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Busato M, Distefano R, Bates F, Karim K, Bossi AM, López Vilariño JM, Piletsky S, Bombieri N, Giorgetti A. MIRATE: MIps RATional dEsign Science Gateway. J Integr Bioinform 2018; 15:/j/jib.ahead-of-print/jib-2017-0075/jib-2017-0075.xml. [PMID: 29897885 PMCID: PMC6348745 DOI: 10.1515/jib-2017-0075] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Accepted: 04/09/2018] [Indexed: 11/15/2022] Open
Abstract
Molecularly imprinted polymers (MIPs) are high affinity robust synthetic receptors, which can be optimally synthesized and manufactured more economically than their biological equivalents (i.e. antibody). In MIPs production, rational design based on molecular modeling is a commonly employed technique. This mostly aids in (i) virtual screening of functional monomers (FMs), (ii) optimization of monomer-template ratio, and (iii) selectivity analysis. We present MIRATE, an integrated science gateway for the intelligent design of MIPs. By combining and adapting multiple state-of-the-art bioinformatics tools into automated and innovative pipelines, MIRATE guides the user through the entire process of MIPs' design. The platform allows the user to fully customize each stage involved in the MIPs' design, with the main goal to support the synthesis in the wet-laboratory. Availability: MIRATE is freely accessible with no login requirement at http://mirate.di.univr.it/. All major browsers are supported.
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Affiliation(s)
- Mirko Busato
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
- Mirko Busato and Rosario Distefano contributed equally to this work
| | - Rosario Distefano
- Department Computer Science, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
- Mirko Busato and Rosario Distefano contributed equally to this work
| | - Ferdia Bates
- Institute of Technological Investigations, University of Coruña (UDC), Campus Esteiro, Ferrol 15402, Spain
| | - Kal Karim
- Leicester Biotechnology Group, Department of Chemistry, University of Leicester, LE1 7RH, Leicester, UK
| | - Alessandra Maria Bossi
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - José Manuel López Vilariño
- Institute of Technological Investigations, University of Coruña (UDC), Campus Esteiro, Ferrol 15402, Spain
| | - Sergey Piletsky
- Leicester Biotechnology Group, Department of Chemistry, University of Leicester, LE1 7RH, Leicester, UK
| | - Nicola Bombieri
- Department Computer Science, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Alejandro Giorgetti
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
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Bates F, Busato M, Piletska E, Whitcombe MJ, Karim K, Guerreiro A, del Valle M, Giorgetti A, Piletsky S. Computational design of molecularly imprinted polymer for direct detection of melamine in milk. SEP SCI TECHNOL 2017. [DOI: 10.1080/01496395.2017.1287197] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Ferdia Bates
- Sensors and Biosensors Group, Department of Chemistry, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Mirko Busato
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Elena Piletska
- Chemical Biology, Department of Chemistry, University of Leicester, Leicester, UK
| | - Michael J. Whitcombe
- Chemical Biology, Department of Chemistry, University of Leicester, Leicester, UK
| | - Kal Karim
- Chemical Biology, Department of Chemistry, University of Leicester, Leicester, UK
| | - Antonio Guerreiro
- Chemical Biology, Department of Chemistry, University of Leicester, Leicester, UK
| | - Manel del Valle
- Sensors and Biosensors Group, Department of Chemistry, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | | | - Sergey Piletsky
- Chemical Biology, Department of Chemistry, University of Leicester, Leicester, UK
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Cowen T, Busato M, Karim K, Piletsky SA. In Silico Synthesis of Synthetic Receptors: A Polymerization Algorithm. Macromol Rapid Commun 2016; 37:2011-2016. [DOI: 10.1002/marc.201600515] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 09/22/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Todd Cowen
- Leicester Biotechnology Group; Department of Chemistry; University of Leicester; Leicester LE1 7RH UK
| | - Mirko Busato
- Department of Biotechnology; University of Verona; Strada le Grazie 15 Verona 37134 Italy
| | - Kal Karim
- Leicester Biotechnology Group; Department of Chemistry; University of Leicester; Leicester LE1 7RH UK
| | - Sergey A. Piletsky
- Leicester Biotechnology Group; Department of Chemistry; University of Leicester; Leicester LE1 7RH UK
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Busato M, Giorgetti A. Structural modeling of G-protein coupled receptors: An overview on automatic web-servers. Int J Biochem Cell Biol 2016; 77:264-74. [PMID: 27102413 DOI: 10.1016/j.biocel.2016.04.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 04/09/2016] [Accepted: 04/15/2016] [Indexed: 12/27/2022]
Abstract
Despite the significant efforts and discoveries during the last few years in G protein-coupled receptor (GPCR) expression and crystallization, the receptors with known structures to date are limited only to a small fraction of human GPCRs. The lack of experimental three-dimensional structures of the receptors represents a strong limitation that hampers a deep understanding of their function. Computational techniques are thus a valid alternative strategy to model three-dimensional structures. Indeed, recent advances in the field, together with extraordinary developments in crystallography, in particular due to its ability to capture GPCRs in different activation states, have led to encouraging results in the generation of accurate models. This, prompted the community of modelers to render their methods publicly available through dedicated databases and web-servers. Here, we present an extensive overview on these services, focusing on their advantages, drawbacks and their role in successful applications. Future challenges in the field of GPCR modeling, such as the predictions of long loop regions and the modeling of receptor activation states are presented as well.
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Affiliation(s)
- Mirko Busato
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy.
| | - Alejandro Giorgetti
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy; Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Computational Biomedicine, Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich, Germany.
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Serena M, Giorgetti A, Busato M, Gasparini F, Diani E, Romanelli MG, Zipeto D. Molecular characterization of HIV-1 Nef and ACOT8 interaction: insights from in silico structural predictions and in vitro functional assays. Sci Rep 2016; 6:22319. [PMID: 26927806 PMCID: PMC4772117 DOI: 10.1038/srep22319] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [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: 08/11/2015] [Accepted: 02/11/2016] [Indexed: 11/29/2022] Open
Abstract
HIV-1 Nef interacts with several cellular proteins, among which the human peroxisomal thioesterase 8 (ACOT8). This interaction may be involved in the endocytosis regulation of membrane proteins and might modulate lipid composition in membrane rafts. Nef regions involved in the interaction have been experimentally characterized, whereas structural details of the ACOT8 protein are unknown. The lack of structural information hampers the comprehension of the functional consequences of the complex formation during HIV-1 infection. We modelled, through in silico predictions, the ACOT8 structure and we observed a high charge complementarity between Nef and ACOT8 surfaces, which allowed the identification of the ACOT8 putative contact points involved in the interaction. The predictions were validated by in vitro assays through the development of ACOT8 deletion mutants. Coimmunoprecipitation and immunofluorescence analyses showed that ACOT8 Arg45-Phe55 and Arg86-Pro93 regions are involved in Nef association. In addition, K91S mutation abrogated the interaction with Nef, indicating that Lys91 plays a key role in the interaction. Finally, when associated with ACOT8, Nef may be preserved from degradation. These findings improve the comprehension of the association between HIV-1 Nef and ACOT8, helping elucidating the biological effect of their interaction.
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Affiliation(s)
- Michela Serena
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Strada le Grazie 8, 37134 Verona, Italy
| | - Alejandro Giorgetti
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Mirko Busato
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Francesca Gasparini
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Strada le Grazie 8, 37134 Verona, Italy.,Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Erica Diani
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Strada le Grazie 8, 37134 Verona, Italy
| | - Maria Grazia Romanelli
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Strada le Grazie 8, 37134 Verona, Italy
| | - Donato Zipeto
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Strada le Grazie 8, 37134 Verona, Italy
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Ceccon A, Busato M, Pérez Santero S, D'Onofrio M, Musiani F, Giorgetti A, Assfalg M. Inside Back Cover: Transient Interactions of a Cytosolic Protein with Macromolecular and Vesicular Cosolutes: Unspecific and Specific Effects (ChemBioChem 18/2015). Chembiochem 2015. [DOI: 10.1002/cbic.201500637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Alberto Ceccon
- Department of Biotechnology; Biomolecular NMR Laboratory; University of Verona; Strada Le Grazie 15 37134 Verona Italy
| | - Mirko Busato
- Department of Biotechnology; Applied Bioinformatics Laboratory; University of Verona; Strada Le Grazie 15 37134 Verona Italy
| | - Silvia Pérez Santero
- Department of Biotechnology; Biomolecular NMR Laboratory; University of Verona; Strada Le Grazie 15 37134 Verona Italy
| | - Mariapina D'Onofrio
- Department of Biotechnology; Biomolecular NMR Laboratory; University of Verona; Strada Le Grazie 15 37134 Verona Italy
| | - Francesco Musiani
- Department of Pharmacy and Biotechnology; Laboratory of Bioinorganic Chemistry; University of Bologna; Viale G. Fanin 40 40127 Bologna Italy
| | - Alejandro Giorgetti
- Department of Biotechnology; Applied Bioinformatics Laboratory; University of Verona; Strada Le Grazie 15 37134 Verona Italy
| | - Michael Assfalg
- Department of Biotechnology; Biomolecular NMR Laboratory; University of Verona; Strada Le Grazie 15 37134 Verona Italy
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Cenci L, Anesi A, Busato M, Guella G, Bossi AM. Molecularly imprinted polymers coupled to matrix assisted laser desorption ionization mass spectrometry for femtomoles detection of cardiac troponin I peptides. J Mol Recognit 2015; 29:41-50. [PMID: 26373625 DOI: 10.1002/jmr.2494] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [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: 05/05/2015] [Revised: 07/21/2015] [Accepted: 07/29/2015] [Indexed: 12/20/2022]
Abstract
Molecularly imprinted polymers (MIPs) were combined to MALDI-TOF-MS to evaluate a selective enrichment (SE) method for the determination of clinically relevant biomarkers from complex biological samples. The concept was proven with the myocardial injury marker Troponin I (cTnI). In a first part, MIP materials entailed for the recognition of cTnI epitopes (three peptides selected) were prepared and characterized in dimensions (0.7-2μm), dissociation constants (58-817 nM), kinetics of binding (5-60 min), binding capacity (ca. 1.5 µg/mg polymer), imprinting factors (3 > IF > 5) and selectivity for the peptide epitope. Then, the MIPs, incubated with cTnI peptides and spotted on the target with the DHB matrix, were assayed for the desorption of the peptides in MALDI-TOF-MS. The measured detection limit was ca. 300 femtomols. Finally, the MIP-SE MALDI-TOF-MS was tested for its ability to enrich in the cTnI peptides from a complex sample, mimic of serum (i.e. 81 peptides of digested albumin). The MIP-SE MALDI-TOF-MS successfully enriched in cTnI peptides from the complex sample proving the technique could offer a flexible platform to prepare entailed materials suitable for diagnostic purposes.
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Affiliation(s)
- Lucia Cenci
- University of Verona, Department of Biotechnology, Strada Le Grazie 15, 37134, Verona, Italy
| | - Andrea Anesi
- University of Trento, Department of Physics, Via Sommarive 14, 38123, Trento, Italy
| | - Mirko Busato
- University of Verona, Department of Biotechnology, Strada Le Grazie 15, 37134, Verona, Italy
| | - Graziano Guella
- University of Trento, Department of Physics, Via Sommarive 14, 38123, Trento, Italy
| | - Alessandra Maria Bossi
- University of Verona, Department of Biotechnology, Strada Le Grazie 15, 37134, Verona, Italy
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Cenci L, Andreetto E, Vestri A, Bovi M, Barozzi M, Iacob E, Busato M, Castagna A, Girelli D, Bossi AM. Surface plasmon resonance based on molecularly imprinted nanoparticles for the picomolar detection of the iron regulating hormone Hepcidin-25. J Nanobiotechnology 2015; 13:51. [PMID: 26311037 PMCID: PMC4549936 DOI: 10.1186/s12951-015-0115-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 08/10/2015] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Molecularly imprinted polymer (MIP) technique is a powerful mean to produce tailor made synthetic recognition sites. Here precipitation polymerization was exploited to produce a library of MIP nanoparticles (NPs) targeting the N terminus of the hormone Hepcidin-25, whose serum levels correlate with iron dis-metabolisms and doping. Biotinylated MIP NPs were immobilized to NeutrAvidin™ SPR sensor chip. The response of the MIP NP sensor to Hepcidin-25 was studied. FINDINGS Morphological analysis showed MIP NPs of 20-50 nm; MIP NP exhibited high affinity and selectivity for the target analyte: low nanomolar Kds for the interaction NP/Hepcidin-25, but none for the NP/non regulative Hepcidin-20. The MIP NP were integrated as recognition element in SPR allowing the detection of Hepcidin-25 in 3 min. Linearity was observed with the logarithm of Hepcidin-25 concentration in the range 7.2-720 pM. LOD was 5 pM. The response for Hepcidin-20 was limited. Hepcidin-25 determination in real serum samples spiked with known analyte concentrations was also attempted. CONCLUSION The integration of MIP NP to SPR allowed the determination of Hepcidin-25 at picomolar concentrations in short times outperforming the actual state of art. Optimization is still needed for real sample measurements in view of future clinical applications.
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Affiliation(s)
- Lucia Cenci
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy.
| | - Erika Andreetto
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy.
| | - Ambra Vestri
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy.
| | - Michele Bovi
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy.
| | - Mario Barozzi
- Center for Materials and Microsystems CMM-MNF, FBK Fondazione Bruno Kessler, Via Sommarive 18, 38123, Povo-Trento, Italy.
| | - Erica Iacob
- Center for Materials and Microsystems CMM-MNF, FBK Fondazione Bruno Kessler, Via Sommarive 18, 38123, Povo-Trento, Italy.
| | - Mirko Busato
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy.
| | - Annalisa Castagna
- Department of Medicine, University of Verona, Section of Internal Medicine B, 37134, Verona, Italy.
| | - Domenico Girelli
- Department of Medicine, University of Verona, Section of Internal Medicine B, 37134, Verona, Italy.
| | - Alessandra Maria Bossi
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy.
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Castellini A, Zucchelli M, Busato M, Manca V. From time series to biological network regulations: an evolutionary approach. Mol Biosyst 2013; 9:225-33. [PMID: 23165363 DOI: 10.1039/c2mb25191d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this paper we present a new methodology, based on genetic algorithms and multiple linear regression, for discovering regulation mechanisms responsible for observed time series in biological networks. The modeling framework employed is called Metabolic P systems; they are deterministic and time-discrete dynamical systems proposed as an effective alternative to ordinary differential equations for modeling biochemical systems. Our methodology is here successfully applied to the mitotic oscillator in early amphibian embryos. Starting from the time series of substances involved in this system, we are able to reconstruct an MP system reproducing the observed dynamics, where the regulatory components were discovered by our evolutionary methodology. In particular, genetic algorithms are used as a variable selection technique to identify the best representation of any regulation function in terms of some given primitive functions.
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Affiliation(s)
- Alberto Castellini
- Center for Biomedical Computing, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy.
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