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Understanding and Modulating Antibody Fine Specificity: Lessons from Combinatorial Biology. Antibodies (Basel) 2022; 11:antib11030048. [PMID: 35892708 PMCID: PMC9326607 DOI: 10.3390/antib11030048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 02/01/2023] Open
Abstract
Combinatorial biology methods such as phage and yeast display, suitable for the generation and screening of huge numbers of protein fragments and mutated variants, have been useful when dissecting the molecular details of the interactions between antibodies and their target antigens (mainly those of protein nature). The relevance of these studies goes far beyond the mere description of binding interfaces, as the information obtained has implications for the understanding of the chemistry of antibody–antigen binding reactions and the biological effects of antibodies. Further modification of the interactions through combinatorial methods to manipulate the key properties of antibodies (affinity and fine specificity) can result in the emergence of novel research tools and optimized therapeutics.
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Nasir A, Shaukat K, Hameed IA, Luo S, Alam TM, Iqbal F. A Bibliometric Analysis of Corona Pandemic in Social Sciences: A Review of Influential Aspects and Conceptual Structure. IEEE ACCESS : PRACTICAL INNOVATIONS, OPEN SOLUTIONS 2020; 8:133377-133402. [PMID: 34812340 PMCID: PMC8545329 DOI: 10.1109/access.2020.3008733] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 07/06/2020] [Indexed: 05/07/2023]
Abstract
Corona pandemic has affected the whole world, and it is a highly researched area in biological sciences. As the current pandemic has affected countries socially and economically, the purpose of this bibliometric analysis is to provide a holistic review of the corona pandemic in the field of social sciences. This study aims to highlight significant, influential aspects, research streams, and themes. We have reviewed 395 journal articles related to coronavirus in the field of social sciences from 2003 to 2020. We have deployed 'biblioshiny' a web-interface of the 'bibliometrix 3.0' package of R-studio to conduct bibliometric analysis and visualization. In the field of social sciences, we have reported influential aspects of coronavirus literature. We have found that the 'Morbidity and Mortality Weekly Report' is the top journal. The core article of coronavirus literature is 'Guidelines for preventing health-care-associated pneumonia'. The most commonly used word, in titles, abstracts, author's keywords, and keywords plus, is 'SARS'. Top affiliation is 'The University of Hong Kong'. Hong Kong is a leading country based on citations, and the USA is on top based on total publications. We have used a conceptual framework to identify potential research streams and themes in coronavirus literature. Four research streams are found by deploying a co-occurrence network. These research streams are 'Social and economic effects of epidemic disease', 'Infectious disease calamities and control', 'Outbreak of COVID 19,' and 'Infectious diseases and the role of international organizations'. Finally, a thematic map is used to provide a holistic understanding by dividing significant themes into basic or transversal, emerging or declining, motor, highly developed, but isolated themes. These themes and subthemes have proposed future directions and critical areas of research.
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Affiliation(s)
- Adeel Nasir
- Department of Management SciencesLahore College for Women UniversityLahore54000Pakistan
| | - Kamran Shaukat
- School of Electrical Engineering and ComputingThe University of NewcastleCallaghanNSW2308Australia
- Punjab University College of Information Technology, University of the PunjabLahore54590Pakistan
| | - Ibrahim A. Hameed
- Department of ICT and Natural SciencesNorwegian University of Science and Technology7491TrondheimNorway
| | - Suhuai Luo
- School of Electrical Engineering and ComputingThe University of NewcastleCallaghanNSW2308Australia
| | - Talha Mahboob Alam
- Department of Computer ScienceUniversity of Engineering and TechnologyLahore54890Pakistan
| | - Farhat Iqbal
- Punjab University College of Information Technology, University of the PunjabLahore54590Pakistan
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Expression and epitope identification of myosin light chain isoform 1, an allergen in Procambarus clarkii. Food Chem 2020; 317:126422. [DOI: 10.1016/j.foodchem.2020.126422] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 02/09/2020] [Accepted: 02/15/2020] [Indexed: 12/17/2022]
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Yang Y, Hu MJ, Jin TC, Zhang YX, Liu GY, Li YB, Zhang ML, Cao MJ, Su WJ, Liu GM. A comprehensive analysis of the allergenicity and IgE epitopes of myosinogen allergens in Scylla paramamosain. Clin Exp Allergy 2018; 49:108-119. [PMID: 30187588 DOI: 10.1111/cea.13266] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 08/26/2018] [Accepted: 08/29/2018] [Indexed: 12/22/2022]
Abstract
BACKGROUND Scylla paramamosain is one of the most common and serious food allergens in Asia. Therefore, research on its prevalence, accurate diagnosis, and IgE-binding pattern of the allergens is crucial. OBJECTIVE To identify the IgE epitopes of the myosinogen allergens in S. paramamosain using phage peptide library. METHODS The prevalence of allergy to crabs (AC) and of sensitization was analysed using a questionnaire and a serological assay. BAT was performed by flow cytometry, and its diagnostic performance was evaluated in relation to allergens purified from crab myosinogen. IgE-binding epitopes were identified by phage display using the IgE from patients with AC. Sequence- and structure-based bioinformatics analyses were performed to identify allergenic epitopes. RESULTS Crab was the most common cause of food allergies in this study. Subjects with AC (n = 30) with clear clinical symptoms were identified by immunoblotting and BAT. All of the myosinogen allergens triggered basophil activation; surface expression of CD63 and CD203c was higher in patients allergic to AK and FLN c than in patients allergic to SCP and TIM. In addition to six conformational epitopes of SCP, six linear epitopes and eight conformational epitopes of AK were identified. Five linear epitopes and three conformational epitopes of TIM, nine linear and ten conformational epitopes of FLN c were also identified, and the sequence VH(I/T) L was appeared in epitopes of both TIM and FLN c. The number of epitopes showed consistency with the value of BAT. CONCLUSIONS AND CLINICAL RELEVANCE BAT can be used for accurate diagnosis of AC. Identification of particular allergenic motifs could be a valuable tool for prevention, diagnosis, and treatment of food allergies.
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Affiliation(s)
- Yang Yang
- College of Food and Biological Engineering, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Jimei University, Xiamen, China
| | - Meng Jun Hu
- College of Food and Biological Engineering, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Jimei University, Xiamen, China
| | - Teng Chuan Jin
- University of Science and Technology of China, Hefei, China
| | - Yong Xia Zhang
- College of Food and Biological Engineering, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Jimei University, Xiamen, China
| | - Guang Yu Liu
- College of Food and Biological Engineering, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Jimei University, Xiamen, China
| | - Yu Bao Li
- Medical center of Jimei University, Xiamen, China
| | | | - Min Jie Cao
- College of Food and Biological Engineering, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Jimei University, Xiamen, China
| | - Wen Jin Su
- College of Food and Biological Engineering, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Jimei University, Xiamen, China
| | - Guang Ming Liu
- College of Food and Biological Engineering, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Jimei University, Xiamen, China
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Liu GY, Mei XJ, Hu MJ, Yang Y, Liu M, Li MS, Zhang ML, Cao MJ, Liu GM. Analysis of the Allergenic Epitopes of Tropomyosin from Mud Crab Using Phage Display and Site-Directed Mutagenesis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:9127-9137. [PMID: 30107732 DOI: 10.1021/acs.jafc.8b03466] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Mud crab ( Scylla serrata), which is widely consumed, can cause severe allergic symptoms. Eight linear epitopes and seven conformational epitopes of tropomyosin (TM) from S. serrata were identified using phage display. The conformational epitopes were formed based on the coiled-coil structure of TM. Most of the epitopes were located in the regions where primary structures were conserved among crustacean TM. Twelve synthetic peptides were designed according to the epitopes and trypsin-cutting sites of TM, among them, three synthetic peptides (including one linear epitope and two conformational epitopes) were recognized by all of the patient sera using inhibitory dot blotting. A triple-variant (R90A-E164A-Y267A) was constructed based on the critical amino acids of the TM epitope. The IgE-binding activity of the triple-variant was significantly reduced compared with that of native TM. The results of phage display and site-directed mutagenesis offered new information regarding conformational epitopes of TM.
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Affiliation(s)
- Guang-Yu Liu
- College of Food and Biological Engineering, Xiamen Key Laboratory of Marine Functional Food, Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources , Jimei University , Xiamen , Fujian China
| | - Xue-Jiao Mei
- College of Food and Biological Engineering, Xiamen Key Laboratory of Marine Functional Food, Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources , Jimei University , Xiamen , Fujian China
| | - Meng-Jun Hu
- College of Food and Biological Engineering, Xiamen Key Laboratory of Marine Functional Food, Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources , Jimei University , Xiamen , Fujian China
| | - Yang Yang
- College of Food and Biological Engineering, Xiamen Key Laboratory of Marine Functional Food, Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources , Jimei University , Xiamen , Fujian China
| | - Meng Liu
- College of Food and Biological Engineering, Xiamen Key Laboratory of Marine Functional Food, Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources , Jimei University , Xiamen , Fujian China
| | - Meng-Si Li
- College of Food and Biological Engineering, Xiamen Key Laboratory of Marine Functional Food, Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources , Jimei University , Xiamen , Fujian China
| | - Ming-Li Zhang
- Xiamen Second Hospital , Xiamen , Fujian 361021 , China
| | - Min-Jie Cao
- College of Food and Biological Engineering, Xiamen Key Laboratory of Marine Functional Food, Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources , Jimei University , Xiamen , Fujian China
| | - Guang-Ming Liu
- College of Food and Biological Engineering, Xiamen Key Laboratory of Marine Functional Food, Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources , Jimei University , Xiamen , Fujian China
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Yang Y, Chen ZW, Hurlburt BK, Li GL, Zhang YX, Fei DX, Shen HW, Cao MJ, Liu GM. Identification of triosephosphate isomerase as a novel allergen in Octopus fangsiao. Mol Immunol 2017; 85:35-46. [PMID: 28208072 DOI: 10.1016/j.molimm.2017.02.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 01/21/2017] [Accepted: 02/06/2017] [Indexed: 11/19/2022]
Abstract
Octopus is an important mollusk in human dietary for its nutritional value, however it also causes allergic reactions in humans. Major allergens from octopus have been identified, while the knowledge of novel allergens remains poor. In the present study, a novel allergen with molecular weight of 28kDa protein was purified from octopus (Octopus fangsiao) and identified as triosephosphate isomerase (TIM) by mass spectrometry. TIM aggregated beyond 45°C, and its IgE-binding activity was affected under extreme pH conditions due to the altered secondary structure. In simulated gastric fluid digestion, TIM can be degraded into small fragments, while retaining over 80% of the IgE-binding activity. The full-length cDNA of O. fangsiao TIM (1140bp) was cloned, which encodes 247 amino acid residues, and the entire recombinant TIM was successfully expressed in Escherichia coli BL21, which showed similar immunoreactivity to the native TIM. Different intensity of cross-reactivity among TIM from related species revealed the complexity of its epitopes. Eight linear epitopes of TIM were predicted following bioinformatic analysis. Furthermore, a conformational epitope (A71G74S69D75T73F72V67) was confirmed by the phage display technology. The results revealed the physicochemical and immunological characteristics of TIM, which is significant in the development of hyposensitivity food and allergy diagnosis.
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Affiliation(s)
- Yang Yang
- College of Food and Biological Engineering, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen Key Laboratory of Marine Functional Food, Jimei University, 43 Yindou Road, Xiamen, Fujian, 361021, China
| | - Zhong-Wei Chen
- College of Food and Biological Engineering, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen Key Laboratory of Marine Functional Food, Jimei University, 43 Yindou Road, Xiamen, Fujian, 361021, China
| | - Barry K Hurlburt
- U.S. Department of Agriculture, Agriculture Research Service, Southern Regional Research Center, 1100 Robert E. Lee Boulevard, New Orleans, LA, 70124, USA
| | - Gui-Ling Li
- College of Food and Biological Engineering, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen Key Laboratory of Marine Functional Food, Jimei University, 43 Yindou Road, Xiamen, Fujian, 361021, China
| | - Yong-Xia Zhang
- College of Food and Biological Engineering, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen Key Laboratory of Marine Functional Food, Jimei University, 43 Yindou Road, Xiamen, Fujian, 361021, China
| | - Dan-Xia Fei
- College of Food and Biological Engineering, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen Key Laboratory of Marine Functional Food, Jimei University, 43 Yindou Road, Xiamen, Fujian, 361021, China
| | - Hai-Wang Shen
- College of Food and Biological Engineering, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen Key Laboratory of Marine Functional Food, Jimei University, 43 Yindou Road, Xiamen, Fujian, 361021, China
| | - Min-Jie Cao
- College of Food and Biological Engineering, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen Key Laboratory of Marine Functional Food, Jimei University, 43 Yindou Road, Xiamen, Fujian, 361021, China
| | - Guang-Ming Liu
- College of Food and Biological Engineering, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen Key Laboratory of Marine Functional Food, Jimei University, 43 Yindou Road, Xiamen, Fujian, 361021, China.
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Yang Y, Zhang YX, Liu M, Maleki SJ, Zhang ML, Liu QM, Cao MJ, Su WJ, Liu GM. Triosephosphate Isomerase and Filamin C Share Common Epitopes as Novel Allergens of Procambarus clarkii. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:950-963. [PMID: 28072528 DOI: 10.1021/acs.jafc.6b04587] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Triosephosphate isomerase (TIM) is a key enzyme in glycolysis and has been identified as an allergen in saltwater products. In this study, TIM with a molecular mass of 28 kDa was purified from the freshwater crayfish (Procambarus clarkii) muscle. A 90-kDa protein that showed IgG/IgE cross-reactivity with TIM was purified and identified as filamin C (FLN c), which is an actin-binding protein. TIM showed similar thermal and pH stability with better digestion resistance compared with FLN c. The result of the surface plasmon resonance (SPR) experiment demonstrated the infinity of anti-TIM polyclonal antibody (pAb) to both TIM and FLN c. Five linear and 3 conformational epitopes of TIM, as well as 9 linear and 10 conformational epitopes of FLN c, were mapped by phage display. Epitopes of TIM and FLN c demonstrated the sharing of certain residues; the occurrence of common epitopes in the two allergens accounts for their cross-reactivity.
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Affiliation(s)
- Yang Yang
- College of Food and Biological Engineering, Xiamen Key Laboratory of Marine Functional Food, Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Jimei University , Xiamen, Fujian 361021, China
| | - Yong-Xia Zhang
- College of Food and Biological Engineering, Xiamen Key Laboratory of Marine Functional Food, Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Jimei University , Xiamen, Fujian 361021, China
| | - Meng Liu
- College of Food and Biological Engineering, Xiamen Key Laboratory of Marine Functional Food, Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Jimei University , Xiamen, Fujian 361021, China
| | - Soheila J Maleki
- Agricultural Research Service, Southern Regional Research Center, U. S. Department of Agriculture , New Orleans, Louisiana 70124, United States
| | - Ming-Li Zhang
- Xiamen Second Hospital , Xiamen, Fujian 361021, China
| | - Qing-Mei Liu
- College of Food and Biological Engineering, Xiamen Key Laboratory of Marine Functional Food, Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Jimei University , Xiamen, Fujian 361021, China
| | - Min-Jie Cao
- College of Food and Biological Engineering, Xiamen Key Laboratory of Marine Functional Food, Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Jimei University , Xiamen, Fujian 361021, China
| | - Wen-Jin Su
- College of Food and Biological Engineering, Xiamen Key Laboratory of Marine Functional Food, Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Jimei University , Xiamen, Fujian 361021, China
| | - Guang-Ming Liu
- College of Food and Biological Engineering, Xiamen Key Laboratory of Marine Functional Food, Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Jimei University , Xiamen, Fujian 361021, China
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Potocnakova L, Bhide M, Pulzova LB. An Introduction to B-Cell Epitope Mapping and In Silico Epitope Prediction. J Immunol Res 2016; 2016:6760830. [PMID: 28127568 PMCID: PMC5227168 DOI: 10.1155/2016/6760830] [Citation(s) in RCA: 198] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 11/21/2016] [Accepted: 12/13/2016] [Indexed: 01/09/2023] Open
Abstract
Identification of B-cell epitopes is a fundamental step for development of epitope-based vaccines, therapeutic antibodies, and diagnostic tools. Epitope-based antibodies are currently the most promising class of biopharmaceuticals. In the last decade, in-depth in silico analysis and categorization of the experimentally identified epitopes stimulated development of algorithms for epitope prediction. Recently, various in silico tools are employed in attempts to predict B-cell epitopes based on sequence and/or structural data. The main objective of epitope identification is to replace an antigen in the immunization, antibody production, and serodiagnosis. The accurate identification of B-cell epitopes still presents major challenges for immunologists. Advances in B-cell epitope mapping and computational prediction have yielded molecular insights into the process of biorecognition and formation of antigen-antibody complex, which may help to localize B-cell epitopes more precisely. In this paper, we have comprehensively reviewed state-of-the-art experimental methods for B-cell epitope identification, existing databases for epitopes, and novel in silico resources and prediction tools available online. We have also elaborated new trends in the antibody-based epitope prediction. The aim of this review is to assist researchers in identification of B-cell epitopes.
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Affiliation(s)
- Lenka Potocnakova
- Laboratory of Biomedical Microbiology and Immunology, Department of Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy in Kosice, 041 81 Kosice, Slovakia
| | - Mangesh Bhide
- Laboratory of Biomedical Microbiology and Immunology, Department of Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy in Kosice, 041 81 Kosice, Slovakia
- Institute of Neuroimmunology of Slovak Academy of Sciences, 845 10 Bratislava, Slovakia
| | - Lucia Borszekova Pulzova
- Laboratory of Biomedical Microbiology and Immunology, Department of Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy in Kosice, 041 81 Kosice, Slovakia
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Yang Y, Cao MJ, Alcocer M, Liu QM, Fei DX, Mao HY, Liu GM. Mapping and characterization of antigenic epitopes of arginine kinase of Scylla paramamosain. Mol Immunol 2015; 65:310-20. [DOI: 10.1016/j.molimm.2015.02.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 02/05/2015] [Accepted: 02/09/2015] [Indexed: 01/30/2023]
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Gómez-Casado C, Roth-Walter F, Jensen-Jarolim E, Díaz-Perales A, Pacios LF. Modeling iron-catecholates binding to NGAL protein. J Mol Graph Model 2013; 45:111-21. [DOI: 10.1016/j.jmgm.2013.08.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 08/08/2013] [Accepted: 08/12/2013] [Indexed: 10/26/2022]
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12
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Zhang W, Zeng X, Zhang L, Peng H, Jiao Y, Zeng J, Treutlein HR. Computational identification of epitopes in the glycoproteins of novel bunyavirus (SFTS virus) recognized by a human monoclonal antibody (MAb 4-5). J Comput Aided Mol Des 2013; 27:539-50. [PMID: 23838839 DOI: 10.1007/s10822-013-9661-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 06/24/2013] [Indexed: 12/12/2022]
Abstract
In this work, we have developed a new approach to predict the epitopes of antigens that are recognized by a specific antibody. Our method is based on the "multiple copy simultaneous search" (MCSS) approach which identifies optimal locations of small chemical functional groups on the surfaces of the antibody, and identifying sequence patterns of peptides that can bind to the surface of the antibody. The identified sequence patterns are then used to search the amino-acid sequence of the antigen protein. The approach was validated by reproducing the binding epitope of HIV gp120 envelop glycoprotein for the human neutralizing antibody as revealed in the available crystal structure. Our method was then applied to predict the epitopes of two glycoproteins of a newly discovered bunyavirus recognized by an antibody named MAb 4-5. These predicted epitopes can be verified by experimental methods. We also discuss the involvement of different amino acids in the antigen-antibody recognition based on the distributions of MCSS minima of different functional groups.
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Affiliation(s)
- Wenshuai Zhang
- Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Prevention and Control, Institute of Pathogenic Microbiology, Ministry Health, Nanjing 210009, China
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Abstract
Tremendous technological advances in peptide synthesis and modification in recent years have resolved the major limitations of peptide-based vaccines. B-cell epitopes are major components of these vaccines (besides having other biological applications). Researchers have been developing in silico or computational models for the prediction of both linear and conformational B-cell epitopes, enabling immunologists and clinicians to identify the most promising epitopes for characterization in the laboratory. Attempts are also ongoing in systems biology to delineate the signaling networks in immune cells. Here we present all possible in silico models developed thus far in these areas.
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Huang J, Ru B, Zhu P, Nie F, Yang J, Wang X, Dai P, Lin H, Guo FB, Rao N. MimoDB 2.0: a mimotope database and beyond. Nucleic Acids Res 2011; 40:D271-7. [PMID: 22053087 PMCID: PMC3245166 DOI: 10.1093/nar/gkr922] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Mimotopes are peptides with affinities to given targets. They are readily obtained through biopanning against combinatorial peptide libraries constructed by phage display and other display technologies such as mRNA display, ribosome display, bacterial display and yeast display. Mimotopes have been used to infer the protein interaction sites and networks; they are also ideal candidates for developing new diagnostics, therapeutics and vaccines. However, such valuable peptides are not collected in the central data resources such as UniProt and NCBI GenPept due to their ‘unnatural’ short sequences. The MimoDB database is an information portal to biopanning results of random libraries. In version 2.0, it has 15 633 peptides collected from 849 papers and grouped into 1818 sets. Besides the core data on panning experiments and their results, broad background information on target, template, library and structure is included. An accompanied benchmark has also been compiled for bioinformaticians to develop and evaluate their new models, algorithms and programs. In addition, the MimoDB database provides tools for simple and advanced searches, structure visualization, BLAST and alignment view on the fly. The experimental biologists can easily use the database as a virtual control to exclude possible target-unrelated peptides. The MimoDB database is freely available at http://immunet.cn/mimodb.
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Affiliation(s)
- Jian Huang
- Key Laboratory for Neuroinformation of Ministry of Education, School of Life Science and Technology, University of Electronic Science and Technology of China, No 4, 2nd Section, North Jianshe Road, Chengdu, Sichuan 610054, China.
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