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Capelli R, Serapian SA, Colombo G. Computational Epitope Prediction and Design for Antibody Development and Detection. Methods Mol Biol 2023; 2552:255-266. [PMID: 36346596 DOI: 10.1007/978-1-0716-2609-2_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The design of optimized protein antigens is a fundamental step in the development of new vaccine candidates and in the detection of therapeutic antibodies. A fundamental prerequisite is the identification of antigenic regions that are most prone to interact with antibodies, namely, B-cell epitopes. Here, we describe an efficient structure-based computational method for epitope prediction, called MLCE. In this approach, all that is required is the 3D structure of the antigen of interest. MLCE can be applied to glycosylated proteins, facilitating the identification of immunoreactive versus immune-shielding carbohydrates.
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Affiliation(s)
- Riccardo Capelli
- SCITEC-CNR, Milan, Italy
- Politecnico di Torino, Department of Applied Science and Technology, Torino, Italy
| | | | - Giorgio Colombo
- SCITEC-CNR, Milan, Italy.
- Università di Pavia, Dipartimento di Chimica, Pavia, Italy.
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Quilici G, Berardi A, Fabris C, Ghitti M, Punta M, Gourlay LJ, Bolognesi M, Musco G. Solution Structure of the BPSL1445 Protein of Burkholderia pseudomallei Reveals the SYLF Domain Three-Dimensional Fold. ACS Chem Biol 2022; 17:230-239. [PMID: 34968022 DOI: 10.1021/acschembio.1c00886] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The SYLF domain is an evolutionary conserved protein domain with phosphatidylinositol binding ability, whose three-dimensional structure is unknown. Here, we present the solution structure and the dynamics characterization of the SYLF domain of the bacterial BPSL1445 protein. BPSL1445 is a seroreactive antigen and a diagnostic marker of Burkholderia pseudomallei, the etiological agent of melioidosis, a severe infectious disease in the tropics. The BPSL1445 SYLF domain (BPSL1445-SYLF) consists of a β-barrel core, with two flexible loops protruding out of the barrel and three helices packing on its surface. Our structure allows for a more precise definition of the boundaries of the SYLF domain compared to the previously reported one and suggests common ancestry with bacterial EipA domains. We also demonstrate by phosphatidyl-inositol phosphate arrays and nuclear magnetic resonance titrations that BPSL1445-SYLF weakly interacts with phosphoinositides, thus supporting lipid binding abilities of this domain also in prokaryotes.
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Affiliation(s)
- Giacomo Quilici
- Biomolecular NMR Laboratory, I.R.C.C.S. Ospedale San Raffaele, Via Olgettina 58, 20132 Milan, Italy
| | - Andrea Berardi
- Biomolecular NMR Laboratory, I.R.C.C.S. Ospedale San Raffaele, Via Olgettina 58, 20132 Milan, Italy
| | - Chantal Fabris
- Biomolecular NMR Laboratory, I.R.C.C.S. Ospedale San Raffaele, Via Olgettina 58, 20132 Milan, Italy
| | - Michela Ghitti
- Biomolecular NMR Laboratory, I.R.C.C.S. Ospedale San Raffaele, Via Olgettina 58, 20132 Milan, Italy
| | - Marco Punta
- Unit of Immunogenetics, Leukemia Genomics and Immunobiology and Center for Omics Sciences, I.R.C.C.S. Ospedale San Raffaele, Via Olgettina 58, 20132 Milan, Italy
| | - Louise J. Gourlay
- Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milan, Italy
- Centro di Ricerca Pediatrica Romeo ed Enrica Invernizzi, Università degli Studi di Milano, 20133 Milan, Italy
| | - Martino Bolognesi
- Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milan, Italy
- Centro di Ricerca Pediatrica Romeo ed Enrica Invernizzi, Università degli Studi di Milano, 20133 Milan, Italy
| | - Giovanna Musco
- Biomolecular NMR Laboratory, I.R.C.C.S. Ospedale San Raffaele, Via Olgettina 58, 20132 Milan, Italy
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Postgenomic Approaches and Bioinformatics Tools to Advance the Development of Vaccines against Bacteria of the Burkholderia cepacia Complex. Vaccines (Basel) 2018; 6:vaccines6020034. [PMID: 29890657 PMCID: PMC6027386 DOI: 10.3390/vaccines6020034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 06/05/2018] [Accepted: 06/06/2018] [Indexed: 12/19/2022] Open
Abstract
Bacteria of the Burkholderia cepacia complex (Bcc) remain an important cause of morbidity and mortality among patients suffering from cystic fibrosis. Eradication of these pathogens by antimicrobial therapy often fails, highlighting the need to develop novel strategies to eradicate infections. Vaccines are attractive since they can confer protection to particularly vulnerable patients, as is the case of cystic fibrosis patients. Several studies have identified specific virulence factors and proteins as potential subunit vaccine candidates. So far, no vaccine is available to protect from Bcc infections. In the present work, we review the most promising postgenomic approaches and selected web tools available to speed up the identification of immunogenic proteins with the potential of conferring protection against Bcc infections.
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Titball RW, Burtnick MN, Bancroft GJ, Brett P. Burkholderia pseudomallei and Burkholderia mallei vaccines: Are we close to clinical trials? Vaccine 2017; 35:5981-5989. [DOI: 10.1016/j.vaccine.2017.03.022] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 02/17/2017] [Accepted: 03/07/2017] [Indexed: 10/19/2022]
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Gori A, Bolognesi M, Colombo G, Gourlay LJ. Structural Vaccinology for Melioidosis Vaccine Design and Immunodiagnostics. CURRENT TROPICAL MEDICINE REPORTS 2017. [DOI: 10.1007/s40475-017-0117-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Paladino A, Marchetti F, Rinaldi S, Colombo G. Protein design: from computer models to artificial intelligence. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2017. [DOI: 10.1002/wcms.1318] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Antonella Paladino
- Biomolecular Simulations & Computational Chemistry Group; Istituto Istituto di Chimica del Riconoscimento Molecolare, CNR; Milano Italy
| | - Filippo Marchetti
- Biomolecular Simulations & Computational Chemistry Group; Istituto Istituto di Chimica del Riconoscimento Molecolare, CNR; Milano Italy
| | - Silvia Rinaldi
- Biomolecular Simulations & Computational Chemistry Group; Istituto Istituto di Chimica del Riconoscimento Molecolare, CNR; Milano Italy
| | - Giorgio Colombo
- Biomolecular Simulations & Computational Chemistry Group; Istituto Istituto di Chimica del Riconoscimento Molecolare, CNR; Milano Italy
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Capelli R, Marchetti F, Tiana G, Colombo G. SAGE: A Fast Computational Tool for Linear Epitope Grafting onto a Foreign Protein Scaffold. J Chem Inf Model 2017; 57:6-10. [PMID: 27992203 DOI: 10.1021/acs.jcim.6b00584] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Computational design is becoming a driving force of structural vaccinology, whereby protein antigens are engineered to generate new biomolecules with optimized immunological properties. In particular, the design of new proteins that contain multiple, different epitopes can potentially provide novel highly efficient vaccine candidates. In this context, epitope grafting, which entails the transplantation of an antibody recognition motif from one protein onto a different protein scaffold (possibly containing other immunoreactive sequences) holds great promise for the realization of superantigens. Herein, we present SAGE (strategy for alignment and grafting of epitopes), an automated computational tool for the implantation of immunogenic epitopes onto a given scaffold. It is based on the comparison between the expected secondary structures of the candidates to be grafted with all the secondary structures in the target scaffold. Evaluating the differences both in sequence and in structure between the epitope and the scaffold returns a ranking of most probable molecules containing the new antigenic sequence. We validate this approach identifying the grafting positions obtained in previous works by experimental and computational methods, proving an efficient, flexible, and fast tool to perform the initial scanning for epitope grafting. This approach is fully general and may be applied to any target antigen and candidate epitopes with known 3D structures.
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Affiliation(s)
- Riccardo Capelli
- Center for Complexity & Biosystems and Dipartimento di Fisica, Università degli Studi di Milano and INFN , via Celoria 16, 20133 Milan, Italy.,Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche , via Mario Bianco 9, 20131 Milan, Italy
| | - Filippo Marchetti
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche , via Mario Bianco 9, 20131 Milan, Italy
| | - Guido Tiana
- Center for Complexity & Biosystems and Dipartimento di Fisica, Università degli Studi di Milano and INFN , via Celoria 16, 20133 Milan, Italy
| | - Giorgio Colombo
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche , via Mario Bianco 9, 20131 Milan, Italy
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Peri C, Gori A, Gagni P, Sola L, Girelli D, Sottotetti S, Cariani L, Chiari M, Cretich M, Colombo G. Evolving serodiagnostics by rationally designed peptide arrays: the Burkholderia paradigm in Cystic Fibrosis. Sci Rep 2016; 6:32873. [PMID: 27615705 PMCID: PMC5018727 DOI: 10.1038/srep32873] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 08/16/2016] [Indexed: 01/05/2023] Open
Abstract
Efficient diagnosis of emerging and novel bacterial infections is fundamental to guide decisions on therapeutic treatments. Here, we engineered a novel rational strategy to design peptide microarray platforms, which combines structural and genomic analyses to predict the binding interfaces between diverse protein antigens and antibodies against Burkholderia cepacia complex infections present in the sera of Cystic Fibrosis (CF) patients. The predicted binding interfaces on the antigens are synthesized in the form of isolated peptides and chemically optimized for controlled orientation on the surface. Our platform displays multiple Burkholderia-related epitopes and is shown to diagnose infected individuals even in presence of superinfections caused by other prevalent CF pathogens, with limited cost and time requirements. Moreover, our data point out that the specific patterns determined by combined probe responses might provide a characterization of Burkholderia infections even at the subtype level (genomovars). The method is general and immediately applicable to other bacteria.
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Affiliation(s)
- Claudio Peri
- Istituto di Chimica del Riconoscimento Molecolare, ICRM, CNR. Via Mario Bianco 9, 20131, Milano (Italy)
| | - Alessandro Gori
- Istituto di Chimica del Riconoscimento Molecolare, ICRM, CNR. Via Mario Bianco 9, 20131, Milano (Italy)
| | - Paola Gagni
- Istituto di Chimica del Riconoscimento Molecolare, ICRM, CNR. Via Mario Bianco 9, 20131, Milano (Italy)
| | - Laura Sola
- Istituto di Chimica del Riconoscimento Molecolare, ICRM, CNR. Via Mario Bianco 9, 20131, Milano (Italy)
| | - Daniela Girelli
- Cystic Fibrosis Microbiology Laboratory, Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, via San Barnaba 8, 20122, Milano (Italy)
| | - Samantha Sottotetti
- Cystic Fibrosis Microbiology Laboratory, Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, via San Barnaba 8, 20122, Milano (Italy)
| | - Lisa Cariani
- Cystic Fibrosis Microbiology Laboratory, Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, via San Barnaba 8, 20122, Milano (Italy)
| | - Marcella Chiari
- Istituto di Chimica del Riconoscimento Molecolare, ICRM, CNR. Via Mario Bianco 9, 20131, Milano (Italy)
| | - Marina Cretich
- Istituto di Chimica del Riconoscimento Molecolare, ICRM, CNR. Via Mario Bianco 9, 20131, Milano (Italy)
| | - Giorgio Colombo
- Istituto di Chimica del Riconoscimento Molecolare, ICRM, CNR. Via Mario Bianco 9, 20131, Milano (Italy)
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Peri C, Morra G, Colombo G. Surface energetics and protein-protein interactions: analysis and mechanistic implications. Sci Rep 2016; 6:24035. [PMID: 27050828 PMCID: PMC4822145 DOI: 10.1038/srep24035] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 03/16/2016] [Indexed: 12/17/2022] Open
Abstract
Understanding protein-protein interactions (PPI) at the molecular level is a fundamental task in the design of new drugs, the prediction of protein function and the clarification of the mechanisms of (dis)regulation of biochemical pathways. In this study, we use a novel computational approach to investigate the energetics of aminoacid networks located on the surface of proteins, isolated and in complex with their respective partners. Interestingly, the analysis of individual proteins identifies patches of surface residues that, when mapped on the structure of their respective complexes, reveal regions of residue-pair couplings that extend across the binding interfaces, forming continuous motifs. An enhanced effect is visible across the proteins of the dataset forming larger quaternary assemblies. The method indicates the presence of energetic signatures in the isolated proteins that are retained in the bound form, which we hypothesize to determine binding orientation upon complex formation. We propose our method, BLUEPRINT, as a complement to different approaches ranging from the ab-initio characterization of PPIs, to protein-protein docking algorithms, for the physico-chemical and functional investigation of protein-protein interactions.
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Affiliation(s)
- Claudio Peri
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, via Mario Bianco, 9, 20131, Milan, Italy
| | - Giulia Morra
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, via Mario Bianco, 9, 20131, Milan, Italy
| | - Giorgio Colombo
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, via Mario Bianco, 9, 20131, Milan, Italy
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Gourlay LJ, Peano C, Deantonio C, Perletti L, Pietrelli A, Villa R, Matterazzo E, Lassaux P, Santoro C, Puccio S, Sblattero D, Bolognesi M. Selecting soluble/foldable protein domains through single-gene or genomic ORF filtering: structure of the head domain of Burkholderia pseudomallei antigen BPSL2063. ACTA ACUST UNITED AC 2015; 71:2227-35. [PMID: 26527140 DOI: 10.1107/s1399004715015680] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 08/21/2015] [Indexed: 11/10/2022]
Abstract
The 1.8 Å resolution crystal structure of a conserved domain of the potential Burkholderia pseudomallei antigen and trimeric autotransporter BPSL2063 is presented as a structural vaccinology target for melioidosis vaccine development. Since BPSL2063 (1090 amino acids) hosts only one conserved domain, and the expression/purification of the full-length protein proved to be problematic, a domain-filtering library was generated using β-lactamase as a reporter gene to select further BPSL2063 domains. As a result, two domains (D1 and D2) were identified and produced in soluble form in Escherichia coli. Furthermore, as a general tool, a genomic open reading frame-filtering library from the B. pseudomallei genome was also constructed to facilitate the selection of domain boundaries from the entire ORFeome. Such an approach allowed the selection of three potential protein antigens that were also produced in soluble form. The results imply the further development of ORF-filtering methods as a tool in protein-based research to improve the selection and production of soluble proteins or domains for downstream applications such as X-ray crystallography.
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Affiliation(s)
- Louise J Gourlay
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy
| | - Clelia Peano
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20090 Segrate, Italy
| | - Cecilia Deantonio
- Department of Health Sciences and IRCAD, University of Eastern Piedmont, Via Solaroli 17, 28100 Novara, Italy
| | - Lucia Perletti
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy
| | - Alessandro Pietrelli
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20090 Segrate, Italy
| | - Riccardo Villa
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy
| | - Elena Matterazzo
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy
| | - Patricia Lassaux
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy
| | - Claudio Santoro
- Department of Health Sciences and IRCAD, University of Eastern Piedmont, Via Solaroli 17, 28100 Novara, Italy
| | - Simone Puccio
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20090 Segrate, Italy
| | - Daniele Sblattero
- Department of Life Sciences, University of Trieste, Via Weiss 2, 34128 Trieste, Italy
| | - Martino Bolognesi
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy
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Structural and Computational Biology in the Design of Immunogenic Vaccine Antigens. J Immunol Res 2015; 2015:156241. [PMID: 26526043 PMCID: PMC4615220 DOI: 10.1155/2015/156241] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 08/02/2015] [Indexed: 01/08/2023] Open
Abstract
Vaccination is historically one of the most important medical interventions for the prevention of infectious disease. Previously, vaccines were typically made of rather crude mixtures of inactivated or attenuated causative agents. However, over the last 10–20 years, several important technological and computational advances have enabled major progress in the discovery and design of potently immunogenic recombinant protein vaccine antigens. Here we discuss three key breakthrough approaches that have potentiated structural and computational vaccine design. Firstly, genomic sciences gave birth to the field of reverse vaccinology, which has enabled the rapid computational identification of potential vaccine antigens. Secondly, major advances in structural biology, experimental epitope mapping, and computational epitope prediction have yielded molecular insights into the immunogenic determinants defining protective antigens, enabling their rational optimization. Thirdly, and most recently, computational approaches have been used to convert this wealth of structural and immunological information into the design of improved vaccine antigens. This review aims to illustrate the growing power of combining sequencing, structural and computational approaches, and we discuss how this may drive the design of novel immunogens suitable for future vaccines urgently needed to increase the global prevention of infectious disease.
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