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Sadeghi S, Deshpande S, Vallerinteavide Mavelli G, Aksoyoglu A, Bafna J, Winterhalter M, Kini RM, Lane DP, Drum CL. A general approach to protein folding using thermostable exoshells. Nat Commun 2021; 12:5720. [PMID: 34588451 DOI: 10.1038/s41467-021-25996-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 09/07/2021] [Indexed: 02/08/2023] Open
Abstract
In vitro protein folding is a complex process which often results in protein aggregation, low yields and low specific activity. Here we report the use of nanoscale exoshells (tES) to provide complementary nanoenvironments for the folding and release of 12 highly diverse protein substrates ranging from small protein toxins to human albumin, a dimeric protein (alkaline phosphatase), a trimeric ion channel (Omp2a) and the tetrameric tumor suppressor, p53. These proteins represent a unique diversity in size, volume, disulfide linkages, isoelectric point and multi versus monomeric nature of their functional units. Protein encapsulation within tES increased crude soluble yield (3-fold to >100-fold), functional yield (2-fold to >100-fold) and specific activity (3-fold to >100-fold) for all the proteins tested. The average soluble yield was 6.5 mg/100 mg of tES with charge complementation between the tES internal cavity and the protein substrate being the primary determinant of functional folding. Our results confirm the importance of nanoscale electrostatic effects and provide a solution for folding proteins in vitro.
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Lopes-Rodrigues M, Matagne A, Zanuy D, Alemán C, Perpète EA, Michaux C. Structural and functional characterization of Solanum tuberosum VDAC36. Proteins 2019; 88:729-739. [PMID: 31833115 DOI: 10.1002/prot.25861] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 11/26/2019] [Accepted: 12/06/2019] [Indexed: 11/05/2022]
Abstract
As it forms water-filled channel in the mitochondria outer membrane and diffuses essential metabolites such as NADH and ATP, the voltage-dependent anion channel (VDAC) protein family plays a central role in all eukaryotic cells. In comparison with their mammalian homologues, little is known about the structural and functional properties of plant VDACs. In the present contribution, one of the two VDACs isoforms of Solanum tuberosum, stVDAC36, has been successfully overexpressed and refolded by an in-house method, as demonstrated by the information on its secondary and tertiary structure gathered from circular dichroism and intrinsic fluorescence. Cross-linking and molecular modeling studies have evidenced the presence of dimers and tetramers, and they suggest the formation of an intermolecular disulfide bond between two stVDAC36 monomers. The pore-forming activity was also assessed by liposome swelling assays, indicating a typical pore diameter between 2.0 and 2.7 nm. Finally, insights about the ATP binding inside the pore are given by docking studies and electrostatic calculations.
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Affiliation(s)
- Maximilien Lopes-Rodrigues
- Laboratoire de Chimie Physique des Biomolécules, Unité de Chimie Physique Théorique et Structurale (UCPTS), University of Namur, Namur, Belgium.,Namur Institute of Structured Matter, University of Namur, Namur, Belgium.,Departament d'Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, C/Eduard Maristany, Barcelona, Spain.,Barcelona Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, Eduard Maristany, Barcelona, Spain
| | - André Matagne
- Laboratoire d'Enzymologie et Repliement des Protéines, Centre d'Ingénierie des Protéines (CIP), Université de Liège, Liège, Belgium
| | - David Zanuy
- Departament d'Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, C/Eduard Maristany, Barcelona, Spain
| | - Carlos Alemán
- Departament d'Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, C/Eduard Maristany, Barcelona, Spain.,Barcelona Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, Eduard Maristany, Barcelona, Spain
| | - Eric A Perpète
- Laboratoire de Chimie Physique des Biomolécules, Unité de Chimie Physique Théorique et Structurale (UCPTS), University of Namur, Namur, Belgium.,Namur Institute of Structured Matter, University of Namur, Namur, Belgium.,Namur Research Institute for Life Sciences, University of Namur, Namur, Belgium
| | - Catherine Michaux
- Laboratoire de Chimie Physique des Biomolécules, Unité de Chimie Physique Théorique et Structurale (UCPTS), University of Namur, Namur, Belgium.,Namur Institute of Structured Matter, University of Namur, Namur, Belgium.,Institute of Life-Earth-Environment, University of Namur, Namur, Belgium
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Puiggalí-Jou A, Del Valle LJ, Alemán C. Biomimetic hybrid membranes: incorporation of transport proteins/peptides into polymer supports. Soft Matter 2019; 15:2722-2736. [PMID: 30869096 DOI: 10.1039/c8sm02513d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Molecular sensing, water purification and desalination, drug delivery, and DNA sequencing are some striking applications of biomimetic hybrid membranes. These devices take advantage of biomolecules, which have gained excellence in their specificity and efficiency during billions of years, and of artificial materials that load the purified biological molecules and provide technological properties, such as robustness, scalability, and suitable nanofeatures to confine the biomolecules. Recent methodological advances allow more precise control of polymer membranes that support the biomacromolecules, and are expected to improve the design of the next generation of membranes as well as their applicability. In the first section of this review we explain the biological relevance of membranes, membrane proteins, and the classification used for the latter. After this, we critically analyse the different approaches employed for the production of highly selective hybrid membranes, focusing on novel materials made of self-assembled block copolymers and nanostructured polymers. Finally, a summary of the advantages and disadvantages of the different methodologies is presented and the main characteristics of biomimetic hybrid membranes are highlighted.
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Affiliation(s)
- Anna Puiggalí-Jou
- Departament d'Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, C/Eduard Maristany, 10-14, Ed. I2, 08019, Barcelona, Spain. and Barcelona Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, C/Eduard Maristany, 10-14, Ed. C, 08019, Barcelona, Spain
| | - Luis J Del Valle
- Departament d'Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, C/Eduard Maristany, 10-14, Ed. I2, 08019, Barcelona, Spain. and Barcelona Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, C/Eduard Maristany, 10-14, Ed. C, 08019, Barcelona, Spain
| | - Carlos Alemán
- Departament d'Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, C/Eduard Maristany, 10-14, Ed. I2, 08019, Barcelona, Spain. and Barcelona Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, C/Eduard Maristany, 10-14, Ed. C, 08019, Barcelona, Spain
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Lopes-Rodrigues M, Zanuy D, Alemán C, Michaux C, Perpète EA. 3D structure of a Brucella melitensis porin: molecular modelling in lipid membranes. J Biomol Struct Dyn 2018; 37:3923-3935. [DOI: 10.1080/07391102.2018.1529627] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Maximilien Lopes-Rodrigues
- Laboratoire de Chimie Physique des Biomolécules, Unité de Chimie Physique Théorique et Structurale (UCPTS), University of Namur, Namur, Belgium
- Namur Institute of Structured Matter, University of Namur, Namur, Belgium
- Departament d’Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, Barcelona, Spain
- Barcelona Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, Barcelona, Spain
| | - David Zanuy
- Departament d’Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, Barcelona, Spain
| | - Carlos Alemán
- Departament d’Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, Barcelona, Spain
- Barcelona Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, Barcelona, Spain
| | - Catherine Michaux
- Laboratoire de Chimie Physique des Biomolécules, Unité de Chimie Physique Théorique et Structurale (UCPTS), University of Namur, Namur, Belgium
- Namur Institute of Structured Matter, University of Namur, Namur, Belgium
- Namur Research Institute for Life Sciences, University of Namur, Namur, Belgium
| | - Eric A. Perpète
- Laboratoire de Chimie Physique des Biomolécules, Unité de Chimie Physique Théorique et Structurale (UCPTS), University of Namur, Namur, Belgium
- Namur Institute of Structured Matter, University of Namur, Namur, Belgium
- Institute of Life-Earth-Environment, University of Namur, Namur, Belgium
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Lopes-Rodrigues M, Puiggalí-Jou A, Martí-Balleste D, del Valle LJ, Michaux C, Perpète EA, Alemán C. Thermomechanical Response of a Representative Porin for Biomimetics. ACS Omega 2018; 3:7856-7867. [PMID: 31458928 PMCID: PMC6644815 DOI: 10.1021/acsomega.8b00463] [Citation(s) in RCA: 5] [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] [Received: 03/12/2018] [Accepted: 07/02/2018] [Indexed: 06/09/2023]
Abstract
The thermomechanical response of Omp2a, a representative porin used for the fabrication of smart biomimetic nanomembranes, has been characterized using microcantilever technology and compared with standard proteins. For this purpose, thermally induced transitions involving the conversion of stable trimers to bigger aggregates, local reorganizations based on the strengthening or weakening of intermolecular interactions, and protein denaturation have been detected by the microcantilever resonance frequency and deflection as a function of the temperature. Measurements have been carried out on arrays of 8-microcantilevers functionalized with proteins (Omp2a, lysozyme and bovine serum albumin). To interpret the measured nanofeatures, the response of proteins to temperature has been also examined using other characterization techniques, including real time wide angle X-ray diffraction. Results not only demonstrate the complex behavior of porins, which exhibit multiple local thermal transitions before undergoing denaturation at temperatures higher than 105 °C, but also suggest a posttreatment to control the orientation of immobilized Omp2a molecules in functionalized biomimetic nanomembranes and, thus, increase their efficacy in ion transport.
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Affiliation(s)
- Maximilien Lopes-Rodrigues
- Departament
d’Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, C/ Eduard Maristany, 10-14, Ed.
I2, 08019 Barcelona, Spain
- Barcelona
Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, Eduard Maristany, 10-14, 08019 Barcelona, Spain
- Laboratoire
de Chimie Physique des Biomolécules, Unité de Chimie
Physique Théorique et Structurale (UCPTS), University of Namur, Rue de Bruxelles, 61, 5000 Namur, Belgium
| | - Anna Puiggalí-Jou
- Departament
d’Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, C/ Eduard Maristany, 10-14, Ed.
I2, 08019 Barcelona, Spain
- Barcelona
Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, Eduard Maristany, 10-14, 08019 Barcelona, Spain
| | - Didac Martí-Balleste
- Departament
d’Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, C/ Eduard Maristany, 10-14, Ed.
I2, 08019 Barcelona, Spain
- Barcelona
Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, Eduard Maristany, 10-14, 08019 Barcelona, Spain
| | - Luis J. del Valle
- Departament
d’Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, C/ Eduard Maristany, 10-14, Ed.
I2, 08019 Barcelona, Spain
- Barcelona
Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, Eduard Maristany, 10-14, 08019 Barcelona, Spain
| | - Catherine Michaux
- Laboratoire
de Chimie Physique des Biomolécules, Unité de Chimie
Physique Théorique et Structurale (UCPTS), University of Namur, Rue de Bruxelles, 61, 5000 Namur, Belgium
| | - Eric A. Perpète
- Laboratoire
de Chimie Physique des Biomolécules, Unité de Chimie
Physique Théorique et Structurale (UCPTS), University of Namur, Rue de Bruxelles, 61, 5000 Namur, Belgium
| | - Carlos Alemán
- Departament
d’Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, C/ Eduard Maristany, 10-14, Ed.
I2, 08019 Barcelona, Spain
- Barcelona
Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, Eduard Maristany, 10-14, 08019 Barcelona, Spain
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Lopes-Rodrigues M, Triguero J, Torras J, Perpète EA, Michaux C, Zanuy D, Alemán C. Influence of the surrounding environment in re-naturalized β-barrel membrane proteins. Biophys Chem 2018; 234:6-15. [DOI: 10.1016/j.bpc.2017.12.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 12/20/2017] [Accepted: 12/23/2017] [Indexed: 10/18/2022]
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Puiggalí-Jou A, Pérez-Madrigal MM, Del Valle LJ, Armelin E, Casas MT, Michaux C, Perpète EA, Estrany F, Alemán C. Confinement of a β-barrel protein in nanoperforated free-standing nanomembranes for ion transport. Nanoscale 2016; 8:16922-16935. [PMID: 27714137 DOI: 10.1039/c6nr04948f] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Bioinspired free-standing nanomembranes (FSNMs) for selective ion transport have been tailored by immobilizing the Omp2a β-barrel membrane protein inside nanoperforations created in flexible poly(lactic acid) (PLA) nanomembranes. Perforated PLA FSNMs have been prepared by spin-coating a 99 : 1 PLA : poly(vinyl alcohol) mixture, and through a phase segregation process nanofeatures with dimensions similar to the entire nanomembrane thickness (∼110 nm) were induced. These nanofeatures have subsequently been transformed into nanoperforations (diameter: ∼51 nm) by selective solvent etching. The protein confined inside the nanopores of PLA FSNMs preserves the β-barrel structure and organizes in ovoid aggregates. The transport properties of Na+, K+, and Ca2+ across non-perforated PLA, nanoperforated PLA, and Omp2a-filled nanoperforated PLA have been monitored by measuring the nanomembrane resistance with electrochemical impedance spectroscopy (EIS). The incorporation of nanoperforations enhances the transport of ions across PLA nanomembranes, whereas the functionality of immobilized Omp2a is essential to exhibit effects similar to those observed in biological nanomembranes. Indeed, Omp2a-filled nanoperforated PLA nanomembranes exhibit stronger affinity towards Na+ and Ca2+ ions than towards K+. In summary, this work provides a novel bioinspired strategy to develop mechanically stable and flexible FSNMs with channels for ion transport, which are precisely located inside artificial nanoperforations, thus holding great potential for applications in biofiltration and biosensing.
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Affiliation(s)
- Anna Puiggalí-Jou
- Departament d'Enginyeria Química, ETSEIB, Universitat Politècnica de Catalunya, Avda. Diagonal 647, Barcelona E-08028, Spain. and Center for Research in Nano-Engineering, Universitat Politècnica de Catalunya, Campus Sud, Edifici C', C/Pasqual i Vila s/n, Barcelona E-08028, Spain
| | - Maria M Pérez-Madrigal
- Departament d'Enginyeria Química, ETSEIB, Universitat Politècnica de Catalunya, Avda. Diagonal 647, Barcelona E-08028, Spain. and Center for Research in Nano-Engineering, Universitat Politècnica de Catalunya, Campus Sud, Edifici C', C/Pasqual i Vila s/n, Barcelona E-08028, Spain
| | - Luis J Del Valle
- Departament d'Enginyeria Química, ETSEIB, Universitat Politècnica de Catalunya, Avda. Diagonal 647, Barcelona E-08028, Spain. and Center for Research in Nano-Engineering, Universitat Politècnica de Catalunya, Campus Sud, Edifici C', C/Pasqual i Vila s/n, Barcelona E-08028, Spain
| | - Elaine Armelin
- Departament d'Enginyeria Química, ETSEIB, Universitat Politècnica de Catalunya, Avda. Diagonal 647, Barcelona E-08028, Spain. and Center for Research in Nano-Engineering, Universitat Politècnica de Catalunya, Campus Sud, Edifici C', C/Pasqual i Vila s/n, Barcelona E-08028, Spain
| | - María T Casas
- Departament d'Enginyeria Química, ETSEIB, Universitat Politècnica de Catalunya, Avda. Diagonal 647, Barcelona E-08028, Spain.
| | - Catherine Michaux
- Laboratoire de Chimie Physique des Biomolécules, Unité de Chimie Physique Théorique et Structurale (UCPTS), University of Namur, Rue de Bruxelles, 61, 5000 Namur, Belgium
| | - Eric A Perpète
- Laboratoire de Chimie Physique des Biomolécules, Unité de Chimie Physique Théorique et Structurale (UCPTS), University of Namur, Rue de Bruxelles, 61, 5000 Namur, Belgium
| | - Francesc Estrany
- Center for Research in Nano-Engineering, Universitat Politècnica de Catalunya, Campus Sud, Edifici C', C/Pasqual i Vila s/n, Barcelona E-08028, Spain and Departament d'Enginyeria Química, Escola Universitària d'Enginyeria Tècnica Industrial de Barcelona, Universitat Politècnica de Catalunya, Comte d'Urgell 187, 08036 Barcelona, Spain
| | - Carlos Alemán
- Departament d'Enginyeria Química, ETSEIB, Universitat Politècnica de Catalunya, Avda. Diagonal 647, Barcelona E-08028, Spain. and Center for Research in Nano-Engineering, Universitat Politècnica de Catalunya, Campus Sud, Edifici C', C/Pasqual i Vila s/n, Barcelona E-08028, Spain
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Abstract
The global emergence of multidrug-resistant Gram-negative bacteria is a growing threat to antibiotic therapy. The chromosomally encoded drug efflux mechanisms that are ubiquitous in these bacteria greatly contribute to antibiotic resistance and present a major challenge for antibiotic development. Multidrug pumps, particularly those represented by the clinically relevant AcrAB-TolC and Mex pumps of the resistance-nodulation-division (RND) superfamily, not only mediate intrinsic and acquired multidrug resistance (MDR) but also are involved in other functions, including the bacterial stress response and pathogenicity. Additionally, efflux pumps interact synergistically with other resistance mechanisms (e.g., with the outer membrane permeability barrier) to increase resistance levels. Since the discovery of RND pumps in the early 1990s, remarkable scientific and technological advances have allowed for an in-depth understanding of the structural and biochemical basis, substrate profiles, molecular regulation, and inhibition of MDR pumps. However, the development of clinically useful efflux pump inhibitors and/or new antibiotics that can bypass pump effects continues to be a challenge. Plasmid-borne efflux pump genes (including those for RND pumps) have increasingly been identified. This article highlights the recent progress obtained for organisms of clinical significance, together with methodological considerations for the characterization of MDR pumps.
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Pérez-Madrigal MM, del Valle LJ, Armelin E, Michaux C, Roussel G, Perpète EA, Alemán C. Polypyrrole-supported membrane proteins for bio-inspired ion channels. ACS Appl Mater Interfaces 2015; 7:1632-43. [PMID: 25585165 DOI: 10.1021/am507142f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Biomedical platforms constructed by immobilizing membrane proteins in matrixes made of synthetic organic polymers is a challenge because the structure and function of these proteins are affected by environmental conditions. In this work, an operative composite that regulates the diffusion of alkali ions has been prepared by functionalizing a supporting matrix made of poly(N-methylpyrrole) (PNMPy) with a β-barrel membrane protein (Omp2a) that forms channels and pores. The protein has been unequivocally identified in the composite, and its structure has been shown to remain unaltered. The PNMPy-Omp2a platform fulfills properties typically associated with functional bio-interfaces with biomedical applications (e.g., biocompatibility, biodegrabadility, and hydrophilicity). The functionality of the immobilized protein has been examined by studying the passive ion transport response in the presence of electrolytic solutions with Na(+) and K(+) concentrations close to those found in blood. Although the behavior of PNMPy and PNMPy-Omp2a is very similar for solutions with very low concentration, the resistance of the latter decreases drastically when the concentration of ions increases to ∼100 mM. This reduction reflects an enhanced ion exchange between the biocomposite and the electrolytic medium, which is not observed in PNMPy, evidencing that PNMPy-Omp2a is particularly well suited to prepare bioinspired channels and smart biosensors.
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Affiliation(s)
- Maria M Pérez-Madrigal
- Departament d'Enginyeria Química, ETSEIB, Universitat Politècnica de Catalunya , Avda. Diagonal 647, Barcelona E-08028, Spain
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Roussel G, Perpète EA, Matagne A, Tinti E, Michaux C. Towards a universal method for protein refolding: The trimeric beta barrel membrane Omp2a as a test case. Biotechnol Bioeng 2012; 110:417-23. [DOI: 10.1002/bit.24722] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 08/09/2012] [Accepted: 08/20/2012] [Indexed: 12/31/2022]
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