Johannes R. Loeffler
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - James A. Ferguson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hailee R. Perrett
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Klaus R. Liedl
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Julianna Han
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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3
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Thakur S, Mehra R. Computational Insight into Substrate-Induced Conformational Changes in Methionyl-tRNA Synthetase of Mycobacterium Tuberculosis. Protein J 2023; 42:533-546. [PMID: 37402109 DOI: 10.1007/s10930-023-10135-3] [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] [Accepted: 06/26/2023] [Indexed: 07/05/2023]
Abstract
Tuberculosis caused by Mycobacterium tuberculosis (M.tb) has killed millions worldwide. Antibiotic resistance leads to the ineffectiveness of the current therapies. Aminoacyl tRNA synthetase (aaRS) class of proteins involved in protein synthesis are promising bacterial targets for developing new therapies. Here, we carried out a systematic comparative study on the aaRS sequences from M.tb and human. We listed important M.tb aaRS that could be explored as potential M.tb targets alongside the detailed conformational space analysis of methionyl-tRNA synthetase (MetRS) in apo- and substrate-bound form, which is among the proposed targets. Understanding the conformational dynamics is central to the mechanistic understanding of MetRS, as the substrate binding leads to the conformational changes causing the reaction to proceed. We performed the most complete simulation study of M.tb MetRS for 6 microseconds (2 systems × 3 runs × 1 microsecond) in the apo and substrate-bound states. Interestingly, we observed differential features, showing comparatively large dynamics for the holo simulations, whereas the apo structures became slightly compact with reduced solvent exposed area. In contrast, the ligand size decreased significantly in holo structures possibly to relax ligand conformation. Our findings correlate with experimental studies, thus validating our protocol. Adenosine monophosphate moiety of the substrate exhibited quite higher fluctuations than the methionine. His21 and Lys54 were found to be the important residues forming prominent hydrogen bond and salt-bridge interactions with the ligand. The ligand-protein affinity decreased during simulations as computed by MMGBSA analysis over the last 500 ns trajectories, which indicates the conformational changes upon ligand binding. These differential features could be further explored for designing new M.tb inhibitors.
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Affiliation(s)
- Shivani Thakur
- Department of Chemistry, Indian Institute of Technology Bhilai, Sejbahar, Raipur, Chhattisgarh, 492015, India
| | - Rukmankesh Mehra
- Department of Chemistry, Indian Institute of Technology Bhilai, Sejbahar, Raipur, Chhattisgarh, 492015, India.
- Department of Bioscience and Biomedical Engineering, Indian Institute of Technology Bhilai, Sejbahar, Raipur, Chhattisgarh, 492015, India.
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4
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Jaiswal D, Verma S, Nair DT, Salunke DM. Antibody multispecificity: A necessary evil? Mol Immunol 2022; 152:153-161. [DOI: 10.1016/j.molimm.2022.10.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/20/2022] [Accepted: 10/24/2022] [Indexed: 11/09/2022]
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5
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Immunoinformatics Approach for Epitope-Based Vaccine Design: Key Steps for Breast Cancer Vaccine. Diagnostics (Basel) 2022; 12:diagnostics12122981. [PMID: 36552988 PMCID: PMC9777080 DOI: 10.3390/diagnostics12122981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022] Open
Abstract
Vaccines are an upcoming medical intervention for breast cancer. By targeting the tumor antigen, cancer vaccines can be designed to train the immune system to recognize tumor cells. Therefore, along with technological advances, the vaccine design process is now starting to be carried out with more rational methods such as designing epitope-based peptide vaccines using immunoinformatics methods. Immunoinformatics methods can assist vaccine design in terms of antigenicity and safety. Common protocols used to design epitope-based peptide vaccines include tumor antigen identification, protein structure analysis, T cell epitope prediction, epitope characterization, and evaluation of protein-epitope interactions. Tumor antigen can be divided into two types: tumor associated antigen and tumor specific antigen. We will discuss the identification of tumor antigens using high-throughput technologies. Protein structure analysis comprises the physiochemical, hydrochemical, and antigenicity of the protein. T cell epitope prediction models are widely available with various prediction parameters as well as filtering tools for the prediction results. Epitope characterization such as allergenicity and toxicity can be done in silico as well using allergenicity and toxicity predictors. Evaluation of protein-epitope interactions can also be carried out in silico with molecular simulation. We will also discuss current and future developments of breast cancer vaccines using an immunoinformatics approach. Finally, although prediction models have high accuracy, the opposite can happen after being tested in vitro and in vivo. Therefore, further studies are needed to ensure the effectiveness of the vaccine to be developed. Although epitope-based peptide vaccines have the disadvantage of low immunogenicity, the addition of adjuvants can be a solution.
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Fernández-Quintero ML, Georges G, Varga JM, Liedl KR. Ensembles in solution as a new paradigm for antibody structure prediction and design. MAbs 2021; 13:1923122. [PMID: 34030577 PMCID: PMC8158028 DOI: 10.1080/19420862.2021.1923122] [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] [Indexed: 11/05/2022] Open
Abstract
The rise of antibodies as a promising and rapidly growing class of biotherapeutic proteins has motivated numerous studies to characterize and understand antibody structures. In the past decades, the number of antibody crystal structures increased substantially, which revolutionized the atomistic understanding of antibody functions. Even though numerous static structures are known, various biophysical properties of antibodies (i.e., specificity, hydrophobicity and stability) are governed by their dynamic character. Additionally, the importance of high-quality structures in structure–function relationship studies has substantially increased. These structure–function relationship studies have also created a demand for precise homology models of antibody structures, which allow rational antibody design and engineering when no crystal structure is available. Here, we discuss various aspects and challenges in antibody design and extend the paradigm of describing antibodies with only a single static structure to characterizing them as dynamic ensembles in solution.
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Affiliation(s)
- Monica L Fernández-Quintero
- Department of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Guy Georges
- Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Janos M Varga
- Department of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Klaus R Liedl
- Department of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
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7
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Filby BW, Hardman MJ, Paunov VN. Antibody‐free bioimprint aided sandwich ELISA technique for cell recognition and rapid screening for bacteria. NANO SELECT 2020. [DOI: 10.1002/nano.202000113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Benjamin W. Filby
- Department of Chemistry and Biochemistry University of Hull Hull HU6 7RX UK
| | - Matthew J. Hardman
- Department of Chemistry and Biochemistry University of Hull Hull HU6 7RX UK
| | - Vesselin N. Paunov
- Department of Chemistry and Biochemistry University of Hull Hull HU6 7RX UK
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8
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Antibody specificity and promiscuity. Biochem J 2019; 476:433-447. [PMID: 30723137 DOI: 10.1042/bcj20180670] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 01/06/2019] [Accepted: 01/07/2019] [Indexed: 12/16/2022]
Abstract
The immune system is capable of making antibodies against anything that is foreign, yet it does not react against components of self. In that sense, a fundamental requirement of the body's immune defense is specificity. Remarkably, this ability to specifically attack foreign antigens is directed even against antigens that have not been encountered a priori by the immune system. The specificity of an antibody for the foreign antigen evolves through an iterative process of somatic mutations followed by selection. There is, however, accumulating evidence that the antibodies are often functionally promiscuous or multi-specific which can lead to their binding to more than one antigen. An important cause of antibody cross-reactivity is molecular mimicry. Molecular mimicry has been implicated in the generation of autoimmune response. When foreign antigen shares similarity with the component of self, the antibodies generated could result in an autoimmune response. The focus of this review is to capture the contrast between specificity and promiscuity and the structural mechanisms employed by the antibodies to accomplish promiscuity, at the molecular level. The conundrum between the specificity of the immune system for foreign antigens on the one hand and the multi-reactivity of the antibody on the other has been addressed. Antibody specificity in the context of the rapid evolution of the antigenic determinants and molecular mimicry displayed by antigens are also discussed.
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9
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Fernández-Quintero ML, Loeffler JR, Kraml J, Kahler U, Kamenik AS, Liedl KR. Characterizing the Diversity of the CDR-H3 Loop Conformational Ensembles in Relationship to Antibody Binding Properties. Front Immunol 2019; 9:3065. [PMID: 30666252 PMCID: PMC6330313 DOI: 10.3389/fimmu.2018.03065] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 12/11/2018] [Indexed: 11/23/2022] Open
Abstract
We present an approach to assess antibody CDR-H3 loops according to their dynamic properties using molecular dynamics simulations. We selected six antibodies in three pairs differing substantially in their individual promiscuity respectively specificity. For two pairs of antibodies crystal structures are available in different states of maturation and used as starting structures for the analyses. For a third pair we chose two antibody CDR sequences obtained from a synthetic library and predicted the respective structures. For all three pairs of antibodies we performed metadynamics simulations to overcome the limitations in conformational sampling imposed by high energy barriers. Additionally, we used classic molecular dynamics simulations to describe nano- to microsecond flexibility and to estimate up to millisecond kinetics of captured conformational transitions. The methodology represents the antibodies as conformational ensembles and allows comprehensive analysis of structural diversity, thermodynamics of conformations and kinetics of structural transitions. Referring to the concept of conformational selection we investigated the link between promiscuity and flexibility of the antibodies' binding interfaces. The obtained detailed characterization of the binding interface clearly indicates a link between structural flexibility and binding promiscuity for this set of antibodies.
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Affiliation(s)
- Monica L Fernández-Quintero
- Center for Molecular Biosciences Innsbruck (CMBI), Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Johannes R Loeffler
- Center for Molecular Biosciences Innsbruck (CMBI), Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Johannes Kraml
- Center for Molecular Biosciences Innsbruck (CMBI), Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Ursula Kahler
- Center for Molecular Biosciences Innsbruck (CMBI), Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Anna S Kamenik
- Center for Molecular Biosciences Innsbruck (CMBI), Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Klaus R Liedl
- Center for Molecular Biosciences Innsbruck (CMBI), Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
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10
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Chen H, Li J, Zhang X, Li X, Yao M, Zheng G. Automated in Vivo Nanosensing of Breath-Borne Protein Biomarkers. NANO LETTERS 2018; 18:4716-4726. [PMID: 29995423 DOI: 10.1021/acs.nanolett.8b01070] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Toxicology and bedside medical condition monitoring is often desired to be both ultrasensitive and noninvasive. However, current biomarker analyses for these purposes are mostly offline and fail to detect low marker quantities. Here, we report a system called dLABer (detection of living animal's exhaled breath biomarker) that integrates living rats, breath sampling, microfluidics, and biosensors for the automated tracking of breath-borne biomarkers. Our data show that dLABer could selectively detect (online) and report differences (of up to 103-fold) in the levels of inflammation agent interleukin-6 (IL-6) exhaled by rats injected with different ambient particulate matter (PM). The dLABer system was further shown to have an up to 104 higher signal-to-noise ratio than that of the enzyme-linked immunosorbent assay (ELISA) when analyzing the same breath samples. In addition, both blood-borne IL-6 levels analyzed via ELISA in rats injected with different PM extracts and PM toxicity determined by a dithiothreitol (DTT) assay agreed well with those determined by the dLABer system. Video recordings further verified that rats exposed to PM with higher toxicity (according to a DTT assay and as revealed by dLABer) appeared to be less physically active. All the data presented here suggest that the dLABer system is capable of real-time, noninvasive monitoring of breath-borne biomarkers with ultrasensitivity. The dLABer system is expected to revolutionize pollutant health effect studies and bedside disease diagnosis as well as physiological condition monitoring at the single-protein level.
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Affiliation(s)
- Haoxuan Chen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering , Peking University , Beijing 100871 , China
| | - Jing Li
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering , Peking University , Beijing 100871 , China
| | - Xiangyu Zhang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering , Peking University , Beijing 100871 , China
| | - Xinyue Li
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering , Peking University , Beijing 100871 , China
| | - Maosheng Yao
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering , Peking University , Beijing 100871 , China
| | - Gengfeng Zheng
- Laboratory of Advanced Materials, Department of Chemistry and State Key Laboratory of Medical Neurobiology , Fudan University , Shanghai 200438 , China
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11
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Berto M, Casalini S, Di Lauro M, Marasso SL, Cocuzza M, Perrone D, Pinti M, Cossarizza A, Pirri CF, Simon DT, Berggren M, Zerbetto F, Bortolotti CA, Biscarini F. Biorecognition in Organic Field Effect Transistors Biosensors: The Role of the Density of States of the Organic Semiconductor. Anal Chem 2016; 88:12330-12338. [DOI: 10.1021/acs.analchem.6b03522] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Marcello Berto
- Dipartimento
di Scienze della Vita, Università di Modena e Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Stefano Casalini
- Dipartimento
di Scienze della Vita, Università di Modena e Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Michele Di Lauro
- Dipartimento
di Scienze della Vita, Università di Modena e Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Simone L. Marasso
- Dipartimento
di Scienza Applicata e Tecnologia (DISAT), Politecnico di Torino, C.so Duca degli Abruzzi 24, 10129 Torino, Italy
- IMEM-CNR, Parco Area delle Scienze 37, 43124 Parma, Italy
| | - Matteo Cocuzza
- Dipartimento
di Scienza Applicata e Tecnologia (DISAT), Politecnico di Torino, C.so Duca degli Abruzzi 24, 10129 Torino, Italy
- IMEM-CNR, Parco Area delle Scienze 37, 43124 Parma, Italy
| | - Denis Perrone
- Istituto Italiano di Tecnologia, Center for Sustainable
Futures, Corso Trento
21, 10129 Torino, Italy
| | - Marcello Pinti
- Dipartimento
di Scienze della Vita, Università di Modena e Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Andrea Cossarizza
- Dipartimento
di Scienze Mediche e Chirurgiche Materno-Infantili e dell’Adulto, Università di Modena e Reggio Emilia, Via Campi 287, 41125 Modena, Italy
| | - Candido F. Pirri
- Dipartimento
di Scienza Applicata e Tecnologia (DISAT), Politecnico di Torino, C.so Duca degli Abruzzi 24, 10129 Torino, Italy
- Istituto Italiano di Tecnologia, Center for Sustainable
Futures, Corso Trento
21, 10129 Torino, Italy
| | - Daniel T. Simon
- Laboratory
of Organic Electronics, Department of Science and Technology, ITN, Linköping University, S-601 74 Norrköping, Sweden
| | - Magnus Berggren
- Laboratory
of Organic Electronics, Department of Science and Technology, ITN, Linköping University, S-601 74 Norrköping, Sweden
| | - Francesco Zerbetto
- Dipartimento
di Chimica “G. Ciamician”, Università di Bologna, Via Selmi 2, 40126 Bologna, Italy
| | - Carlo A. Bortolotti
- Dipartimento
di Scienze della Vita, Università di Modena e Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Fabio Biscarini
- Dipartimento
di Scienze della Vita, Università di Modena e Reggio Emilia, Via Campi 103, 41125 Modena, Italy
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12
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Zhou C, Przedborski S. Intrabody and Parkinson's disease. Biochim Biophys Acta Mol Basis Dis 2008; 1792:634-42. [PMID: 18834937 DOI: 10.1016/j.bbadis.2008.09.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2008] [Revised: 08/22/2008] [Accepted: 09/03/2008] [Indexed: 10/21/2022]
Abstract
The intrabody technology has become a promising therapeutic avenue for a variety of incurable diseases. This technology is an intracellular application of gene-engineered antibodies, aimed at ablating the abnormal function of intracellular molecules. Parkinson's disease (PD) is a common neurodegenerative disease with no cure. Recent studies have explored possible intrabody applications against alpha-synuclein (alpha-syn), whose misfolding is believed to cause a familial form of PD. Here, we review the origin, production, and therapeutic mechanisms of intrabodies and the potential of intrabody protection against alpha-syn toxicity. Furthermore, we propose possible intrabody applications against leucine-rich repeat kinase 2 (LRRK2), whose mutations are the most frequent known cause of familial and sporadic PD.
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Affiliation(s)
- Chun Zhou
- Department of Neurology, Columbia University, New York, NY 10032, USA
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13
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The immunoglobulin constant region contributes to affinity and specificity. Trends Immunol 2008; 29:91-7. [PMID: 18191616 DOI: 10.1016/j.it.2007.11.004] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2007] [Revised: 11/06/2007] [Accepted: 11/07/2007] [Indexed: 11/22/2022]
Abstract
A central dogma in immunology is that antibody specificity is solely the result of variable (V)-region interactions with an antigen. However, this view is not tenable in light of numerous reports that constant heavy (C(H)) domains can affect binding affinity and specificity and V-region structure. Kinetic and thermodynamic proof for the occurrence of this phenomenon is now available. C(H)-region effects on affinity and specificity suggest new mechanisms for generating antibody diversity and polyreactivity (multispecificity) that impact current views on idiotype regulation, autoimmunity, and B cell selection and change our understanding of vaccine responses.
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14
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Meeks SL, Healey JF, Parker ET, Barrow RT, Lollar P. Antihuman factor VIII C2 domain antibodies in hemophilia A mice recognize a functionally complex continuous spectrum of epitopes dominated by inhibitors of factor VIII activation. Blood 2007; 110:4234-42. [PMID: 17848617 PMCID: PMC2234776 DOI: 10.1182/blood-2007-06-096842] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The diversity of factor VIII (fVIII) C2 domain antibody epitopes was investigated by competition enzyme-linked immunosorbent assay (ELISA) using a panel of 56 antibodies. The overlap patterns produced 5 groups of monoclonal antibodies (MAbs), designated A, AB, B, BC, and C, and yielded a set of 18 distinct epitopes. Group-specific loss of antigenicity was associated with mutations at the Met2199/Phe2200 phospholipid binding beta-hairpin (group AB MAbs) and at Lys2227 (group BC MAbs), which allowed orientation of the epitope structure as a continuum that covers one face of the C2 beta-sandwich. MAbs from groups A, AB, and B inhibit the binding of fVIIIa to phospholipid membranes. Group BC was the most common group and displayed the highest specific fVIII inhibitor activities. MAbs in this group are type II inhibitors that inhibit the activation of fVIII by either thrombin or factor Xa and poorly inhibit the binding of fVIII to phospholipid membranes or von Willebrand factor (VWF). Group BC MAbs are epitopically and mechanistically distinct from the extensively studied group C MAb, ESH8. These results reveal the structural and functional complexity of the anti-C2 domain antibody response and indicate that interference with fVIII activation is a major attribute of the inhibitor landscape.
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Affiliation(s)
- Shannon L Meeks
- Aflac Cancer Center and Blood Disorders Service, Children's Healthcare of Atlanta, Department of Pediatrics, Emory University, Atlanta, GA, USA
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15
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Stábeli RG, Magalhães LMP, Selistre-de-Araujo HS, Oliveira EB. Antibodies to a fragment of the Bothrops moojenil-amino acid oxidase cross-react with snake venom components unrelated to the parent protein. Toxicon 2005; 46:308-17. [PMID: 16026810 DOI: 10.1016/j.toxicon.2005.04.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2004] [Accepted: 04/26/2005] [Indexed: 10/25/2022]
Abstract
It is widely accepted that immunological cross-reactivity of snake venoms is mediated by antibodies that recognize venom components bearing either amino acid sequence homology or similar biological functions. However, here we demonstrate that polyspecific Bothrops antivenom is a source of cross-reactive antibodies that interact with venom proteins of distinctive primary structures and biological functions. The homoserine lactone derivative of the undecapeptide IQRWSLDKYAM (Ile1-Hse11), excised from the l-amino acid oxidase (LAAO) of the Bothrops moojeni venom, was the ligand of an affinity resin used to isolate specific anti-Ile1-Hse11 antibodies which were instrumental in revealing immunological cross-reactivity among unrelated venom proteins. We examined the extent of the cross-reactivity of these antibodies by probing electroblots of venoms from representative snakes of genera Bothrops, Lachesis, Crotalus and Micrurus, and by unambiguous structural characterization of the affinity-purified proteins of B. moojeni venom recovered from an agarose-anti-Ile1-Hse11 column. Our results indicate that all venoms tested had at least three reactive components toward anti-Ile1-Hse11 antibodies, among which we identified two serine proteases, one phospholipase A2 homologue, and LAAO. We hypothesize that the cross-reactivity of the anti-Ile1-Hse11 antibodies to unrelated venom proteins derives from their mechanism of antigen recognition, whereby complementarity is achieved through reciprocal conformational adaptation of the reacting molecules. Also, we believe these findings have implications both in the development of improved antivenoms and the preparation of immunochemical reagents for diagnostic and scientific investigation purposes in the field of snake venoms.
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Affiliation(s)
- Rodrigo Guerino Stábeli
- Departamento de Bioquímica e Imunologia, Faculdade de Medicina, USP, Ribeirão Preto, SP, Brazil
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16
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Rotariu O, Strachan NJC, Bădescu V. A stochastic model simulating the capture of pathogenic micro-organisms by superparamagnetic particles in an isodynamic magnetic field. Phys Med Biol 2004; 49:3971-8. [PMID: 15470917 DOI: 10.1088/0031-9155/49/17/010] [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: 11/11/2022]
Abstract
The method of immunomagnetic separation (IMS) has become an established technique to concentrate and separate animal cells, biologically active compounds and pathogenic micro-organisms from clinical, food and environmental matrices. One drawback of this technique is that the analysis is only possible for small sample volumes. We have developed a stochastic model that involves numerical simulations to optimize the process of concentration of pathogenic micro-organisms onto superparamagnetic carrier particles (SCPs) in a gradient magnetic field. Within the range of the system parameters varied in the simulations, optimal conditions favour larger particles with higher magnetite concentrations. The dependence on magnetic field intensity and gradient together with concentration of particles and micro-organisms was found to be less important for larger SCPs but these parameters can influence the values of the collision time for small particles. These results will be useful in aiding the design of apparatus for immunomagnetic separation from large volume samples.
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Affiliation(s)
- O Rotariu
- School of Biological Sciences, University of Aberdeen, Aberdeen, Scotland, AB24 3UU UK.
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17
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Li Y, Lipschultz CA, Mohan S, Smith-Gill SJ. Mutations of an epitope hot-spot residue alter rate limiting steps of antigen-antibody protein-protein associations. Biochemistry 2001; 40:2011-22. [PMID: 11329268 DOI: 10.1021/bi0014148] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The antibodies, HyHEL-10 and HyHEL-26 (H10 and H26, respectively), share over 90% sequence homology and recognize with high affinity the same epitope on hen egg white lysozyme (HEL) but differ in degree of cross-reactivity with mutant lysozymes. The binding kinetics, as measured by BIAcore surface plasmon resonance, of monovalent Fab from both Abs (Fab10 and Fab26) to HEL and mutant lysozymes are best described by a two-step association model consistent with an encounter followed by docking that may include conformational changes. In their complexes with HEL, both Abs make the transition to the docked phase rapidly. For H10, the encounter step is rate limiting, whereas docking is also partially rate limiting for H26. The forward rate constants of H10 are higher than those of H26. The docking equilibrium as well as the overall equilibrium constant are also higher for H10 than for H26. Most of the free energy change of association (Delta G degrees) occurs during the encounter phase (Delta G1) of both Abs. H10 derives a greater amount and proportion of free energy change from the docking phase (Delta G2) than does H26. In the H10--HEL(R21Q) complex, a significant slowing of docking results in lowered affinity, a loss of most of Delta G2, and apparently faster dissociation. Slower encounter and docking cause lowered affinity and a loss of free energy change primarily in the encounter step (Delta G1) of H26 with mutant HEL(R21Q). Overall, in the process of complex formation with lysozyme, the mutations HEL(R21X) affect primarily the docking phase of H10 association and both phases of H26. Our results are consistent with the interpretation that the free energy barriers to conformational rearrangement are highest in H26, especially with mutant antigen.
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MESH Headings
- Amino Acid Substitution/genetics
- Animals
- Antibodies, Monoclonal/metabolism
- Antibody Affinity/genetics
- Antigen-Antibody Reactions/genetics
- Binding Sites, Antibody/genetics
- Chickens
- Dose-Response Relationship, Immunologic
- Enzymes, Immobilized/genetics
- Enzymes, Immobilized/immunology
- Enzymes, Immobilized/metabolism
- Epitopes/genetics
- Epitopes/immunology
- Epitopes/metabolism
- Kinetics
- Ligands
- Models, Chemical
- Models, Immunological
- Models, Statistical
- Muramidase/genetics
- Muramidase/immunology
- Muramidase/metabolism
- Mutagenesis, Site-Directed
- Ovum
- Thermodynamics
- Time Factors
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Affiliation(s)
- Y Li
- Basic Research Laboratory, Program in Structural Biology, National Cancer Institute, Frederick Cancer Research and Development Center, P.O. Box B, Building 469, Room 206, Frederick, Maryland 21702-1201, USA
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18
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Jin L, Shieh JJ, Grabbe E, Adimoolam S, Durbin D, Jonas A. Surface plasmon resonance biosensor studies of human wild-type and mutant lecithin cholesterol acyltransferase interactions with lipoproteins. Biochemistry 1999; 38:15659-65. [PMID: 10569952 DOI: 10.1021/bi9916729] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Binding of lecithin cholesterol acyltransferase (LCAT) to lipoprotein surfaces is a key step in the reverse cholesterol transport process, as the subsequent cholesterol esterification reaction drives the removal of cholesterol from tissues into plasma. In this study, the surface plasmon resonance method was used to investigate the binding kinetics and affinity of LCAT for lipoproteins. Reconstituted high-density lipoproteins (rHDL) containing apolipoprotein A-I or A-II, (apoA-I or apoA-II), low-density lipoproteins (LDL), and small unilamellar phosphatidylcholine vesicles, with biotin tags, were immobilized on biosensor chips containing streptavidin, and the binding kinetics of pure recombinant LCAT were examined as a function of LCAT concentration. In addition, three mutants of LCAT (T123I, N228K, and (Delta53-71) were examined in their interactions with LDL. For the wild-type LCAT, binding to all lipid surfaces had the same association rate constant, k(a), but different dissociation rate constants, k(d), that depended on the presence of apoA-I (k(d) decreased) and different lipids in LDL. Furthermore, increased ionic strength of the buffer decreased k(a) for the binding of LCAT to apoA-I rHDL. For the LCAT mutants, the Delta53-71 (lid-deletion mutant) exhibited no binding to LDL, while the LCAT-deficiency mutants (T123I and N228K) had nearly normal binding to LDL. In conclusion, the association of LCAT to lipoprotein surfaces is essentially independent of their composition but has a small electrostatic contribution, while dissociation of LCAT from lipoproteins is decreased due to the presence of apoA-I, suggesting protein-protein interactions. Also, the region of LCAT between residues 53 and 71 is essential for interfacial binding.
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Affiliation(s)
- L Jin
- Department of Biochemistry, University of Illinois at Urbana-Champaign 61801, USA
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Böhm HJ, Klebe G. Was läßt sich aus der molekularen Erkennung in Protein-Ligand-Komplexen für das Design neuer Wirkstoffe lernen? Angew Chem Int Ed Engl 1996. [DOI: 10.1002/ange.19961082205] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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