1
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Rarick KR, Li K, Teng RJ, Jing X, Martin DP, Xu H, Jones DW, Hogg N, Hillery CA, Garcia G, Day BW, Naylor S, Pritchard KA. Sterile inflammation induces vasculopathy and chronic lung injury in murine sickle cell disease. Free Radic Biol Med 2024; 215:112-126. [PMID: 38336101 DOI: 10.1016/j.freeradbiomed.2024.01.052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/11/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024]
Abstract
Murine sickle cell disease (SCD) results in damage to multiple organs, likely mediated first by vasculopathy. While the mechanisms inducing vascular damage remain to be determined, nitric oxide bioavailability and sterile inflammation are both considered to play major roles in vasculopathy. Here, we investigate the effects of high mobility group box-1 (HMGB1), a pro-inflammatory damage-associated molecular pattern (DAMP) molecule on endothelial-dependent vasodilation and lung morphometrics, a structural index of damage in sickle (SS) mice. SS mice were treated with either phosphate-buffered saline (PBS), hE-HMGB1-BP, an hE dual-domain peptide that binds and removes HMGB1 from the circulation via the liver, 1-[4-(aminocarbonyl)-2-methylphenyl]-5-[4-(1H-imidazol-1-yl)phenyl]-1H-pyrrole-2-propanoic acid (N6022) or N-acetyl-lysyltyrosylcysteine amide (KYC) for three weeks. Human umbilical vein endothelial cells (HUVEC) were treated with recombinant HMGB1 (r-HMGB1), which increases S-nitrosoglutathione reductase (GSNOR) expression by ∼80%, demonstrating a direct effect of HMGB1 to increase GSNOR. Treatment of SS mice with hE-HMGB1-BP reduced plasma HMGB1 in SS mice to control levels and reduced GSNOR expression in facialis arteries isolated from SS mice by ∼20%. These changes were associated with improved endothelial-dependent vasodilation. Treatment of SS mice with N6022 also improved vasodilation in SS mice suggesting that targeting GSNOR also improves vasodilation. SCD decreased protein nitrosothiols (SNOs) and radial alveolar counts (RAC) and increased GSNOR expression and mean linear intercepts (MLI) in lungs from SS mice. The marked changes in pulmonary morphometrics and GSNOR expression throughout the lung parenchyma in SS mice were improved by treating with either hE-HMGB1-BP or KYC. These data demonstrate that murine SCD induces vasculopathy and chronic lung disease by an HMGB1- and GSNOR-dependent mechanism and suggest that HMGB1 and GSNOR might be effective therapeutic targets for reducing vasculopathy and chronic lung disease in humans with SCD.
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Affiliation(s)
- Kevin R Rarick
- Department of Pediatrics, Division of Critical Care, Medical College of Wisconsin, Milwaukee, WI, 53226, USA; Childrens' Research Institute, Children's Wisconsin, Milwaukee, WI, 53226, USA
| | - Keguo Li
- Department of Surgery, Division of Pediatric Surgery, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Ru-Jeng Teng
- Department of Pediatrics, Division of Neonatology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA; Childrens' Research Institute, Children's Wisconsin, Milwaukee, WI, 53226, USA
| | - Xigang Jing
- Department of Pediatrics, Division of Neonatology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Dustin P Martin
- Department of Surgery, Division of Pediatric Surgery, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Hao Xu
- Department of Medicine, Division of Endocrinology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Deron W Jones
- Department of Surgery, Division of Pediatric Surgery, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Neil Hogg
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Cheryl A Hillery
- Department of Pediatrics, Division of Hematology and Oncology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA; Department of Pediatrics, Division of Hematology/Oncology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15224, USA
| | - Guilherme Garcia
- Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | | | | | - Kirkwood A Pritchard
- Department of Surgery, Division of Pediatric Surgery, Medical College of Wisconsin, Milwaukee, WI, 53226, USA; ReNeuroGen LLC, Milwaukee, WI, 53122, USA; Childrens' Research Institute, Children's Wisconsin, Milwaukee, WI, 53226, USA.
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2
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Miller J, Urvoas A, Gigant B, Ouldali M, Arteni A, Mesneau A, Valerio-Lepiniec M, Artzner F, Dujardin E, Minard P. Engineering of brick and staple components for ordered assembly of synthetic repeat proteins. J Struct Biol 2023; 215:108012. [PMID: 37567372 DOI: 10.1016/j.jsb.2023.108012] [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] [Received: 04/26/2023] [Revised: 07/27/2023] [Accepted: 08/07/2023] [Indexed: 08/13/2023]
Abstract
Synthetic ɑRep repeat proteins are engineered as Brick and Staple protein pairs that together self-assemble into helical filaments. In most cases, the filaments spontaneously form supercrystals. Here, we describe an expanded series of ɑRep Bricks designed to stabilize the interaction between consecutive Bricks, to control the length of the assembled multimers, or to alter the spatial distribution of the Staple on the filaments. The effects of these Brick modifications on the assembly, on the final filament structure and on the crystal symmetry are analyzed by biochemical methods, electron microscopy and small angle X-ray scattering. We further extend the concept of Brick/Staple protein origami by designing a new type of "Janus"-like Brick protein that is equally assembled by orthogonal staples binding its inner or outer surfaces and thus ending inside or outside the filaments. The relative roles of longitudinal and lateral associations in the assembly process are discussed. This set of results demonstrates important proofs-of-principle for engineering these remarkably versatile proteins toward nanometer-to-micron scale constructions.
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Affiliation(s)
- Jessalyn Miller
- Emory University Department of Chemistry, 1515 Dickey Drive, Atlanta, GA 30322, USA(1); Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, F-91198 Gif-sur-Yvette CEDEX, France
| | - Agathe Urvoas
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, F-91198 Gif-sur-Yvette CEDEX, France
| | - Benoit Gigant
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, F-91198 Gif-sur-Yvette CEDEX, France
| | - Malika Ouldali
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, F-91198 Gif-sur-Yvette CEDEX, France
| | - Ana Arteni
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, F-91198 Gif-sur-Yvette CEDEX, France
| | - Agnes Mesneau
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, F-91198 Gif-sur-Yvette CEDEX, France
| | - Marie Valerio-Lepiniec
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, F-91198 Gif-sur-Yvette CEDEX, France
| | - Franck Artzner
- Institut de Physique de Rennes (IPR), CNRS, UMR 6251, Université de Rennes 1, F-35042 Rennes, France
| | - Erik Dujardin
- Laboratoire Interdisciplinaire Carnot de Bourgogne, CNRS UMR 6303, Université de Bourgogne Franche-Comté, 21000 Dijon, France.
| | - Philippe Minard
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, F-91198 Gif-sur-Yvette CEDEX, France.
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3
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Moreaud L, Viollet S, Urvoas A, Valerio-Lepiniec M, Mesneau A, Li de la Sierra-Gallay I, Miller J, Ouldali M, Marcelot C, Balor S, Soldan V, Meriadec C, Artzner F, Dujardin E, Minard P. Design, synthesis, and characterization of protein origami based on self-assembly of a brick and staple artificial protein pair. Proc Natl Acad Sci U S A 2023; 120:e2218428120. [PMID: 36893280 PMCID: PMC10089216 DOI: 10.1073/pnas.2218428120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 02/03/2023] [Indexed: 03/11/2023] Open
Abstract
A versatile strategy to create an inducible protein assembly with predefined geometry is demonstrated. The assembly is triggered by a binding protein that staples two identical protein bricks together in a predictable spatial conformation. The brick and staple proteins are designed for mutual directional affinity and engineered by directed evolution from a synthetic modular repeat protein library. As a proof of concept, this article reports on the spontaneous, extremely fast and quantitative self-assembly of two designed alpha-repeat (αRep) brick and staple proteins into macroscopic tubular superhelices at room temperature. Small-angle X-ray scattering (SAXS) and transmission electron microscopy (TEM with staining agent and cryoTEM) elucidate the resulting superhelical arrangement that precisely matches the a priori intended 3D assembly. The highly ordered, macroscopic biomolecular construction sustains temperatures as high as 75 °C thanks to the robust αRep building blocks. Since the α-helices of the brick and staple proteins are highly programmable, their design allows encoding the geometry and chemical surfaces of the final supramolecular protein architecture. This work opens routes toward the design and fabrication of multiscale protein origami with arbitrarily programmed shapes and chemical functions.
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Affiliation(s)
- Laureen Moreaud
- Centre d’Elaboration des Matériaux et d’Etudes Structurales, CNRS UPR8011F-31055, Toulouse, France
| | - Sébastien Viollet
- CEA, CNRS, Institute for Integrative Biology of the Cell, Université Paris-Saclay91198, Gif-sur-Yvette, France
| | - Agathe Urvoas
- CEA, CNRS, Institute for Integrative Biology of the Cell, Université Paris-Saclay91198, Gif-sur-Yvette, France
| | - Marie Valerio-Lepiniec
- CEA, CNRS, Institute for Integrative Biology of the Cell, Université Paris-Saclay91198, Gif-sur-Yvette, France
| | - Agnès Mesneau
- CEA, CNRS, Institute for Integrative Biology of the Cell, Université Paris-Saclay91198, Gif-sur-Yvette, France
| | - Inès Li de la Sierra-Gallay
- CEA, CNRS, Institute for Integrative Biology of the Cell, Université Paris-Saclay91198, Gif-sur-Yvette, France
| | - Jessalyn Miller
- CEA, CNRS, Institute for Integrative Biology of the Cell, Université Paris-Saclay91198, Gif-sur-Yvette, France
- Department of Chemistry, Emory University, Atlanta, GA30322
| | - Malika Ouldali
- CEA, CNRS, Institute for Integrative Biology of the Cell, Université Paris-Saclay91198, Gif-sur-Yvette, France
| | - Cécile Marcelot
- Centre d’Elaboration des Matériaux et d’Etudes Structurales, CNRS UPR8011F-31055, Toulouse, France
| | - Stéphanie Balor
- Microscopie Electronique Intégrative Toulouse, Centre de Biologie Intégrative, Université de Toulouse, CNRS, 31062, Toulouse, France
| | - Vanessa Soldan
- Microscopie Electronique Intégrative Toulouse, Centre de Biologie Intégrative, Université de Toulouse, CNRS, 31062, Toulouse, France
| | - Cristelle Meriadec
- Institut de Physique de Rennes, CNRS, UMR6251, Université de Rennes 1F-35042, Rennes, France
| | - Franck Artzner
- Institut de Physique de Rennes, CNRS, UMR6251, Université de Rennes 1F-35042, Rennes, France
| | - Erik Dujardin
- Centre d’Elaboration des Matériaux et d’Etudes Structurales, CNRS UPR8011F-31055, Toulouse, France
- Laboratoire Interdisciplinaire Carnot de Bourgogne, CNRS, UMR6303, Université de Bourgogne Franche-Comté21000, Dijon, France
| | - Philippe Minard
- CEA, CNRS, Institute for Integrative Biology of the Cell, Université Paris-Saclay91198, Gif-sur-Yvette, France
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4
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Design of an artificial phage-display library based on a new scaffold improved for average stability of the randomized proteins. Sci Rep 2023; 13:1339. [PMID: 36693880 PMCID: PMC9873692 DOI: 10.1038/s41598-023-27710-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 01/06/2023] [Indexed: 01/25/2023] Open
Abstract
Scaffold-based protein libraries are designed to be both diverse and rich in functional/folded proteins. However, introducing an extended diversity while preserving stability of the initial scaffold remains a challenge. Here we developed an original approach to select the ensemble of folded proteins from an initial library. The thermostable CheY protein from Thermotoga maritima was chosen as scaffold. Four loops of CheY were diversified to create a new binding surface. The subset of the library giving rise to folded proteins was first selected using a natural protein partner of the template scaffold. Then, a gene shuffling approach based on a single restriction enzyme was used to recombine DNA sequences encoding these filtrated variants. Taken together, the filtration strategy and the shuffling of the filtrated sequences were shown to enrich the library in folded and stable sequences while maintaining a large diversity in the final library (Lib-Cheytins 2.1). Binders of the Oplophorus luciferase Kaz domain were then selected by phage display from the final library, showing affinities in the μM range. One of the best variants induced a loss of 92% of luminescent activity, suggesting that this Cheytin preferentially binds to the Kaz active site.
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5
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Thébault S, Lejal N, Dogliani A, Donchet A, Urvoas A, Valerio-Lepiniec M, Lavie M, Baronti C, Touret F, Da Costa B, Bourgon C, Fraysse A, Saint-Albin-Deliot A, Morel J, Klonjkowski B, de Lamballerie X, Dubuisson J, Roussel A, Minard P, Le Poder S, Meunier N, Delmas B. Biosynthetic proteins targeting the SARS-CoV-2 spike as anti-virals. PLoS Pathog 2022; 18:e1010799. [PMID: 36067253 PMCID: PMC9481167 DOI: 10.1371/journal.ppat.1010799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 09/16/2022] [Accepted: 08/06/2022] [Indexed: 12/04/2022] Open
Abstract
The binding of the SARS-CoV-2 spike to angiotensin-converting enzyme 2 (ACE2) promotes virus entry into the cell. Targeting this interaction represents a promising strategy to generate antivirals. By screening a phage-display library of biosynthetic protein sequences build on a rigid alpha-helicoidal HEAT-like scaffold (named αReps), we selected candidates recognizing the spike receptor binding domain (RBD). Two of them (F9 and C2) bind the RBD with affinities in the nM range, displaying neutralisation activity in vitro and recognizing distinct sites, F9 overlapping the ACE2 binding motif. The F9-C2 fusion protein and a trivalent αRep form (C2-foldon) display 0.1 nM affinities and EC50 of 8–18 nM for neutralization of SARS-CoV-2. In hamsters, F9-C2 instillation in the nasal cavity before or during infections effectively reduced the replication of a SARS-CoV-2 strain harbouring the D614G mutation in the nasal epithelium. Furthermore, F9-C2 and/or C2-foldon effectively neutralized SARS-CoV-2 variants (including delta and omicron variants) with EC50 values ranging from 13 to 32 nM. With their high stability and their high potency against SARS-CoV-2 variants, αReps provide a promising tool for SARS-CoV-2 therapeutics to target the nasal cavity and mitigate virus dissemination in the proximal environment. The entry of SARS-CoV-2 in permissive cells is mediated by the binding of its spike to angiotensin-converting enzyme 2 (ACE2) on the cell surface. To select ligands able to block this interaction, we screened a library of phages encoding biosynthetic proteins (named αReps) for binding to its receptor binding domain (RBD). Two of them were able to bind the RBD with high affinity and block efficiently the virus entry in cultured cells. Assembled αReps through covalent or non-covalent linkages blocked virus entry at lower concentration than their precursors (with around 20-fold activity increase for a trimeric αRep). These αReps derivates neutralize efficiently SARS-CoV-2 β, γ, δ and Omicron virus variants. Instillation of an αRep dimer in the nasal cavity effectively reduced virus replication in the hamster model of SARS-CoV-2 and pathogenicity.
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Affiliation(s)
- Stéphanie Thébault
- Unité de Virologie et Immunologie Moléculaires, INRAE, Université Paris-Saclay, Jouy-en-Josas, France
| | - Nathalie Lejal
- Unité de Virologie et Immunologie Moléculaires, INRAE, Université Paris-Saclay, Jouy-en-Josas, France
| | - Alexis Dogliani
- Centre National de la Recherche Scientifique, Architecture et Fonction des Macromolécules Biologiques, UMR, Marseille, France
| | - Amélie Donchet
- Unité de Virologie et Immunologie Moléculaires, INRAE, Université Paris-Saclay, Jouy-en-Josas, France
| | - Agathe Urvoas
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette cedex, France
| | - Marie Valerio-Lepiniec
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette cedex, France
| | - Muriel Lavie
- Université Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, Lille, France
| | - Cécile Baronti
- Unité des Virus Émergents (UVE), Aix Marseille Université, IRD 190, INSERM 1207, Marseille, France
| | - Franck Touret
- Unité des Virus Émergents (UVE), Aix Marseille Université, IRD 190, INSERM 1207, Marseille, France
| | - Bruno Da Costa
- Unité de Virologie et Immunologie Moléculaires, INRAE, Université Paris-Saclay, Jouy-en-Josas, France
| | - Clara Bourgon
- Unité de Virologie et Immunologie Moléculaires, INRAE, Université Paris-Saclay, Jouy-en-Josas, France
| | - Audrey Fraysse
- Unité de Virologie et Immunologie Moléculaires, INRAE, Université Paris-Saclay, Jouy-en-Josas, France
| | - Audrey Saint-Albin-Deliot
- Unité de Virologie et Immunologie Moléculaires, INRAE, Université Paris-Saclay, Jouy-en-Josas, France
| | - Jessica Morel
- Unité de Virologie et Immunologie Moléculaires, INRAE, Université Paris-Saclay, Jouy-en-Josas, France
| | - Bernard Klonjkowski
- UMR Virologie, INRAE-ENVA-ANSES, École Nationale Vétérinaire d’Alfort, Université Paris-Est, Maisons-Alfort, Paris, France
| | - Xavier de Lamballerie
- Unité des Virus Émergents (UVE), Aix Marseille Université, IRD 190, INSERM 1207, Marseille, France
| | - Jean Dubuisson
- Université Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, Lille, France
| | - Alain Roussel
- Centre National de la Recherche Scientifique, Architecture et Fonction des Macromolécules Biologiques, UMR, Marseille, France
| | - Philippe Minard
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette cedex, France
| | - Sophie Le Poder
- UMR Virologie, INRAE-ENVA-ANSES, École Nationale Vétérinaire d’Alfort, Université Paris-Est, Maisons-Alfort, Paris, France
| | - Nicolas Meunier
- Unité de Virologie et Immunologie Moléculaires, INRAE, Université Paris-Saclay, Jouy-en-Josas, France
| | - Bernard Delmas
- Unité de Virologie et Immunologie Moléculaires, INRAE, Université Paris-Saclay, Jouy-en-Josas, France
- * E-mail:
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6
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Programmable DARPin-based receptors for the detection of thrombotic markers. Nat Chem Biol 2022; 18:1125-1134. [PMID: 35941237 PMCID: PMC9512699 DOI: 10.1038/s41589-022-01095-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 06/23/2022] [Indexed: 11/08/2022]
Abstract
Cellular therapies remain constrained by the limited availability of sensors for disease markers. Here we present an integrated target-to-receptor pipeline for constructing a customizable advanced modular bispecific extracellular receptor (AMBER) that combines our generalized extracellular molecule sensor (GEMS) system with a high-throughput platform for generating designed ankyrin repeat proteins (DARPins). For proof of concept, we chose human fibrin degradation products (FDPs) as markers with high clinical relevance and screened a DARPin library for FDP binders. We built AMBERs equipped with 19 different DARPins selected from 160 hits, and found 4 of them to be functional as heterodimers with a known single-chain variable fragments binder. Tandem receptors consisting of combinations of the validated DARPins are also functional. We demonstrate applications of these AMBER receptors in vitro and in vivo by constructing designer cell lines that detect pathological concentrations of FDPs and respond with the production of a reporter and a therapeutic anti-thrombotic protein. ![]()
Merging the generalized extracellular molecule sensor (GEMS) system with screening designed ankyrin repeat proteins (DARPins) identifies an advanced modular bispecific extracellular receptor (AMBER) for detection of fibrinogen degradation products.
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7
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ComFC mediates transport and handling of single-stranded DNA during natural transformation. Nat Commun 2022; 13:1961. [PMID: 35414142 PMCID: PMC9005727 DOI: 10.1038/s41467-022-29494-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 03/17/2022] [Indexed: 11/09/2022] Open
Abstract
The ComFC protein is essential for natural transformation, a process that plays a major role in the spread of antibiotic resistance genes and virulence factors across bacteria. However, its role remains largely unknown. Here, we show that Helicobacter pylori ComFC is involved in DNA transport through the cell membrane, and is required for the handling of the single-stranded DNA once it is delivered into the cytoplasm. The crystal structure of ComFC includes a zinc-finger motif and a putative phosphoribosyl transferase domain, both necessary for the protein's in vivo activity. Furthermore, we show that ComFC is a membrane-associated protein with affinity for single-stranded DNA. Our results suggest that ComFC provides the link between the transport of the transforming DNA into the cytoplasm and its handling by the recombination machinery.
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8
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Deryusheva EI, Machulin AV, Galzitskaya OV. Structural, Functional, and Evolutionary Characteristics of Proteins with Repeats. Mol Biol 2021. [DOI: 10.1134/s0026893321040038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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9
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Macromolecular interactions in vitro, comparing classical and novel approaches. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2021; 50:313-330. [PMID: 33792745 DOI: 10.1007/s00249-021-01517-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 02/15/2021] [Accepted: 03/08/2021] [Indexed: 01/11/2023]
Abstract
Biophysical quantification of protein interactions is central to unveil the molecular mechanisms of cellular processes. Researchers can choose from a wide panel of biophysical methods that quantify molecular interactions in different ways, including both classical and more novel techniques. We report the outcome of an ARBRE-MOBIEU training school held in June 2019 in Gif-sur-Yvette, France ( https://mosbio.sciencesconf.org/ ). Twenty European students benefited from a week's training with theoretical and practical sessions in six complementary approaches: (1) analytical ultracentrifugation with or without a fluorescence detector system (AUC-FDS), (2) isothermal titration calorimetry (ITC), (3) size exclusion chromatography coupled to multi-angle light scattering (SEC-MALS), (4) bio-layer interferometry (BLI), (5) microscale thermophoresis (MST) and, (6) switchSENSE. They implemented all these methods on two examples of macromolecular interactions with nanomolar affinity: first, a protein-protein interaction between an artificial alphaRep binder, and its target protein, also an alphaRep; second, a protein-DNA interaction between a DNA repair complex, Ku70/Ku80 (hereafter called Ku), and its cognate DNA ligand. We report the approaches used to analyze the two systems under study and thereby showcase application of each of the six techniques. The workshop provided students with improved understanding of the advantages and limitations of different methods, enabling future choices concerning approaches that are most relevant or informative for specific kinds of sample and interaction.
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10
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Sciortino G, Maréchal JD, Garribba E. Integrated experimental/computational approaches to characterize the systems formed by vanadium with proteins and enzymes. Inorg Chem Front 2021. [DOI: 10.1039/d0qi01507e] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
An integrated instrumental/computational approach to characterize metallodrug–protein adducts at the molecular level is reviewed. A series of applications are described, focusing on potential vanadium drugs with a generalization to other metals.
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Affiliation(s)
- Giuseppe Sciortino
- Departament de Química
- Universitat Autònoma de Barcelona
- Cerdanyola del Vallès
- Barcelona 08193
- Spain
| | - Jean-Didier Maréchal
- Departament de Química
- Universitat Autònoma de Barcelona
- Cerdanyola del Vallès
- Barcelona 08193
- Spain
| | - Eugenio Garribba
- Dipartimento di Chimica e Farmacia
- Università di Sassari
- 07100 Sassari
- Italy
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11
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Kariyawasam K, Di Meo T, Hammerer F, Valerio-Lepiniec M, Sciortino G, Maréchal JD, Minard P, Mahy JP, Urvoas A, Ricoux R. An Artificial Hemoprotein with Inducible Peroxidase- and Monooxygenase-Like Activities. Chemistry 2020; 26:14929-14937. [PMID: 32588931 DOI: 10.1002/chem.202002434] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 06/25/2020] [Indexed: 12/24/2022]
Abstract
A novel inducible artificial metalloenzyme obtained by covalent attachment of a manganese(III)-tetraphenylporphyrin (MnTPP) to the artificial bidomain repeat protein, (A3A3')Y26C, is reported. The protein is part of the αRep family. The biohybrid was fully characterized by MALDI-ToF mass spectrometry, circular dichroism and UV/Vis spectroscopies. The peroxidase and monooxygenase activities were evaluated on the original and modified scaffolds including those that have a) an additional imidazole, b) a specific αRep bA3-2 that is known to induce the opening of the (A3A3') interdomain region and c) a derivative of the αRep bA3-2 inducer extended with a His6 -Tag (His6 -bA3-2). Catalytic profiles are highly dependent on the presence of co-catalysts with the best activity obtained with His6 -bA3-2. The entire mechanism was rationalized by an integrative molecular modeling study that includes protein-ligand docking and large-scale molecular dynamics. This constitutes the first example of an entirely artificial metalloenzyme with inducible peroxidase and monooxygenase activities, reminiscent of allosteric regulation of natural enzymatic pathways.
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Affiliation(s)
- Kalani Kariyawasam
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), UMR 8182 CNRS, Laboratoire de Chimie Bioorganique et Bioinorganique, Bât. 420, Université Paris-sud, Université Paris-Saclay, 91405, Orsay cedex, France
| | - Thibault Di Meo
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), UMR 8182 CNRS, Laboratoire de Chimie Bioorganique et Bioinorganique, Bât. 420, Université Paris-sud, Université Paris-Saclay, 91405, Orsay cedex, France.,Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette cedex, France
| | - Fabien Hammerer
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), UMR 8182 CNRS, Laboratoire de Chimie Bioorganique et Bioinorganique, Bât. 420, Université Paris-sud, Université Paris-Saclay, 91405, Orsay cedex, France
| | - Marie Valerio-Lepiniec
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette cedex, France
| | - Giuseppe Sciortino
- Departament de Química, Universitat Autònoma de Barcelona, Edifici C.n., 08193, Cerdanyola del Vallés, Barcelona, Spain
| | - Jean-Didier Maréchal
- Departament de Química, Universitat Autònoma de Barcelona, Edifici C.n., 08193, Cerdanyola del Vallés, Barcelona, Spain
| | - Philippe Minard
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette cedex, France
| | - Jean-Pierre Mahy
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), UMR 8182 CNRS, Laboratoire de Chimie Bioorganique et Bioinorganique, Bât. 420, Université Paris-sud, Université Paris-Saclay, 91405, Orsay cedex, France
| | - Agathe Urvoas
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette cedex, France
| | - Rémy Ricoux
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), UMR 8182 CNRS, Laboratoire de Chimie Bioorganique et Bioinorganique, Bât. 420, Université Paris-sud, Université Paris-Saclay, 91405, Orsay cedex, France
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12
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Occupation of a thermoresistant-scaffold (αRep) at SP1-NC cleavage site disturbs the function of HIV-1 protease. Biosci Rep 2020; 40:225239. [PMID: 32519747 PMCID: PMC7313444 DOI: 10.1042/bsr20201131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 06/06/2020] [Accepted: 06/09/2020] [Indexed: 11/25/2022] Open
Abstract
HIV-1 nucleocapsid (NC) becomes an attractive target for the development of novel anti-HIV-1 agents. Discovering of non-antibody scaffolds that disrupt the function of NC will be a potential aspect for disturbing viral maturation process. Correspondingly, we explored the specific binding site of the thermoresistant-scaffold protein, αRep9A8 which formerly demonstrated the inhibitory effect on HIV-1 replication. The portion of Gag, CA21-SP1-NC has been used as a template for designing nine overlapping peptides (P4–P12). The P9 peptide showed the strongest binding activity followed by P8 and P12 respectively. The amino acid sequences on those peptides resemble the N-terminal domain of the NC proximity to the SP1-NC initial cleavage site and across the conserved CCHC zinc finger 1 (ZF1) of NC. The interaction KD between αRep9A8 with its target was 224.9 ± 57.4 nM. Consequently, αRep9A8 demonstrated the interference of the HIV-1 protease function by hindering a protease cleavage site. The released NC product from CA21-SP1-NC was diminished. The present study provided an additional information of αRep9A8 function in interfering of viral maturation processes resulting in the decremental efficiency of viral infectivity.
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13
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Léger C, Yahia-Ammar A, Susumu K, Medintz IL, Urvoas A, Valerio-Lepiniec M, Minard P, Hildebrandt N. Picomolar Biosensing and Conformational Analysis Using Artificial Bidomain Proteins and Terbium-to-Quantum Dot Förster Resonance Energy Transfer. ACS NANO 2020; 14:5956-5967. [PMID: 32216328 DOI: 10.1021/acsnano.0c01410] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Although antibodies remain a primary recognition element in all forms of biosensing, functional limitations arising from their size, stability, and structure have motivated the development and production of many different artificial scaffold proteins for biological recognition. However, implementing such artificial binders into functional high-performance biosensors remains a challenging task. Here, we present the design and application of Förster resonance energy transfer (FRET) nanoprobes comprising small artificial proteins (αRep bidomains) labeled with a Tb complex (Tb) donor on the C-terminus and a semiconductor quantum dot (QD) acceptor on the N-terminus. Specific binding of one or two protein targets to the αReps induced a conformational change that could be detected by time-resolved Tb-to-QD FRET. These single-probe FRET switches were used in a separation-free solution-phase assay to quantify different protein targets at sub-nanomolar concentrations and to measure the conformational changes with sub-nanometer resolution. Probing ligand-receptor binding under physiological conditions at very low concentrations in solution is a special feature of FRET that can be efficiently combined with other structural characterization methods to develop, understand, and optimize artificial biosensors. Our results suggest that the αRep FRET nanoprobes have a strong potential for their application in advanced diagnostics and intracellular live-cell imaging of ligand-receptor interactions.
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Affiliation(s)
- Corentin Léger
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Akram Yahia-Ammar
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | | | | | - Agathe Urvoas
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Marie Valerio-Lepiniec
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Philippe Minard
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Niko Hildebrandt
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
- nanoFRET.com, Laboratoire COBRA (Chimie Organique, Bioorganique, Réactivité et Analyse), Université de Rouen Normandie, CNRS, INSA, 76821 Mont-Saint-Aignan, France
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14
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Fernandez M, Urvoas A, Even-Hernandez P, Burel A, Mériadec C, Artzner F, Bouceba T, Minard P, Dujardin E, Marchi V. Hybrid gold nanoparticle-quantum dot self-assembled nanostructures driven by complementary artificial proteins. NANOSCALE 2020; 12:4612-4621. [PMID: 32043516 DOI: 10.1039/c9nr09987e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Hybrid nanostructures are constructed by the direct coupling of fluorescent quantum dots and plasmonic gold nanoparticles. Self-assembly is directed by the strong affinity between two artificial α-repeat proteins that are introduced in the capping layers of the nanoparticles at a controlled surface density. The proteins have been engineered to exhibit a high mutual affinity, corresponding to a dissociation constant in the nanomolar range, towards the protein-functionalized quantum dots and gold nanoparticles. Protein-mediated self-assembly is evidenced by surface plasmon resonance and gel electrophoresis. The size and the structure of colloidal superstructures of complementary nanoparticles are analyzed by transmission electron microscopy and small angle X-ray scattering. The size of the superstructures is determined by the number of proteins per nanoparticle. The well-defined geometry of the rigid protein complex sets a highly uniform interparticle distance of 8 nm that affects the emission properties of the quantum dots in the hybrid ensembles. Our results open the route to the design of hybrid emitter-plasmon colloidal assemblies with controlled near-field coupling and better optical response.
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Affiliation(s)
- Maxence Fernandez
- University Rennes 1, Institute of Chemical Sciences, UMR 6226 CNRS, Campus Beaulieu, F-35042 Rennes, France.
| | - Agathe Urvoas
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Pascale Even-Hernandez
- University Rennes 1, Institute of Chemical Sciences, UMR 6226 CNRS, Campus Beaulieu, F-35042 Rennes, France.
| | - Agnès Burel
- University Rennes 1, Microscopy Rennes Imaging Center, UMS3480 BIOSIT, Campus Villejean, Rennes, France
| | - Cristelle Mériadec
- University Rennes 1, Institut de Physique de Rennes, UMR 6251 CNRS, Campus Beaulieu, F-35042 Rennes, France
| | - Franck Artzner
- University Rennes 1, Institut de Physique de Rennes, UMR 6251 CNRS, Campus Beaulieu, F-35042 Rennes, France
| | - Tahar Bouceba
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Protein engineering platform, Molecular Interaction Service, F-75005 Paris, France
| | - Philippe Minard
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Erik Dujardin
- Groupe NanoSciences-CEMES, CNRS UPR 8011, 29 rue J. Marvig, B.P. 94347, F-31055 Toulouse, France
| | - Valérie Marchi
- University Rennes 1, Institute of Chemical Sciences, UMR 6226 CNRS, Campus Beaulieu, F-35042 Rennes, France.
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15
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Prasad J, Viollet S, Gurunatha KL, Urvoas A, Fournier AC, Valerio-Lepiniec M, Marcelot C, Baris B, Minard P, Dujardin E. Directed evolution of artificial repeat proteins as habit modifiers for the morphosynthesis of (111)-terminated gold nanocrystals. NANOSCALE 2019; 11:17485-17497. [PMID: 31532442 DOI: 10.1039/c9nr04497c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Natural biocomposites are shaped by proteins that have evolved to interact with inorganic materials. Protein directed evolution methods which mimic Darwinian evolution have proven highly successful to generate improved enzymes or therapeutic antibodies but have rarely been used to evolve protein-material interactions. Indeed, most reported studies have focused on short peptides and a wide range of oligopeptides with chemical binding affinity for inorganic materials have been uncovered by phage display methods. However, their small size and flexible unfolded structure prevent them from dictating the shape and crystallinity of the growing material. In the present work, a specific set of artificial repeat proteins (αRep), which exhibit highly stable 3D folding with a well-defined hypervariable interacting surface, is selected by directed evolution of a very efficient home-built protein library for their high and selective affinity for the Au(111) surface. The proteins are built from the extendable concatenation of self-compatible repeated motifs idealized from natural HEAT proteins. The high-yield synthesis of Au(111)-faceted nanostructures mediated by these αRep proteins demonstrates their chemical affinity and structural selectivity that endow them with high crystal habit modification performances. Importantly, we further exploit the protein shell spontaneously assembled on the nanocrystal facets to drive protein-mediated colloidal self-assembly and on-surface enzymatic catalysis. Our method constitutes a generic tool for producing nanocrystals with determined faceting, superior biocompatibility and versatile bio-functionalization towards plasmon-based devices and (bio)molecular sensors.
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Affiliation(s)
- Janak Prasad
- CEMES, CNRS UPR 8011, 29 rue J. Marvig, B.P. 94347, F-31055 Toulouse, France.
| | - Sébastien Viollet
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette Cedex, France.
| | - Kargal L Gurunatha
- CEMES, CNRS UPR 8011, 29 rue J. Marvig, B.P. 94347, F-31055 Toulouse, France.
| | - Agathe Urvoas
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette Cedex, France.
| | - Agathe C Fournier
- CEMES, CNRS UPR 8011, 29 rue J. Marvig, B.P. 94347, F-31055 Toulouse, France.
| | - Marie Valerio-Lepiniec
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette Cedex, France.
| | - Cécile Marcelot
- CEMES, CNRS UPR 8011, 29 rue J. Marvig, B.P. 94347, F-31055 Toulouse, France.
| | - Bulent Baris
- CEMES, CNRS UPR 8011, 29 rue J. Marvig, B.P. 94347, F-31055 Toulouse, France.
| | - Philippe Minard
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette Cedex, France.
| | - Erik Dujardin
- CEMES, CNRS UPR 8011, 29 rue J. Marvig, B.P. 94347, F-31055 Toulouse, France.
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16
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Abstract
Nucleation is one of the least understood steps of microtubule dynamics. It is a kinetically unfavorable process that is templated in the cell by the γ-tubulin ring complex or by preexisting microtubules; it also occurs in vitro from pure tubulin. Here we study the nucleation inhibition potency of natural or artificial proteins in connection with their binding mode to the longitudinal surface of α- or β-tubulin. The structure of tubulin-bound CopN, a Chlamydia protein that delays nucleation, suggests that this protein may interfere with two protofilaments at the (+) end of a nucleus. Designed ankyrin repeat proteins that share a binding mode similar to that of CopN also impede nucleation, whereas those that target only one protofilament do not. In addition, an αRep protein predicted to target two protofilaments at the (-) end does not delay nucleation, pointing to different behaviors at both ends of the nucleus. Our results link the interference with protofilaments at the (+) end and the inhibition of nucleation.
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17
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Agnew HD, Coppock MB, Idso MN, Lai BT, Liang J, McCarthy-Torrens AM, Warren CM, Heath JR. Protein-Catalyzed Capture Agents. Chem Rev 2019; 119:9950-9970. [PMID: 30838853 DOI: 10.1021/acs.chemrev.8b00660] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Protein-catalyzed capture agents (PCCs) are synthetic and modular peptide-based affinity agents that are developed through the use of single-generation in situ click chemistry screens against large peptide libraries. In such screens, the target protein, or a synthetic epitope fragment of that protein, provides a template for selectively promoting the noncopper catalyzed azide-alkyne dipolar cycloaddition click reaction between either a library peptide and a known ligand or a library peptide and the synthetic epitope. The development of epitope-targeted PCCs was motivated by the desire to fully generalize pioneering work from the Sharpless and Finn groups in which in situ click screens were used to develop potent, divalent enzymatic inhibitors. In fact, a large degree of generality has now been achieved. Various PCCs have demonstrated utility for selective protein detection, as allosteric or direct inhibitors, as modulators of protein folding, and as tools for in vivo tumor imaging. We provide a historical context for PCCs and place them within the broader scope of biological and synthetic aptamers. The development of PCCs is presented as (i) Generation I PCCs, which are branched ligands engineered through an iterative, nonepitope-targeted process, and (ii) Generation II PCCs, which are typically developed from macrocyclic peptide libraries and are precisely epitope-targeted. We provide statistical comparisons of Generation II PCCs relative to monoclonal antibodies in which the protein target is the same. Finally, we discuss current challenges and future opportunities of PCCs.
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Affiliation(s)
- Heather D Agnew
- Indi Molecular, Inc. , 6162 Bristol Parkway , Culver City , California 90230 , United States
| | - Matthew B Coppock
- Sensors and Electron Devices Directorate , U.S. Army Research Laboratory , Adelphi , Maryland 20783 , United States
| | - Matthew N Idso
- Institute for Systems Biology , 401 Terry Avenue North , Seattle , Washington 98109-5234 , United States
| | - Bert T Lai
- Indi Molecular, Inc. , 6162 Bristol Parkway , Culver City , California 90230 , United States
| | - JingXin Liang
- Institute for Systems Biology , 401 Terry Avenue North , Seattle , Washington 98109-5234 , United States
| | - Amy M McCarthy-Torrens
- Institute for Systems Biology , 401 Terry Avenue North , Seattle , Washington 98109-5234 , United States
| | - Carmen M Warren
- Indi Molecular, Inc. , 6162 Bristol Parkway , Culver City , California 90230 , United States
| | - James R Heath
- Institute for Systems Biology , 401 Terry Avenue North , Seattle , Washington 98109-5234 , United States
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18
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Ligand-induced conformational switch in an artificial bidomain protein scaffold. Sci Rep 2019; 9:1178. [PMID: 30718544 PMCID: PMC6362204 DOI: 10.1038/s41598-018-37256-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 11/28/2018] [Indexed: 11/15/2022] Open
Abstract
Artificial proteins binding any predefined “target” protein can now be efficiently generated using combinatorial libraries based on robust protein scaffolds. αRep is such a family of artificial proteins, based on an α-solenoid protein repeat scaffold. The low aggregation propensity of the specific “binders” generated from this library opens new protein engineering opportunities such as the creation of biosensors within multidomain constructions. Here, we have explored the properties of two new types of artificial bidomain proteins based on αRep structures. Their structural and functional properties are characterized in detail using biophysical methods. The results clearly show that both bidomain proteins adopt a closed bivalve shell-like conformation, in the ligand free form. However, the presence of ligands induces a conformational transition, and the proteins adopt an open form in which each domain can bind its cognate protein partner. The open/closed equilibria alter the affinities of each domain and induce new cooperative effects. The binding-induced relative domain motion was monitored by FRET. Crystal structures of the chimeric proteins indicate that the conformation of each constituting domain is conserved but that their mutual interactions explain the emergent properties of these artificial bidomain proteins. The ligand-induced structural transition observed in these bidomain proteins should be transferable to other αRep proteins with different specificity and could provide the basis of a new generic biosensor design.
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19
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Campanacci V, Urvoas A, Consolati T, Cantos-Fernandes S, Aumont-Nicaise M, Valerio-Lepiniec M, Surrey T, Minard P, Gigant B. Selection and Characterization of Artificial Proteins Targeting the Tubulin α Subunit. Structure 2019; 27:497-506.e4. [PMID: 30661854 PMCID: PMC6408325 DOI: 10.1016/j.str.2018.12.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 10/24/2018] [Accepted: 12/03/2018] [Indexed: 11/08/2022]
Abstract
Microtubules are cytoskeletal filaments of eukaryotic cells made of αβ-tubulin heterodimers. Structural studies of non-microtubular tubulin rely mainly on molecules that prevent its self-assembly and are used as crystallization chaperones. Here we identified artificial proteins from an αRep library that are specific to α-tubulin. Turbidity experiments indicate that these αReps impede microtubule assembly in a dose-dependent manner and total internal reflection fluorescence microscopy further shows that they specifically block growth at the microtubule (−) end. Structural data indicate that they do so by targeting the α-tubulin longitudinal surface. Interestingly, in one of the complexes studied, the α subunit is in a conformation that is intermediate between the ones most commonly observed in X-ray structures of tubulin and those seen in the microtubule, emphasizing the plasticity of tubulin. These α-tubulin-specific αReps broaden the range of tools available for the mechanistic study of microtubule dynamics and its regulation. Selection of α-tubulin-specific artificial αRep proteins The αReps inhibit microtubule assembly and specifically block growth at the (−) end The αReps target the longitudinal surface of α-tubulin The αReps are useful tools for the mechanistic study of microtubule dynamics
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Affiliation(s)
- Valérie Campanacci
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette Cedex 91198, France
| | - Agathe Urvoas
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette Cedex 91198, France
| | - Tanja Consolati
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Soraya Cantos-Fernandes
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette Cedex 91198, France
| | - Magali Aumont-Nicaise
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette Cedex 91198, France
| | - Marie Valerio-Lepiniec
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette Cedex 91198, France
| | - Thomas Surrey
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Philippe Minard
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette Cedex 91198, France.
| | - Benoît Gigant
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette Cedex 91198, France.
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20
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Shi L, Cavagnino A, Rabefiraisana JL, Lazar N, Li de la Sierra-Gallay I, Ochsenbein F, Valerio-Lepiniec M, Urvoas A, Minard P, Mijakovic I, Nessler S. Structural Analysis of the Hanks-Type Protein Kinase YabT From Bacillus subtilis Provides New Insights in its DNA-Dependent Activation. Front Microbiol 2019; 9:3014. [PMID: 30671027 PMCID: PMC6333020 DOI: 10.3389/fmicb.2018.03014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 11/21/2018] [Indexed: 12/19/2022] Open
Abstract
YabT is a serine/threonine kinase of the Hanks family from Bacillus subtilis, which lacks the canonical extracellular signal receptor domain but is anchored to the membrane through a C-terminal transmembrane helix. A previous study demonstrated that a basic juxtamembrane region corresponds to a DNA-binding motif essential for the activation of YabT trans-autophosphorylation. YabT is expressed during spore development and localizes to the asymmetric septum where it specifically phosphorylates essential proteins involved in genome maintenance, such as RecA, SsbA, and YabA. YabT has also been shown to phosphorylate proteins involved in protein synthesis, such as AbrB and Ef-Tu, suggesting a possible regulatory role in the progressive metabolic quiescence of the forespore. Finally, cross phosphorylations with other protein kinases implicate YabT in the regulation of numerous other cellular processes. Using an artificial protein scaffold as crystallization helper, we determined the first crystal structure of this DNA-dependent bacterial protein kinase. This allowed us to trap the active conformation of the kinase domain of YabT. Using NMR, we showed that the basic juxtamembrane region of YabT is disordered in the absence of DNA in solution, just like it is in the crystal, and that it is stabilized upon DNA binding. In comparison with its closest structural homolog, the mycobacterial kinase PknB allowed us to discuss the dimerization mode of YabT. Together with phosphorylation assays and DNA-binding experiments, this structural analysis helped us to gain new insights into the regulatory activation mechanism of YabT.
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Affiliation(s)
- Lei Shi
- Division of Systems and Synthetic Biology, Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Andrea Cavagnino
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Jean-Luc Rabefiraisana
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Noureddine Lazar
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Inès Li de la Sierra-Gallay
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Françoise Ochsenbein
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Marie Valerio-Lepiniec
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Agathe Urvoas
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Philippe Minard
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Ivan Mijakovic
- Division of Systems and Synthetic Biology, Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Sylvie Nessler
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
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21
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Broad-Spectrum Antiviral Activity of an Ankyrin Repeat Protein on Viral Assembly against Chimeric NL4-3 Viruses Carrying Gag/PR Derived from Circulating Strains among Northern Thai Patients. Viruses 2018; 10:v10110625. [PMID: 30428529 PMCID: PMC6265948 DOI: 10.3390/v10110625] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 11/08/2018] [Accepted: 11/09/2018] [Indexed: 01/06/2023] Open
Abstract
Certain proteins have demonstrated proficient human immunodeficiency virus (HIV-1) life cycle disturbance. Recently, the ankyrin repeat protein targeting the HIV-1 capsid, AnkGAG1D4, showed a negative effect on the viral assembly of the HIV-1NL4-3 laboratory strain. To extend its potential for future clinical application, the activity of AnkGAG1D4 in the inhibition of other HIV-1 circulating strains was evaluated. Chimeric NL4-3 viruses carrying patient-derived Gag/PR-coding regions were generated from 131 antiretroviral drug-naïve HIV-1 infected individuals in northern Thailand during 2001–2012. SupT1, a stable T-cell line expressing AnkGAG1D4 and ankyrin non-binding control (AnkA32D3), were challenged with these chimeric viruses. The p24CA sequences were analysed and classified using the K-means clustering method. Among all the classes of virus classified using the p24CA sequences, SupT1/AnkGAG1D4 demonstrated significantly lower levels of p24CA than SupT1/AnkA32D3, which was found to correlate with the syncytia formation. This result suggests that AnkGAG1D4 can significantly interfere with the chimeric viruses derived from patients with different sequences of the p24CA domain. It supports the possibility of ankyrin-based therapy as a broad alternative therapeutic molecule for HIV-1 gene therapy in the future.
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Chevrel A, Mesneau A, Sanchez D, Celma L, Quevillon-Cheruel S, Cavagnino A, Nessler S, Li de la Sierra-Gallay I, van Tilbeurgh H, Minard P, Valerio-Lepiniec M, Urvoas A. Alpha repeat proteins (αRep) as expression and crystallization helpers. J Struct Biol 2018; 201:88-99. [DOI: 10.1016/j.jsb.2017.08.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 07/28/2017] [Accepted: 08/14/2017] [Indexed: 12/30/2022]
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23
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Chang HJ, Mayonove P, Zavala A, De Visch A, Minard P, Cohen-Gonsaud M, Bonnet J. A Modular Receptor Platform To Expand the Sensing Repertoire of Bacteria. ACS Synth Biol 2018; 7:166-175. [PMID: 28946740 PMCID: PMC5880506 DOI: 10.1021/acssynbio.7b00266] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
Engineered
bacteria promise to revolutionize diagnostics and therapeutics,
yet many applications are precluded by the limited number of detectable
signals. Here we present a general framework to engineer synthetic
receptors enabling bacterial cells to respond to novel ligands. These
receptors are activated via ligand-induced dimerization
of a single-domain antibody fused to monomeric DNA-binding domains
(split-DBDs). Using E. coli as a model system,
we engineer both transmembrane and cytosolic receptors using a VHH
for ligand detection and demonstrate the scalability of our platform
by using the DBDs of two different transcriptional regulators. We
provide a method to optimize receptor behavior by finely tuning protein
expression levels and optimizing interdomain linker regions. Finally,
we show that these receptors can be connected to downstream synthetic
gene circuits for further signal processing. The general nature of
the split-DBD principle and the versatility of antibody-based detection
should support the deployment of these receptors into various hosts
to detect ligands for which no receptor is found in nature.
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Affiliation(s)
- Hung-Ju Chang
- Centre
de Biochimie Structurale, INSERM U1054, CNRS UMR5048, University of Montpellier, 34090 Montpellier, France
| | - Pauline Mayonove
- Centre
de Biochimie Structurale, INSERM U1054, CNRS UMR5048, University of Montpellier, 34090 Montpellier, France
| | - Agustin Zavala
- Centre
de Biochimie Structurale, INSERM U1054, CNRS UMR5048, University of Montpellier, 34090 Montpellier, France
| | - Angelique De Visch
- Centre
de Biochimie Structurale, INSERM U1054, CNRS UMR5048, University of Montpellier, 34090 Montpellier, France
| | - Philippe Minard
- Institute
for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - Martin Cohen-Gonsaud
- Centre
de Biochimie Structurale, INSERM U1054, CNRS UMR5048, University of Montpellier, 34090 Montpellier, France
| | - Jerome Bonnet
- Centre
de Biochimie Structurale, INSERM U1054, CNRS UMR5048, University of Montpellier, 34090 Montpellier, France
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24
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Hadpech S, Nangola S, Chupradit K, Fanhchaksai K, Furnon W, Urvoas A, Valerio-Lepiniec M, Minard P, Boulanger P, Hong SS, Tayapiwatana C. Alpha-helicoidal HEAT-like Repeat Proteins (αRep) Selected as Interactors of HIV-1 Nucleocapsid Negatively Interfere with Viral Genome Packaging and Virus Maturation. Sci Rep 2017; 7:16335. [PMID: 29180782 PMCID: PMC5703948 DOI: 10.1038/s41598-017-16451-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 11/13/2017] [Indexed: 12/21/2022] Open
Abstract
A new generation of artificial proteins, derived from alpha-helicoidal HEAT-like repeat protein scaffolds (αRep), was previously characterized as an effective source of intracellular interfering proteins. In this work, a phage-displayed library of αRep was screened on a region of HIV-1 Gag polyprotein encompassing the C-terminal domain of the capsid, the SP1 linker and the nucleocapsid. This region is known to be essential for the late steps of HIV-1 life cycle, Gag oligomerization, viral genome packaging and the last cleavage step of Gag, leading to mature, infectious virions. Two strong αRep binders were isolated from the screen, αRep4E3 (32 kDa; 7 internal repeats) and αRep9A8 (28 kDa; 6 internal repeats). Their antiviral activity against HIV-1 was evaluated in VLP-producer cells and in human SupT1 cells challenged with HIV-1. Both αRep4E3 and αRep9A8 showed a modest but significant antiviral effects in all bioassays and cell systems tested. They did not prevent the proviral integration reaction, but negatively interfered with late steps of the HIV-1 life cycle: αRep4E3 blocked the viral genome packaging, whereas αRep9A8 altered both virus maturation and genome packaging. Interestingly, SupT1 cells stably expressing αRep9A8 acquired long-term resistance to HIV-1, implying that αRep proteins can act as antiviral restriction-like factors.
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Affiliation(s)
- Sudarat Hadpech
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand.,Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand.,Faculty of Pharmaceutical Science, Burapha University, Muang District, Chonburi Province, 20131, Thailand.,University Lyon 1, UMR754-INRA-EPHE, Viral Infections and Comparative Pathology, 50, Avenue Tony Garnier, 69366, Lyon Cedex 07, France
| | - Sawitree Nangola
- Division of Clinical Immunology and Transfusion Sciences, School of Allied Health Sciences, University of Phayao, Phayao, 56000, Thailand
| | - Koollawat Chupradit
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand.,Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Kanda Fanhchaksai
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand.,Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Wilhelm Furnon
- University Lyon 1, UMR754-INRA-EPHE, Viral Infections and Comparative Pathology, 50, Avenue Tony Garnier, 69366, Lyon Cedex 07, France
| | - Agathe Urvoas
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Marie Valerio-Lepiniec
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Philippe Minard
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Pierre Boulanger
- University Lyon 1, UMR754-INRA-EPHE, Viral Infections and Comparative Pathology, 50, Avenue Tony Garnier, 69366, Lyon Cedex 07, France
| | - Saw-See Hong
- University Lyon 1, UMR754-INRA-EPHE, Viral Infections and Comparative Pathology, 50, Avenue Tony Garnier, 69366, Lyon Cedex 07, France. .,Institut National de la Santé et de la Recherche Médicale, 101, rue de Tolbiac, 75654, Paris Cedex 13, France.
| | - Chatchai Tayapiwatana
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand. .,Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand.
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25
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Design and applications of a clamp for Green Fluorescent Protein with picomolar affinity. Sci Rep 2017; 7:16292. [PMID: 29176615 PMCID: PMC5701241 DOI: 10.1038/s41598-017-15711-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 10/31/2017] [Indexed: 01/15/2023] Open
Abstract
Green fluorescent protein (GFP) fusions are pervasively used to study structures and processes. Specific GFP-binders are thus of great utility for detection, immobilization or manipulation of GFP-fused molecules. We determined structures of two designed ankyrin repeat proteins (DARPins), complexed with GFP, which revealed different but overlapping epitopes. Here we show a structure-guided design strategy that, by truncation and computational reengineering, led to a stable construct where both can bind simultaneously: by linkage of the two binders, fusion constructs were obtained that “wrap around” GFP, have very high affinities of about 10–30 pM, and extremely slow off-rates. They can be natively produced in E. coli in very large amounts, and show excellent biophysical properties. Their very high stability and affinity, facile site-directed functionalization at introduced unique lysines or cysteines facilitate many applications. As examples, we present them as tight yet reversible immobilization reagents for surface plasmon resonance, as fluorescently labelled monomeric detection reagents in flow cytometry, as pull-down ligands to selectively enrich GFP fusion proteins from cell extracts, and as affinity column ligands for inexpensive large-scale protein purification. We have thus described a general design strategy to create a “clamp” from two different high-affinity repeat proteins, even if their epitopes overlap.
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26
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Di Meo T, Ghattas W, Herrero C, Velours C, Minard P, Mahy JP, Ricoux R, Urvoas A. αRep A3: A Versatile Artificial Scaffold for Metalloenzyme Design. Chemistry 2017; 23:10156-10166. [PMID: 28543753 DOI: 10.1002/chem.201701518] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Indexed: 12/19/2022]
Abstract
αRep refers to a new family of artificial proteins based on a thermostable α-helical repeated motif. One of its members, αRep A3, forms a stable homo-dimer with a wide cleft that is able to accommodate metal complexes and thus appears to be suitable for generating new artificial biocatalysts. Based on the crystal structure of αRep A3, two positions (F119 and Y26) were chosen, and independently changed into cysteine residues. A phenanthroline ligand was covalently attached to the unique cysteine residue of each protein variant, and the corresponding biohybrids were purified and characterized. Once mutated and coupled to phenanthroline, the protein remained folded and dimeric. Copper(II) was specifically bound by the two biohybrids with two different binding modes. Furthermore, the holo-biohybrid A3F119NPH was found to be capable of enantioselectively catalyzing Diels-Alder (D-A) cycloadditions with up to 62 % ee. This study validates the choice of the αRep A3 dimer as a protein scaffold and provides a promising new route for the design and production of new enantioselective biohybrids based on entirely artificial proteins obtained from a highly diverse library.
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Affiliation(s)
- Thibault Di Meo
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), UMR 8182, CNRS, Univ. Paris Sud, Université Paris-Saclay, Bât. 420, rue du Doyen Georges Poitou, 91405, Orsay cedex, France.,Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Wadih Ghattas
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), UMR 8182, CNRS, Univ. Paris Sud, Université Paris-Saclay, Bât. 420, rue du Doyen Georges Poitou, 91405, Orsay cedex, France
| | - Christian Herrero
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), UMR 8182, CNRS, Univ. Paris Sud, Université Paris-Saclay, Bât. 420, rue du Doyen Georges Poitou, 91405, Orsay cedex, France
| | - Christophe Velours
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Philippe Minard
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Jean-Pierre Mahy
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), UMR 8182, CNRS, Univ. Paris Sud, Université Paris-Saclay, Bât. 420, rue du Doyen Georges Poitou, 91405, Orsay cedex, France
| | - Rémy Ricoux
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), UMR 8182, CNRS, Univ. Paris Sud, Université Paris-Saclay, Bât. 420, rue du Doyen Georges Poitou, 91405, Orsay cedex, France
| | - Agathe Urvoas
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
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27
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Abstract
Advances in protein engineering tools, both computational and experimental, has afforded many new protein structures and functions. Here, we present a snapshot of repeat-protein engineering efforts towards new, versatile, alternative binding scaffolds for use in analytical sensors and as imaging agents. Analytical assays, sensors and imaging agents based on the direct binding of analyte are increasingly important for research and diagnostics in medicine, food safety, and national security.
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28
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Figueroa M, Sleutel M, Vandevenne M, Parvizi G, Attout S, Jacquin O, Vandenameele J, Fischer AW, Damblon C, Goormaghtigh E, Valerio-Lepiniec M, Urvoas A, Durand D, Pardon E, Steyaert J, Minard P, Maes D, Meiler J, Matagne A, Martial JA, Van de Weerdt C. The unexpected structure of the designed protein Octarellin V.1 forms a challenge for protein structure prediction tools. J Struct Biol 2016; 195:19-30. [PMID: 27181418 DOI: 10.1016/j.jsb.2016.05.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 04/19/2016] [Accepted: 05/12/2016] [Indexed: 12/26/2022]
Abstract
Despite impressive successes in protein design, designing a well-folded protein of more 100 amino acids de novo remains a formidable challenge. Exploiting the promising biophysical features of the artificial protein Octarellin V, we improved this protein by directed evolution, thus creating a more stable and soluble protein: Octarellin V.1. Next, we obtained crystals of Octarellin V.1 in complex with crystallization chaperons and determined the tertiary structure. The experimental structure of Octarellin V.1 differs from its in silico design: the (αβα) sandwich architecture bears some resemblance to a Rossman-like fold instead of the intended TIM-barrel fold. This surprising result gave us a unique and attractive opportunity to test the state of the art in protein structure prediction, using this artificial protein free of any natural selection. We tested 13 automated webservers for protein structure prediction and found none of them to predict the actual structure. More than 50% of them predicted a TIM-barrel fold, i.e. the structure we set out to design more than 10years ago. In addition, local software runs that are human operated can sample a structure similar to the experimental one but fail in selecting it, suggesting that the scoring and ranking functions should be improved. We propose that artificial proteins could be used as tools to test the accuracy of protein structure prediction algorithms, because their lack of evolutionary pressure and unique sequences features.
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Affiliation(s)
- Maximiliano Figueroa
- GIGA-Research, Molecular Biomimetics and Protein Engineering, University of Liège, Liège, Belgium.
| | - Mike Sleutel
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Marylene Vandevenne
- GIGA-Research, Molecular Biomimetics and Protein Engineering, University of Liège, Liège, Belgium
| | - Gregory Parvizi
- GIGA-Research, Molecular Biomimetics and Protein Engineering, University of Liège, Liège, Belgium
| | - Sophie Attout
- GIGA-Research, Molecular Biomimetics and Protein Engineering, University of Liège, Liège, Belgium
| | - Olivier Jacquin
- GIGA-Research, Molecular Biomimetics and Protein Engineering, University of Liège, Liège, Belgium
| | - Julie Vandenameele
- Laboratoire d'Enzymologie et Repliement des Protéines, Centre for Protein Engineering, University of Liège, Liège, Belgium
| | - Axel W Fischer
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN, United States
| | | | - Erik Goormaghtigh
- Laboratory for the Structure and Function of Biological Membranes, Center for Structural Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium
| | - Marie Valerio-Lepiniec
- Institute for Integrative Biology of the Cell (I2BC), UMT 9198, CEA, CNRS, Université Paris-Sud, Orsay, France
| | - Agathe Urvoas
- Institute for Integrative Biology of the Cell (I2BC), UMT 9198, CEA, CNRS, Université Paris-Sud, Orsay, France
| | - Dominique Durand
- Institute for Integrative Biology of the Cell (I2BC), UMT 9198, CEA, CNRS, Université Paris-Sud, Orsay, France
| | - Els Pardon
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Philippe Minard
- Institute for Integrative Biology of the Cell (I2BC), UMT 9198, CEA, CNRS, Université Paris-Sud, Orsay, France
| | - Dominique Maes
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Jens Meiler
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN, United States
| | - André Matagne
- Laboratoire d'Enzymologie et Repliement des Protéines, Centre for Protein Engineering, University of Liège, Liège, Belgium
| | - Joseph A Martial
- GIGA-Research, Molecular Biomimetics and Protein Engineering, University of Liège, Liège, Belgium
| | - Cécile Van de Weerdt
- GIGA-Research, Molecular Biomimetics and Protein Engineering, University of Liège, Liège, Belgium.
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29
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Gurunatha KL, Fournier AC, Urvoas A, Valerio-Lepiniec M, Marchi V, Minard P, Dujardin E. Nanoparticles Self-Assembly Driven by High Affinity Repeat Protein Pairing. ACS NANO 2016; 10:3176-3185. [PMID: 26863288 DOI: 10.1021/acsnano.5b04531] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Proteins are the most specific yet versatile biological self-assembling agents with a rich chemistry. Nevertheless, the design of new proteins with recognition capacities is still in its infancy and has seldom been exploited for the self-assembly of functional inorganic nanoparticles. Here, we report on the protein-directed assembly of gold nanoparticles using purpose-designed artificial repeat proteins having a rigid but modular 3D architecture. αRep protein pairs are selected for their high mutual affinity from a library of 10(9) variants. Their conjugation onto gold nanoparticles drives the massive colloidal assembly of free-standing, one-particle thick films. When the average number of proteins per nanoparticle is lowered, the extent of self-assembly is limited to oligomeric particle clusters. Finally, we demonstrate that the aggregates are reversibly disassembled by an excess of one free protein. Our approach could be optimized for applications in biosensing, cell targeting, or functional nanomaterials engineering.
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Affiliation(s)
- Kargal L Gurunatha
- Groupe NanoSciences-CEMES, CNRS UPR 8011 , 29 rue J. Marvig, B.P. 94347, F-31055 Toulouse, France
| | - Agathe C Fournier
- Groupe NanoSciences-CEMES, CNRS UPR 8011 , 29 rue J. Marvig, B.P. 94347, F-31055 Toulouse, France
| | - Agathe Urvoas
- I2BC, Univ Paris Sud, CNRS, CEA UMR 9198 , Bât. 430, F-91405 Orsay, France
| | | | - Valérie Marchi
- University Rennes 1, Institut of Chemical Sciences, UMR 6226 CNRS , Campus Beaulieu, F- 35042 Rennes, France
| | - Philippe Minard
- I2BC, Univ Paris Sud, CNRS, CEA UMR 9198 , Bât. 430, F-91405 Orsay, France
| | - Erik Dujardin
- Groupe NanoSciences-CEMES, CNRS UPR 8011 , 29 rue J. Marvig, B.P. 94347, F-31055 Toulouse, France
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30
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Ghattas W, Cotchico-Alonso L, Maréchal JD, Urvoas A, Rousseau M, Mahy JP, Ricoux R. Artificial Metalloenzymes with the Neocarzinostatin Scaffold: Toward a Biocatalyst for the Diels-Alder Reaction. Chembiochem 2016; 17:433-40. [DOI: 10.1002/cbic.201500445] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Indexed: 01/17/2023]
Affiliation(s)
- Wadih Ghattas
- Institute de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO); UMR 8182, CNRS, Université Paris-Sud; Bât. 420, rue du Doyen Georges Poitou 91405 Orsay Cedex France
| | - Lur Cotchico-Alonso
- Departament de Química; Universitat Autònoma de Barcelona; Edifici C.n. 08193, Cerdonyola del Vallès Barcelona Spain
| | - Jean-Didier Maréchal
- Departament de Química; Universitat Autònoma de Barcelona; Edifici C.n. 08193, Cerdonyola del Vallès Barcelona Spain
| | - Agathe Urvoas
- Institute for Integrative Biology of the Cell (I2BC); UMR 9198, CEA, CNRS, Université Paris-Sud; Bât. 430, rue du Doyen Georges Poitou 91405 Orsay Cedex France
| | - Maëva Rousseau
- Institute de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO); UMR 8182, CNRS, Université Paris-Sud; Bât. 420, rue du Doyen Georges Poitou 91405 Orsay Cedex France
| | - Jean-Pierre Mahy
- Institute de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO); UMR 8182, CNRS, Université Paris-Sud; Bât. 420, rue du Doyen Georges Poitou 91405 Orsay Cedex France
| | - Rémy Ricoux
- Institute de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO); UMR 8182, CNRS, Université Paris-Sud; Bât. 420, rue du Doyen Georges Poitou 91405 Orsay Cedex France
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31
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Bakail M, Ochsenbein F. Targeting protein–protein interactions, a wide open field for drug design. CR CHIM 2016. [DOI: 10.1016/j.crci.2015.12.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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32
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The αRep artificial repeat protein scaffold: a new tool for crystallization and live cell applications. Biochem Soc Trans 2015; 43:819-24. [DOI: 10.1042/bst20150075] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We have designed a new family of artificial proteins, named αRep, based on HEAT (acronym for Huntingtin, elongation factor 3 (EF3), protein pphosphatase 2A (PP2A), yeast kinase Tor1) repeat proteins containing an α-helical repeated motif. The sequence of the repeated motifs, first identified in a thermostable archae protein was optimized using a consensus design strategy and used for the construction of a library of artificial proteins. All proteins from this library share the same general fold but differ both in the number of repeats and in five highly randomized amino acid positions within each repeat. The randomized side chains altogether provide a hypervariable surface on αRep variants. Sequences from this library are efficiently expressed as soluble, folded and very stable proteins. αRep binders with high affinity for various protein targets were selected by phage display. Low micromolar to nanomolar dissociation constants between partners were measured and the structures of several complexes (specific αRep/protein target) were solved by X-ray crystallography. Using GFP as a model target, it was demonstrated that αReps can be used as bait in pull-down experiments. αReps can be expressed in eukaryotic cells and specifically interact with their target addressed to different cell compartments.
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33
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Specific GFP-binding artificial proteins (αRep): a new tool for in vitro to live cell applications. Biosci Rep 2015; 35:BSR20150080. [PMID: 26182430 PMCID: PMC4613692 DOI: 10.1042/bsr20150080] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 04/23/2015] [Indexed: 02/08/2023] Open
Abstract
Artificial proteins, named αRep, binding tightly and specifically to EGFP are described. The structures of αRep–EGFP complexes explain how αRep recognize their cognate partner. Specific αRep can be used for biochemical or live cells experiments. A family of artificial proteins, named αRep, based on a natural family of helical repeat was previously designed. αRep members are efficiently expressed, folded and extremely stable proteins. A large αRep library was constructed creating proteins with a randomized interaction surface. In the present study, we show that the αRep library is an efficient source of tailor-made specific proteins with direct applications in biochemistry and cell biology. From this library, we selected by phage display αRep binders with nanomolar dissociation constants against the GFP. The structures of two independent αRep binders in complex with the GFP target were solved by X-ray crystallography revealing two totally different binding modes. The affinity of the selected αReps for GFP proved sufficient for practically useful applications such as pull-down experiments. αReps are disulfide free proteins and are efficiently and functionally expressed in eukaryotic cells: GFP-specific αReps are clearly sequestrated by their cognate target protein addressed to various cell compartments. These results suggest that αRep proteins with tailor-made specificity can be selected and used in living cells to track, modulate or interfere with intracellular processes.
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Tiouajni M, Durand D, Blondeau K, Graille M, Urvoas A, Valerio-Lepiniec M, Guellouz A, Aumont-Nicaise M, Minard P, van Tilbeurgh H. Structural and functional analysis of the fibronectin-binding protein FNE from Streptococcus equi spp. equi. FEBS J 2014; 281:5513-31. [PMID: 25290767 DOI: 10.1111/febs.13092] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 09/24/2014] [Accepted: 09/30/2014] [Indexed: 12/17/2022]
Abstract
Streptococcus equi is a horse pathogen belonging to Lancefield group C. Infection by S. equi ssp. equi causes strangles, a serious and highly contagious disease of the upper respiratory tract. S. equi ssp. equi secretes a fibronectin (Fn)-binding protein, FNE, that does not contain cell wall-anchoring motifs. FNE binds to the gelatin-binding domain (GBD) of Fn, composed of the motifs (6) FI (12) FII (789) FI . FNE lacks the canonical Fn-binding peptide repeats observed in many microbial surface components recognizing adhesive matrix molecules. We found that the interaction between FNE and the human GBD is mediated by the binding of the disordered C-terminal region (residues 208-262) of FNE to the (789) FI GBD subfragment. The crystal structure of FNE showed that it is similar to the minor pilus protein Spy0125 of Streptococcus pyogenes, found at the end of pilus polymers and responsible for adhesion. FNE and Spy0125 both have a superimposable internal thioester bond between highly conserved Cys and Gln residues. Small-angle X-ray scattering of the FNE-(789) FI complex provided a model that aligns the C-terminal peptide of FNE with the E-strands of the FI domains, adopting the β-zipper extension model observed in previous structures of microbial surface components recognizing adhesive matrix molecule adhesion peptides bound to FI domains.
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Affiliation(s)
- Mounira Tiouajni
- Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, UMR 8619 CNRS, Université Paris Sud, Orsay, France
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Lensink MF, Wodak SJ. Score_set: A CAPRI benchmark for scoring protein complexes. Proteins 2014; 82:3163-9. [DOI: 10.1002/prot.24678] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 08/05/2014] [Accepted: 08/22/2014] [Indexed: 12/26/2022]
Affiliation(s)
- Marc F. Lensink
- CNRS USR3078; University Lille North of France, Parc de la Haute Borne; F-59658 Villeneuve d'Ascq France
| | - Shoshana J. Wodak
- Structural Biology Program; Hospital for Sick Children; Toronto Ontario M5G 1X8 Canada
- Department of Biochemistry; University of Toronto; Ontario Canada
- Department of Molecular Genetics; University of Toronto; Ontario Canada
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Ferrandez Y, Dezi M, Bosco M, Urvoas A, Valerio-Lepiniec M, Le Bon C, Giusti F, Broutin I, Durand G, Polidori A, Popot JL, Picard M, Minard P. Amphipol-mediated screening of molecular orthoses specific for membrane protein targets. J Membr Biol 2014; 247:925-40. [PMID: 25086771 DOI: 10.1007/s00232-014-9707-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 07/14/2014] [Indexed: 12/11/2022]
Abstract
Specific, tight-binding protein partners are valuable helpers to facilitate membrane protein (MP) crystallization, because they can i) stabilize the protein, ii) reduce its conformational heterogeneity, and iii) increase the polar surface from which well-ordered crystals can grow. The design and production of a new family of synthetic scaffolds (dubbed αReps, for "artificial alpha repeat protein") have been recently described. The stabilization and immobilization of MPs in a functional state are an absolute prerequisite for the screening of binders that recognize specifically their native conformation. We present here a general procedure for the selection of αReps specific of any MP. It relies on the use of biotinylated amphipols, which act as a universal "Velcro" to stabilize, and immobilize MP targets onto streptavidin-coated solid supports, thus doing away with the need to tag the protein itself.
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Affiliation(s)
- Yann Ferrandez
- Laboratoire de Modélisation et Ingénierie des Protéines, IBBMC UMR 8619, CNRS/Université Paris Sud, 91405, Orsay, France
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Huang SY, Yan C, Grinter SZ, Chang S, Jiang L, Zou X. Inclusion of the orientational entropic effect and low-resolution experimental information for protein-protein docking in Critical Assessment of PRedicted Interactions (CAPRI). Proteins 2013; 81:2183-91. [PMID: 24227686 PMCID: PMC3916956 DOI: 10.1002/prot.24435] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 09/23/2013] [Accepted: 09/25/2013] [Indexed: 01/20/2023]
Abstract
Inclusion of entropy is important and challenging for protein-protein binding prediction. Here, we present a statistical mechanics-based approach to empirically consider the effect of orientational entropy. Specifically, we globally sample the possible binding orientations based on a simple shape-complementarity scoring function using an FFT-type docking method. Then, for each generated orientation, we calculate the probability through the partition function of the ensemble of accessible states, which are assumed to be represented by the set of nearby binding modes. For each mode, the interaction energy is calculated using our ITScorePP scoring function that was developed in our laboratory based on principles of statistical mechanics. Using the above protocol, we present the results of our participation in Rounds 22-27 of the Critical Assessment of PRedicted Interactions (CAPRI) experiment for 10 targets (T46-T58). Additional experimental information, such as low-resolution small-angle X-ray scattering data, was used when available. In the prediction (or docking) experiments of the 10 target complexes, we achieved correct binding modes for six targets: one with high accuracy (T47), two with medium accuracy (T48 and T57), and three with acceptable accuracy (T49, T50, and T58). In the scoring experiments of seven target complexes, we obtained correct binding modes for six targets: one with high accuracy (T47), two with medium accuracy (T49 and T50), and three with acceptable accuracy (T46, T51, and T53).
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Affiliation(s)
- Sheng-You Huang
- Department of Physics and Astronomy, Department of Biochemistry, Dalton Cardiovascular Research Center, and Informatics Institute, University of Missouri, Columbia, MO 65211
| | | | | | - Shan Chang
- Department of Physics and Astronomy, Department of Biochemistry, Dalton Cardiovascular Research Center, and Informatics Institute, University of Missouri, Columbia, MO 65211
| | - Lin Jiang
- Department of Physics and Astronomy, Department of Biochemistry, Dalton Cardiovascular Research Center, and Informatics Institute, University of Missouri, Columbia, MO 65211
| | - Xiaoqin Zou
- Department of Physics and Astronomy, Department of Biochemistry, Dalton Cardiovascular Research Center, and Informatics Institute, University of Missouri, Columbia, MO 65211
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Lensink MF, Wodak SJ. Docking, scoring, and affinity prediction in CAPRI. Proteins 2013; 81:2082-95. [DOI: 10.1002/prot.24428] [Citation(s) in RCA: 199] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 09/12/2013] [Accepted: 09/13/2013] [Indexed: 01/28/2023]
Affiliation(s)
- Marc F. Lensink
- Interdisciplinary Research Institute, USR3078 CNRS; University Lille North of France, Parc de la Haute Borne; 50 avenue de Halley F-59658 Villeneuve d'Ascq cedex France
| | - Shoshana J. Wodak
- Structure and Function Program; Hospital for Sick Children; Toronto Ontario M5G 1X8 Canada
- Department of Biochemistry; University of Toronto; Toronto Ontario Canada
- Department of Molecular Genetics; University of Toronto; Toronto Ontario Canada
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