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Tandiana R, Barletta GP, Soler MA, Fortuna S, Rocchia W. Computational Mutagenesis of Antibody Fragments: Disentangling Side Chains from ΔΔ G Predictions. J Chem Theory Comput 2024; 20:2630-2642. [PMID: 38445482 DOI: 10.1021/acs.jctc.3c01225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
The development of highly potent antibodies and antibody fragments as binding agents holds significant implications in fields such as biosensing and biotherapeutics. Their binding strength is intricately linked to the arrangement and composition of residues at the binding interface. Computational techniques offer a robust means to predict the three-dimensional structure of these complexes and to assess the affinity changes resulting from mutations. Given the interdependence of structure and affinity prediction, our objective here is to disentangle their roles. We aim to evaluate independently six side-chain reconstruction methods and ten binding affinity estimation techniques. This evaluation was pivotal in predicting affinity alterations due to single mutations, a key step in computational affinity maturation protocols. Our analysis focuses on a data set comprising 27 distinct antibody/hen egg white lysozyme complexes, each with crystal structures and experimentally determined binding affinities. Using six different side-chain reconstruction methods, we transformed each structure into its corresponding mutant via in silico single-point mutations. Subsequently, these structures undergo minimization and molecular dynamics simulation. We therefore estimate ΔΔG values based on the original crystal structure, its energy-minimized form, and the ensuing molecular dynamics trajectories. Our research underscores the critical importance of selecting reliable side-chain reconstruction methods and conducting thorough molecular dynamics simulations to accurately predict the impact of mutations. In summary, our study demonstrates that the integration of conformational sampling and scoring is a potent approach to precisely characterizing mutation processes in single-point mutagenesis protocols and crucial for computational antibody design.
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Affiliation(s)
- Rika Tandiana
- Computational MOdelling of NanosCalE and BioPhysical SysTems─CONCEPT Lab Istituto Italiano di Tecnologia (IIT), Via Melen-83, B Block, 16152 Genoa, Italy
| | - German P Barletta
- Computational MOdelling of NanosCalE and BioPhysical SysTems─CONCEPT Lab Istituto Italiano di Tecnologia (IIT), Via Melen-83, B Block, 16152 Genoa, Italy
- The Abdus Salam International Centre for Theoretical Physics─ICTP, Strada Costiera 11, 34151 Trieste, Italy
| | - Miguel Angel Soler
- Dipartimento di Scienze Matematiche, Informatiche e Fisiche, Universita' di Udine, Via delle Scienze 206, 33100 Udine, Italy
| | - Sara Fortuna
- Computational MOdelling of NanosCalE and BioPhysical SysTems─CONCEPT Lab Istituto Italiano di Tecnologia (IIT), Via Melen-83, B Block, 16152 Genoa, Italy
| | - Walter Rocchia
- Computational MOdelling of NanosCalE and BioPhysical SysTems─CONCEPT Lab Istituto Italiano di Tecnologia (IIT), Via Melen-83, B Block, 16152 Genoa, Italy
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2
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Zhang D, Chen L, Lin H, Hao T, Wu Y, Xie J, Shi X, Jiang X, Guo Z. Well plate-based LF-NMR/colorimetric dual-mode homogeneous immunosensor for Vibrio parahaemolyticus detection. Food Chem 2024; 436:137757. [PMID: 37890347 DOI: 10.1016/j.foodchem.2023.137757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 09/22/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023]
Abstract
A 96-well plate-based low-field nuclear magnetic resonance (LF-NMR)/colorimetric dual-mode homogeneous immunosensor was developed for the detection of pathogen bacteria, using Vibrio parahaemolyticus (VP) as a detection template. The signal unit MNS@Ab2 is graphene oxide (GO) simultaneously loaded with VP antibody and Fe3O4 nanoparticles. A 96-well plate coated with VP antibody captures the target VP, which then binds the signal unit to form the immunocomplex. After acidolysed, Fe3O4 nanoparticles are transformed into Fe3+ and Fe2+, so the non-homogeneous system is transformed into a homogeneous one. The addition of KMnO4 can not only convert Fe2+ into Fe3+ but also provide Mn2+, improving the detection sensitivity. And, colorimetric analysis can be achieved by the quantitative reduction of KMnO4. Under the optimal experimental conditions, the limit of detection was 60 CFU/mL with good selectivity, stability, precision, accuracy, and consistency, providing a simple and reliable detection platform for pathogenic bacteria in food.
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Affiliation(s)
- Dongyu Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, PR China
| | - Le Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, PR China
| | - Han Lin
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, PR China
| | - Tingting Hao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, PR China
| | - Yangbo Wu
- Faculty of Electrical Engineering and Computer Science, Ningbo University, Ningbo 315211, PR China.
| | - Jianjun Xie
- Faculty of Electrical Engineering and Computer Science, Ningbo University, Ningbo 315211, PR China
| | - Xizhi Shi
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Marine Science, Ningbo University, Ningbo 315211, PR China
| | - Xiaohua Jiang
- School of Materials & Environmental Engineering, Shenzhen Polytechnic, Shenzhen 518055, PR China
| | - Zhiyong Guo
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, PR China.
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3
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Shirani E, Razmjou A, Asadnia M, Nordon RE, Inglis DW. Surface Modification of Polystyrene with Boronic Acid for Immunoaffinity-Based Cell Enrichment. Langmuir 2024; 40:4361-4372. [PMID: 38357828 DOI: 10.1021/acs.langmuir.3c03644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
Obtaining an enriched and phenotypically pure cell population from heterogeneous cell mixtures is important for diagnostics and biosensing. Existing techniques such as fluorescent-activated cell sorting (FACS) and magnetic-activated cell sorting (MACS) require preincubation with antibodies (Ab) and specialized equipment. Cell immunopanning removes the need for preincubation and can be done with no specialized equipment. The majority of the available antibody-mediated analyte capture techniques require a modification to the Abs for binding. In this work, no antibody modification is used because we take advantage of the carbohydrate chain in the Fc region of Ab. We use boronic acid as a cross-linker to bind the Ab to a modified surface. The process allows for functional orientation and cleavable binding of the Ab. In this study, we created an immunoaffinity matrix on polystyrene (PS), an inexpensive and ubiquitous plastic. We observed a 37% increase in Ab binding compared with that of a passive adsorption approach. The method also displayed a more consistent antibody binding with 17 times less variation in Ab loading among replicates than did the passive adsorption approach. Surface topography analysis revealed that a dextran coating reduced nonspecific antibody binding. Elemental analysis (XPS) was used to characterize the surface at different stages and showed that APBA molecules can bind upside-down on the surface. While upside-down antibodies likely remain functional, their elution behavior might differ from those bound in the desired way. Cell capture experiments show that the new surface has 43% better selectivity and 2.4-fold higher capture efficiency compared to a control surface of passively adsorbed Abs. This specific surface chemistry modification will allow the targeted capture of cells or analytes with the option of chemical detachment for further research and characterization.
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Affiliation(s)
- Elham Shirani
- School of Engineering, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Amir Razmjou
- Mineral Recovery Research Center (MRRC), School of Engineering, Edith Cowan University, Joondalup, Perth, Western Australia 6027, Australia
| | - Mohsen Asadnia
- School of Engineering, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Robert E Nordon
- Graduate School of Biomedical Engineering, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - David W Inglis
- School of Engineering, Macquarie University, Sydney, New South Wales 2109, Australia
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4
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Brasiunas B, Popov A, Lisyte V, Kausaite-Minkstimiene A, Ramanaviciene A. ZnO nanostructures: A promising frontier in immunosensor development. Biosens Bioelectron 2024; 246:115848. [PMID: 38042053 DOI: 10.1016/j.bios.2023.115848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 11/01/2023] [Accepted: 11/15/2023] [Indexed: 12/04/2023]
Abstract
This review addresses the design of immunosensors, which employ ZnO nanostructures. Various methods of modifying ZnO nanostructures with antibodies or antigens are discussed, including covalent and non-covalent approaches and cross-linking techniques. Immunosensors based on different properties of ZnO nanomaterials are described and compared. This article provides a comprehensive review of electrochemical immunosensors based on ZnO nanostructures and various detection techniques, including cyclic voltammetry (CV), differential pulse voltammetry (DPV), photoelectrochemical (PEC) detection, electrochemical impedance spectroscopy (EIS), and other electrochemical methods. In addition, this review article examines the application of optical detection techniques, including photoluminescence (PL) and electrochemiluminescence (ECL), in the development of immunosensors based on ZnO nanostructures.
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Affiliation(s)
- Benediktas Brasiunas
- NanoTechnas - Nanotechnology and Materials Science Center, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko St. 24, LT 03225, Vilnius, Lithuania
| | - Anton Popov
- NanoTechnas - Nanotechnology and Materials Science Center, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko St. 24, LT 03225, Vilnius, Lithuania
| | - Viktorija Lisyte
- NanoTechnas - Nanotechnology and Materials Science Center, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko St. 24, LT 03225, Vilnius, Lithuania
| | - Asta Kausaite-Minkstimiene
- NanoTechnas - Nanotechnology and Materials Science Center, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko St. 24, LT 03225, Vilnius, Lithuania
| | - Almira Ramanaviciene
- NanoTechnas - Nanotechnology and Materials Science Center, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko St. 24, LT 03225, Vilnius, Lithuania.
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Wang JJ, van der Neut Kolfschoten M, Rutten L, Armour B, Tan CW, Chataway T, Bos R, Koornneef A, Abeywickrema P, Kapur R, Porcelijn L, Khalifa M, Sadi A, Bouchier P, Kourkouta E, Perkasa A, Kwaks T, Zahn R, Solforosi L, Gordon TP. Characterization of reverse-engineered anti-PF4 stereotypic antibodies derived from serum of patients with VITT. Blood 2024; 143:370-374. [PMID: 37976451 DOI: 10.1182/blood.2023021307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 10/26/2023] [Accepted: 10/31/2023] [Indexed: 11/19/2023] Open
Affiliation(s)
- Jing Jing Wang
- Department of Immunology, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia
- Department of Immunology, SA Pathology, Flinders Medical Centre, Bedford Park, SA, Australia
| | | | - Lucy Rutten
- Janssen Vaccines & Prevention B.V., Leiden, The Netherlands
| | - Bridie Armour
- Department of Immunology, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia
- Department of Immunology, SA Pathology, Flinders Medical Centre, Bedford Park, SA, Australia
| | - Chee Wee Tan
- Department of Medicine, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
- Department of Hematology, SA Pathology, Adelaide, SA, Australia
- Department of Hematology, Royal Adelaide Hospital, Central Area Local Health Network, Adelaide, SA, Australia
| | - Tim Chataway
- Flinders Proteomics Facility, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia
| | - Rinke Bos
- Janssen Vaccines & Prevention B.V., Leiden, The Netherlands
| | | | - Pravien Abeywickrema
- Structural & Protein Sciences, Janssen Research and Development, Spring House, PA
| | - Rick Kapur
- Sanquin Research, Department of Experimental Immunohematology, and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Leendert Porcelijn
- Department of Immunohematology Diagnostics, Sanquin Diagnostic Services, Amsterdam, The Netherlands
| | - Midia Khalifa
- Janssen Vaccines & Prevention B.V., Leiden, The Netherlands
| | - Ava Sadi
- Janssen Vaccines & Prevention B.V., Leiden, The Netherlands
| | | | | | - Aditya Perkasa
- Janssen Vaccines & Prevention B.V., Leiden, The Netherlands
| | - Ted Kwaks
- Janssen Vaccines & Prevention B.V., Leiden, The Netherlands
| | - Roland Zahn
- Janssen Vaccines & Prevention B.V., Leiden, The Netherlands
| | | | - Tom P Gordon
- Department of Immunology, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia
- Department of Immunology, SA Pathology, Flinders Medical Centre, Bedford Park, SA, Australia
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6
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Dang M, Wu L, Jin G, Yang C, Isah MB, Zhang X. Quantum Dot-Based Immunoassays: Unraveling Sensitivity Discrepancies and Charting Future Frontiers. Anal Chem 2024; 96:980-984. [PMID: 38194441 DOI: 10.1021/acs.analchem.3c04791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
The 2023 Nobel Prize in Chemistry honors the groundbreaking contributions of Alexei Ekimov, Louis Brus, and Moungi Bawendi to the field of quantum dots (QDs). In this spirit, we developed a direct competitive QD fluorescence immunoassay (dc-QD-FLISA) to detect aristolochic acid type I (AAI), a potent carcinogen found in herbal remedies. Unexpectedly, the dc-QD-FLISA exhibited lower sensitivity than that of an indirect competitive enzyme-linked immunosorbent assay (ic-ELISA), contrary to our initial expectations. This discrepancy in the sensitivity prompted a comprehensive analysis of the entire experimental process. We propose that steric hindrance between QDs and antigen-binding sites on antibodies may significantly diminish the binding efficiency, reducing sensitivity within the dc-QD-FLISA method. Furthermore, issues such as buffer conditions, antibody handling, and separation methods are also contributing factors. We recommend site-directed QD modification and stringent consideration of the experimental conditions. This study not only provides insights into QD-based immunoassays but also highlights the need for future advancements in immunoassay technology in terms of augmenting sensitivity and specificity, potentially revolutionizing disease diagnosis, biomarker discovery, and biomedical research.
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Affiliation(s)
- Mei Dang
- College of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723000, Shaanxi, China
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 10 Keng Ridge Crescent, 119260 Singapore
| | - Longjiang Wu
- College of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723000, Shaanxi, China
| | - Gelin Jin
- College of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723000, Shaanxi, China
| | - Chenxuan Yang
- College of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723000, Shaanxi, China
| | - Murtala Bindawa Isah
- College of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723000, Shaanxi, China
| | - Xiaoying Zhang
- College of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723000, Shaanxi, China
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, N1G 2W1 Guelph, Ontario, Canada
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7
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Quinchia J, Blázquez-García M, Torrente-Rodríguez RM, Ruiz-Valdepeñas Montiel V, Serafín V, Rejas-González R, Montero-Calle A, Orozco J, Pingarrón JM, Barderas R, Campuzano S. Disposable electrochemical immunoplatform to shed light on the role of the multifunctional glycoprotein TIM-1 in cancer cells invasion. Talanta 2024; 267:125155. [PMID: 37696234 DOI: 10.1016/j.talanta.2023.125155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/24/2023] [Accepted: 09/02/2023] [Indexed: 09/13/2023]
Abstract
Detecting overexpression of cancer biomarkers is an excellent tool for diagnostic/prognostic and follow-up of patients with cancer or their response to treatment. This work illustrates the relevance of interrogating the levels of T-cell immunoglobulin and mucin domain 1 (TIM-1) protein as a diagnostic/prognostic biomarker of high-prevalence breast and lung cancers by using an amperometric disposable magnetic microparticles-assisted immunoplatform. The developed method integrates the inherent advantages of carboxylic acid-functionalized magnetic beads (HOOC-MBs) as pre-concentrator support and the amperometric transduction at screen-printed carbon electrodes (SPCEs). The immunoplatform involves a sandwich-type immunoassay assembled on HOOC-MBs through the specific capture/labeling of TIM-1 using capture antibodies and horseradish peroxidase (HRP)-conjugated biotinylated detection antibodies as biorecognition elements. The magnetic immunoconjugates were confined onto the working electrode (WE) surface of the SPCEs for amperometric detection using the hydroquinone/hydrogen peroxide/HRP (HQ/H2O2/HRP) redox system. The method allows the selective detection of TIM-1 protein over the 87-7500 pg mL-1 concentration range in only 45 min, with a limit of detection of 26 pg mL-1. The developed bioplatform was successfully applied to the analysis of breast and lung cancer cell extracts, providing the first quantitative results of the target glycoprotein in these types of samples.
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Affiliation(s)
- Jennifer Quinchia
- Department of Analytical Chemistry, Faculty of Chemistry, Complutense University of Madrid, Pza. de Las Ciencias 2, 28040, Madrid, Spain; Max Planck Tandem Group in Nanobioengineering, Institute of Chemistry, Faculty of Natural and Exact Sciences, University of Antioquia. Complejo Ruta N, Calle 67 No. 52-20, Medellín, 050010, Colombia
| | - Marina Blázquez-García
- Department of Analytical Chemistry, Faculty of Chemistry, Complutense University of Madrid, Pza. de Las Ciencias 2, 28040, Madrid, Spain
| | - Rebeca M Torrente-Rodríguez
- Department of Analytical Chemistry, Faculty of Chemistry, Complutense University of Madrid, Pza. de Las Ciencias 2, 28040, Madrid, Spain
| | - Víctor Ruiz-Valdepeñas Montiel
- Department of Analytical Chemistry, Faculty of Chemistry, Complutense University of Madrid, Pza. de Las Ciencias 2, 28040, Madrid, Spain
| | - Verónica Serafín
- Department of Analytical Chemistry, Faculty of Chemistry, Complutense University of Madrid, Pza. de Las Ciencias 2, 28040, Madrid, Spain
| | | | - Ana Montero-Calle
- UFIEC, Instituto de Salud Carlos III, 28220, Majadahonda, Madrid, Spain
| | - Jahir Orozco
- Max Planck Tandem Group in Nanobioengineering, Institute of Chemistry, Faculty of Natural and Exact Sciences, University of Antioquia. Complejo Ruta N, Calle 67 No. 52-20, Medellín, 050010, Colombia
| | - José M Pingarrón
- Department of Analytical Chemistry, Faculty of Chemistry, Complutense University of Madrid, Pza. de Las Ciencias 2, 28040, Madrid, Spain
| | - Rodrigo Barderas
- UFIEC, Instituto de Salud Carlos III, 28220, Majadahonda, Madrid, Spain.
| | - Susana Campuzano
- Department of Analytical Chemistry, Faculty of Chemistry, Complutense University of Madrid, Pza. de Las Ciencias 2, 28040, Madrid, Spain.
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Lee SH, Back JH, Joo HJ, Lim DS, Lee JE, Lee HJ. Simultaneous detection method for two cardiac disease protein biomarkers on a single chip modified with mixed aptamers using surface plasmon resonance. Talanta 2024; 267:125232. [PMID: 37806108 DOI: 10.1016/j.talanta.2023.125232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 09/18/2023] [Accepted: 09/21/2023] [Indexed: 10/10/2023]
Abstract
A simultaneous detection method for two cardiac disease protein biomarkers present in serum samples on a single planar gold chip using surface plasmon resonance (SPR) is described. The detection of N-terminal pro-brain natriuretic peptide (NT-proBNP) and tumor necrosis factor α (TNF-α), which are known as acute myocardial infarction (AMI) biomarkers, with predetermined clinically relevant concentrations was performed using mixed aptamers specific to each protein tethered on a single gold surface. After the binding of NT-proBNP and/or TNF-α to the mixed aptamers, an antibody specific to each target protein was injected to form a surface sandwich complex to improve selectivity. In order to adjust the dynamic ranges in the known clinically relevant concentration significantly different for NT-proBNP (0.13-0.24 nM) and TNF-α (0.5-3 pM), the surface density ratios of the corresponding pair of aptamer and antibody were first systematically determined, which were the 1:1 mixed aptamer chip with 40 nM anti-NT-proBNP and 100 nM anti-TNF-α. This allowed to establish the distinct dynamic ranges of 0.05-0.5 nM for NT-proBNP and 0.1-5 pM for TNF-α in a buffer, along with detection and quantification limits of 0.03 and 0.19 nM for NT-proBNP and 0.06 and 0.21 pM for TNF-α, respectively. The changes in refractive unit (RU) values observed when exposing both proteins at different concentrations alongside the corresponding fixed concentration of antibodies onto the 1:1 mixed aptamer chip were then correlated to the sum of RU values measured when using the injection of individual protein for evaluating each protein concentration. With a complete characterization of the simultaneous quantification of two protein concentrations in the buffer, the mixed aptamer chip was finally employed for direct measurements of NT-proBNP and TNF-α concentrations in undiluted serum samples from healthy controls and AMI patients. The results of simultaneous SPR measurements for the two proteins in the serum samples were further compared to the individual protein concentration results using an enzyme-linked immunosorbent assay.
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Affiliation(s)
- Sang Hyuk Lee
- Department of Chemistry and Green-Nano Materials Research Center, Kyungpook National University, 80 Daehakro, Buk-gu, Daegu, 41566, Republic of Korea
| | - Ji Hyun Back
- Chemical & Biological integrative Research Center, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea; Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Hyung Joon Joo
- Department of Cardiology, Cardiovascular Center, College of Medicine, Korea University, Seoul, 02841, Republic of Korea
| | - Do-Sun Lim
- Department of Cardiology, Cardiovascular Center, College of Medicine, Korea University, Seoul, 02841, Republic of Korea
| | - Ji Eun Lee
- Chemical & Biological integrative Research Center, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea
| | - Hye Jin Lee
- Department of Chemistry and Green-Nano Materials Research Center, Kyungpook National University, 80 Daehakro, Buk-gu, Daegu, 41566, Republic of Korea.
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Yin Y, Yajima M, Campbell JD. Characterization and decontamination of background noise in droplet-based single-cell protein expression data with DecontPro. Nucleic Acids Res 2024; 52:e4. [PMID: 37973397 PMCID: PMC10783508 DOI: 10.1093/nar/gkad1032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 09/19/2023] [Accepted: 10/20/2023] [Indexed: 11/19/2023] Open
Abstract
Assays such as CITE-seq can measure the abundance of cell surface proteins on individual cells using antibody derived tags (ADTs). However, many ADTs have high levels of background noise that can obfuscate down-stream analyses. In an exploratory analysis of PBMC datasets, we find that some droplets that were originally called 'empty' due to low levels of RNA contained high levels of ADTs and likely corresponded to neutrophils. We identified a novel type of artifact in the empty droplets called a 'spongelet' which has medium levels of ADT expression and is distinct from ambient noise. ADT expression levels in the spongelets correlate to ADT expression levels in the background peak of true cells in several datasets suggesting that they can contribute to background noise along with ambient ADTs. We then developed DecontPro, a novel Bayesian hierarchical model that can decontaminate ADT data by estimating and removing contamination from these sources. DecontPro outperforms other decontamination tools in removing aberrantly expressed ADTs while retaining native ADTs and in improving clustering specificity. Overall, these results suggest that identification of empty drops should be performed separately for RNA and ADT data and that DecontPro can be incorporated into CITE-seq workflows to improve the quality of downstream analyses.
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Affiliation(s)
- Yuan Yin
- Section of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Masanao Yajima
- Department of Mathematics and Statistics, Boston University, Boston, MA 02115, USA
| | - Joshua D Campbell
- Section of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
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10
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Abanades B, Olsen T, Raybould MJ, Aguilar-Sanjuan B, Wong W, Georges G, Bujotzek A, Deane C. The Patent and Literature Antibody Database (PLAbDab): an evolving reference set of functionally diverse, literature-annotated antibody sequences and structures. Nucleic Acids Res 2024; 52:D545-D551. [PMID: 37971316 PMCID: PMC10767817 DOI: 10.1093/nar/gkad1056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 10/20/2023] [Accepted: 10/30/2023] [Indexed: 11/19/2023] Open
Abstract
Antibodies are key proteins of the adaptive immune system, and there exists a large body of academic literature and patents dedicated to their study and concomitant conversion into therapeutics, diagnostics, or reagents. These documents often contain extensive functional characterisations of the sets of antibodies they describe. However, leveraging these heterogeneous reports, for example to offer insights into the properties of query antibodies of interest, is currently challenging as there is no central repository through which this wide corpus can be mined by sequence or structure. Here, we present PLAbDab (the Patent and Literature Antibody Database), a self-updating repository containing over 150,000 paired antibody sequences and 3D structural models, of which over 65 000 are unique. We describe the methods used to extract, filter, pair, and model the antibodies in PLAbDab, and showcase how PLAbDab can be searched by sequence, structure, or keyword. PLAbDab uses include annotating query antibodies with potential antigen information from similar entries, analysing structural models of existing antibodies to identify modifications that could improve their properties, and facilitating the compilation of bespoke datasets of antibody sequences/structures that bind to a specific antigen. PLAbDab is freely available via Github (https://github.com/oxpig/PLAbDab) and as a searchable webserver (https://opig.stats.ox.ac.uk/webapps/plabdab/).
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Affiliation(s)
- Brennan Abanades
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, 24-29 St Giles’, Oxford OX1 3LB, UK
| | - Tobias H Olsen
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, 24-29 St Giles’, Oxford OX1 3LB, UK
| | - Matthew I J Raybould
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, 24-29 St Giles’, Oxford OX1 3LB, UK
| | - Broncio Aguilar-Sanjuan
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, 24-29 St Giles’, Oxford OX1 3LB, UK
| | - Wing Ki Wong
- Large Molecule Research, Roche Pharma Research and Early Development, Roche Innovation Center Munich, DE-82377 Penzberg, Germany
| | - Guy Georges
- Large Molecule Research, Roche Pharma Research and Early Development, Roche Innovation Center Munich, DE-82377 Penzberg, Germany
| | - Alexander Bujotzek
- Large Molecule Research, Roche Pharma Research and Early Development, Roche Innovation Center Munich, DE-82377 Penzberg, Germany
| | - Charlotte M Deane
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, 24-29 St Giles’, Oxford OX1 3LB, UK
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11
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Tennenhouse A, Khmelnitsky L, Khalaila R, Yeshaya N, Noronha A, Lindzen M, Makowski EK, Zaretsky I, Sirkis YF, Galon-Wolfenson Y, Tessier PM, Abramson J, Yarden Y, Fass D, Fleishman SJ. Computational optimization of antibody humanness and stability by systematic energy-based ranking. Nat Biomed Eng 2024; 8:30-44. [PMID: 37550425 PMCID: PMC10842793 DOI: 10.1038/s41551-023-01079-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 07/13/2023] [Indexed: 08/09/2023]
Abstract
Conventional methods for humanizing animal-derived antibodies involve grafting their complementarity-determining regions onto homologous human framework regions. However, this process can substantially lower antibody stability and antigen-binding affinity, and requires iterative mutational fine-tuning to recover the original antibody properties. Here we report a computational method for the systematic grafting of animal complementarity-determining regions onto thousands of human frameworks. The method, which we named CUMAb (for computational human antibody design; available at http://CUMAb.weizmann.ac.il ), starts from an experimental or model antibody structure and uses Rosetta atomistic simulations to select designs by energy and structural integrity. CUMAb-designed humanized versions of five antibodies exhibited similar affinities to those of the parental animal antibodies, with some designs showing marked improvement in stability. We also show that (1) non-homologous frameworks are often preferred to highest-homology frameworks, and (2) several CUMAb designs that differ by dozens of mutations and that use different human frameworks are functionally equivalent.
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Affiliation(s)
- Ariel Tennenhouse
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Lev Khmelnitsky
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Razi Khalaila
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Noa Yeshaya
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Ashish Noronha
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - Moshit Lindzen
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Emily K Makowski
- Biointerfaces Institute and Departments of Chemical Engineering, Pharmaceutical Sciences and Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Ira Zaretsky
- Antibody Engineering Unit, Weizmann Institute of Science, Rehovot, Israel
| | | | | | - Peter M Tessier
- Biointerfaces Institute and Departments of Chemical Engineering, Pharmaceutical Sciences and Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Jakub Abramson
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yosef Yarden
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Deborah Fass
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Sarel J Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.
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12
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Yang Y, He X, Xu S, Wang D, Liu Z, Xu Z. Post-imprinting modification of molecularly imprinted polymer for proteins detection: A review. Int J Biol Macromol 2023; 253:127104. [PMID: 37769758 DOI: 10.1016/j.ijbiomac.2023.127104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/17/2023] [Accepted: 09/25/2023] [Indexed: 10/02/2023]
Abstract
Inspired by protein post-translational modification (PTM), post-imprinting modification (PIM) has been proposed and developed to prepare novel molecularly imprinted polymers (MIPs), which are similar to functionalized biosynthetic proteins. The PIM involves site-directed modifications in the imprinted cavity of the MIP, such as introducing high-affinity binding sites and introducing fluorescent signal molecules. This modification makes the MIP further functionalized and improves the shortcomings of general molecular imprinting, such as single function, low selectivity, low sensitivity, and inability to fully restore the complex function of natural antibodies. This paper describes the characteristics of PIM strategies, reviews the latest research progress in the recognition and detection of protein biomarkers such as lysozyme, prostate-specific antigen, alpha-fetoprotein, human serum albumin, and peptides, and further discusses the importance, main challenges, and development prospects of PIM. The PIM technology has the potential to develop a new generation of biomimetic recognition materials beyond natural antibodies. It can be used in bioanalysis and other multitudinous fields for its unique features in molecule recognition.
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Affiliation(s)
- Yi Yang
- Faculty of Science, Kunming University of Science and Technology, Kunming 650500, China
| | - Xiaomei He
- Faculty of Science, Kunming University of Science and Technology, Kunming 650500, China
| | - Shufang Xu
- Faculty of Science, Kunming University of Science and Technology, Kunming 650500, China
| | - Dan Wang
- Faculty of Science, Kunming University of Science and Technology, Kunming 650500, China
| | - Zhimin Liu
- Faculty of Science, Kunming University of Science and Technology, Kunming 650500, China.
| | - Zhigang Xu
- Faculty of Science, Kunming University of Science and Technology, Kunming 650500, China.
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13
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Saputri DS, Ismanto HS, Nugraha DK, Xu Z, Horiguchi Y, Sakakibara S, Standley DM. Deciphering the antigen specificities of antibodies by clustering their complementarity determining region sequences. mSystems 2023; 8:e0072223. [PMID: 37975681 PMCID: PMC10734444 DOI: 10.1128/msystems.00722-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 10/06/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE Determining antigen and epitope specificity is an essential step in the discovery of therapeutic antibodies as well as in the analysis adaptive immune responses to disease or vaccination. Despite extensive efforts, deciphering antigen specificity solely from BCR amino acid sequence remains a challenging task, requiring a combination of experimental and computational approaches. Here, we describe and experimentally validate a simple and straightforward approach for grouping antibodies that share antigen and epitope specificities based on their CDR sequence similarity. This approach allows us to identify the specificities of a large number of antibodies whose antigen targets are unknown, using a small fraction of antibodies with well-annotated binding specificities.
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Affiliation(s)
- Dianita S. Saputri
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
- Graduate School of Medicine, Osaka University, Suita, Japan
| | - Hendra S. Ismanto
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Dendi K. Nugraha
- Department of Molecular Bacteriology, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Zichang Xu
- Immunology Frontier Research Center, Osaka University, Suita, Japan
| | - Yasuhiko Horiguchi
- Graduate School of Medicine, Osaka University, Suita, Japan
- Department of Molecular Bacteriology, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
- Center for Infectious Disease Education and Research, Osaka University, Suita, Japan
| | - Shuhei Sakakibara
- Immunology Frontier Research Center, Osaka University, Suita, Japan
- Graduate School of Medical Safety Management, Jikei University of Health Care Sciences, Osaka, Japan
| | - Daron M. Standley
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
- Graduate School of Medicine, Osaka University, Suita, Japan
- Immunology Frontier Research Center, Osaka University, Suita, Japan
- Center for Infectious Disease Education and Research, Osaka University, Suita, Japan
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14
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López de Sá A, Díaz-Tejeiro C, Poyatos-Racionero E, Nieto-Jiménez C, Paniagua-Herranz L, Sanvicente A, Calvo E, Pérez-Segura P, Moreno V, Moris F, Ocana A. Considerations for the design of antibody drug conjugates (ADCs) for clinical development: lessons learned. J Hematol Oncol 2023; 16:118. [PMID: 38087293 PMCID: PMC10717055 DOI: 10.1186/s13045-023-01519-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 12/01/2023] [Indexed: 12/18/2023] Open
Abstract
Antibody-drug conjugates (ADCs) have emerged as a novel therapeutic strategy that has successfully reached patient treatment in different clinical scenarios. ADCs are formed by an antibody against a specific tumor-associated antigen (TAA), a cytotoxic payload, and a chemical linker that binds both. To this regard, most efforts have been focused on target identification, antibody design and linker optimization, but other relevant aspects for clinical development have not received the necessary attention. In this article using data from approved ADCs, we evaluated all characteristics of these agents, including payload physicochemical properties, in vitro potency, drug antibody ratio (DAR), exposure-response relationships, and clinical development strategies. We suggest that compounds with best options for clinical development include those with optimal payload physicochemical properties and cleavable linkers that would lead to a bystander effect. These modalities can facilitate the development of ADCs in indications with low expression of the TAA. Early clinical development strategies including changes in the schedule of administration with more frequent doses are also discussed in the context of an efficient strategy. In conclusion, we highlight relevant aspects that are needed for the optimal development of ADCs in cancer, proposing options for improvement.
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Affiliation(s)
- Alfonso López de Sá
- Medical Oncology Department, Hospital Clínico Universitario San Carlos, Instituto de Investigación Sanitaria San Carlos (IdISSC), and CIBERONC, Madrid, Spain
| | - Cristina Díaz-Tejeiro
- Experimental Therapeutics in Cancer Unit, Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
| | | | - Cristina Nieto-Jiménez
- Experimental Therapeutics in Cancer Unit, Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
| | - Lucía Paniagua-Herranz
- Experimental Therapeutics in Cancer Unit, Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
| | - Adrián Sanvicente
- Experimental Therapeutics in Cancer Unit, Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
- Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Emiliano Calvo
- START Madrid-HM Centro Integral Oncológico Clara Campal (CIOCC), Early Phase Program, HM Sanchinarro University Hospital, Madrid, Spain
| | - Pedro Pérez-Segura
- Medical Oncology Department, Hospital Clínico Universitario San Carlos, Instituto de Investigación Sanitaria San Carlos (IdISSC), and CIBERONC, Madrid, Spain
| | - Víctor Moreno
- START Madrid-Fundación Jiménez Díaz (FJD) Early Phase Program, Fundación Jiménez Díaz Hospital, Madrid, Spain
| | | | - Alberto Ocana
- Medical Oncology Department, Hospital Clínico Universitario San Carlos, Instituto de Investigación Sanitaria San Carlos (IdISSC), and CIBERONC, Madrid, Spain.
- Experimental Therapeutics in Cancer Unit, Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain.
- START Madrid-Fundación Jiménez Díaz (FJD) Early Phase Program, Fundación Jiménez Díaz Hospital, Madrid, Spain.
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15
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Liang S, Zhang C, Zhu M. Ab Initio Prediction of 3-D Conformations for Protein Long Loops with High Accuracy and Applications to Antibody CDRH3 Modeling. J Chem Inf Model 2023; 63:7568-7577. [PMID: 38018130 DOI: 10.1021/acs.jcim.3c01051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023]
Abstract
Residue-level potentials of mean force were widely used for protein backbone refinements to avoid simultaneous sampling of side-chain conformations. The interaction energy between the reduced side chains and backbone atoms was not considered explicitly. In this study, we developed novel methods to calculate the residue-atom interaction energy in combination with atomic and residue-level terms. The parameters were optimized step by step to remove the overcounting or overlap problem between different energy terms. The mixing energy functions were then used to evaluate the generated backbone conformations at the initial sampling stage of protein loop modeling (OSCAR-loop), including the interaction energy between the reduced loop residues and full atoms of the protein framework. The accuracies of top-ranked decoys were 1.18 and 2.81 Å for 8-residue and 12-residue loops, respectively. We then selected diverse decoys for side-chain modeling, backbone refinement, and energy minimization. The procedure was repeated multiple times to select one prediction with the lowest energy. Consequently, we obtained an accuracy of 0.74 Å for a prevailing test set of 12-residue loops, compared with >1.4 Å reported by other researchers. The OSCAR-loop was also effective for modeling the H3 loops of antibody complementary determining regions (CDRs) in the crystal environment. The prediction accuracy of OSCAR-loop (1.74 Å) was better than the accuracy of the Rosetta NGK method (3.11 Å) or those achieved by deep learning methods (>2.2 Å) for the CDRH3 loops of 49 targets in the Rosetta antibody benchmark. The performance of OSCAR-loop in a model environment was also discussed.
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Affiliation(s)
- Shide Liang
- Department of Computational Biology, 20n Bio Limited, Hangzhou 310018, P. R. China
- Department of Research and Development, Bio-Thera Solutions, Guangzhou 510530, P. R. China
| | - Chi Zhang
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska 68588, United States
| | - Mingfu Zhu
- Department of Computational Biology, 20n Bio Limited, Hangzhou 310018, P. R. China
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16
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Ayoubi R, Ryan J, Biddle MS, Alshafie W, Fotouhi M, Bolivar SG, Ruiz Moleon V, Eckmann P, Worrall D, McDowell I, Southern K, Reintsch W, Durcan TM, Brown C, Bandrowski A, Virk H, Edwards AM, McPherson P, Laflamme C. Scaling of an antibody validation procedure enables quantification of antibody performance in major research applications. eLife 2023; 12:RP91645. [PMID: 37995198 PMCID: PMC10666931 DOI: 10.7554/elife.91645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2023] Open
Abstract
Antibodies are critical reagents to detect and characterize proteins. It is commonly understood that many commercial antibodies do not recognize their intended targets, but information on the scope of the problem remains largely anecdotal, and as such, feasibility of the goal of at least one potent and specific antibody targeting each protein in a proteome cannot be assessed. Focusing on antibodies for human proteins, we have scaled a standardized characterization approach using parental and knockout cell lines (Laflamme et al., 2019) to assess the performance of 614 commercial antibodies for 65 neuroscience-related proteins. Side-by-side comparisons of all antibodies against each target, obtained from multiple commercial partners, have demonstrated that: (i) more than 50% of all antibodies failed in one or more applications, (ii) yet, ~50-75% of the protein set was covered by at least one high-performing antibody, depending on application, suggesting that coverage of human proteins by commercial antibodies is significant; and (iii) recombinant antibodies performed better than monoclonal or polyclonal antibodies. The hundreds of underperforming antibodies identified in this study were found to have been used in a large number of published articles, which should raise alarm. Encouragingly, more than half of the underperforming commercial antibodies were reassessed by the manufacturers, and many had alterations to their recommended usage or were removed from the market. This first study helps demonstrate the scale of the antibody specificity problem but also suggests an efficient strategy toward achieving coverage of the human proteome; mine the existing commercial antibody repertoire, and use the data to focus new renewable antibody generation efforts.
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Affiliation(s)
- Riham Ayoubi
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill UniversityMontrealCanada
| | - Joel Ryan
- Advanced BioImaging Facility (ABIF), McGill UniversityMontrealCanada
| | - Michael S Biddle
- NIHR Respiratory BRC, Department of Respiratory Sciences, University of LeicesterLeicesterUnited Kingdom
| | - Walaa Alshafie
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill UniversityMontrealCanada
| | - Maryam Fotouhi
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill UniversityMontrealCanada
| | - Sara Gonzalez Bolivar
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill UniversityMontrealCanada
| | - Vera Ruiz Moleon
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill UniversityMontrealCanada
| | - Peter Eckmann
- Department of Neuroscience, UC San DiegoLa JollaUnited States
| | - Donovan Worrall
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill UniversityMontrealCanada
| | - Ian McDowell
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill UniversityMontrealCanada
| | - Kathleen Southern
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill UniversityMontrealCanada
| | - Wolfgang Reintsch
- The Neuro's Early Drug Discovery Unit (EDDU), Structural Genomics Consortium, McGill UniversityMontrealCanada
| | - Thomas M Durcan
- The Neuro's Early Drug Discovery Unit (EDDU), Structural Genomics Consortium, McGill UniversityMontrealCanada
| | - Claire Brown
- Advanced BioImaging Facility (ABIF), McGill UniversityMontrealCanada
| | | | - Harvinder Virk
- NIHR Respiratory BRC, Department of Respiratory Sciences, University of LeicesterLeicesterUnited Kingdom
| | - Aled M Edwards
- Structural Genomics Consortium, University of TorontoTorontoCanada
| | - Peter McPherson
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill UniversityMontrealCanada
| | - Carl Laflamme
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill UniversityMontrealCanada
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17
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Vessella T, Zhang H, Zhou Z, Cui F, Zhou HS. In-situ synthesized V 2CT x MXene-based immune tag for the electrochemical detection of Interleukin 6 (IL-6) from breast cancer cells. Biosens Bioelectron 2023; 237:115512. [PMID: 37421796 DOI: 10.1016/j.bios.2023.115512] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 06/21/2023] [Accepted: 07/03/2023] [Indexed: 07/10/2023]
Abstract
Interleukin-6 (IL-6) is a proinflammatory cytokine with a critical role in immune regulation and treatment of many diseases, including breast cancer. Herein, we developed a novel V2CTx MXene-based immunosensor for rapid and accurate IL-6 detection. The chosen substrate was V2CTx, a 2-dimensional (2D) MXene nanomaterial with excellent electronic properties. Prussian blue (Fe4[Fe(CN)6]3), used for its electrochemical properties, and spindle-shaped gold nanoparticles (Au SSNPs), used to combine with antibodies, were in-situ synthesized on the surface of the MXene. The in-situ synthesis ensures a firm chemical connection compared to other tags formed by a less stable physical absorption. Inspired by a sandwich ELISA test, the modified V2CTx tag was captured by the electrode surface with cysteamine to detect the analyte, IL-6, after being attached with a capture antibody (cAb). Benefiting from an increased surface area, an enhanced charge transfer rate, and a firm connection of the tag, this biosensor exhibited excellent analytical performance. The high sensitivity, high selectivity, and wide detection range covering the IL-6 level of both healthy individuals and breast cancer patients were obtained to meet clinical demands. Herein, this V2CTx MXene-based immunosensor is a potential therapeutic and diagnostic point-of-care alternative to routine ELISA IL-6 detection methods.
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Affiliation(s)
- Theadora Vessella
- Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, MA, 01609, USA
| | - Hui Zhang
- Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, MA, 01609, USA
| | - Zhiru Zhou
- Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, MA, 01609, USA
| | - Feiyun Cui
- Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, MA, 01609, USA.
| | - Hong Susan Zhou
- Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, MA, 01609, USA.
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18
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Zhao Y, Chudasama V, Baker JR. Trifunctional Dibromomaleimide Reagents Built Around A Lysine Scaffold Deliver Site-selective Dual-modality Antibody Conjugation. Chembiochem 2023; 24:e202300356. [PMID: 37548625 DOI: 10.1002/cbic.202300356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/11/2023] [Indexed: 08/08/2023]
Abstract
We describe the synthesis and application of a selection of trifunctional reagents for the dual-modality modification of native, solvent accessible disulfide bonds in trastuzumab. The reagents were developed from the dibromomaleimide (DBM) platform with two orthogonal clickable functional groups built around a lysine core. We also describe the development of an aryl diselenide additive which enables antibody disulfide reduction in 4 minutes and a rapid overall reduction-bridging-double click sequence.
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Affiliation(s)
- Yanbo Zhao
- Department of Chemistry, University College London, 20 Gordon St, London, WC1H 0AJ, UK
| | - Vijay Chudasama
- Department of Chemistry, University College London, 20 Gordon St, London, WC1H 0AJ, UK
| | - James R Baker
- Department of Chemistry, University College London, 20 Gordon St, London, WC1H 0AJ, UK
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19
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Flajnik MF, Stanfield R, Pokidysheva EN, Boudko SP, Wilson I, Ohta Y. An Ancient MHC-Linked Gene Encodes a Nonrearranging Shark Antibody, UrIg, Convergent with IgG. J Immunol 2023; 211:1042-1051. [PMID: 37540118 PMCID: PMC10530332 DOI: 10.4049/jimmunol.2300361] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 07/12/2023] [Indexed: 08/05/2023]
Abstract
Gnathostome adaptive immunity is defined by the Ag receptors, Igs and TCRs, and the MHC. Cartilaginous fish are the oldest vertebrates with these adaptive hallmarks. We and others have unearthed nonrearranging Ag receptor-like genes in several vertebrates, some of which are encoded in the MHC or in MHC paralogous regions. One of these genes, named UrIg, was detected in the class III region of the shark MHC that encodes a protein with typical V and C domains such as those found in conventional Igs and TCRs. As no transmembrane region was detected in gene models or cDNAs, the protein does not appear to act as a receptor. Unlike some other shark Ig genes, the UrIg V region shows no evidence of RAG-mediated rearrangement, and thus it is likely related to other V genes that predated the invasion of the RAG transposon. The UrIg gene is present in all elasmobranchs and evolves conservatively, unlike Igs and TCRs. Also, unlike Ig/TCR, the gene is not expressed in secondary lymphoid tissues, but mainly in the liver. Recombinant forms of the molecule form disulfide-linked homodimers, which is the form also detected in many shark tissues by Western blotting. mAbs specific for UrIg identify the protein in the extracellular matrix of several shark tissues by immunohistochemistry. We propose that UrIg is related to the V gene invaded by the RAG transposon, consistent with the speculation of emergence of Ig/TCR within the MHC or proto-MHC.
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Affiliation(s)
- Martin F Flajnik
- Department of Microbiology and Immunology, University of Maryland, Baltimore, MD
| | - Robyn Stanfield
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA
| | - Elena N Pokidysheva
- Division of Nephrology and Hypertension, Department of Medicine, Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, TN
| | - Sergei P Boudko
- Division of Nephrology and Hypertension, Department of Medicine, Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, TN
- Department of Biochemistry, Vanderbilt University, Nashville, TN
| | - Ian Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA
| | - Yuko Ohta
- Department of Microbiology and Immunology, University of Maryland, Baltimore, MD
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20
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Erramilli SK, Dominik PK, Deneka D, Tokarz P, Kim SS, Reddy BG, Skrobek BM, Dalmas O, Perozo E, Kossiakoff AA. Conformation-specific Synthetic Antibodies Discriminate Multiple Functional States of the Ion Channel CorA. J Mol Biol 2023; 435:168192. [PMID: 37394032 PMCID: PMC10529903 DOI: 10.1016/j.jmb.2023.168192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/20/2023] [Accepted: 06/26/2023] [Indexed: 07/04/2023]
Abstract
CorA, the primary magnesium ion channel in prokaryotes and archaea, is a prototypical homopentameric ion channel that undergoes ion-dependent conformational transitions. CorA adopts five-fold symmetric non-conductive states in the presence of high concentrations of Mg2+, and highly asymmetric flexible states in its complete absence. However, the latter were of insufficient resolution to be thoroughly characterized. In order to gain additional insights into the relationship between asymmetry and channel activation, we exploited phage display selection strategies to generate conformation-specific synthetic antibodies (sABs) against CorA in the absence of Mg2+. Two sABs from these selections, C12 and C18, showed different degrees of Mg2+-sensitivity. Through structural, biochemical, and biophysical characterization, we found the sABs are both conformation-specific but probe different features of the channel under open-like conditions. C18 is highly specific to the Mg2+-depleted state of CorA and through negative-stain electron microscopy (ns-EM), we show sAB binding reflects the asymmetric arrangement of CorA protomers in Mg2+-depleted conditions. We used X-ray crystallography to determine a structure at 2.0 Å resolution of sAB C12 bound to the soluble N-terminal regulatory domain of CorA. The structure shows C12 is a competitive inhibitor of regulatory magnesium binding through its interaction with the divalent cation sensing site. We subsequently exploited this relationship to capture and visualize asymmetric CorA states in different [Mg2+] using ns-EM. We additionally utilized these sABs to provide insights into the energy landscape that governs the ion-dependent conformational transitions of CorA.
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Affiliation(s)
- Satchal K Erramilli
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Pawel K Dominik
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Dawid Deneka
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Piotr Tokarz
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Sangwoo S Kim
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Bharat G Reddy
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Blazej M Skrobek
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA; Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - Olivier Dalmas
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Eduardo Perozo
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA; Grossman Institute for Neuroscience, Quantitative Biology and Human Behavior, The University of Chicago, Chicago, IL, USA
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA; Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.
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21
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Islam J, Conroy P, Fercher C, Kim M, Yaari Z, Jones M, Bell TDM, Caradoc-Davies T, Law R, Whisstock J, Heller D, Mahler S, Corrie S. Design of Polarity-Dependent Immunosensors Based on the Structural Analysis of Engineered Antibodies. ACS Chem Biol 2023; 18:1863-1871. [PMID: 37440171 DOI: 10.1021/acschembio.3c00303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
"Reagentless" immunosensors are emerging to address the challenge of practical and sensitive detection of important biomarkers in real biological samples without the need for multistep assays and user intervention, with applications ranging from research tools to point-of-care diagnostics. Selective target binding to an affinity reagent is detected and reported in one step without the need for washing or additional reporters. In this study, we used a structure-guided approach to identify a mutation site in an antibody fragment for the polarity-dependent fluorophore, Anap, such that upon binding of the protein target cardiac troponin I, the Anap-labeled antibody would produce a detectable and dose-dependent shift in emission wavelength. We observed a significant emission wavelength shift of the Anap-labeled anti-cTnI mutant, with a blue shift of up to 37 nm, upon binding to the cTnI protein. Key differences in the resulting emission spectra between target peptides in comparison to whole proteins were also found; however, the affinity and binding characteristics remained unaffected when compared to the wild-type antibody. We also highlighted the potential flexibility of the approach by incorporating a near-infrared dye, IRDye800CW, into the same mutation site, which also resulted in a dose-dependent wavelength shift upon target incubation. These reagents can be used in experiments and devices to create simpler and more efficient biosensors across a range of research, medical laboratory, and point-of-care platforms.
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Affiliation(s)
- Jiaul Islam
- Department of Chemical and Biological Engineering, Monash University, Melbourne 3800, Australia
| | - Paul Conroy
- Dept. of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne 3800, Australia
| | - Christian Fercher
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane 4072, Australia
- ARC Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane 4072, Australia
| | - Mijin Kim
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Centre, New York 10065, United States
| | - Zvi Yaari
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Centre, New York 10065, United States
- School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91905, Israel
| | - Martina Jones
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane 4072, Australia
- ARC Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane 4072, Australia
| | - Toby D M Bell
- School of Chemistry, Monash University, Melbourne 3800, Australia
| | - Tom Caradoc-Davies
- Dept. of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne 3800, Australia
- Australian Synchrotron - ANSTO, Melbourne 3168, Australia
| | - Ruby Law
- Dept. of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne 3800, Australia
| | - James Whisstock
- Dept. of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne 3800, Australia
| | - Daniel Heller
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Centre, New York 10065, United States
| | - Stephen Mahler
- Dept. of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne 3800, Australia
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane 4072, Australia
| | - Simon Corrie
- Department of Chemical and Biological Engineering, Monash University, Melbourne 3800, Australia
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22
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Ang YS, Yung LYL. Protein-DNA Conjugates with a Discrete Number of Oligonucleotide Strands for Highly Reproducible Protein Quantification by the DNA Proximity Assay. Anal Chem 2023; 95:12071-12079. [PMID: 37523447 DOI: 10.1021/acs.analchem.3c02033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Protein-oligonucleotide conjugates are increasingly used as detection probes in biological applications such as proximity sensing and spatial biology. The preparation of high-quality conjugate probes as starting reagents is critical for achieving good and consistent performance, which we demonstrate via the DNA proximity assay (DPA) for the one-pot quantification of protein targets. We first established a complete conjugation and anion-exchange chromatography purification workflow to reproducibly obtain pure subpopulations of protein probes carrying a discrete number of oligonucleotide strands. A systematic study using the purified conjugate sub-populations confirmed that the order of conjugate (number of oligonucleotides per protein) and its purity (the absence of the unconjugated antibody) were important for ensuring optimal and reproducible assay performance. The streamlined workflow was then successfully used to conjugate a pair of universal DPA initiator oligonucleotides onto a wide range of binders including antibodies, nanobodies, and antigens which enabled the versatile detection of different types of proteins such as cytokines, total antibodies, and specific antibody isotypes. The good assay robustness (the inter-assay coefficient of variation lower than 5%) and linear calibration curve was achieved across all targets with just a single mix-and-incubate reaction step and a short reaction time of 30 min. We anticipate the streamlined protein-oligonucleotide probe preparation workflow developed in this work to have broad utility across applications leveraging the specificity of protein bio-recognition with the programmability of DNA hybridization.
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Affiliation(s)
- Yan Shan Ang
- Department of Chemical & Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore
| | - Lin-Yue Lanry Yung
- Department of Chemical & Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore
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23
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Liu X, Zhang Y, Li X, Xu J, Zhao C, Yang J. Raman Spectroscopy Combined with Malaria Protein for Early Capture and Recognition of Broad-Spectrum Circulating Tumor Cells. Int J Mol Sci 2023; 24:12072. [PMID: 37569448 PMCID: PMC10419290 DOI: 10.3390/ijms241512072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/22/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
Early identification of tumors can significantly reduce the mortality rate. Circulating tumor cells (CTCs) are a type of tumor cell that detaches from the primary tumor and circulates through the bloodstream. Monitoring CTCs may allow the early identification of tumor progression. However, due to their rarity and heterogeneity, the enrichment and identification of CTCs is still challenging. Studies have shown that Raman spectroscopy could distinguish CTCs from metastatic cancer patients. VAR2CSA, a class of malaria proteins, has a strong broad-spectrum binding effect on various tumor cells and is a promising candidate biomarker for cancer detection. Here, recombinant malaria VAR2CSA proteins were synthesized, expressed, and purified. After confirming that various types of tumor cells can be isolated from blood by recombinant malaria VAR2CSA proteins, we further proved that the VAR2CSA combined with Raman spectroscopy could be used efficiently for tumor capture and type recognition using A549 cell lines spiked into the blood. This would allow the early screening and detection of a broad spectrum of CTCs. Finally, we synthesized and purified the malaria protein fusion antibody and confirmed its in vitro tumor-killing activity. Herein, this paper exploits the theoretical basis of a novel strategy to capture, recognize, and kill broad-spectrum types of CTCs from the peripheral blood.
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Affiliation(s)
- Xinning Liu
- Key Laboratory of Marine Drugs, Ministry of Education, Qingdao Marine Biomedical Research Institute, Ocean University of China, Qingdao 266071, China; (X.L.)
- Innovation Platform of Marine Drug Screening & Evaluation, Qingdao Marine Science and Technology Center, Qingdao 266100, China
| | - Yidan Zhang
- Key Laboratory of Marine Drugs, Ministry of Education, Qingdao Marine Biomedical Research Institute, Ocean University of China, Qingdao 266071, China; (X.L.)
- Innovation Platform of Marine Drug Screening & Evaluation, Qingdao Marine Science and Technology Center, Qingdao 266100, China
| | - Xunrong Li
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100000, China
| | - Jian Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100000, China
| | - Chenyang Zhao
- Key Laboratory of Marine Drugs, Ministry of Education, Qingdao Marine Biomedical Research Institute, Ocean University of China, Qingdao 266071, China; (X.L.)
- Innovation Platform of Marine Drug Screening & Evaluation, Qingdao Marine Science and Technology Center, Qingdao 266100, China
| | - Jinbo Yang
- Key Laboratory of Marine Drugs, Ministry of Education, Qingdao Marine Biomedical Research Institute, Ocean University of China, Qingdao 266071, China; (X.L.)
- Innovation Platform of Marine Drug Screening & Evaluation, Qingdao Marine Science and Technology Center, Qingdao 266100, China
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24
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Das P, Pujals S, Ali LMA, Gary-Bobo M, Albertazzi L, Durand JO. Super-resolution imaging of antibody-conjugated biodegradable periodic mesoporous organosilica nanoparticles for targeted chemotherapy of prostate cancer. Nanoscale 2023; 15:12008-12024. [PMID: 37403617 DOI: 10.1039/d3nr01571h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/06/2023]
Abstract
Biodegradable periodic mesoporous organosilica nanoparticles (nanoPMOs) are widely used as responsive drug delivery platforms for targeted chemotherapy of cancer. However, the evaluation of their properties such as surface functionality and biodegradability is still challenging, which has a significant impact on the efficiency of chemotherapy. In this study, we have applied direct stochastic optical reconstruction microscopy (dSTORM), a single-molecule super-resolution microscopy technique, to quantify the degradation of nanoPMOs triggered by glutathione and the multivalency of antibody-conjugated nanoPMOs. Subsequently, the effect of these properties on cancer cell targeting, drug loading and release capability, and anticancer activity is also studied. Due to the higher spatial resolution at the nanoscale, dSTORM imaging is able to reveal the structural properties (i.e., size and shape) of fluorescent and biodegradable nanoPMOs. The quantification of nanoPMOs' biodegradation using dSTORM imaging demonstrates their excellent structure-dependent degradation behavior at a higher glutathione concentration. The surface functionality of anti-M6PR antibody-conjugated nanoPMOs as quantified by dSTORM imaging plays a key role in prostate cancer cell labeling: oriented antibody is more effective than random ones, while high multivalency is also effective. The higher biodegradability and cancer cell-targeting properties of nanorods conjugated with oriented antibody (EAB4H) effectively deliver the anticancer drug doxorubicin to cancer cells, exhibiting potent anticancer effects.
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Affiliation(s)
- Pradip Das
- Institute Charles Gerhardt Montpellier (ICGM), University of Montpellier, CNRS, ENSCM, Montpellier 34293, France.
- Nanoscopy for Nanomedicine Group, Institute for Bioengineering of Catalonia (IBEC), Barcelona 08036, Spain
| | - Silvia Pujals
- Department of Biological Chemistry, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Barcelona, Spain.
| | - Lamiaa M A Ali
- IBMM, University of Montpellier, CNRS, ENSCM, 34093 Montpellier, France
| | - Magali Gary-Bobo
- IBMM, University of Montpellier, CNRS, ENSCM, 34093 Montpellier, France
| | - Lorenzo Albertazzi
- Nanoscopy for Nanomedicine Group, Institute for Bioengineering of Catalonia (IBEC), Barcelona 08036, Spain
- Department of Biomedical Engineering, Institute of Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Jean-Olivier Durand
- Institute Charles Gerhardt Montpellier (ICGM), University of Montpellier, CNRS, ENSCM, Montpellier 34293, France.
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25
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Suderman RJ, Gibson SD, Strecker M, Bonner AM, Chao DM. Protein engineering of a nanoCLAMP antibody mimetic scaffold as a platform for producing bioprocess-compatible affinity capture ligands. J Biol Chem 2023; 299:104910. [PMID: 37315789 PMCID: PMC10404686 DOI: 10.1016/j.jbc.2023.104910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 05/17/2023] [Accepted: 06/06/2023] [Indexed: 06/16/2023] Open
Abstract
Protein A affinity chromatography is widely used for the large-scale purification of antibodies because of its high yield, selectivity, and compatibility with NaOH sanitation. A general platform to produce robust affinity capture ligands for proteins beyond antibodies would improve bioprocessing efficiency. We previously developed nanoCLAMPs (nano Clostridial Antibody Mimetic Proteins), a class of antibody mimetic proteins useful as lab-scale affinity capture reagents. This work describes a protein engineering campaign to develop a more robust nanoCLAMP scaffold compatible with harsh bioprocessing conditions. The campaign generated an improved scaffold with dramatically improved resistance to heat, proteases, and NaOH. To isolate additional nanoCLAMPs based on this scaffold, we constructed a randomized library of 1 × 1010 clones and isolated binders to several targets. We then performed an in-depth characterization of nanoCLAMPs recognizing yeast SUMO, a fusion partner used for the purification of recombinant proteins. These second-generation nanoCLAMPs typically had a Kd of <80 nM, a Tm of >70 °C, and a t1/2 in 0.1 mg/ml trypsin of >20 h. Affinity chromatography resins bearing these next-generation nanoCLAMPs enabled single-step purifications of SUMO fusions. Bound target proteins could be eluted at neutral or acidic pH. These affinity resins maintained binding capacity and selectivity over 20 purification cycles, each including 10 min of cleaning-in-place with 0.1 M NaOH, and remained functional after exposure to 100% DMF and autoclaving. The improved nanoCLAMP scaffold will enable the development of robust, high-performance affinity chromatography resins against a wide range of protein targets.
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Affiliation(s)
| | - Shane D Gibson
- Nectagen, Inc, Kansas City, Kansas, USA; University of Washington, Seattle, Washington, USA
| | - Mary Strecker
- Nectagen, Inc, Kansas City, Kansas, USA; Two Dot Consulting, Arvada, Colorado, USA
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26
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Das R, Dey A, Uppal S. A method for in situ visualization of Protein-Nascent RNA interactions in single cell using Proximity Ligation Assay (IPNR-PLA) in mammalian cells. Transcription 2023; 14:146-157. [PMID: 36927323 PMCID: PMC10807467 DOI: 10.1080/21541264.2023.2190296] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 03/06/2023] [Accepted: 03/08/2023] [Indexed: 03/18/2023] Open
Abstract
Proximity ligation assay (PLA) is an immunofluorescence assay, which determines in situ interaction of two biomolecules present within 40 nm close proximity. Here, we describe a modification of PLA for visual detection of in situ protein interactions with nascent RNA in a single cell (IPNR-PLA). In IPNR-PLA, nascent RNA is labeled by incorporating 5-fluorouridine (FU), a uridine nucleotide analogue, followed by covalent cross-linking of the interacting partners in proximity to newly synthesized RNA. By using combination of anti-BrdU antibody, which specifically binds to FU, and primary antibody against a protein of interest, the IPNR reaction results in fluorescent puncta as a positive signal, only if the candidate proteins are in proximity to nascent RNA. We have validated this method by demonstrating known CDK9 and elongating RNA pol II interaction with nascent RNA. Finally, we used this method to test for the presence of DNA double strand breaks as well as Poly (ADP-ribose) polymerase 1 (PARP1), an RNA binding protein, in the vicinity of nascent RNA in cancer cells. The capability of performing parallel IF labeling and quantifiable multiparameter measurements within heterogeneous cell populations makes IPNR-PLA very attractive for use in biological studies. Overall, we have developed the IPNR-PLA method for analysis of protein association with nascent RNA with single-cell resolution, which is highly sensitive, quantitative, efficient, and requires little starting experimental material.
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Affiliation(s)
- Rituparna Das
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay,Mumbai, India
- Life Sciences, Homi Bhabha National Institute, Anushakti Nagar, Mumbai, India
| | - Anusree Dey
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay,Mumbai, India
- Life Sciences, Homi Bhabha National Institute, Anushakti Nagar, Mumbai, India
| | - Sheetal Uppal
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay,Mumbai, India
- Life Sciences, Homi Bhabha National Institute, Anushakti Nagar, Mumbai, India
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27
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Chen W, Liu F, Zhang C, Duan Y, Ma J, Wang Y, Chen G. A review of advances in aptamer-based cell detection technology. Mol Biol Rep 2023; 50:5425-5438. [PMID: 37101007 DOI: 10.1007/s11033-023-08410-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 03/24/2023] [Indexed: 04/28/2023]
Abstract
Since cells are the basic structural and functional units of organisms, the detection or quantitation of cells is one of the most common basic problems in life science research. The established cell detection techniques mainly include fluorescent dye labeling, colorimetric assay, and lateral flow assay, all of which employ antibodies as cell recognition elements. However, the widespread application of the established methods generally dependent on antibodies is limited, because the preparation of antibodies is complicated and time-consuming, and unrecoverable denaturation is prone to occur with antibodies. By contrast, aptamers that are generally selected through the systematic evolution of ligands by exponential enrichment can avoid the disadvantages of antibodies due to their controllable synthesis, thermostability, and long shelf life, etc. Accordingly, aptamers may serve as novel molecular recognition elements like antibodies in combination with various techniques for cell detection. This paper reviews the developed aptamer-based cell detection methods, mainly including aptamer-fluorescent labeling, aptamer-isothermal amplification assay, electrochemical aptamer sensor, aptamer-based lateral flow analysis, and aptamer-colorimetric assay. The principles, advantages, progress of application in cell detection and future development trend of these methods were specially discussed. Overall, different assays are suitable for different detection purposes, and the development of more accurate, economical, efficient, and rapid aptamer-based cell detection methods is always on the road in the future. This review is expected to provide a reference for achieving efficient and accurate detection of cells as well as improving the usefulness of aptamers in the field of analytical applications.
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Affiliation(s)
- Wenrong Chen
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Wenhua West Road, 2#, Weihai, 264209, PR China
| | - Fuguo Liu
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Wenhua West Road, 2#, Weihai, 264209, PR China
- School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China
| | - Chunyun Zhang
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Wenhua West Road, 2#, Weihai, 264209, PR China.
| | - Yu Duan
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Wenhua West Road, 2#, Weihai, 264209, PR China
- School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China
| | - Jinju Ma
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Wenhua West Road, 2#, Weihai, 264209, PR China
- School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China
| | - Yuanyuan Wang
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Wenhua West Road, 2#, Weihai, 264209, PR China
| | - Guofu Chen
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Wenhua West Road, 2#, Weihai, 264209, PR China.
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28
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Calcaterra A, Polli F, Lamelza L, Del Plato C, Cammarone S, Ghirga F, Botta B, Mazzei F, Quaglio D. Resorc[4]arene-Modified Gold-Decorated Magnetic Nanoparticles for Immunosensor Development. Bioconjug Chem 2023; 34:529-537. [PMID: 36753752 PMCID: PMC10020960 DOI: 10.1021/acs.bioconjchem.2c00605] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
In recent years, several efforts have been made to develop selective, sensitive, fast response, and miniaturized immunosensors with improved performance for the monitoring and screening of analytes in several matrices, significantly expanding the use of this technology in a broad range of applications. However, one of the main technical challenges in developing immunosensors is overcoming the complexity of binding antibodies (Abs) to the sensor surface. Most immobilizing approaches lead to a random orientation of Abs, resulting in lower binding site density and immunoaffinity. In this context, supramolecular chemistry has emerged as a suitable surface modification tool to achieve the preorganization of artificial receptors and to improve the functional properties of self-assembled monolayers. Herein, a supramolecular chemistry/nanotechnology-based platform was conceived to develop sensitive label-free electrochemical immunosensors, by using a resorcarene macrocycle as an artificial linker for the oriented antibody immobilization. To this aim, a water-soluble bifunctional resorc[4]arene architecture (RW) was rationally designed and synthesized to anchor gold-coated magnetic nanoparticles (Au@MNPs) and to maximize the amount of the active immobilized antibody (Ab) in the proper "end-on" orientation. The resulting supramolecular chemistry-modified nanoparticles, RW@Au@MNPs, were deposited onto graphite screen printed electrodes which were then employed to immobilize three different Abs. Furthermore, an immunosensor for atrazine (ATZ) analysis was realized and characterized by the differential pulse voltammetry technique to demonstrate the validity of the developed biosensing platform as a proof of concept for electrochemical immunosensors. The RW-based immunosensor improved AbATZ loading on Au@MNPs and sensitivity toward ATZ by almost 1.5 times compared to the random platform. Particularly, the electrochemical characterization of the developed immunosensor displays a linearity range toward ATZ within 0.05-1.5 ng/mL, a limit of detection of 0.011 ng/ml, and good reproducibility and stability. The immunosensor was tested by analyzing spiked fortified water samples with a mean recovery ranging from 95.7 to 108.4%. The overall good analytical performances of this immunodevice suggest its application for the screening and monitoring of ATZ in real matrices. Therefore, the results highlighted the successful application of the resorc[4]arene-based sensor design strategy for developing sensitive electrochemical immunosensors with improved analytical performance and simplifying the Ab immobilization procedure.
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29
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Tse Sum Bui B, Mier A, Haupt K. Molecularly Imprinted Polymers as Synthetic Antibodies for Protein Recognition: The Next Generation. Small 2023; 19:e2206453. [PMID: 36650929 DOI: 10.1002/smll.202206453] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/27/2022] [Indexed: 06/17/2023]
Abstract
Molecularly imprinted polymers (MIPs) are chemical antibody mimics obtained by nanomoulding the 3D shape and chemical functionalities of a desired target in a synthetic polymer. Consequently, they possess exquisite molecular recognition cavities for binding the target molecule, often with specificity and affinity similar to those of antigen-antibody interactions. Research on MIPs targeting proteins began in the mid-90s, and this review will evaluate the progress made till now, starting from their synthesis in a monolith bulk format through surface imprinting to biocompatible soluble nanogels prepared by solid-phase synthesis. MIPs in the latter format will be discussed more in detail because of their tremendous potential of replacing antibodies in the biomedical domain like in diagnostics and therapeutics, where the workforce of antibodies is concentrated. Emphasis is also put on the development of epitope imprinting, which consists of imprinting a short surface-exposed fragment of a protein, resulting in MIPs capable of selectively recognizing the whole macromolecule, amidst others in complex biological media, on cells or tissues. Thus selecting the 'best' peptide antigen is crucial and in this context a rational approach, inspired from that used to predict peptide immunogens for peptide antibodies, is described for its unambiguous identification.
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Affiliation(s)
- Bernadette Tse Sum Bui
- Université de Technologie de Compiègne, CNRS Laboratory for Enzyme and Cell Engineering, Rue du Docteur Schweitzer, CS 60319, Compiègne, 60203 Cedex, France
| | - Alejandra Mier
- Université de Technologie de Compiègne, CNRS Laboratory for Enzyme and Cell Engineering, Rue du Docteur Schweitzer, CS 60319, Compiègne, 60203 Cedex, France
| | - Karsten Haupt
- Université de Technologie de Compiègne, CNRS Laboratory for Enzyme and Cell Engineering, Rue du Docteur Schweitzer, CS 60319, Compiègne, 60203 Cedex, France
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30
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Plikusiene I, Ramanaviciene A. Investigation of Biomolecule Interactions: Optical-, Electrochemical-, and Acoustic-Based Biosensors. Biosensors (Basel) 2023; 13:bios13020292. [PMID: 36832058 PMCID: PMC9954023 DOI: 10.3390/bios13020292] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 02/16/2023] [Indexed: 05/24/2023]
Abstract
Today, optical, electrochemical, and acoustic affinity biosensors; immunosensors; and immunoanalytical systems play an important role in the detection and characterization of a number of biological substances, including viral antigens, specific antibodies, and clinically important biomarkers [...].
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Affiliation(s)
- Ieva Plikusiene
- NanoTechnas—Center of Nanotechnology and Materials Science, Faculty of Chemistry and Geosciences, Vilnius University, LT-03225 Vilnius, Lithuania
- State Research Institute Center for Physical Sciences and Technology, LT-10257 Vilnius, Lithuania
| | - Almira Ramanaviciene
- NanoTechnas—Center of Nanotechnology and Materials Science, Faculty of Chemistry and Geosciences, Vilnius University, LT-03225 Vilnius, Lithuania
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31
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Seidler CA, Kokot J, Fernández-Quintero ML, Liedl KR. Structural Characterization of Nanobodies during Germline Maturation. Biomolecules 2023; 13:380. [PMID: 36830754 PMCID: PMC9953242 DOI: 10.3390/biom13020380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/27/2023] [Accepted: 02/14/2023] [Indexed: 02/22/2023] Open
Abstract
Camelid heavy-chain antibody variable domains (VHH), nanobodies, are the smallest-known functional antibody fragments with high therapeutic potential. In this study, we investigate a VHH binding to hen egg-white lysozyme (HEL). We structurally and dynamically characterized the conformational diversity of four VHH variants to elucidate the antigen-binding process. For two of these antibodies, not only are the dissociation constants known, but also the experimentally determined crystal structures of the VHH in complex with HEL are available. We performed well-tempered metadynamics simulations in combination with molecular dynamics simulations to capture a broad conformational space and to reconstruct the thermodynamics and kinetics of conformational transitions in the antigen-binding site, the paratope. By kinetically characterizing the loop movements of the paratope, we found that, with an increase in affinity, the state populations shift towards the binding competent conformation. The contacts contributing to antigen binding, and those who contribute to the overall stability, show a clear trend towards less variable but more intense contacts. Additionally, these investigated nanobodies clearly follow the conformational selection paradigm, as the binding competent conformation pre-exists within the structural ensembles without the presence of the antigen.
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Affiliation(s)
| | | | - Monica L. Fernández-Quintero
- Department of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria
| | - Klaus R. Liedl
- Department of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria
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Desta IT, Kotelnikov S, Jones G, Ghani U, Abyzov M, Kholodov Y, Standley DM, Sabitova M, Beglov D, Vajda S, Kozakov D. Mapping of antibody epitopes based on docking and homology modeling. Proteins 2023; 91:171-182. [PMID: 36088633 PMCID: PMC9822860 DOI: 10.1002/prot.26420] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/25/2022] [Accepted: 09/06/2022] [Indexed: 01/11/2023]
Abstract
Antibodies are key proteins produced by the immune system to target pathogen proteins termed antigens via specific binding to surface regions called epitopes. Given an antigen and the sequence of an antibody the knowledge of the epitope is critical for the discovery and development of antibody based therapeutics. In this work, we present a computational protocol that uses template-based modeling and docking to predict epitope residues. This protocol is implemented in three major steps. First, a template-based modeling approach is used to build the antibody structures. We tested several options, including generation of models using AlphaFold2. Second, each antibody model is docked to the antigen using the fast Fourier transform (FFT) based docking program PIPER. Attention is given to optimally selecting the docking energy parameters depending on the input data. In particular, the van der Waals energy terms are reduced for modeled antibodies relative to x-ray structures. Finally, ranking of antigen surface residues is produced. The ranking relies on the docking results, that is, how often the residue appears in the docking poses' interface, and also on the energy favorability of the docking pose in question. The method, called PIPER-Map, has been tested on a widely used antibody-antigen docking benchmark. The results show that PIPER-Map improves upon the existing epitope prediction methods. An interesting observation is that epitope prediction accuracy starting from antibody sequence alone does not significantly differ from that of starting from unbound (i.e., separately crystallized) antibody structure.
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Affiliation(s)
- Israel T. Desta
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Sergei Kotelnikov
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA
| | - George Jones
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Usman Ghani
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | | | | | - Daron M. Standley
- Department of Genome Informatics, Osaka University, Osaka, 565-0871, Japan
- Center for Infectious Disease Education and Research, Osaka University, Osaka, 565-0871, Japan
| | - Maria Sabitova
- Department of Mathematics, CUNY Queens College, Flushing, NY 11367, USA
| | - Dmitri Beglov
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Sandor Vajda
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Dima Kozakov
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA
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Benešová M, Bernatová S, Mika F, Pokorná Z, Ježek J, Šiler M, Samek O, Růžička F, Rebrošová K, Zemánek P, Pilát Z. SERS-Tags: Selective Immobilization and Detection of Bacteria by Strain-Specific Antibodies and Surface-Enhanced Raman Scattering. Biosensors (Basel) 2023; 13:182. [PMID: 36831948 PMCID: PMC9954015 DOI: 10.3390/bios13020182] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/16/2023] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
Efficient separation and sensitive identification of pathogenic bacterial strains is essential for a prosperous modern society, with direct applications in medical diagnostics, drug discovery, biodefense, and food safety. We developed a fast and reliable method for antibody-based selective immobilization of bacteria from suspension onto a gold-plated glass surface, followed by detection using strain-specific antibodies linked to gold nanoparticles decorated with a reporter molecule. The reporter molecules are subsequently detected by surface-enhanced Raman spectroscopy (SERS). Such a multi-functionalized nanoparticle is called a SERS-tag. The presented procedure uses widely accessible and cheap materials for manufacturing and functionalization of the nanoparticles and the immobilization surfaces. Here, we exemplify the use of the produced SERS-tags for sensitive single-cell detection of opportunistic pathogen Escherichia coli, and we demonstrate the selectivity of our method using two other bacterial strains, Staphylococcus aureus and Serratia marcescens, as negative controls. We believe that the described approach has a potential to inspire the development of novel medical diagnostic tools for rapid identification of bacterial pathogens.
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Affiliation(s)
- Markéta Benešová
- Institute of Scientific Instruments of the Czech Academy of Sciences, v.v.i., Královopolská 147, 612 64 Brno, Czech Republic
| | - Silvie Bernatová
- Institute of Scientific Instruments of the Czech Academy of Sciences, v.v.i., Královopolská 147, 612 64 Brno, Czech Republic
| | - Filip Mika
- Institute of Scientific Instruments of the Czech Academy of Sciences, v.v.i., Královopolská 147, 612 64 Brno, Czech Republic
| | - Zuzana Pokorná
- Institute of Scientific Instruments of the Czech Academy of Sciences, v.v.i., Královopolská 147, 612 64 Brno, Czech Republic
| | - Jan Ježek
- Institute of Scientific Instruments of the Czech Academy of Sciences, v.v.i., Královopolská 147, 612 64 Brno, Czech Republic
| | - Martin Šiler
- Institute of Scientific Instruments of the Czech Academy of Sciences, v.v.i., Královopolská 147, 612 64 Brno, Czech Republic
| | - Ota Samek
- Institute of Scientific Instruments of the Czech Academy of Sciences, v.v.i., Královopolská 147, 612 64 Brno, Czech Republic
| | - Filip Růžička
- Department of Microbiology, Faculty of Medicine of Masaryk University and St. Anne’s University Hospital, Pekařská 53, 656 91 Brno, Czech Republic
| | - Katarina Rebrošová
- Department of Microbiology, Faculty of Medicine of Masaryk University and St. Anne’s University Hospital, Pekařská 53, 656 91 Brno, Czech Republic
| | - Pavel Zemánek
- Institute of Scientific Instruments of the Czech Academy of Sciences, v.v.i., Královopolská 147, 612 64 Brno, Czech Republic
| | - Zdeněk Pilát
- Institute of Scientific Instruments of the Czech Academy of Sciences, v.v.i., Královopolská 147, 612 64 Brno, Czech Republic
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Lee FS, Anderson AG, Olafson BD. Benchmarking TriadAb using targets from the second antibody modeling assessment. Protein Eng Des Sel 2023; 36:gzad013. [PMID: 37864287 DOI: 10.1093/protein/gzad013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 08/10/2023] [Indexed: 10/22/2023] Open
Abstract
Computational modeling and design of antibodies has become an integral part of today's research and development in antibody therapeutics. Here we describe the Triad Antibody Homology Modeling (TriadAb) package, a functionality of the Triad protein design platform that predicts the structure of any heavy and light chain sequences of an antibody Fv domain using template-based modeling. To gauge the performance of TriadAb, we benchmarked against the results of the Second Antibody Modeling Assessment (AMA-II). On average, TriadAb produced main-chain carbonyl root-mean-square deviations between models and experimentally determined structures at 1.10 Å, 1.45 Å, 1.41 Å, 3.04 Å, 1.47 Å, 1.27 Å, 1.63 Å in the framework and the six complementarity-determining regions (H1, H2, H3, L1, L2, L3), respectively. The inaugural results are comparable to those reported in AMA-II, corroborating with our internal bench-based experiences that models generated using TriadAb are sufficiently accurate and useful for antibody engineering using the sequence design capabilities provided by Triad.
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Yang W, Seo J, Kim JH. Protein-mimetic peptoid nanoarchitectures for pathogen recognition and neutralization. Nanoscale 2023; 15:975-986. [PMID: 36541218 DOI: 10.1039/d2nr05326h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Recent outbreaks of both new and existing infectious pathogens have threatened healthcare systems around the world. Therefore, it is vital to detect and neutralize pathogens to prevent their spread and treat infected patients. This consideration has led to the development of biosensors and antibiotics inspired by the structure and function of antibodies and antimicrobial peptides (AMPs), which constitute adaptive and innate immunity, efficiently protecting the human body against invading pathogens. Herein, we provide an overview of recent advances in the detection and neutralization of pathogens using protein-mimetic peptoid nanoarchitectures. Peptoids are bio-inspired and sequence-defined polymers composed of repeating N-substituted glycine units. They can spontaneously fold into well-defined three-dimensional nanostructures that encode chemical information depending on their sequences. Loop-functionalized peptoid nanosheets have been constructed by mimicking antibodies containing chemically variable loops as binding motifs for their respective target pathogen. Furthermore, by mimicking the cationic amphipathic features of natural AMPs, helical peptoids and their assemblies have been developed to achieve selective anti-infective activity owing to their intrinsic ability to interact with bacterial membranes and viral envelopes. We believe that this mini-review furnishes in-depth insight into how to construct protein-like nanostructures via the self-assembly of peptoids for application in the detection of pathogens and the treatment of infectious diseases for future healthcare applications.
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Affiliation(s)
- Woojin Yang
- Soft Hybrid Materials Research Center, Korea Institute of Science and Technology, 5 Hwarang-ro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea.
| | - Jiwon Seo
- Department of Chemistry, Gwangju Institute of Science and Technology, 123 Cheomdan-gwagiro, Buk-gu, Gwangju 61005, Republic of Korea.
| | - Jae Hong Kim
- Soft Hybrid Materials Research Center, Korea Institute of Science and Technology, 5 Hwarang-ro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea.
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36
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Smith CA, Sonneson GJ, Hoey RJ, Hinerman JM, Sheehy K, Walter R, Herr AB, Horn JR. Molecular recognition requires dimerization of a VHH antibody. MAbs 2023; 15:2215363. [PMID: 37243579 PMCID: PMC10228392 DOI: 10.1080/19420862.2023.2215363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 05/02/2023] [Accepted: 05/15/2023] [Indexed: 05/29/2023] Open
Abstract
Camelid heavy-chain-only antibodies are a unique class of antibody that possesses only a single variable domain (termed VHH) for antigen recognition. Despite their apparent canonical mechanism of target recognition, where a single VHH domain binds a single target, an anti-caffeine VHH has been observed to possess 2:1 stoichiometry. Here, the structure of the anti-caffeine VHH/caffeine complex enabled the generation and biophysical analysis of variants that were used to better understand the role of VHH homodimerization in caffeine recognition. VHH interface mutants and caffeine analogs, which were examined to probe the mechanism of caffeine binding, suggested caffeine recognition is only possible with the VHH dimer species. Correspondingly, in the absence of caffeine, the anti-caffeine VHH was found to form a dimer with a dimerization constant comparable to that observed with VH:VL domains in conventional antibody systems, which was most stable near physiological temperature. While the VHH:VHH dimer structure (at 1.13 Å resolution) is reminiscent of conventional VH:VL heterodimers, the homodimeric VHH possesses a smaller angle of domain interaction, as well as a larger amount of apolar surface area burial. To test the general hypothesis that the short complementarity-determining region-3 (CDR3) may help drive VHH:VHH homodimerization, an anti-picloram VHH domain containing a short CDR3 was generated and characterized, which revealed it also existed as dimer species in solution. These results suggest homodimer-driven recognition may represent a more common method of VHH ligand recognition, opening opportunities for novel VHH homodimer affinity reagents and helping to guide their use in chemically induced dimerization applications.
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Affiliation(s)
- Christopher A. Smith
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL, USA
| | - Gregory J. Sonneson
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL, USA
| | - Robert J. Hoey
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL, USA
| | - Jennifer M. Hinerman
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
| | - Kimberly Sheehy
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL, USA
| | - Richard Walter
- Shamrock Structures, LLC, Woodridge, IL, USA
- Joliet XTALPAC LLC, USA
| | - Andrew B. Herr
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH USA
| | - James R. Horn
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL, USA
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Patel R, Verma P, Nagraj AK, Gavade A, Sharma OP, Patil J. Significance of antibody numbering systems in the development of antibody engineering. Hum Antibodies 2023; 31:71-80. [PMID: 38217590 DOI: 10.3233/hab-230014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2024]
Abstract
Immunotherapy has become increasingly popular in recent years for treating a variety of diseases including inflammatory, neurological, oncological, and auto-immune disorders. The significant interest in antibody development is due to the high binding affinity and specificity of an antibody against a specific antigen. Recent advances in antibody engineering have provided a different view on how to engineer antibodies in silico for therapeutic and diagnostic applications. In order to improve the clinical utility of therapeutic antibodies, it is of paramount importance to understand the various molecular properties which impact antigen targeting and its potency. In antibody engineering, antibody numbering (AbN) systems play an important role to identify the complementarity determining regions (CDRs) and the framework regions (FR). Hence, it is crucial to accurately define and understand the CDR, FR and the crucial residues of heavy and light chains that aid in the binding of the antibody to the antigenic site. Detailed understanding of amino acids positions are useful for modifying the binding affinity, specificity, physicochemical features, and half-life of an antibody. In this review, we have summarized the different antibody numbering systems that are widely used in antibody engineering and highlighted their significance. Here, we have systematically explored and mentioned the various tools and servers that harness different AbN systems.
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Affiliation(s)
- Riya Patel
- Innoplexus Consulting Services Pvt Ltd, Pune, Maharashtra, India
| | - Pratibha Verma
- Innoplexus Consulting Services Pvt Ltd, Pune, Maharashtra, India
| | | | - Akshata Gavade
- Innoplexus Consulting Services Pvt Ltd, Pune, Maharashtra, India
| | | | - Jaspal Patil
- Innoplexus Consulting Services Pvt Ltd, Pune, Maharashtra, India
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38
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Mejias-Gomez O, Madsen AV, Skovgaard K, Pedersen LE, Morth JP, Jenkins TP, Kristensen P, Goletz S. A window into the human immune system: comprehensive characterization of the complexity of antibody complementary-determining regions in functional antibodies. MAbs 2023; 15:2268255. [PMID: 37876265 PMCID: PMC10601506 DOI: 10.1080/19420862.2023.2268255] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 10/04/2023] [Indexed: 10/26/2023] Open
Abstract
The human immune system uses antibodies to neutralize foreign antigens. They are composed of heavy and light chains, both with constant and variable regions. The variable region has six hypervariable loops, also known as complementary-determining regions (CDRs) that determine antibody diversity and antigen specificity. Knowledge of their significance, and certain residues present in these areas, is vital for antibody therapeutics development. This study includes an analysis of more than 11,000 human antibody sequences from the International Immunogenetics information system (IMGT). The analysis included parameters such as length distribution, overall amino acid diversity, amino acid frequency per CDR and residue position within antibody chains. Overall, our findings confirm existing knowledge, such as CDRH3's high length diversity and amino acid variability, increased aromatic residue usage, particularly tyrosine, charged and polar residues like aspartic acid, serine, and the flexible residue glycine. Specific residue positions within each CDR influence these occurrences, implying a unique amino acid type distribution pattern. We compared amino acid type usage in CDRs and non-CDR regions, both in globular and transmembrane proteins, which revealed distinguishing features, such as increased frequency of tyrosine, serine, aspartic acid, and arginine. These findings should prove useful for future optimization, improvement of affinity, synthetic antibody library design, or the creation of antibodies de-novo in silico.
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Affiliation(s)
- Oscar Mejias-Gomez
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Andreas V. Madsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Kerstin Skovgaard
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Lasse E. Pedersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - J. Preben Morth
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Timothy P. Jenkins
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Peter Kristensen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Steffen Goletz
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
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Marin FI, Marcatili P. Computational Modeling of Antibody and T-Cell Receptor (CDR3 Loops). Methods Mol Biol 2023; 2552:83-100. [PMID: 36346586 DOI: 10.1007/978-1-0716-2609-2_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Antibodies and T-cell receptors have been a subject of much interest due to their central role in the immune system and their potential applications in several biotechnological and medical applications from cancer therapy to vaccine development. A unique feature of these two lymphocyte receptors is their ability to bind a huge variety of different (pathogen) targets. This ability stems from six short loops in the binding domain that have hypervariable sequence due to genetic recombination mechanism. Particularly one of these loops, the third complementarity determining region (CDR3), has the highest sequence variability and a dominant role in binding the target. However, it has also been proven the most difficult to be modeled structurally, which is vitally important for downstream tasks such as binding prediction. This difficulty stems from its variability in sequence that both reduces the possibility of finding homologues and introduces unique structural features in the loop. We present here a general protocol for modeling such loops in antibodies and T-cell receptors. We also discuss the difficulties in loop modeling and the advantages and limitations of different modeling methods.
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Affiliation(s)
- Frederikke I Marin
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Paolo Marcatili
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark.
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40
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Sarker AH, Cooper PK. Slot Blot Assay for Detection of R Loops. Methods Mol Biol 2023; 2701:149-156. [PMID: 37574480 DOI: 10.1007/978-1-0716-3373-1_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
R loops (DNA-RNA hybrid) are three-stranded nucleic acid structures that comprise of template DNA strand hybridized with the nascent RNA leaving the displaced non-template strand. Although a programmed R loop formation can serve as powerful regulators of gene expression, these structures can also turn into major sources of genomic instability and contribute to the development of diseases. Therefore, understanding how cells prevent the deleterious consequences of R loops yet allow R loop formation to participate in various physiological processes will help to understand how their homeostasis is maintained. Detection and quantitative measurements of R loops are critical that largely relied on S9.6 antibody. Immunofluorescence methods are frequently used to localize and quantify R loops in the cell but they require specialized tools for analysis and relatively expensive; therefore, they are not always useful for initial assessments of R loop accumulation. Here, we describe an improved slot blot protocol to detect and estimate R loops and show its sensitivity and specificity using the S9.6 antibody. Since specific factors protecting cells from harmful R loop accumulation are expanding, this protocol can be used to determine R loop accumulation in research and clinical settings.
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Affiliation(s)
- Altaf H Sarker
- Department of BioEngineering and BioMedical Sciences, Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Priscilla K Cooper
- Department of BioEngineering and BioMedical Sciences, Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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41
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Abstract
The immune systems protect vertebrates from foreign molecules or antigens, and antibodies are important mediators of this system. The sequences and structural features of antibodies vary depending on species. Many of antibodies from vertebrates, including camelids, have both heavy and light chain variable domains, but camelids also have antibodies that lack the light chains. In antibodies that lack light chains, the C-terminal variable region is called the VHH domain. Antibodies recognize antigens through six complementarity-determining regions (CDRs). The third CDR of the heavy chain (CDR-H3) is at the center of the antigen-binding site and is diverse in terms of sequence and structure. Due to the importance of antibodies in basic science as well as in medical applications, there have been many studies of CDR-H3s of antibodies that possess both light and heavy chains. However, nature of CDR-H3s of single-domain VHH antibodies is less well studied. In this chapter, we describe current knowledge of sequence-structure-function correlations of single-domain VHH antibodies with emphasis on CDR-H3. Based on the 370 crystal structures in the Protein Data Bank, we also attempt structural classification of CDR-H3 in single-domain VHH antibodies and discuss lessons learned from the ever-increasing number of the structures.
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Affiliation(s)
- Daisuke Kuroda
- Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, Tokyo, Japan.
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan.
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan.
| | - Kouhei Tsumoto
- Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, Tokyo, Japan.
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan.
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan.
- Laboratory of Medical Proteomics, Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
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42
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Comeau SR, Thorsteinson N, Kumar S. Structural Considerations in Affinity Maturation of Antibody-Based Biotherapeutic Candidates. Methods Mol Biol 2023; 2552:309-321. [PMID: 36346600 DOI: 10.1007/978-1-0716-2609-2_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Affinity maturation is an important stage in biologic drug discovery as is the natural process of generating an immune response inside the human body. In this chapter, we describe in silico approaches to affinity maturation via a worked example. Both advantages and limitations of the computational methods used are critically examined. Furthermore, construction of affinity maturation libraries and how their outputs might be implemented in an experimental setting are also described. It should be noted that structure-based design of biologic drugs is an emerging field and the tools currently available require further development. Furthermore, there are no standardized structure-based strategies yet for antibody affinity maturation as this research relies heavily on scientific logic as well as creative intuition.
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Affiliation(s)
- Stephen R Comeau
- Computational Biochemistry and Bioinformatics Group, Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT, USA
| | - Nels Thorsteinson
- Scientific Services Manager, Biologics, Chemical Computing Group ULC, Montreal, QC, Canada
| | - Sandeep Kumar
- Computational Biochemistry and Bioinformatics Group, Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT, USA.
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43
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Ascher DB, Kaminskas LM, Myung Y, Pires DEV. Using Graph-Based Signatures to Guide Rational Antibody Engineering. Methods Mol Biol 2023; 2552:375-397. [PMID: 36346604 DOI: 10.1007/978-1-0716-2609-2_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Antibodies are essential experimental and diagnostic tools and as biotherapeutics have significantly advanced our ability to treat a range of diseases. With recent innovations in computational tools to guide protein engineering, we can now rationally design better antibodies with improved efficacy, stability, and pharmacokinetics. Here, we describe the use of the mCSM web-based in silico suite, which uses graph-based signatures to rapidly identify the structural and functional consequences of mutations, to guide rational antibody engineering to improve stability, affinity, and specificity.
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Affiliation(s)
- David B Ascher
- Structural Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Parkville, VIC, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
- Department of Biochemistry, Cambridge University, Cambridge, UK
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia
| | - Lisa M Kaminskas
- School of Biological Sciences, University of Queensland, St Lucia, QLD, Australia
| | - Yoochan Myung
- Structural Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Parkville, VIC, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia
| | - Douglas E V Pires
- Structural Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Parkville, VIC, Australia.
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia.
- School of Computing and Information Systems, University of Melbourne, Parkville, VIC, Australia.
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Kakuzaki T, Koga H, Takizawa S, Metsugi S, Shiraiwa H, Sampei Z, Yoshida K, Tsunoda H, Teramoto R. Monte Carlo Thompson sampling-guided design for antibody engineering. MAbs 2023; 15:2244214. [PMID: 37605371 PMCID: PMC10446805 DOI: 10.1080/19420862.2023.2244214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 07/27/2023] [Accepted: 07/29/2023] [Indexed: 08/23/2023] Open
Abstract
Antibodies are one of the predominant treatment modalities for various diseases. To improve the characteristics of a lead antibody, such as antigen-binding affinity and stability, we conducted comprehensive substitutions and exhaustively explored their sequence space. However, it is practically unfeasible to evaluate all possible combinations of mutations owing to combinatorial explosion when multiple amino acid residues are incorporated. It was recently reported that a machine-learning guided protein engineering approach such as Thompson sampling (TS) has been used to efficiently explore sequence space in the framework of Bayesian optimization. For TS, over-exploration occurs when the initial data are biasedly distributed in the vicinity of the lead antibody. We handle a large-scale virtual library that includes numerous mutations. When the number of experiments is limited, this over-exploration causes a serious issue. Thus, we conducted Monte Carlo Thompson sampling (MTS) to balance the exploration-exploitation trade-off by defining the posterior distribution via the Monte Carlo method and compared its performance with TS in antibody engineering. Our results demonstrated that MTS largely outperforms TS in discovering desirable candidates at an earlier round when over-exploration occurs on TS. Thus, the MTS method is a powerful technique for efficiently discovering antibodies with desired characteristics when the number of rounds is limited.
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Affiliation(s)
- Taro Kakuzaki
- Research Division, Chugai Pharmaceutical Co., Ltd., Yokohama, Japan
| | - Hikaru Koga
- Research Division, Chugai Pharmaceutical Co., Ltd., Yokohama, Japan
| | - Shuuki Takizawa
- Research Division, Chugai Pharmaceutical Co., Ltd., Yokohama, Japan
| | - Shoichi Metsugi
- Research Division, Chugai Pharmaceutical Co., Ltd., Yokohama, Japan
| | | | - Zenjiro Sampei
- Research Division, Chugai Pharmaceutical Co., Ltd., Yokohama, Japan
| | - Kenji Yoshida
- Research Division, Chugai Pharmaceutical Co., Ltd., Yokohama, Japan
| | - Hiroyuki Tsunoda
- Research Division, Chugai Pharmaceutical Co., Ltd., Yokohama, Japan
| | - Reiji Teramoto
- Research Division, Chugai Pharmaceutical Co., Ltd., Yokohama, Japan
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Childers MC, Daggett V. Molecular Dynamics Methods for Antibody Design. Methods Mol Biol 2023; 2552:109-124. [PMID: 36346588 DOI: 10.1007/978-1-0716-2609-2_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Complex and coordinated dynamics are closely connected with protein functions, including the binding of antibodies to antigens. Knowledge of such dynamics could improve the design of antibodies. Molecular dynamics (MD) simulations provide a "computational microscope" that can resolve atomic motions and inform antibody design efforts.
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Affiliation(s)
| | - Valerie Daggett
- Department of Bioengineering, University of Washington, Seattle, WA, USA.
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46
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Diwan D, Pajerowska-Mukhtar KM. Preparation and Utilization of a Versatile GFP-Protein Trap-Like System for Protein Complex Immunoprecipitation in Plants. Methods Mol Biol 2023; 2690:59-68. [PMID: 37450136 DOI: 10.1007/978-1-0716-3327-4_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Protein complex immunoprecipitation (co-IP) is an in vitro technique used to study protein-protein interaction between two or more proteins. This method relies on affinity purification of recombinant epitope-tagged proteins followed by western blotting detection using tag-specific antibodies for the confirmation of positive interaction. The traditional co-IP method relies on the use of porous beaded support with immobilized antibodies to precipitate protein complexes. However, this method is time-consuming, labor-intensive, and provides lower reproducibility and yield of protein complexes. Here, we describe the implementation of magnetic beads and high-affinity anti-green fluorescent protein (GFP) antibodies to develop an in vitro GFP-protein trap-like system. This highly reproducible system utilizes a combination of small sample size, versatile lysis buffer, and lower amounts of magnetic beads to obtain protein complexes and aggregates that are compatible with functional assays, Western blotting, and mass spectrometry. In addition to protein-protein interactions, this versatile method can be employed to study protein-nucleic acid interactions. This protocol also highlights troubleshooting and includes recommendations to optimize its application.
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Affiliation(s)
- Danish Diwan
- Department of Biology, University of Alabama, Birmingham, AL, USA
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Zhang X, Liu H, He J, Ou C, Donahue TC, Muthana MM, Su L, Wang LX. Site-Specific Chemoenzymatic Conjugation of High-Affinity M6P Glycan Ligands to Antibodies for Targeted Protein Degradation. ACS Chem Biol 2022; 17:3013-3023. [PMID: 35316032 PMCID: PMC9492806 DOI: 10.1021/acschembio.1c00751] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Lysosome-targeting chimeras (LYTACs) offer an opportunity for the degradation of extracellular and membrane-associated proteins of interest. Here, we report an efficient chemoenzymatic method that enables a single-step and site-specific conjugation of high-affinity mannose-6-phosphate (M6P) glycan ligands to antibodies without the need of protein engineering and conventional click reactions that would introduce "unnatural" moieties, yielding homogeneous antibody-M6P glycan conjugates for targeted degradation of membrane-associated proteins. Using trastuzumab and cetuximab as model antibodies, we showed that the wild-type endoglycosidase S (Endo-S) could efficiently perform the antibody deglycosylation and simultaneous transfer of an M6P-glycan from a synthetic M6P-glycan oxazoline to the deglycosylated antibody in a one-pot manner, giving structurally well-defined antibody-M6P glycan conjugates. A two-step procedure, using wild-type Endo-S2 for deglycosylation followed by transglycosylation with an Endo-S2 mutant (D184M), was also efficient to provide M6P glycan-antibody conjugates. The chemoenzymatic approach was highly specific for Fc glycan remodeling when both Fc and Fab domains were glycosylated, as exemplified by the selective Fc-glycan remodeling of cetuximab. SPR binding analysis indicated that the M6P conjugates possessed a nanomolar range of binding affinities for the cation-independent mannose-6-phosphate receptor (CI-MPR). Preliminary cell-based assays showed that the M6P-trastuzumab and M6P-cetuximab conjugates were able to selectively degrade the membrane-associated HER2 and EGFR, respectively. This modular glycan-remodeling strategy is expected to find wide applications for antibody-based lysosome-targeted degradation of extracellular and membrane proteins.
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Affiliation(s)
- Xiao Zhang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Huiying Liu
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Jia He
- Division of Virology, Pathogenesis, and Cancer, Institute of Human Virology, Departments of Pharmacology, Microbiology, and Immunology, University of Maryland School of Medicine, Baltimore, Maryland 21201, United States
| | - Chong Ou
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Thomas C Donahue
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Musleh M Muthana
- Division of Virology, Pathogenesis, and Cancer, Institute of Human Virology, Departments of Pharmacology, Microbiology, and Immunology, University of Maryland School of Medicine, Baltimore, Maryland 21201, United States
| | - Lishan Su
- Division of Virology, Pathogenesis, and Cancer, Institute of Human Virology, Departments of Pharmacology, Microbiology, and Immunology, University of Maryland School of Medicine, Baltimore, Maryland 21201, United States
| | - Lai-Xi Wang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
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Chen C, Zhou J, Men D, Zhang XE. Promoter-regulated in vivo asymmetric self-assembly strategy to synthesize heterogeneous nanoparticles for signal amplification. Nanoscale 2022; 14:16180-16184. [PMID: 36278831 DOI: 10.1039/d2nr04661j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Signal amplification is commonly used to enhance the sensitivity of biological analysis. Here, we present a strategy involving in vivo asymmetric self-assembly combined with promoter strength regulation to synthesize heterogeneous nanoparticles for signal amplification. Two expression vectors were constructed by genetically inserting, respectively, signal and binding molecules into the hepatitis B core antigen protein (HBcAg) structure. Because of differential expression of the two recombinant proteins in the presence of a strong promoter (T7) and a weak promoter (Tac-1) and spontaneous asymmetric self-assembly in vivo, heterogeneous HBcAg nanoparticles (NPs) with a high ratio of signal-bearing to target-binding molecules were obtained. These nanoparticles contained a large number of green fluorescent proteins as signal molecules and a small number of B1 immunoglobulin-binding domains from protein G for antibody binding, thus enabling sensitive immunoassays. As a proof of concept, improved sensitivity for antibody detection was achieved using the heterogeneous nanoparticle conjugated with a secondary antibody molecule.
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Affiliation(s)
- Chen Chen
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Juan Zhou
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, P. R. China
| | - Dong Men
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Xian-En Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- Faculty of Synthetic Biology and Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
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Jaffe DB, Shahi P, Adams BA, Chrisman AM, Finnegan PM, Raman N, Royall AE, Tsai F, Vollbrecht T, Reyes DS, Hepler NL, McDonnell WJ. Functional antibodies exhibit light chain coherence. Nature 2022; 611:352-357. [PMID: 36289331 PMCID: PMC9607724 DOI: 10.1038/s41586-022-05371-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 09/21/2022] [Indexed: 11/08/2022]
Abstract
The vertebrate adaptive immune system modifies the genome of individual B cells to encode antibodies that bind particular antigens1. In most mammals, antibodies are composed of heavy and light chains that are generated sequentially by recombination of V, D (for heavy chains), J and C gene segments. Each chain contains three complementarity-determining regions (CDR1-CDR3), which contribute to antigen specificity. Certain heavy and light chains are preferred for particular antigens2-22. Here we consider pairs of B cells that share the same heavy chain V gene and CDRH3 amino acid sequence and were isolated from different donors, also known as public clonotypes23,24. We show that for naive antibodies (those not yet adapted to antigens), the probability that they use the same light chain V gene is around 10%, whereas for memory (functional) antibodies, it is around 80%, even if only one cell per clonotype is used. This property of functional antibodies is a phenomenon that we call light chain coherence. We also observe this phenomenon when similar heavy chains recur within a donor. Thus, although naive antibodies seem to recur by chance, the recurrence of functional antibodies reveals surprising constraint and determinism in the processes of V(D)J recombination and immune selection. For most functional antibodies, the heavy chain determines the light chain.
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Liang T, Jiang C, Yuan J, Othman Y, Xie XQ, Feng Z. Differential performance of RoseTTAFold in antibody modeling. Brief Bioinform 2022; 23:bbac152. [PMID: 35598325 PMCID: PMC9487640 DOI: 10.1093/bib/bbac152] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/28/2022] [Accepted: 04/06/2022] [Indexed: 12/31/2023] Open
Abstract
Antibodies are essential to life, and knowing their structures can facilitate the understanding of antibody-antigen recognition mechanisms. Precise antibody structure prediction has been a core challenge for a prolonged period, especially the accuracy of H3 loop prediction. Despite recent progress, existing methods cannot achieve atomic accuracy, especially when the homologous structures required for these methods are not available. Recently, RoseTTAFold, a deep learning-based algorithm, has shown remarkable breakthroughs in predicting the 3D structures of proteins. To assess the antibody modeling ability of RoseTTAFold, we first retrieved the sequences of 30 antibodies as the test set and used RoseTTAFold to model their 3D structures. We then compared the models constructed by RoseTTAFold with those of SWISS-MODEL in a different way, in which we stratified Global Model Quality Estimate (GMQE) into three different ranges. The results indicated that RoseTTAFold could achieve results similar to SWISS-MODEL in modeling most CDR loops, especially the templates with a GMQE score under 0.8. In addition, we also compared the structures modeled by RoseTTAFold, SWISS-MODEL and ABodyBuilder. In brief, RoseTTAFold could accurately predict 3D structures of antibodies, but its accuracy was not as good as the other two methods. However, RoseTTAFold exhibited better accuracy for modeling H3 loop than ABodyBuilder and was comparable to SWISS-MODEL. Finally, we discussed the limitations and potential improvements of the current RoseTTAFold, which may help to further the accuracy of RoseTTAFold's antibody modeling.
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Affiliation(s)
- Tianjian Liang
- Department of Pharmaceutical Sciences, Computational Chemical Genomics Screening Center, and Pharmacometrics & System Pharmacology PharmacoAnalytics, School of Pharmacy; National Center of Excellence for Computational Drug Abuse Research; Drug Discovery Institute; Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Chen Jiang
- Department of Pharmaceutical Sciences, Computational Chemical Genomics Screening Center, and Pharmacometrics & System Pharmacology PharmacoAnalytics, School of Pharmacy; National Center of Excellence for Computational Drug Abuse Research; Drug Discovery Institute; Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Jiayi Yuan
- Department of Pharmaceutical Sciences, Computational Chemical Genomics Screening Center, and Pharmacometrics & System Pharmacology PharmacoAnalytics, School of Pharmacy; National Center of Excellence for Computational Drug Abuse Research; Drug Discovery Institute; Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Yasmin Othman
- Department of Pharmaceutical Sciences, Computational Chemical Genomics Screening Center, and Pharmacometrics & System Pharmacology PharmacoAnalytics, School of Pharmacy; National Center of Excellence for Computational Drug Abuse Research; Drug Discovery Institute; Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Xiang-Qun Xie
- Department of Pharmaceutical Sciences, Computational Chemical Genomics Screening Center, and Pharmacometrics & System Pharmacology PharmacoAnalytics, School of Pharmacy; National Center of Excellence for Computational Drug Abuse Research; Drug Discovery Institute; Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Zhiwei Feng
- Department of Pharmaceutical Sciences, Computational Chemical Genomics Screening Center, and Pharmacometrics & System Pharmacology PharmacoAnalytics, School of Pharmacy; National Center of Excellence for Computational Drug Abuse Research; Drug Discovery Institute; Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
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