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Cappelli L, Cinelli P, Perrotta A, Veggi D, Audagnotto M, Tuscano G, Pansegrau W, Bartolini E, Rinaudo D, Cozzi R. Computational structure-based approach to study chimeric antigens using a new protein scaffold displaying foreign epitopes. FASEB J 2024; 38:e23326. [PMID: 38019196 DOI: 10.1096/fj.202202130r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 10/24/2023] [Accepted: 11/08/2023] [Indexed: 11/30/2023]
Abstract
The identification and recombinant production of functional antigens and/or epitopes of pathogens represent a crucial step for the development of an effective protein-based vaccine. Many vaccine targets are outer membrane proteins anchored into the lipidic bilayer through an extended hydrophobic portion making their recombinant production challenging. Moreover, only the extracellular loops, and not the hydrophobic regions, are naturally exposed to the immune system. In this work, the Domain 3 (D3) from Group B Streptococcus (GBS) pilus 2a backbone protein has been identified and engineered to be used as a scaffold for the display of extracellular loops of two Neisseria gonorrhoeae membrane proteins (PorB.1b and OpaB). A computational structure-based approach has been applied to the design of both the scaffold and the model antigens. Once identified the best D3 engineerable site, several different chimeric D3 displaying PorB.1b and OpaB extracellular loops were produced as soluble proteins. Each molecule has been characterized in terms of solubility, stability, and ability to correctly display the foreign epitope. This antigen dissection strategy allowed the identification of most immunogenic extracellular loops of both PorB.1b and OpaB gonococcal antigens. The crystal structure of chimeric D3 displaying PorB.1b immunodominant loop has been obtained confirming that the engineerization did not alter the predicted native structure of this epitope. Taken together, the reported data suggest that D3 is a novel protein scaffold for epitope insertion and display, and a valid alternative to the production of whole membrane protein antigens. Finally, this work describes a generalized computational structure-based approach for the identification, design, and dissection of epitopes in target antigens through chimeric proteins.
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Affiliation(s)
- Luigia Cappelli
- Dipartimento di Farmacia e Biotecnologie - FaBiT, University of Bologna, Bologna, Italy
- GSK, Siena, Italy
| | - Paolo Cinelli
- Dipartimento di Farmacia e Biotecnologie - FaBiT, University of Bologna, Bologna, Italy
- GSK, Siena, Italy
| | - Andrea Perrotta
- GSK, Siena, Italy
- Dipartimento di Scienze della Vita, University of Siena, Siena, Italy
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Träger S, Tamò G, Aydin D, Fonti G, Audagnotto M, Dal Peraro M. CLoNe: automated clustering based on local density neighborhoods for application to biomolecular structural ensembles. Bioinformatics 2021; 37:921-928. [PMID: 32821900 PMCID: PMC8128458 DOI: 10.1093/bioinformatics/btaa742] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 07/14/2020] [Accepted: 08/18/2020] [Indexed: 11/14/2022] Open
Abstract
Motivation Proteins are intrinsically dynamic entities. Flexibility sampling methods, such as molecular dynamics or those arising from integrative modeling strategies, are now commonplace and enable the study of molecular conformational landscapes in many contexts. Resulting structural ensembles increase in size as technological and algorithmic advancements take place, making their analysis increasingly demanding. In this regard, cluster analysis remains a go-to approach for their classification. However, many state-of-the-art algorithms are restricted to specific cluster properties. Combined with tedious parameter fine-tuning, cluster analysis of protein structural ensembles suffers from the lack of a generally applicable and easy to use clustering scheme. Results We present CLoNe, an original Python-based clustering scheme that builds on the Density Peaks algorithm of Rodriguez and Laio. CLoNe relies on a probabilistic analysis of local density distributions derived from nearest neighbors to find relevant clusters regardless of cluster shape, size, distribution and amount. We show its capabilities on many toy datasets with properties otherwise dividing state-of-the-art approaches and improves on the original algorithm in key aspects. Applied to structural ensembles, CLoNe was able to extract meaningful conformations from membrane binding events and ligand-binding pocket opening as well as identify dominant dimerization motifs or inter-domain organization. CLoNe additionally saves clusters as individual trajectories for further analysis and provides scripts for automated use with molecular visualization software. Availability and implementation www.epfl.ch/labs/lbm/resources, github.com/LBM-EPFL/CLoNe. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Sylvain Träger
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne 1025, Switzerland.,Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Giorgio Tamò
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne 1025, Switzerland.,Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Deniz Aydin
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne 1025, Switzerland.,Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Giulia Fonti
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne 1025, Switzerland.,Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Martina Audagnotto
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne 1025, Switzerland.,Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne 1025, Switzerland.,Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
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Abrami L, Audagnotto M, Ho S, Marcaida MJ, Mesquita FS, Anwar MU, Sandoz PA, Fonti G, Pojer F, Peraro MD, van der Goot FG. Palmitoylated acyl protein thioesterase APT2 deforms membranes to extract substrate acyl chains. Nat Chem Biol 2021; 17:438-447. [PMID: 33707782 PMCID: PMC7610442 DOI: 10.1038/s41589-021-00753-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 12/27/2020] [Accepted: 01/26/2021] [Indexed: 01/31/2023]
Abstract
Many biochemical reactions require controlled recruitment of proteins to membranes. This is largely regulated by posttranslational modifications. A frequent one is S-acylation, which consists of the addition of acyl chains and can be reversed by poorly understood acyl protein thioesterases (APTs). Using a panel of computational and experimental approaches, we dissect the mode of action of the major cellular thioesterase APT2 (LYPLA2). We show that soluble APT2 is vulnerable to proteasomal degradation, from which membrane binding protects it. Interaction with membranes requires three consecutive steps: electrostatic attraction, insertion of a hydrophobic loop and S-acylation by the palmitoyltransferases ZDHHC3 or ZDHHC7. Once bound, APT2 is predicted to deform the lipid bilayer to extract the acyl chain bound to its substrate and capture it in a hydrophobic pocket to allow hydrolysis. This molecular understanding of APT2 paves the way to understand the dynamics of APT2-mediated deacylation of substrates throughout the endomembrane system.
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Affiliation(s)
- Laurence Abrami
- Global Health Institute, School of Life Sciences, EPFL, Lausanne, Switzerland
| | - Martina Audagnotto
- Institute of Bioengineering, School of Life Sciences, EPFL, Lausanne, Switzerland
| | - Sylvia Ho
- Global Health Institute, School of Life Sciences, EPFL, Lausanne, Switzerland
| | - Maria Jose Marcaida
- Institute of Bioengineering, School of Life Sciences, EPFL, Lausanne, Switzerland
| | | | - Muhammad U. Anwar
- Global Health Institute, School of Life Sciences, EPFL, Lausanne, Switzerland
| | - Patrick A. Sandoz
- Global Health Institute, School of Life Sciences, EPFL, Lausanne, Switzerland
| | - Giulia Fonti
- Institute of Bioengineering, School of Life Sciences, EPFL, Lausanne, Switzerland
| | - Florence Pojer
- Protein Production and Structure Core Facility, School of Life Sciences, EPFL, Lausanne, Switzerland
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, EPFL, Lausanne, Switzerland,Corresponding Authors: F. Gisou van der Goot () and Matteo Dal Peraro ()
| | - F. Gisou van der Goot
- Global Health Institute, School of Life Sciences, EPFL, Lausanne, Switzerland,Corresponding Authors: F. Gisou van der Goot () and Matteo Dal Peraro ()
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Watanabe R, Buschauer R, Böhning J, Audagnotto M, Lasker K, Wen Lu T, Boassa D, Taylor SS, Villa E. The In situ Structure of Parkinson's Disease-Linked LRRK2. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.2690] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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Audagnotto M, Kengo Lorkowski A, Dal Peraro M. Recruitment of the amyloid precursor protein by γ-secretase at the synaptic plasma membrane. Biochem Biophys Res Commun 2017; 498:334-341. [PMID: 29097209 DOI: 10.1016/j.bbrc.2017.10.164] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 10/04/2017] [Accepted: 10/29/2017] [Indexed: 10/18/2022]
Abstract
Γ-secretase is a membrane-embedded protease that cleaves single transmembrane helical domains of various integral membrane proteins. The amyloid precursor protein (APP) is an important substrate due to its pathological relevance to Alzheimer's disease. The mechanism of the cleavage of APP by γ-secretase that leads to accumulation of Alzheimer's disease causing amyloid-β (Aβ) is still unknown. Coarse-grained molecular dynamics simulations in this study reveal initial lipids raft formation near the catalytic site of γ-secretase as well as changes in dynamic behavior of γ-secretase once interacting with APP. The results suggest a precursor of the APP binding mode and hint at conformational changes of γ-secretase in the nicastrin (NCT) domain upon APP binding.
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Affiliation(s)
- Martina Audagnotto
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland; Swiss Institute of Bioinformatcs (SIB), Lausanne 1015, Switzerland
| | - Alexander Kengo Lorkowski
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland; Swiss Institute of Bioinformatcs (SIB), Lausanne 1015, Switzerland
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland; Swiss Institute of Bioinformatcs (SIB), Lausanne 1015, Switzerland.
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Audagnotto M, Dal Peraro M. Protein post-translational modifications: In silico prediction tools and molecular modeling. Comput Struct Biotechnol J 2017; 15:307-319. [PMID: 28458782 PMCID: PMC5397102 DOI: 10.1016/j.csbj.2017.03.004] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Revised: 03/17/2017] [Accepted: 03/21/2017] [Indexed: 02/09/2023] Open
Abstract
Post-translational modifications (PTMs) occur in almost all proteins and play an important role in numerous biological processes by significantly affecting proteins' structure and dynamics. Several computational approaches have been developed to study PTMs (e.g., phosphorylation, sumoylation or palmitoylation) showing the importance of these techniques in predicting modified sites that can be further investigated with experimental approaches. In this review, we summarize some of the available online platforms and their contribution in the study of PTMs. Moreover, we discuss the emerging capabilities of molecular modeling and simulation that are able to complement these bioinformatics methods, providing deeper molecular insights into the biological function of post-translational modified proteins.
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Affiliation(s)
- Martina Audagnotto
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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Audagnotto M, Lemmin T, Barducci A, Dal Peraro M. Effect of the Synaptic Plasma Membrane on the Stability of the Amyloid Precursor Protein Homodimer. J Phys Chem Lett 2016; 7:3572-3578. [PMID: 27518597 DOI: 10.1021/acs.jpclett.6b01721] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The proteolytic cleavage of the transmembrane (TM) domain of the amyloid precursor protein (APP) releases amyloid-β (Aβ) peptides, which accumulation in the brain tissue is an early indicator of Alzheimer's disease. We used multiscale molecular dynamics simulations to investigate the stability of APP-TM dimer in realistic models of the synaptic plasma membrane (SPM). Between the two possible dimerization motifs proposed by NMR and EPR, namely G709XXXA713 and G700XXXG704XXXG708, our study revealed that the dimer promoted by the G709XXXA713 motif is not stable in the SPM due to the competition with highly unsaturated lipids that constitute the SPM. Under the same conditions, the dimer promoted by the G700XXXG704XXXG708 motif is instead the most stable species and likely the most biologically relevant. Independently of the dimerization state, both these motifs can be involved in the recruitment of cholesterol molecules.
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Affiliation(s)
- Martina Audagnotto
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL) , Lausanne 1015, Switzerland
- Swiss Institute of Bioinformatics (SIB) , Lausanne 1015, Switzerland
| | - Thomas Lemmin
- Department of Pharmaceutical Chemistry, University of California-San Francisco , San Francisco, California 94143, United States
| | - Alessandro Barducci
- Inserm, U1054 Montpellier, France
- Université de Montpellier, CNRS, UMR 5048 , Centre de Biochimie Structurale, U1054 Montpellier, France
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL) , Lausanne 1015, Switzerland
- Swiss Institute of Bioinformatics (SIB) , Lausanne 1015, Switzerland
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Audagnotto M, Ho S, Sandoz P, Andenmatten N, van der Goot G, Dal Peraro M. New Insight into the Catalytic and Inhibition Mechanism of the Human Acyl Protein Thioesterase. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.2929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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