101
|
Gori A, Longhi R, Peri C, Colombo G. Peptides for immunological purposes: design, strategies and applications. Amino Acids 2013; 45:257-68. [DOI: 10.1007/s00726-013-1526-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 05/24/2013] [Indexed: 12/30/2022]
|
102
|
Brinks V, Weinbuch D, Baker M, Dean Y, Stas P, Kostense S, Rup B, Jiskoot W. Preclinical Models Used for Immunogenicity Prediction of Therapeutic Proteins. Pharm Res 2013; 30:1719-28. [DOI: 10.1007/s11095-013-1062-z] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Accepted: 04/15/2013] [Indexed: 02/06/2023]
|
103
|
Yao B, Zheng D, Liang S, Zhang C. Conformational B-cell epitope prediction on antigen protein structures: a review of current algorithms and comparison with common binding site prediction methods. PLoS One 2013; 8:e62249. [PMID: 23620816 PMCID: PMC3631208 DOI: 10.1371/journal.pone.0062249] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 03/18/2013] [Indexed: 11/19/2022] Open
Abstract
Accurate prediction of B-cell antigenic epitopes is important for immunologic research and medical applications, but compared with other bioinformatic problems, antigenic epitope prediction is more challenging because of the extreme variability of antigenic epitopes, where the paratope on the antibody binds specifically to a given epitope with high precision. In spite of the continuing efforts in the past decade, the problem remains unsolved and therefore still attracts a lot of attention from bioinformaticists. Recently, several discontinuous epitope prediction servers became available, and it is intriguing to review all existing methods and evaluate their performances on the same benchmark. In addition, these methods are also compared against common binding site prediction algorithms, since they have been frequently used as substitutes in the absence of good epitope prediction methods.
Collapse
Affiliation(s)
- Bo Yao
- School of Biological Sciences, Center for Plant Science and Innovation, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Dandan Zheng
- Department of Radiation Oncology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Shide Liang
- Systems Immunology Lab, Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan
- * E-mail: (CZ); (SL)
| | - Chi Zhang
- School of Biological Sciences, Center for Plant Science and Innovation, University of Nebraska, Lincoln, Nebraska, United States of America
- * E-mail: (CZ); (SL)
| |
Collapse
|
104
|
Lo YT, Pai TW, Wu WK, Chang HT. Prediction of conformational epitopes with the use of a knowledge-based energy function and geometrically related neighboring residue characteristics. BMC Bioinformatics 2013; 14 Suppl 4:S3. [PMID: 23514199 PMCID: PMC3599093 DOI: 10.1186/1471-2105-14-s4-s3] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background A conformational epitope (CE) in an antigentic protein is composed of amino acid residues that are spatially near each other on the antigen's surface but are separated in sequence; CEs bind their complementary paratopes in B-cell receptors and/or antibodies. CE predication is used during vaccine design and in immuno-biological experiments. Here, we develop a novel system, CE-KEG, which predicts CEs based on knowledge-based energy and geometrical neighboring residue contents. The workflow applied grid-based mathematical morphological algorithms to efficiently detect the surface atoms of the antigens. After extracting surface residues, we ranked CE candidate residues first according to their local average energy distributions. Then, the frequencies at which geometrically related neighboring residue combinations in the potential CEs occurred were incorporated into our workflow, and the weighted combinations of the average energies and neighboring residue frequencies were used to assess the sensitivity, accuracy, and efficiency of our prediction workflow. Results We prepared a database containing 247 antigen structures and a second database containing the 163 non-redundant antigen structures in the first database to test our workflow. Our predictive workflow performed better than did algorithms found in the literature in terms of accuracy and efficiency. For the non-redundant dataset tested, our workflow achieved an average of 47.8% sensitivity, 84.3% specificity, and 80.7% accuracy according to a 10-fold cross-validation mechanism, and the performance was evaluated under providing top three predicted CE candidates for each antigen. Conclusions Our method combines an energy profile for surface residues with the frequency that each geometrically related amino acid residue pair occurs to identify possible CEs in antigens. This combination of these features facilitates improved identification for immuno-biological studies and synthetic vaccine design. CE-KEG is available at http://cekeg.cs.ntou.edu.tw.
Collapse
Affiliation(s)
- Ying-Tsang Lo
- Department of Computer Science and Engineering, National Taiwan Ocean University, Keelung, Taiwan, ROC
| | | | | | | |
Collapse
|
105
|
Abstract
The varied landscape of the adaptive immune response is determined by the peptides presented by immune cells, derived from viral or microbial pathogens or cancerous cells. The study of immune biomarkers or antigens is not new and classical methods such as agglutination, enzyme-linked immunosorbent assay, or Western blotting have been used for many years to study the immune response to vaccination or disease. However, in many of these traditional techniques, protein or peptide identification has often been the bottleneck. Recent advances in genomics and proteomics, has led to many of the rapid advances in proteomics approaches. Immunoproteomics describes a rapidly growing collection of approaches that have the common goal of identifying and measuring antigenic peptides or proteins. This includes gel based, array based, mass spectrometry, DNA based, or in silico approaches. Immunoproteomics is yielding an understanding of disease and disease progression, vaccine candidates, and biomarkers. This review gives an overview of immunoproteomics and closely related technologies that are used to define the full set of antigens targeted by the immune system during disease.
Collapse
Affiliation(s)
- Kelly M Fulton
- Human Health Therapeutics, National Research Council Canada, Ottawa, ON, Canada
| | | |
Collapse
|
106
|
Structural and functional analysis of multi-interface domains. PLoS One 2012; 7:e50821. [PMID: 23272073 PMCID: PMC3522720 DOI: 10.1371/journal.pone.0050821] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2012] [Accepted: 10/29/2012] [Indexed: 02/03/2023] Open
Abstract
A multi-interface domain is a domain that can shape multiple and distinctive binding sites to contact with many other domains, forming a hub in domain-domain interaction networks. The functions played by the multiple interfaces are usually different, but there is no strict bijection between the functions and interfaces as some subsets of the interfaces play the same function. This work applies graph theory and algorithms to discover fingerprints for the multiple interfaces of a domain and to establish associations between the interfaces and functions, based on a huge set of multi-interface proteins from PDB. We found that about 40% of proteins have the multi-interface property, however the involved multi-interface domains account for only a tiny fraction (1.8%) of the total number of domains. The interfaces of these domains are distinguishable in terms of their fingerprints, indicating the functional specificity of the multiple interfaces in a domain. Furthermore, we observed that both cooperative and distinctive structural patterns, which will be useful for protein engineering, exist in the multiple interfaces of a domain.
Collapse
|
107
|
Whiteaker JR, Paulovich AG. Peptide immunoaffinity enrichment coupled with mass spectrometry for peptide and protein quantification. Clin Lab Med 2012; 31:385-96. [PMID: 21907104 DOI: 10.1016/j.cll.2011.07.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|
108
|
Greiff V, Redestig H, Lück J, Bruni N, Valai A, Hartmann S, Rausch S, Schuchhardt J, Or-Guil M. A minimal model of peptide binding predicts ensemble properties of serum antibodies. BMC Genomics 2012; 13:79. [PMID: 22353141 PMCID: PMC3311590 DOI: 10.1186/1471-2164-13-79] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2011] [Accepted: 02/21/2012] [Indexed: 12/16/2022] Open
Affiliation(s)
- Victor Greiff
- Systems Immunology Lab, Department of Biology, Humboldt University Berlin, and Research Center ImmunoSciences, Charité University Medicine Berlin, Berlin, Germany
| | | | | | | | | | | | | | | | | |
Collapse
|
109
|
Van Regenmortel MHV. Limitations to the structure-based design of HIV-1 vaccine immunogens. J Mol Recognit 2012; 24:741-53. [PMID: 21812050 DOI: 10.1002/jmr.1116] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In spite of 25 years of intensive research, no effective human immunodeficiency virus type 1 (HIV-1) vaccine has yet been developed. One reason for this is that investigators have concentrated mainly on the structural analysis of HIV-1 antigens because they assumed that it should be possible to deduce vaccine-relevant immunogens from the structure of viral antigens bound to neutralizing monoclonal antibodies. This unwarranted assumption arises from misconceptions regarding the nature of protein epitopes and from the belief that it is justified to extrapolate from the antigenicity to the immunogenicity of proteins. Although the structure of the major HIV-1 antigenic sites has been elucidated, this knowledge has been of little use for designing an HIV-1 vaccine. Little attention has been given to the fact that protective immune responses tend to be polyclonal and involve antibodies directed to several different epitopes. It is concluded that only trial and error, empirical investigations using numerous immunization protocols may eventually allow us to identify which mixtures of immunogens are likely to be the best candidates for an HIV-1 vaccine.
Collapse
|
110
|
Ramaraj T, Angel T, Dratz EA, Jesaitis AJ, Mumey B. Antigen-antibody interface properties: composition, residue interactions, and features of 53 non-redundant structures. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1824:520-32. [PMID: 22246133 DOI: 10.1016/j.bbapap.2011.12.007] [Citation(s) in RCA: 115] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2011] [Revised: 12/22/2011] [Accepted: 12/23/2011] [Indexed: 11/17/2022]
Abstract
The structures of protein antigen-antibody (Ag-Ab) interfaces contain information about how Ab recognize Ag as well as how Ag are folded to present surfaces for Ag recognition. As such, the Ab surface holds information about Ag folding that resides with the Ab-Ag interface residues and how they interact. In order to gain insight into the nature of such interactions, a data set comprised of 53 non-redundant 3D structures of Ag-Ab complexes was analyzed. We assessed the physical and biochemical features of the Ag-Ab interfaces and the degree to which favored interactions exist between amino acid residues on the corresponding interface surfaces. Amino acid compositional analysis of the interfaces confirmed the dominance of TYR in the Ab paratope-containing surface (PCS), with almost two fold greater abundance than any other residue. Additionally TYR had a much higher than expected presence in the PCS compared to the surface of the whole antibody (defined as the occurrence propensity), along with aromatics PHE, TRP, and to a lesser degree HIS and ILE. In the Ag epitope-containing surface (ECS), there were slightly increased occurrence propensities of TRP and TYR relative to the whole Ag surface, implying an increased significance over the compositionally most abundant LYS>ASN>GLU>ASP>ARG. This examination encompasses a large, diverse set of unique Ag-Ab crystal structures that help explain the biological range and specificity of Ag-Ab interactions. This analysis may also provide a measure of the significance of individual amino acid residues in phage display analysis of Ag binding.
Collapse
|
111
|
Zhao L, Wong L, Li J. Antibody-specified B-cell epitope prediction in line with the principle of context-awareness. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2011; 8:1483-1494. [PMID: 21383422 DOI: 10.1109/tcbb.2011.49] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Context-awareness is a characteristic in the recognition between antigens and antibodies, highlighting the reconfiguration of epitope residues when an antigen interacts with a different antibody. A coarse binary classification of antigen regions into epitopes, or nonepitopes without specifying antibodies may not accurately reflect this biological reality. Therefore, we study an antibody-specified epitope prediction problem in line with this principle. This problem is new and challenging as we pinpoint a subset of the antigenic residues from an antigen when it binds to a specific antibody. We introduce two kinds of associations of the contextual awareness: 1) residues-residues pairing preference, and 2) the dependence between sets of contact residue pairs. Preference plays a bridging role to link interacting paratope and epitope residues while dependence is used to extend the association from one-dimension to two-dimension. The paratope/epitope residues' relative composition, cooperativity ratios, and Markov properties are also utilized to enhance our method. A nonredundant data set containing 80 antibody-antigen complexes is compiled and used in the evaluation. The results show that our method yields a good performance on antibody-specified epitope prediction. On the traditional antibody-ignored epitope prediction problem, a simplified version of our method can produce a competitive, sometimes much better, performance in comparison with three structure-based predictors.
Collapse
Affiliation(s)
- Liang Zhao
- School of Computer Engineering, Bioinformatics Research Center, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798.
| | | | | |
Collapse
|
112
|
Van Regenmortel MHV. Requirements for empirical immunogenicity trials, rather than structure-based design, for developing an effective HIV vaccine. Arch Virol 2011; 157:1-20. [PMID: 22012269 PMCID: PMC7087187 DOI: 10.1007/s00705-011-1145-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Accepted: 10/07/2011] [Indexed: 11/29/2022]
Abstract
The claim that it is possible to rationally design a structure-based HIV-1 vaccine is based on misconceptions regarding the nature of protein epitopes and of immunological specificity. Attempts to use reverse vaccinology to generate an HIV-1 vaccine on the basis of the structure of viral epitopes bound to monoclonal neutralizing antibodies have failed so far because it was not possible to extrapolate from an observed antigenic structure to the immunogenic structure required in a vaccine. Vaccine immunogenicity depends on numerous extrinsic factors such as the host immunoglobulin gene repertoire, the presence of various cellular and regulatory mechanisms in the immunized host and the process of antibody affinity maturation. All these factors played a role in the appearance of the neutralizing antibody used to select the epitope to be investigated as potential vaccine immunogen, but they cannot be expected to be present in identical form in the host to be vaccinated. It is possible to rationally design and optimize an epitope to fit one particular antibody molecule or to improve the paratope binding efficacy of a monoclonal antibody intended for passive immunotherapy. What is not possible is to rationally design an HIV-1 vaccine immunogen that will elicit a protective polyclonal antibody response of predetermined efficacy. An effective vaccine immunogen can only be discovered by investigating experimentally the immunogenicity of a candidate molecule and demonstrating its ability to induce a protective immune response. It cannot be discovered by determining which epitopes of an engineered antigen molecule are recognized by a neutralizing monoclonal antibody. This means that empirical immunogenicity trials rather than structural analyses of antigens offer the best hope of discovering an HIV-1 vaccine.
Collapse
Affiliation(s)
- Marc H V Van Regenmortel
- Stellenbosch Institute of Advanced Study, Wallenberg Research Center at Stellenbosch University, Stellenbosch 7600, South Africa.
| |
Collapse
|
113
|
Barbarini N, Tiengo A, Bellazzi R. Prediction of peptide reactivity with human IVIg through a knowledge-based approach. PLoS One 2011; 6:e23616. [PMID: 21887285 PMCID: PMC3160895 DOI: 10.1371/journal.pone.0023616] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Accepted: 07/21/2011] [Indexed: 11/18/2022] Open
Abstract
The prediction of antibody-protein (antigen) interactions is very difficult due to the huge variability that characterizes the structure of the antibodies. The region of the antigen bound to the antibodies is called epitope. Experimental data indicate that many antibodies react with a panel of distinct epitopes (positive reaction). The Challenge 1 of DREAM5 aims at understanding whether there exists rules for predicting the reactivity of a peptide/epitope, i.e., its capability to bind to human antibodies. DREAM 5 provided a training set of peptides with experimentally identified high and low reactivities to human antibodies. On the basis of this training set, the participants to the challenge were asked to develop a predictive model of reactivity. A test set was then provided to evaluate the performance of the model implemented so far.We developed a logistic regression model to predict the peptide reactivity, by facing the challenge as a machine learning problem. The initial features have been generated on the basis of the available knowledge and the information reported in the dataset. Our predictive model had the second best performance of the challenge. We also developed a method, based on a clustering approach, able to "in-silico" generate a list of positive and negative new peptide sequences, as requested by the DREAM5 "bonus round" additional challenge.The paper describes the developed model and its results in terms of reactivity prediction, and highlights some open issues concerning the propensity of a peptide to react with human antibodies.
Collapse
Affiliation(s)
- Nicola Barbarini
- Laboratory of Biomedical Informatics Mario Stefanelli, Department of Computer Engineering and Systems Science, University of Pavia, Pavia, Italy.
| | | | | |
Collapse
|
114
|
Prediction of B-cell linear epitopes with a combination of support vector machine classification and amino acid propensity identification. J Biomed Biotechnol 2011; 2011:432830. [PMID: 21876642 PMCID: PMC3163029 DOI: 10.1155/2011/432830] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Accepted: 06/28/2011] [Indexed: 12/29/2022] Open
Abstract
Epitopes are antigenic determinants that are useful because they induce B-cell antibody production and stimulate T-cell activation. Bioinformatics can enable rapid, efficient prediction of potential epitopes. Here, we designed a novel B-cell linear epitope prediction system called LEPS, Linear Epitope Prediction by Propensities and Support Vector Machine, that combined physico-chemical propensity identification and support vector machine (SVM) classification. We tested the LEPS on four datasets: AntiJen, HIV, a newly generated PC, and AHP, a combination of these three datasets. Peptides with globally or locally high physicochemical propensities were first identified as primitive linear epitope (LE) candidates. Then, candidates were classified with the SVM based on the unique features of amino acid segments. This reduced the number of predicted epitopes and enhanced the positive prediction value (PPV). Compared to four other well-known LE prediction systems, the LEPS achieved the highest accuracy (72.52%), specificity (84.22%), PPV (32.07%), and Matthews' correlation coefficient (10.36%).
Collapse
|
115
|
Epitope prediction based on random peptide library screening: benchmark dataset and prediction tools evaluation. Molecules 2011; 16:4971-93. [PMID: 21681149 PMCID: PMC6264216 DOI: 10.3390/molecules16064971] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Revised: 06/01/2011] [Accepted: 06/10/2011] [Indexed: 11/16/2022] Open
Abstract
Epitope prediction based on random peptide library screening has become a focus as a promising method in immunoinformatics research. Some novel software and web-based servers have been proposed in recent years and have succeeded in given test cases. However, since the number of available mimotopes with the relevant structure of template-target complex is limited, a systematic evaluation of these methods is still absent. In this study, a new benchmark dataset was defined. Using this benchmark dataset and a representative dataset, five examples of the most popular epitope prediction software products which are based on random peptide library screening have been evaluated. Using the benchmark dataset, in no method did performance exceed a 0.42 precision and 0.37 sensitivity, and the MCC scores suggest that the epitope prediction results of these software programs are greater than random prediction about 0.09–0.13; while using the representative dataset, most of the values of these performance measures are slightly improved, but the overall performance is still not satisfactory. Many test cases in the benchmark dataset cannot be applied to these pieces of software due to software limitations. Moreover chances are that these software products are overfitted to the small dataset and will fail in other cases. Therefore finding the correlation between mimotopes and genuine epitope residues is still far from resolved and much larger dataset for mimotope-based epitope prediction is desirable.
Collapse
|
116
|
MimoPro: a more efficient Web-based tool for epitope prediction using phage display libraries. BMC Bioinformatics 2011; 12:199. [PMID: 21609501 PMCID: PMC3124435 DOI: 10.1186/1471-2105-12-199] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2010] [Accepted: 05/25/2011] [Indexed: 11/24/2022] Open
Abstract
Background A B-cell epitope is a group of residues on the surface of an antigen which stimulates humoral responses. Locating these epitopes on antigens is important for the purpose of effective vaccine design. In recent years, mapping affinity-selected peptides screened from a random phage display library to the native epitope has become popular in epitope prediction. These peptides, also known as mimotopes, share the similar structure and function with the corresponding native epitopes. Great effort has been made in using this similarity between such mimotopes and native epitopes in prediction, which has resulted in better outcomes than statistics-based methods can. However, it cannot maintain a high degree of satisfaction in various circumstances. Results In this study, we propose a new method that maps a group of mimotopes back to a source antigen so as to locate the interacting epitope on the antigen. The core of this method is a searching algorithm that is incorporated with both dynamic programming (DP) and branch and bound (BB) optimization and operated on a series of overlapping patches on the surface of a protein. These patches are then transformed to a number of graphs using an adaptable distance threshold (ADT) regulated by an appropriate compactness factor (CF), a novel parameter proposed in this study. Compared with both Pep-3D-Search and PepSurf, two leading graph-based search tools, on average from the results of 18 test cases, MimoPro, the Web-based implementation of our proposed method, performed better in sensitivity, precision, and Matthews correlation coefficient (MCC) than both did in epitope prediction. In addition, MimoPro is significantly faster than both Pep-3D-Search and PepSurf in processing. Conclusions Our search algorithm designed for processing well constructed graphs using an ADT regulated by CF is more sensitive and significantly faster than other graph-based approaches in epitope prediction. MimoPro is a viable alternative to both PepSurf and Pep-3D-Search for epitope prediction in the same kind, and freely accessible through the MimoPro server located at http://informatics.nenu.edu.cn/MimoPro.
Collapse
|
117
|
Pacios LF, Tordesillas L, Palacín A, Sánchez-Monge R, Salcedo G, Díaz-Perales A. LocaPep: Localization of Epitopes on Protein Surfaces Using Peptides from Phage Display Libraries. J Chem Inf Model 2011; 51:1465-73. [DOI: 10.1021/ci200059c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Luis F. Pacios
- Department Biotecnología, ETSI Montes, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Leticia Tordesillas
- Department Biotecnología, ETSI Agrónomos, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Arantxa Palacín
- Department Biotecnología, ETSI Agrónomos, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Rosa Sánchez-Monge
- Department Biotecnología, ETSI Agrónomos, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Gabriel Salcedo
- Department Biotecnología, ETSI Agrónomos, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Araceli Díaz-Perales
- Department Biotecnología, ETSI Agrónomos, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| |
Collapse
|
118
|
Kumar S, Singh SK, Wang X, Rup B, Gill D. Coupling of Aggregation and Immunogenicity in Biotherapeutics: T- and B-Cell Immune Epitopes May Contain Aggregation-Prone Regions. Pharm Res 2011; 28:949-61. [DOI: 10.1007/s11095-011-0414-9] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Accepted: 03/01/2011] [Indexed: 11/29/2022]
|
119
|
In silico proteomic characterization of human epidermal growth factor receptor 2 (HER-2) for the mapping of high affinity antigenic determinants against breast cancer. Amino Acids 2011; 42:1349-60. [DOI: 10.1007/s00726-010-0830-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2010] [Accepted: 12/23/2010] [Indexed: 10/18/2022]
|
120
|
Tai DF, Ho YF, Wu CH, Lin TC, Lu KH, Lin KS. Artificial-epitope mapping for CK-MB assay. Analyst 2011; 136:2230-3. [DOI: 10.1039/c0an00919a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
121
|
Magnan CN, Zeller M, Kayala MA, Vigil A, Randall A, Felgner PL, Baldi P. High-throughput prediction of protein antigenicity using protein microarray data. Bioinformatics 2010; 26:2936-43. [PMID: 20934990 PMCID: PMC2982151 DOI: 10.1093/bioinformatics/btq551] [Citation(s) in RCA: 322] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2010] [Revised: 09/08/2010] [Accepted: 09/23/2010] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Discovery of novel protective antigens is fundamental to the development of vaccines for existing and emerging pathogens. Most computational methods for predicting protein antigenicity rely directly on homology with previously characterized protective antigens; however, homology-based methods will fail to discover truly novel protective antigens. Thus, there is a significant need for homology-free methods capable of screening entire proteomes for the antigens most likely to generate a protective humoral immune response. RESULTS Here we begin by curating two types of positive data: (i) antigens that elicit a strong antibody response in protected individuals but not in unprotected individuals, using human immunoglobulin reactivity data obtained from protein microarray analyses; and (ii) known protective antigens from the literature. The resulting datasets are used to train a sequence-based prediction model, ANTIGENpro, to predict the likelihood that a protein is a protective antigen. ANTIGENpro correctly classifies 82% of the known protective antigens when trained using only the protein microarray datasets. The accuracy on the combined dataset is estimated at 76% by cross-validation experiments. Finally, ANTIGENpro performs well when evaluated on an external pathogen proteome for which protein microarray data were obtained after the initial development of ANTIGENpro. AVAILABILITY ANTIGENpro is integrated in the SCRATCH suite of predictors available at http://scratch.proteomics.ics.uci.edu. CONTACT pfbaldi@ics.uci.edu
Collapse
Affiliation(s)
- Christophe N Magnan
- Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California, Irvine, CA 92697, USA
| | | | | | | | | | | | | |
Collapse
|
122
|
Denisova GF, Denisov DA, Bramson JL. Applying bioinformatics for antibody epitope prediction using affinity-selected mimotopes - relevance for vaccine design. Immunome Res 2010; 6 Suppl 2:S6. [PMID: 21067548 PMCID: PMC2981875 DOI: 10.1186/1745-7580-6-s2-s6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
To properly characterize protective polyclonal antibody responses, it is necessary to examine epitope specificity. Most antibody epitopes are conformational in nature and, thus, cannot be identified using synthetic linear peptides. Cyclic peptides can function as mimetics of conformational epitopes (termed mimotopes), thereby providing targets, which can be selected by immunoaffinity purification. However, the management of large collections of random cyclic peptides is cumbersome. Filamentous bacteriophage provides a useful scaffold for the expression of random peptides (termed phage display) facilitating both the production and manipulation of complex peptide libraries. Immunoaffinity selection of phage displaying random cyclic peptides is an effective strategy for isolating mimotopes with specificity for a given antiserum. Further epitope prediction based on mimotope sequence is not trivial since mimotopes generally display only small homologies with the target protein. Large numbers of unique mimotopes are required to provide sufficient sequence coverage to elucidate the target epitope. We have developed a method based on pattern recognition theory to deal with the complexity of large collections of conformational mimotopes. The analysis consists of two phases: 1) The learning phase where a large collection of epitope-specific mimotopes is analyzed to identify epitope specific “signs” and 2) The identification phase where immunoaffinity-selected mimotopes are interrogated for the presence of the epitope specific “signs” and assigned to specific epitopes. We are currently using computational methods to define epitope “signs” without the need for prior knowledge of specific mimotopes. This technology provides an important tool for characterizing the breadth of antibody specificities within polyclonal antisera.
Collapse
Affiliation(s)
- Galina F Denisova
- Department of Pathology and Molecular Medicine, Centre for Gene Therapeutics, McMaster University, 1200 Main Street West, Hamilton, Ontario, Canada, L8N 3Z5.
| | | | | |
Collapse
|
123
|
Abstract
Identification of epitopes that invoke strong responses from B-cells is one of the key steps in designing effective vaccines against pathogens. Because experimental determination of epitopes is expensive in terms of cost, time, and effort involved, there is an urgent need for computational methods for reliable identification of B-cell epitopes. Although several computational tools for predicting B-cell epitopes have become available in recent years, the predictive performance of existing tools remains far from ideal. We review recent advances in computational methods for B-cell epitope prediction, identify some gaps in the current state of the art, and outline some promising directions for improving the reliability of such methods.
Collapse
|
124
|
Ponomarenko J, Papangelopoulos N, Zajonc DM, Peters B, Sette A, Bourne PE. IEDB-3D: structural data within the immune epitope database. Nucleic Acids Res 2010; 39:D1164-70. [PMID: 21030437 PMCID: PMC3013771 DOI: 10.1093/nar/gkq888] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
IEDB-3D is the 3D structural component of the Immune Epitope Database (IEDB) available via the 'Browse by 3D Structure' page at http://www.iedb.org. IEDB-3D catalogs B- and T-cell epitopes and Major Histocompatibility Complex (MHC) ligands for which 3D structures of complexes with antibodies, T-cell receptors or MHC molecules are available in the Protein Data Bank (PDB). Journal articles that are primary citations of PDB structures and that define immune epitopes are curated within IEDB as any other reference along with accompanying functional assays and immunologically relevant information. For each curated structure, IEDB-3D provides calculated data on intermolecular contacts and interface areas and includes an application, EpitopeViewer, to visualize the structures. IEDB-3D is fully embedded within IEDB, thus allowing structural data, both curated and calculated, and all accompanying information to be queried using multiple search interfaces. These include queries for epitopes recognized in different pathogens, eliciting different functional immune responses, and recognized by different components of the immune system. The query results can be downloaded in Microsoft Excel format, or the entire database, together with structural data both curated and calculated, can be downloaded in either XML or MySQL formats.
Collapse
Affiliation(s)
- Julia Ponomarenko
- San Diego Supercomputer Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, CA 92093, USA.
| | | | | | | | | | | |
Collapse
|
125
|
Tomar N, De RK. Immunoinformatics: an integrated scenario. Immunology 2010; 131:153-68. [PMID: 20722763 PMCID: PMC2967261 DOI: 10.1111/j.1365-2567.2010.03330.x] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2009] [Revised: 06/12/2010] [Accepted: 06/21/2010] [Indexed: 12/11/2022] Open
Abstract
Genome sequencing of humans and other organisms has led to the accumulation of huge amounts of data, which include immunologically relevant data. A large volume of clinical data has been deposited in several immunological databases and as a result immunoinformatics has emerged as an important field which acts as an intersection between experimental immunology and computational approaches. It not only helps in dealing with the huge amount of data but also plays a role in defining new hypotheses related to immune responses. This article reviews classical immunology, different databases and prediction tools. It also describes applications of immunoinformatics in designing in silico vaccination and immune system modelling. All these efforts save time and reduce cost.
Collapse
Affiliation(s)
- Namrata Tomar
- Machine Intelligence Unit, Indian Statistical Institute, Kolkata, India
| | | |
Collapse
|
126
|
Fiorucci S, Zacharias M. Prediction of protein-protein interaction sites using electrostatic desolvation profiles. Biophys J 2010; 98:1921-30. [PMID: 20441756 DOI: 10.1016/j.bpj.2009.12.4332] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2009] [Revised: 11/30/2009] [Accepted: 12/23/2009] [Indexed: 01/15/2023] Open
Abstract
Protein-protein complex formation involves removal of water from the interface region. Surface regions with a small free energy penalty for water removal or desolvation may correspond to preferred interaction sites. A method to calculate the electrostatic free energy of placing a neutral low-dielectric probe at various protein surface positions has been designed and applied to characterize putative interaction sites. Based on solutions of the finite-difference Poisson equation, this method also includes long-range electrostatic contributions and the protein solvent boundary shape in contrast to accessible-surface-area-based solvation energies. Calculations on a large set of proteins indicate that in many cases (>90%), the known binding site overlaps with one of the six regions of lowest electrostatic desolvation penalty (overlap with the lowest desolvation region for 48% of proteins). Since the onset of electrostatic desolvation occurs even before direct protein-protein contact formation, it may help guide proteins toward the binding region in the final stage of complex formation. It is interesting that the probe desolvation properties associated with residue types were found to depend to some degree on whether the residue was outside of or part of a binding site. The probe desolvation penalty was on average smaller if the residue was part of a binding site compared to other surface locations. Applications to several antigen-antibody complexes demonstrated that the approach might be useful not only to predict protein interaction sites in general but to map potential antigenic epitopes on protein surfaces.
Collapse
Affiliation(s)
- Sébastien Fiorucci
- School of Engineering and Science, Jacobs University Bremen, Bremen, Germany.
| | | |
Collapse
|
127
|
Predicting interaction sites from the energetics of isolated proteins: a new approach to epitope mapping. Biophys J 2010; 98:1966-75. [PMID: 20441761 DOI: 10.1016/j.bpj.2010.01.014] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2009] [Revised: 01/08/2010] [Accepted: 01/11/2010] [Indexed: 02/02/2023] Open
Abstract
An increasing number of functional studies of proteins have shown that sequence and structural similarities alone may not be sufficient for reliable prediction of their interaction properties. This is particularly true for proteins recognizing specific antibodies, where the prediction of antibody-binding sites, called epitopes, has proven challenging. The antibody-binding properties of an antigen depend on its structure and related dynamics. Aiming to predict the antibody-binding regions of a protein, we investigate a new approach based on the integrated analysis of the dynamical and energetic properties of antigens, to identify nonoptimized, low-intensity energetic interaction networks in the protein structure isolated in solution. The method is based on the idea that recognition sites may correspond to localized regions with low-intensity energetic couplings with the rest of the protein, which allows them to undergo conformational changes, to be recognized by a binding partner, and to tolerate mutations with minimal energetic expense. Upon analyzing the results on isolated proteins and benchmarking against antibody complexes, it is found that the method successfully identifies binding sites located on the protein surface that are accessible to putative binding partners. The combination of dynamics and energetics can thus discriminate between epitopes and other substructures based only on physical properties. We discuss implications for vaccine design.
Collapse
|
128
|
Scientific Opinion on the assessment of allergenicity of GM plants and microorganisms and derived food and feed. EFSA J 2010. [DOI: 10.2903/j.efsa.2010.1700] [Citation(s) in RCA: 243] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
|
129
|
Liang S, Zheng D, Standley DM, Yao B, Zacharias M, Zhang C. EPSVR and EPMeta: prediction of antigenic epitopes using support vector regression and multiple server results. BMC Bioinformatics 2010; 11:381. [PMID: 20637083 PMCID: PMC2910724 DOI: 10.1186/1471-2105-11-381] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2010] [Accepted: 07/16/2010] [Indexed: 11/10/2022] Open
Abstract
Background Accurate prediction of antigenic epitopes is important for immunologic research and medical applications, but it is still an open problem in bioinformatics. The case for discontinuous epitopes is even worse - currently there are only a few discontinuous epitope prediction servers available, though discontinuous peptides constitute the majority of all B-cell antigenic epitopes. The small number of structures for antigen-antibody complexes limits the development of reliable discontinuous epitope prediction methods and an unbiased benchmark to evaluate developed methods. Results In this work, we present two novel server applications for discontinuous epitope prediction: EPSVR and EPMeta, where EPMeta is a meta server. EPSVR, EPMeta, and datasets are available at http://sysbio.unl.edu/services. Conclusion The server application for discontinuous epitope prediction, EPSVR, uses a Support Vector Regression (SVR) method to integrate six scoring terms. Furthermore, we combined EPSVR with five existing epitope prediction servers to construct EPMeta. All methods were benchmarked by our curated independent test set, in which all antigens had no complex structures with the antibody, and their epitopes were identified by various biochemical experiments. The area under the receiver operating characteristic curve (AUC) of EPSVR was 0.597, higher than that of any other existing single server, and EPMeta had a better performance than any single server - with an AUC of 0.638, significantly higher than PEPITO and Disctope (p-value < 0.05).
Collapse
|
130
|
Xu X, Sun J, Liu Q, Wang X, Xu T, Zhu R, Wu D, Cao Z. Evaluation of spatial epitope computational tools based on experimentally-confirmed dataset for protein antigens. ACTA ACUST UNITED AC 2010. [DOI: 10.1007/s11434-010-3199-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
131
|
Zhao L, Li J. Mining for the antibody-antigen interacting associations that predict the B cell epitopes. BMC STRUCTURAL BIOLOGY 2010; 10 Suppl 1:S6. [PMID: 20487513 PMCID: PMC2873829 DOI: 10.1186/1472-6807-10-s1-s6] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background Predicting B-cell epitopes is very important for designing vaccines and drugs to fight against the infectious agents. However, due to the high complexity of this problem, previous prediction methods that focus on linear and conformational epitope prediction are both unsatisfactory. In addition, antigen interacting with antibody is context dependent and the coarse binary classification of antigen residues into epitope and non-epitope without the corresponding antibody may not reveal the biological reality. Therefore, we take a novel way to identify epitopes by using associations between antibodies and antigens. Results Given a pair of antibody-antigen sequences, the epitope residues can be identified by two types of associations: paratope-epitope interacting biclique and cooccurrent pattern of interacting residue pairs. As the association itself does not include the neighborhood information on the primary sequence, residues' cooperativity and relative composition are then used to enhance our method. Evaluation carried out on a benchmark data set shows that the proposed method produces very good performance in terms of accuracy. After compared with other two structure-based B-cell epitope prediction methods, results show that the proposed method is competitive to, sometimes even better than, the structure-based methods which have much smaller applicability scope. Conclusions The proposed method leads to a new way of identifying B-cell epitopes. Besides, this antibody-specified epitope prediction can provide more precise and helpful information for wet-lab experiments.
Collapse
Affiliation(s)
- Liang Zhao
- Bioinformatics Research Center, & School of Computer Engineering, Nanyang Technological University, Nanyang Avenue, Singapore 639798
| | | |
Collapse
|
132
|
Innovative bioinformatic approaches for developing peptide-based vaccines against hypervariable viruses. Immunol Cell Biol 2010; 89:81-9. [PMID: 20458336 DOI: 10.1038/icb.2010.65] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The application of the fields of pharmacogenomics and pharmacogenetics to vaccine design has been recently labeled 'vaccinomics'. This newly named area of vaccine research, heavily intertwined with bioinformatics, seems to be leading the charge in developing novel vaccines for currently unmet medical needs against hypervariable viruses such as human immunodeficiency virus (HIV), hepatitis C and emerging avian and swine influenza. Some of the more recent bioinformatic approaches in the area of vaccine research include the use of epitope determination and prediction algorithms for exploring the use of peptide epitopes as vaccine immunogens. This paper briefly discusses and explores some current uses of bioinformatics in vaccine design toward the pursuit of peptide vaccines for hypervariable viruses. The various informatics and vaccine design strategies attempted by other groups toward hypervariable viruses will also be briefly examined, along with the strategy used by our group in the design and synthesis of peptide immunogens for candidate HIV and influenza vaccines.
Collapse
|
133
|
Inflammatory and autoimmune reactions in atherosclerosis and vaccine design informatics. J Biomed Biotechnol 2010; 2010:459798. [PMID: 20414374 PMCID: PMC2858284 DOI: 10.1155/2010/459798] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2009] [Revised: 01/15/2010] [Accepted: 01/28/2010] [Indexed: 12/14/2022] Open
Abstract
Atherosclerosis is the leading pathological contributor to cardiovascular morbidity and mortality worldwide. As its complex pathogenesis has been gradually unwoven, the regime of treatments and therapies has increased with still much ground to cover. Active research in the past decade has attempted to develop antiatherosclerosis vaccines with some positive results. Nevertheless, it remains to develop a vaccine against atherosclerosis with high affinity, specificity, efficiency, and minimal undesirable pathology. In this review, we explore vaccine development against atherosclerosis by interpolating a number of novel findings in the fields of vascular biology, immunology, and bioinformatics. With recent technological breakthroughs, vaccine development affords precision in specifying the nature of the desired immune response—useful when addressing a disease as complex as atherosclerosis with a manifold of inflammatory and autoimmune components. Moreover, our exploration of available bioinformatic tools for epitope-based vaccine design provides a method to avoid expenditure of excess time or resources.
Collapse
|
134
|
Benchmarking B-cell epitope prediction for the design of peptide-based vaccines: problems and prospects. J Biomed Biotechnol 2010; 2010:910524. [PMID: 20368996 PMCID: PMC2847767 DOI: 10.1155/2010/910524] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2009] [Revised: 12/12/2009] [Accepted: 02/18/2010] [Indexed: 11/18/2022] Open
Abstract
To better support the design of peptide-based vaccines, refinement of methods to predict B-cell epitopes necessitates meaningful benchmarking against empirical data on the cross-reactivity of polyclonal antipeptide antibodies with proteins, such that the positive data reflect functionally relevant cross-reactivity (which is consistent with antibody-mediated change in protein function) and the negative data reflect genuine absence of cross-reactivity (rather than apparent absence of cross-reactivity due to artifactual masking of B-cell epitopes in immunoassays). These data are heterogeneous in view of multiple factors that complicate B-cell epitope prediction, notably physicochemical factors that define key structural differences between immunizing peptides and their cognate proteins (e.g., unmatched electrical charges along the peptide-protein sequence alignments). If the data are partitioned with respect to these factors, iterative parallel benchmarking against the resulting subsets of data provides a basis for systematically identifying and addressing the limitations of methods for B-cell epitope prediction as applied to vaccine design.
Collapse
|
135
|
Black M, Trent A, Tirrell M, Olive C. Advances in the design and delivery of peptide subunit vaccines with a focus on toll-like receptor agonists. Expert Rev Vaccines 2010; 9:157-73. [PMID: 20109027 DOI: 10.1586/erv.09.160] [Citation(s) in RCA: 132] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Considerable success has been made with many peptide antigen formulations, and peptide-based vaccines are emerging as the next generation of prophylactic and remedial immunotherapy. However, finding an optimal platform balancing all of the requirements for an effective, specific and safe immune response remains a major challenge for many infectious and chronic diseases. This review outlines how peptide immunogenicity is influenced by the way in which peptides are presented to the immune system, underscoring the need for multifunctional delivery systems that couple antigen and adjuvant into a single construct. Particular attention is given to the ability of Toll-like receptor agonists to act as adjuvants. A survey of recent approaches to developing peptide antigen delivery systems is given, many of which incorporate Toll-like receptor agonists into the design.
Collapse
Affiliation(s)
- Matthew Black
- University of California, Santa Barbara, CA 93106, USA.
| | | | | | | |
Collapse
|
136
|
Salimi N, Fleri W, Peters B, Sette A. Design and utilization of epitope-based databases and predictive tools. Immunogenetics 2010; 62:185-96. [PMID: 20213141 PMCID: PMC2843836 DOI: 10.1007/s00251-010-0435-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2009] [Accepted: 02/11/2010] [Indexed: 11/30/2022]
Abstract
In the last decade, significant progress has been made in expanding the scope and depth of publicly available immunological databases and online analysis resources, which have become an integral part of the repertoire of tools available to the scientific community for basic and applied research. Herein, we present a general overview of different resources and databases currently available. Because of our association with the Immune Epitope Database and Analysis Resource, this resource is reviewed in more detail. Our review includes aspects such as the development of formal ontologies and the type and breadth of analytical tools available to predict epitopes and analyze immune epitope data. A common feature of immunological databases is the requirement to host large amounts of data extracted from disparate sources. Accordingly, we discuss and review processes to curate the immunological literature, as well as examples of how the curated data can be used to generate a meta-analysis of the epitope knowledge currently available for diseases of worldwide concern, such as influenza and malaria. Finally, we review the impact of immunological databases, by analyzing their usage and citations, and by categorizing the type of citations. Taken together, the results highlight the growing impact and utility of immunological databases for the scientific community.
Collapse
Affiliation(s)
- Nima Salimi
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA.
| | | | | | | |
Collapse
|
137
|
Cysteine-free proteins in the immunobiology of arthropod-borne diseases. J Biomed Biotechnol 2010; 2010:171537. [PMID: 20069123 PMCID: PMC2804111 DOI: 10.1155/2010/171537] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2009] [Accepted: 10/13/2009] [Indexed: 11/21/2022] Open
Abstract
One approach to identify epitopes that could be used in the design of vaccines to control several arthropod-borne diseases simultaneously is to look for common structural features in the secretome of the pathogens that cause them. Using a novel bioinformatics technique, cysteine-abundance and distribution analysis, we found that many different proteins secreted by several arthropod-borne pathogens, including Plasmodium falciparum, Borrelia burgdorferi, and eight species of Proteobacteria, are devoid of cysteine residues. The identification of three cysteine-abundance and distribution patterns in several families of proteins secreted by pathogenic and nonpathogenic Proteobacteria, and not found when the amino acid analyzed was tryptophan, provides evidence of forces restricting the content of cysteine residues in microbial proteins during evolution. We discuss these findings in the context of protein structure and function, antigenicity and immunogenicity, and host-parasite relationships.
Collapse
|
138
|
Zhang ZW, Zhang YG, Wang YL, Pan L, Fang YZ, Jiang ST, Lü JL, Zhou P. Screening and identification of B cell epitopes of structural proteins of foot-and-mouth disease virus serotype Asia1. Vet Microbiol 2010; 140:25-33. [PMID: 19699594 DOI: 10.1016/j.vetmic.2009.07.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2009] [Revised: 06/24/2009] [Accepted: 07/03/2009] [Indexed: 11/24/2022]
|
139
|
In silico DNA vaccine designing against human papillomavirus (HPV) causing cervical cancer. Vaccine 2009; 28:120-31. [DOI: 10.1016/j.vaccine.2009.09.095] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2009] [Revised: 09/17/2009] [Accepted: 09/22/2009] [Indexed: 12/15/2022]
|
140
|
Removal of B cell epitopes as a practical approach for reducing the immunogenicity of foreign protein-based therapeutics. Adv Drug Deliv Rev 2009; 61:977-85. [PMID: 19679153 DOI: 10.1016/j.addr.2009.07.014] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2009] [Revised: 07/09/2009] [Accepted: 07/14/2009] [Indexed: 11/23/2022]
Abstract
Immunogenicity of non-human proteins with useful therapeutic properties has prevented their development for use in the therapy of disease. However, this class of proteins could be very useful, if their immunogenicity could be markedly reduced so that many treatment cycles could be administered. One approach to reduce the immunogenicity of foreign proteins is to identify B cell epitopes on the protein and eliminate them by mutagenesis. In this article, theoretical aspects and experimental evidence for the feasibility of B cell epitope removal is reviewed. A special focus is given to our results with deimmunization of recombinant immunotoxins in which Fvs are fused to a 38kDa portion of the bacterial protein, Pseudomonas exotoxin A (PE38). Immunotoxins targeting CD22 and CD25 have produced complete remissions in many patients with drug resistant Hairy Cell Leukemia and are being evaluated in other malignancies. Experimental data summarized in this review indicates that removal of B cell epitopes is a practical approach for making less immunogenic protein therapeutics from non-human functional proteins. This approach requires grouping of the epitopes to identify targets for deimmunization followed by quantitative analysis of the decrease in affinity produced by the mutations in B cell epitopes.
Collapse
|
141
|
Liang S, Zheng D, Zhang C, Zacharias M. Prediction of antigenic epitopes on protein surfaces by consensus scoring. BMC Bioinformatics 2009; 10:302. [PMID: 19772615 PMCID: PMC2761409 DOI: 10.1186/1471-2105-10-302] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2009] [Accepted: 09/22/2009] [Indexed: 12/05/2022] Open
Abstract
Background Prediction of antigenic epitopes on protein surfaces is important for vaccine design. Most existing epitope prediction methods focus on protein sequences to predict continuous epitopes linear in sequence. Only a few structure-based epitope prediction algorithms are available and they have not yet shown satisfying performance. Results We present a new antigen Epitope Prediction method, which uses ConsEnsus Scoring (EPCES) from six different scoring functions - residue epitope propensity, conservation score, side-chain energy score, contact number, surface planarity score, and secondary structure composition. Applied to unbounded antigen structures from an independent test set, EPCES was able to predict antigenic eptitopes with 47.8% sensitivity, 69.5% specificity and an AUC value of 0.632. The performance of the method is statistically similar to other published methods. The AUC value of EPCES is slightly higher compared to the best results of existing algorithms by about 0.034. Conclusion Our work shows consensus scoring of multiple features has a better performance than any single term. The successful prediction is also due to the new score of residue epitope propensity based on atomic solvent accessibility.
Collapse
Affiliation(s)
- Shide Liang
- School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany
| | | | | | | |
Collapse
|
142
|
Toussaint NC, Kohlbacher O. Towards in silico design of epitope-based vaccines. Expert Opin Drug Discov 2009; 4:1047-60. [PMID: 23480396 DOI: 10.1517/17460440903242283] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
BACKGROUND Epitope-based vaccines (EVs) make use of immunogenic peptides (epitopes) to trigger an immune response. Due to their manifold advantages, EVs have recently been attracting growing interest. The success of an EV is determined by the choice of epitopes used as a basis. However, the experimental discovery of candidate epitopes is expensive in terms of time and money. Furthermore, for the final choice of epitopes various immunological requirements have to be considered. METHODS Numerous in silico approaches exist that can guide the design of EVs. In particular, computational methods for MHC binding prediction have already become standard tools in immunology. Apart from binding prediction and prediction of antigen processing, methods for epitope design and selection have been suggested. We review these in silico approaches for epitope discovery and selection along with their strengths and weaknesses. Finally, we discuss some of the obvious problems in the design of EVs. CONCLUSION State-of-the-art in silico approaches to MHC binding prediction yield high accuracies. However, a more thorough understanding of the underlying biological processes and significant amounts of experimental data will be required for the validation and improvement of in silico approaches to the remaining aspects of EV design.
Collapse
Affiliation(s)
- Nora C Toussaint
- Eberhard Karls University, Center for Bioinformatics Tübingen, Division for Simulation of Biological Systems, 72076 Tübingen, Germany +49 7071 2970458 ; +49 7071 295152 ;
| | | |
Collapse
|
143
|
Tong JC, Ren EC. Immunoinformatics: current trends and future directions. Drug Discov Today 2009; 14:684-9. [PMID: 19379830 PMCID: PMC7108239 DOI: 10.1016/j.drudis.2009.04.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2008] [Revised: 03/30/2009] [Accepted: 04/06/2009] [Indexed: 01/28/2023]
Abstract
Immunoinformatics has recently emerged as a critical field for accelerating immunology research. Although still an evolving process, computational models now play instrumental roles, not only in directing the selection of key experiments, but also in the formulation of new testable hypotheses through detailed analysis of complex immunologic data that could not be achieved using traditional approaches alone. Immunomics, which combines traditional immunology with computer science, mathematics, chemistry, biochemistry, genomics and proteomics for the large-scale analysis of immune system function, offers new opportunities for future bench-to-bedside research. In this article, we review the latest trends and future directions of the field.
Collapse
Affiliation(s)
- Joo Chuan Tong
- Institute for Infocomm Research, 1 Fusionopolis Way, #21-01 Connexis, South Tower, Singapore 138632, Singapore.
| | | |
Collapse
|
144
|
Yang X, Yu X. An introduction to epitope prediction methods and software. Rev Med Virol 2009; 19:77-96. [PMID: 19101924 DOI: 10.1002/rmv.602] [Citation(s) in RCA: 127] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
In this paper, current prediction methods and algorithms for both T- and B cell epitopes are reviewed, and a comprehensive summary of epitope prediction software and databases currently available online is also provided. This review can offer researchers in this field a sense of direction and insights for future work. However, our main purpose is to introduce clinical and basic biomedical researchers who are not familiar with these biological analysis tools and databases to these online resources and to provide guidance on how to use them effectively.
Collapse
Affiliation(s)
- Xingdong Yang
- Department of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan, P. R. China
| | | |
Collapse
|
145
|
Lata S, Bhasin M, Raghava GPS. MHCBN 4.0: A database of MHC/TAP binding peptides and T-cell epitopes. BMC Res Notes 2009; 2:61. [PMID: 19379493 PMCID: PMC2679046 DOI: 10.1186/1756-0500-2-61] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2008] [Accepted: 04/20/2009] [Indexed: 11/23/2022] Open
Abstract
Background Many databases housing the information about MHC binders and non-binders have been developed in the past to help the scientific community working in the field of immunology, immune-informatics or vaccine design. As the information about these MHC binding and non-binding peptides continues to grow with the time and there is a need to keep the databases updated. So, in order to provide the immunological fraternity with the most recent information we need to maintain and update our database regularly. In this paper, we describe the updated version of 4.0 of the database MHCBN. Findings MHCBN is a comprehensive database comprising over 25,857 peptide sequences (1053 TAP binding peptides), whose binding affinity with either MHC or TAP molecules has been assayed experimentally. It is a manually curated database where entries are collected & compiled from published literature and existing immunological public databases. MHCBN has a number of web-based tools for the analysis and retrieval of information like mapping of antigenic regions, creation of allele specific dataset, BLAST search, various diseases associated with MHC alleles etc. Further, all entries are hyper linked to major databases like SWISS-PROT, PDB etc. to provide the information beyond the scope of MHCBN. The latest version 4.0 of MHCBN has 6080 more entries than previously published version 1.1. Conclusion MHCBN database updating is meant to facilitate immunologist in understanding the immune system and provide them the latest information. We feel that our database will complement the existing databases in serving scientific community.
Collapse
Affiliation(s)
- Sneh Lata
- Bioinformatics Center, Institute of Microbial Technology, Sector 39A, Chandigarh, India.
| | | | | |
Collapse
|
146
|
|
147
|
Chang HT, Liu CH, Pai TW. Estimation and extraction of B-cell linear epitopes predicted by mathematical morphology approaches. J Mol Recognit 2009; 21:431-41. [PMID: 18680207 DOI: 10.1002/jmr.910] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
B-cell epitope prediction facilitates the design and synthesis of short peptides for various immunological applications. Several algorithms have been developed to predict B-cell linear epitopes (LEs) from primary sequences of antigens, providing important information for immunobiological experiments and antibody design. This paper describes two robust methods, LE prediction with/without local peak extraction (LEP-LP and LEP-NLP), based on antigenicity scale and mathematical morphology for the prediction of B-cell LEs. Previous studies revealed that LEs could occur in regions with low-to-moderate but not globally high antigenicity scales. Hence, we developed a method adopting mathematical morphology to extract local peaks from a linear combination of the propensity scales of physico-chemical characteristics at each antigen residue. Comparison among LEP-LP/LEP-NLP, BepiPred and BEPITOPE revealed that our algorithms performed better in retrieving epitopes with low-to-moderate antigenicity and achieved comparable performance according to receiver operation characteristics (ROC) curve analysis. Of the identified LEs, over 30% were unable to be predicted by BepiPred and BEPITOPE employing an average threshold of antigenicity index or default settings. Our LEP-LP method provides a bioinformatics approach for predicting B-cell LEs with low- to-moderate antigenicity. The web-based server was established at http://biotools.cs.ntou.edu.tw/lepd_antigenicity. php for free use.
Collapse
Affiliation(s)
- Hao-Teng Chang
- Graduate Institute of Molecular Systems Biomedicine, China Medical University, Taichung, Taiwan, ROC
| | | | | |
Collapse
|
148
|
Abstract
The prediction of B-cell epitopes is desirable for designing peptide-based vaccines, or generating antibodies especially if the purified protein is difficult to obtain and immunization has to be performed with protein-derived synthetic peptides. A number of freely available tools predict epitopes from protein sequence or structural information. The handling of these tools is described and the predictive power is assessed using test data based on the proteome of HIV, where comprehensive epitope mapping data are available.
Collapse
Affiliation(s)
- Ulf Reimer
- Computational Chemistry Department, Jerini AG, Invalidenstr. 130, D-10115 Berlin, Germany
| |
Collapse
|
149
|
Davies MN, Flower DR. Computational Vaccinology. BIOINFORMATICS FOR IMMUNOMICS 2009. [PMCID: PMC7121138 DOI: 10.1007/978-1-4419-0540-6_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
150
|
Abstract
The antigenicity of proteins resides in different types of antigenic determinants known as continuous and discontinuous epitopes, cryptotopes, neotopes, and mimotopes. All epitopes have fuzzy boundaries and can be identified only by their ability to bind to certain antibodies. Antigenic cross-reactivity is a common phenomenon because antibodies are always able to recognize a considerable number of related epitopes. This places severe limits to the specificity of antibodies. Antigenicity, which is the ability of an epitope to react with an antibody, must be distinguished from its immunogenicity or ability to induce antibodies in a competent vertebrate host. Failure to make this distinction partly explains why no successful peptide-based vaccines have yet been developed. Methods for predicting the epitopes of proteins are discussed and the reasons for the low success rate of epitope prediction are analyzed.
Collapse
|