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Liang H, Ma Z, Wang Z, Zhong P, Li R, Jiang H, Zong X, Zhong C, Liu X, Liu P, Liu J, Zhu H, Liu R, Ding Y. Structural Insights into the Binding of Red Fluorescent Protein mCherry-Specific Nanobodies. Int J Mol Sci 2023; 24:ijms24086952. [PMID: 37108116 PMCID: PMC10138814 DOI: 10.3390/ijms24086952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/31/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
Red fluorescent proteins (RFPs) have broad applications in life science research, and the manipulation of RFPs using nanobodies can expand their potential uses. However, the structural information available for nanobodies that bind with RFPs is still insufficient. In this study, we cloned, expressed, purified, and crystallized complexes formed by mCherry with LaM1, LaM3, and LaM8. Then, we analyzed the biochemical properties of the complexes using mass spectrometry (MS), fluorescence-detected size exclusion chromatography (FSEC), isothermal titration calorimetry (ITC), and bio-layer interferometry (BLI) technology. We determined the crystal structure of mCherry-LaM1, mCherry-LaM3, and mCherry-LaM8, with resolutions of 2.05 Å, 3.29 Å, and 1.31 Å, respectively. In this study, we systematically compared various parameters of several LaM series nanobodies, including LaM1, LaM3, and LaM8, with previously reported data on LaM2, LaM4, and LaM6, specifically examining their structural information. After designing multivalent tandem LaM1-LaM8 and LaM8-LaM4 nanobodies based on structural information, we characterized their properties, revealing their higher affinity and specificity to mCherry. Our research provides novel structural insights that could aid in understanding nanobodies targeting a specific target protein. This could provide a starting point for developing enhanced mCherry manipulation tools.
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Affiliation(s)
- Hui Liang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Zhiqiang Ma
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Ziying Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Peiyu Zhong
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Ran Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - He Jiang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xin Zong
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Chao Zhong
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xihuan Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Peng Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jiayuan Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Haoran Zhu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Rui Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yu Ding
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
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Yasui N, Nakamura K, Yamashita A. A sweet protein monellin as a non-antibody scaffold for synthetic binding proteins. J Biochem 2021; 169:585-599. [PMID: 33386843 DOI: 10.1093/jb/mvaa147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/07/2020] [Indexed: 11/13/2022] Open
Abstract
Synthetic binding proteins that have the ability to bind with molecules can be generated using various protein domains as non-antibody scaffolds. These designer proteins have been used widely in research studies, as their properties overcome the disadvantages of using antibodies. Here, we describe the first application of a phage display to generate synthetic binding proteins using a sweet protein, monellin, as a non-antibody scaffold. Single-chain monellin (scMonellin), in which two polypeptide chains of natural monellin are connected by a short linker, has two loops on one side of the molecule. We constructed phage display libraries of scMonellin, in which the amino acid sequence of the two loops is diversified. To validate the performance of these libraries, we sorted them against the folding mutant of the green fluorescent protein variant (GFPuv) and yeast small ubiquitin-related modifier. We successfully obtained scMonellin variants exhibiting moderate but significant affinities for these target proteins. Crystal structures of one of the GFPuv-binding variants in complex with GFPuv revealed that the two diversified loops were involved in target recognition. scMonellin, therefore, represents a promising non-antibody scaffold in the design and generation of synthetic binding proteins. We termed the scMonellin-derived synthetic binding proteins 'SWEEPins'.
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Affiliation(s)
- Norihisa Yasui
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1, Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Kazuaki Nakamura
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1, Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Atsuko Yamashita
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1, Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
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Structural insights into two distinct nanobodies recognizing the same epitope of green fluorescent protein. Biochem Biophys Res Commun 2021; 565:57-63. [PMID: 34098312 DOI: 10.1016/j.bbrc.2021.05.089] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 05/27/2021] [Indexed: 01/01/2023]
Abstract
Green fluorescent protein (GFP) and its derivatives are widely used in biomedical research, and the manipulation of GFP-tagged proteins by GFP-specific binders is highly desired. However, structural information on how these binders bind with GFP is still lacking. In this study, we determined the crystal structure of the nanobody Nb2 complexed with superfolder GFP (sfGFP) at a resolution of 2.2 Å. Interestingly, although the complementarity-determining regions (CDRs) of Nb2 and LaG16 sequences were only 29.7% identical, they both bound to the same epitope of GFP and existed in the same orientation. Structural analysis indicated that they achieved similar binding characteristics through different mechanisms. We further verified the kinetics and thermodynamics of binding by biolayer interferometry (BLI) and isothermal titration calorimetry (ITC). Nb2 showed a slightly higher binding affinity for sfGFP than LaG16. The stability of GFP-specific nanobodies was verified by nano differential scanning fluorimetry (nanoDSF). Nb2 exhibited the highest melting temperature (Tm); thus, Nb2 is a promising GFP nanobody candidate for use in applications requiring harsh testing conditions. We also compared the binding sites of available GFP nanobodies and showed that some of them can simultaneously bind with GFP and assemble into multifunctional complexes to manipulate GFP-tagged target proteins. Our results provide atomic-scale binding information for Nb2-sfGFP, which is important for the further development of GFP-nanobody based fusion protein manipulation techniques.
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Kashima D, Kageoka M, Kimura Y, Horikawa M, Miura M, Nakakido M, Tsumoto K, Nagamune T, Kawahara M. A Novel Cell-Based Intracellular Protein-Protein Interaction Detection Platform (SOLIS) for Multimodality Screening. ACS Synth Biol 2021; 10:990-999. [PMID: 33909409 DOI: 10.1021/acssynbio.0c00483] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Intervention in protein-protein interactions (PPIs) has tremendous effects in the molecular therapy of many diseases. To fulfill the requirements for targeting intracellular proteins, here we develop SOS-localization-based interaction screening (SOLIS), which elaborately mimics signaling via the Ras-mitogen-activated protein kinase pathway. SOLIS employs two chimeric proteins in which a membrane localization motif (CaaX) is fused at the C-terminus of a protein of interest and the catalytic domain of SOS is fused at the C-terminus of another protein of interest. Interaction between the two proteins of interest induces membrane localization of the SOS chimera and cell proliferation. Thus, the SOLIS system enables enrichment of superior binders based on cell proliferation in an intracellular PPI-dependent manner. This was verified by three major modalities against intracellular PPIs (small molecules, peptide aptamers, and intrabodies). The system worked over a broad range of affinities (KD = 0.32-140 nM). In a screening of a site-directed randomized library, novel intrabody clones were selected on the basis of the potency of cell proliferation. Three other PPI detection methods (NanoBiT, SPR, and pull-down assays) were employed to characterize the SOLIS system, and several intrabody clones were judged as false negatives in these assays. SOLIS signals would be less sensitive to the orientation/conformation of the chimeric proteins, and this feature emerges as the advantage of SOLIS as a mammalian cytosolic PPI detection system with few false negatives.
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Affiliation(s)
- Daiki Kashima
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Miho Kageoka
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Yosuke Kimura
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Makiko Horikawa
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Masashi Miura
- Laboratory of Cell Vaccine, Center for Vaccine and Adjuvant Research (CVAR), National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki-shi, Osaka 567-0085, Japan
| | - Makoto Nakakido
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Kouhei Tsumoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Medical Proteomics Laboratory, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Teruyuki Nagamune
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Masahiro Kawahara
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Laboratory of Cell Vaccine, Center for Vaccine and Adjuvant Research (CVAR), National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki-shi, Osaka 567-0085, Japan
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5
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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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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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7
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bioPROTACs as versatile modulators of intracellular therapeutic targets including proliferating cell nuclear antigen (PCNA). Proc Natl Acad Sci U S A 2020; 117:5791-5800. [PMID: 32123106 DOI: 10.1073/pnas.1920251117] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Targeted degradation approaches such as proteolysis targeting chimeras (PROTACs) offer new ways to address disease through tackling challenging targets and with greater potency, efficacy, and specificity over traditional approaches. However, identification of high-affinity ligands to serve as PROTAC starting points remains challenging. As a complementary approach, we describe a class of molecules termed biological PROTACs (bioPROTACs)-engineered intracellular proteins consisting of a target-binding domain directly fused to an E3 ubiquitin ligase. Using GFP-tagged proteins as model substrates, we show that there is considerable flexibility in both the choice of substrate binders (binding positions, scaffold-class) and the E3 ligases. We then identified a highly effective bioPROTAC against an oncology target, proliferating cell nuclear antigen (PCNA) to elicit rapid and robust PCNA degradation and associated effects on DNA synthesis and cell cycle progression. Overall, bioPROTACs are powerful tools for interrogating degradation approaches, target biology, and potentially for making therapeutic impacts.
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8
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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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9
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Kongsuwan N, Xiong X, Bai P, You JB, Png CE, Wu L, Hess O. Quantum Plasmonic Immunoassay Sensing. NANO LETTERS 2019; 19:5853-5861. [PMID: 31356753 DOI: 10.1021/acs.nanolett.9b01137] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Plasmon-polaritons are among the most promising candidates for next-generation optical sensors due to their ability to support extremely confined electromagnetic fields and empower strong coupling of light and matter. Here we propose quantum plasmonic immunoassay sensing as an innovative scheme, which embeds immunoassay sensing with recently demonstrated room-temperature strong coupling in nanoplasmonic cavities. In our protocol, the antibody-antigen-antibody complex is chemically linked with a quantum emitter label. Placing the quantum-emitter-enhanced antibody-antigen-antibody complexes inside or close to a nanoplasmonic (hemisphere dimer) cavity facilitates strong coupling between the plasmon-polaritons and the emitter label resulting in signature Rabi splitting. Through rigorous statistical analysis of multiple analytes randomly distributed on the substrate in extensive realistic computational experiments, we demonstrate a drastic enhancement of the sensitivity up to nearly 1500% compared to conventional shifting-type plasmonic sensors. Most importantly and in stark contrast to classical sensing, we achieve in the strong-coupling (quantum) sensing regime an enhanced sensitivity that is no longer dependent on the concentration of antibody-antigen-antibody complexes down to the single-analyte limit. The quantum plasmonic immunoassay scheme thus not only leads to the development of plasmonic biosensing for single molecules but also opens up new pathways toward room-temperature quantum sensing enabled by biomolecular inspired protocols linked with quantum nanoplasmonics.
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Affiliation(s)
- Nuttawut Kongsuwan
- The Blackett Laboratory , Imperial College London , Prince Consort Road, London SW7 2AZ , United Kingdom
| | - Xiao Xiong
- Institute of High Performance Computing, A*STAR (Agency for Science, Technology and Research) , 1 Fusionopolis Way, #16-16 Connexis , Singapore 138632 , Singapore
| | - Ping Bai
- Institute of High Performance Computing, A*STAR (Agency for Science, Technology and Research) , 1 Fusionopolis Way, #16-16 Connexis , Singapore 138632 , Singapore
| | - Jia-Bin You
- Institute of High Performance Computing, A*STAR (Agency for Science, Technology and Research) , 1 Fusionopolis Way, #16-16 Connexis , Singapore 138632 , Singapore
| | - Ching Eng Png
- Institute of High Performance Computing, A*STAR (Agency for Science, Technology and Research) , 1 Fusionopolis Way, #16-16 Connexis , Singapore 138632 , Singapore
| | - Lin Wu
- Institute of High Performance Computing, A*STAR (Agency for Science, Technology and Research) , 1 Fusionopolis Way, #16-16 Connexis , Singapore 138632 , Singapore
| | - Ortwin Hess
- The Blackett Laboratory , Imperial College London , Prince Consort Road, London SW7 2AZ , United Kingdom
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10
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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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11
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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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12
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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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13
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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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14
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Roebroek T, Duwé S, Vandenberg W, Dedecker P. Reduced Fluorescent Protein Switching Fatigue by Binding-Induced Emissive State Stabilization. Int J Mol Sci 2017; 18:ijms18092015. [PMID: 28930199 PMCID: PMC5618663 DOI: 10.3390/ijms18092015] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 09/08/2017] [Accepted: 09/11/2017] [Indexed: 01/12/2023] Open
Abstract
Reversibly switchable fluorescent proteins (RSFPs) enable advanced fluorescence imaging, though the performance of this imaging crucially depends on the properties of the labels. We report on the use of an existing small binding peptide, named Enhancer, to modulate the spectroscopic properties of the recently developed rsGreen series of RSFPs. Fusion constructs of Enhancer with rsGreen1 and rsGreenF revealed an increased molecular brightness and pH stability, although expression in living E. coli or HeLa cells resulted in a decrease of the overall emission. Surprisingly, Enhancer binding also increased off-switching speed and resistance to switching fatigue. Further investigation suggested that the RSFPs can interconvert between fast- and slow-switching emissive states, with the overall protein population gradually converting to the slow-switching state through irradiation. The Enhancer modulates the spectroscopic properties of both states, but also preferentially stabilizes the fast-switching state, supporting the increased fatigue resistance. This work demonstrates how the photo-physical properties of RSFPs can be influenced by their binding to other small proteins, which opens up new horizons for applications that may require such modulation. Furthermore, we provide new insights into the photoswitching kinetics that should be of general consideration when developing new RSFPs with improved or different photochromic properties.
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Affiliation(s)
- Thijs Roebroek
- Laboratory for Nanobiology, Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Leuven, Belgium.
| | - Sam Duwé
- Laboratory for Nanobiology, Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Leuven, Belgium.
| | - Wim Vandenberg
- Laboratory for Nanobiology, Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Leuven, Belgium.
| | - Peter Dedecker
- Laboratory for Nanobiology, Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Leuven, Belgium.
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15
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Yan Y, Wen Z, Wang X, Huang SY. Addressing recent docking challenges: A hybrid strategy to integrate template-based and free protein-protein docking. Proteins 2017; 85:497-512. [PMID: 28026062 DOI: 10.1002/prot.25234] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Revised: 12/15/2016] [Accepted: 12/16/2016] [Indexed: 12/23/2022]
Abstract
Protein-protein docking is an important computational tool for predicting protein-protein interactions. With the rapid development of proteomics projects, more and more experimental binding information ranging from mutagenesis data to three-dimensional structures of protein complexes are becoming available. Therefore, how to appropriately incorporate the biological information into traditional ab initio docking has been an important issue and challenge in the field of protein-protein docking. To address these challenges, we have developed a Hybrid DOCKing protocol of template-based and template-free approaches, referred to as HDOCK. The basic procedure of HDOCK is to model the structures of individual components based on the template complex by a template-based method if a template is available; otherwise, the component structures will be modeled based on monomer proteins by regular homology modeling. Then, the complex structure of the component models is predicted by traditional protein-protein docking. With the HDOCK protocol, we have participated in the CPARI experiment for rounds 28-35. Out of the 25 CASP-CAPRI targets for oligomer modeling, our HDOCK protocol predicted correct models for 16 targets, ranking one of the top algorithms in this challenge. Our docking method also made correct predictions on other CAPRI challenges such as protein-peptide binding for 6 out of 8 targets and water predictions for 2 out of 2 targets. The advantage of our hybrid docking approach over pure template-based docking was further confirmed by a comparative evaluation on 20 CASP-CAPRI targets. Proteins 2017; 85:497-512. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Yumeng Yan
- School of Physics, Huazhong University of Science and Technology, Wuhan Hubei, 430074, People's Republic of China
| | - Zeyu Wen
- School of Physics, Huazhong University of Science and Technology, Wuhan Hubei, 430074, People's Republic of China
| | - Xinxiang Wang
- School of Physics, Huazhong University of Science and Technology, Wuhan Hubei, 430074, People's Republic of China
| | - Sheng-You Huang
- School of Physics, Huazhong University of Science and Technology, Wuhan Hubei, 430074, People's Republic of China
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16
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Lensink MF, Velankar S, Wodak SJ. Modeling protein-protein and protein-peptide complexes: CAPRI 6th edition. Proteins 2016; 85:359-377. [PMID: 27865038 DOI: 10.1002/prot.25215] [Citation(s) in RCA: 156] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 10/07/2016] [Accepted: 10/10/2016] [Indexed: 12/19/2022]
Abstract
We present the sixth report evaluating the performance of methods for predicting the atomic resolution structures of protein complexes offered as targets to the community-wide initiative on the Critical Assessment of Predicted Interactions (CAPRI). The evaluation is based on a total of 20,670 predicted models for 8 protein-peptide complexes, a novel category of targets in CAPRI, and 12 protein-protein targets in CAPRI prediction Rounds held during the years 2013-2016. For two of the protein-protein targets, the focus was on the prediction of side-chain conformation and positions of interfacial water molecules. Seven of the protein-protein targets were particularly challenging owing to their multicomponent nature, to conformational changes at the binding site, or to a combination of both. Encouragingly, the very large multiprotein complex with the nucleosome was correctly predicted, and correct models were submitted for the protein-peptide targets, but not for some of the challenging protein-protein targets. Models of acceptable quality or better were obtained for 14 of the 20 targets, including medium quality models for 13 targets and high quality models for 8 targets, indicating tangible progress of present-day computational methods in modeling protein complexes with increased accuracy. Our evaluation suggests that the progress stems from better integration of different modeling tools with docking procedures, as well as the use of more sophisticated evolutionary information to score models. Nonetheless, adequate modeling of conformational flexibility in interacting proteins remains an important area with a crucial need for improvement. Proteins 2017; 85:359-377. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Marc F Lensink
- University of Lille, CNRS UMR8576 UGSF, Lille, 59000, France
| | - Sameer Velankar
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Shoshana J Wodak
- VIB Structural Biology Research Center, VUB Pleinlaan 2, Brussels, 1050, Belgium
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17
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Xu X, Qiu L, Yan C, Ma Z, Grinter SZ, Zou X. Performance of MDockPP in CAPRI rounds 28-29 and 31-35 including the prediction of water-mediated interactions. Proteins 2016; 85:424-434. [PMID: 27802576 DOI: 10.1002/prot.25203] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 10/24/2016] [Accepted: 10/24/2016] [Indexed: 01/01/2023]
Abstract
Protein-protein interactions are either through direct contacts between two binding partners or mediated by structural waters. Both direct contacts and water-mediated interactions are crucial to the formation of a protein-protein complex. During the recent CAPRI rounds, a novel parallel searching strategy for predicting water-mediated interactions is introduced into our protein-protein docking method, MDockPP. Briefly, a FFT-based docking algorithm is employed in generating putative binding modes, and an iteratively derived statistical potential-based scoring function, ITScorePP, in conjunction with biological information is used to assess and rank the binding modes. Up to 10 binding modes are selected as the initial protein-protein complex structures for MD simulations in explicit solvent. Water molecules near the interface are clustered based on the snapshots extracted from independent equilibrated trajectories. Then, protein-ligand docking is employed for a parallel search for water molecules near the protein-protein interface. The water molecules generated by ligand docking and the clustered water molecules generated by MD simulations are merged, referred to as the predicted structural water molecules. Here, we report the performance of this protocol for CAPRI rounds 28-29 and 31-35 containing 20 valid docking targets and 11 scoring targets. In the docking experiments, we predicted correct binding modes for nine targets, including one high-accuracy, two medium-accuracy, and six acceptable predictions. Regarding the two targets for the prediction of water-mediated interactions, we achieved models ranked as "excellent" in accordance with the CAPRI evaluation criteria; one of these two targets is considered as a difficult target for structural water prediction. Proteins 2017; 85:424-434. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Xianjin Xu
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, 65211, USA
| | - Liming Qiu
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, 65211, USA
| | - Chengfei Yan
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, 65211, USA.,Department of Physics and Astronomy, University of Missouri, Columbia, Missouri, 65211, USA
| | - Zhiwei Ma
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, 65211, USA.,Department of Physics and Astronomy, University of Missouri, Columbia, Missouri, 65211, USA
| | - Sam Z Grinter
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, 65211, USA.,Informatics Institute, University of Missouri, Columbia, Missouri, 65211, USA
| | - Xiaoqin Zou
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, 65211, USA.,Department of Physics and Astronomy, University of Missouri, Columbia, Missouri, 65211, USA.,Department of Biochemistry, University of Missouri, Columbia, Missouri, 65211, USA.,Informatics Institute, University of Missouri, Columbia, Missouri, 65211, USA
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18
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Schindler CEM, Chauvot de Beauchêne I, de Vries SJ, Zacharias M. Protein-protein and peptide-protein docking and refinement using ATTRACT in CAPRI. Proteins 2016; 85:391-398. [PMID: 27785830 DOI: 10.1002/prot.25196] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 09/13/2016] [Accepted: 09/27/2016] [Indexed: 11/06/2022]
Abstract
The ATTRACT coarse-grained docking approach in combination with various types of atomistic, flexible refinement methods has been applied to predict protein-protein and peptide-protein complexes in CAPRI rounds 28-36. For a large fraction of CAPRI targets (12 out of 18), at least one model of acceptable or better quality was generated, corresponding to a success rate of 67%. In particular, for several peptide-protein complexes excellent predictions were achieved. In several cases, a combination of template-based modeling and extensive molecular dynamics-based refinement yielded medium and even high quality solutions. In one particularly challenging case, the structure of an ubiquitylation enzyme bound to the nucleosome was correctly predicted as a set of acceptable quality solutions. Based on the experience with the CAPRI targets, new interface refinement approaches and methods for ab-initio peptide-protein docking have been developed. Failures and possible improvements of the docking method with respect to scoring and protein flexibility will also be discussed. Proteins 2017; 85:391-398. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Christina E M Schindler
- Physics Department T38, Technische Universität München, Garching, 85748, Germany.,Center for Integrated Protein Science Munich, München, 81377, Germany
| | | | - Sjoerd J de Vries
- Physics Department T38, Technische Universität München, Garching, 85748, Germany
| | - Martin Zacharias
- Physics Department T38, Technische Universität München, Garching, 85748, Germany.,Center for Integrated Protein Science Munich, München, 81377, Germany
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19
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Pallara C, Jiménez-García B, Romero M, Moal IH, Fernández-Recio J. pyDock scoring for the new modeling challenges in docking: Protein-peptide, homo-multimers, and domain-domain interactions. Proteins 2016; 85:487-496. [PMID: 27701776 DOI: 10.1002/prot.25184] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 09/22/2016] [Accepted: 10/02/2016] [Indexed: 12/18/2022]
Abstract
The sixth CAPRI edition included new modeling challenges, such as the prediction of protein-peptide complexes, and the modeling of homo-oligomers and domain-domain interactions as part of the first joint CASP-CAPRI experiment. Other non-standard targets included the prediction of interfacial water positions and the modeling of the interactions between proteins and nucleic acids. We have participated in all proposed targets of this CAPRI edition both as predictors and as scorers, with new protocols to efficiently use our docking and scoring scheme pyDock in a large variety of scenarios. In addition, we have participated for the first time in the servers section, with our recently developed webserver, pyDockWeb. Excluding the CASP-CAPRI cases, we submitted acceptable models (or better) for 7 out of the 18 evaluated targets as predictors, 4 out of the 11 targets as scorers, and 6 out of the 18 targets as servers. The overall success rates were below those in past CAPRI editions. This shows the challenging nature of this last edition, with many difficult targets for which no participant submitted a single acceptable model. Interestingly, we submitted acceptable models for 83% of the evaluated protein-peptide targets. As for the 25 cases of the CASP-CAPRI experiment, in which we used a larger variety of modeling techniques (template-based, symmetry restraints, literature information, etc.), we submitted acceptable models for 56% of the targets. In summary, this CAPRI edition showed that pyDock scheme can be efficiently adapted to the increasing variety of problems that the protein interactions field is currently facing. Proteins 2017; 85:487-496. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Chiara Pallara
- Life Sciences Department, Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain
| | - Brian Jiménez-García
- Life Sciences Department, Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain
| | - Miguel Romero
- Life Sciences Department, Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain
| | - Iain H Moal
- Life Sciences Department, Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain.,European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Juan Fernández-Recio
- Life Sciences Department, Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain
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20
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Yu J, Andreani J, Ochsenbein F, Guerois R. Lessons from (co-)evolution in the docking of proteins and peptides for CAPRI Rounds 28-35. Proteins 2016; 85:378-390. [PMID: 27701780 DOI: 10.1002/prot.25180] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 08/25/2016] [Accepted: 08/25/2016] [Indexed: 11/06/2022]
Abstract
Computational protein-protein docking is of great importance for understanding protein interactions at the structural level. Critical assessment of prediction of interactions (CAPRI) experiments provide the protein docking community with a unique opportunity to blindly test methods based on real-life cases and help accelerate methodology development. For CAPRI Rounds 28-35, we used an automatic docking pipeline integrating the coarse-grained co-evolution-based potential InterEvScore. This score was developed to exploit the information contained in the multiple sequence alignments of binding partners and selectively recognize co-evolved interfaces. Together with Zdock/Frodock for rigid-body docking, SOAP-PP for atomic potential and Rosetta applications for structural refinement, this pipeline reached high performance on a majority of targets. For protein-peptide docking and interfacial water position predictions, we also explored different means of taking evolutionary information into account. Overall, our group ranked 1st by correctly predicting 10 targets, composed of 1 High, 7 Medium and 2 Acceptable predictions. Excellent and Outstanding levels of accuracy were reached for each of the two water prediction targets, respectively. Altogether, in 15 out of 18 targets in total, evolutionary information, either through co-evolution or conservation analyses, could provide key constraints to guide modeling towards the most likely assemblies. These results open promising perspectives regarding the way evolutionary information can be valuable to improve docking prediction accuracy. Proteins 2017; 85:378-390. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Jinchao Yu
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, F-91198, France
| | - Jessica Andreani
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, F-91198, France
| | - Françoise Ochsenbein
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, F-91198, France
| | - Raphaël Guerois
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, F-91198, France
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21
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Pratt SE, Speltz EB, Mochrie SGJ, Regan L. Designed Proteins as Novel Imaging Reagents in Living Escherichia coli. Chembiochem 2016; 17:1652-7. [PMID: 27304706 DOI: 10.1002/cbic.201600252] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Indexed: 11/06/2022]
Abstract
Fluorescence imaging is a powerful tool to study protein function in living cells. Here, we introduce a novel imaging strategy that is fully genetically encodable, does not require the use of exogenous substrates, and adds a minimally disruptive tag to the protein of interest (POI). Our method was based on a set of designed tetratricopeptide repeat affinity proteins (TRAPs) that specifically and reversibly interact with a short, extended peptide tag. We co-expressed the TRAPs fused to fluorescent proteins (FPs) and the peptide tags fused to the POIs. We illustrated the method using the Escherichia coli protein FtsZ and showed that our system could track distinct FtsZ structures under both low and high expression conditions in live cells. We anticipate that our imaging strategy will be a useful tool for imaging the subcellular localization of many proteins, especially those recalcitrant to imaging by direct tagging with FPs.
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Affiliation(s)
- Susan E Pratt
- Department of Physics, Yale University, 217 Prospect Street, New Haven, CT, 06511, USA.,Integrated Graduate Program in Physical and Engineering Biology, Yale University, 266 Whitney Avenue, New Haven, CT, 06511, USA
| | - Elizabeth B Speltz
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT, 06511, USA
| | - Simon G J Mochrie
- Department of Physics, Yale University, 217 Prospect Street, New Haven, CT, 06511, USA. .,Integrated Graduate Program in Physical and Engineering Biology, Yale University, 266 Whitney Avenue, New Haven, CT, 06511, USA. .,Department of Applied Physics, Yale University, 15 Prospect Street, New Haven, CT, 06511, USA.
| | - Lynne Regan
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, 266 Whitney Avenue, New Haven, CT, 06511, USA. .,Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT, 06511, USA. .,Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT, 06511, USA.
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22
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Ahmad S, Pecqueur L, Dreier B, Hamdane D, Aumont-Nicaise M, Plückthun A, Knossow M, Gigant B. Destabilizing an interacting motif strengthens the association of a designed ankyrin repeat protein with tubulin. Sci Rep 2016; 6:28922. [PMID: 27380724 PMCID: PMC4933879 DOI: 10.1038/srep28922] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 06/13/2016] [Indexed: 01/10/2023] Open
Abstract
Affinity maturation by random mutagenesis and selection is an established technique to make binding molecules more suitable for applications in biomedical research, diagnostics and therapy. Here we identified an unexpected novel mechanism of affinity increase upon in vitro evolution of a tubulin-specific designed ankyrin repeat protein (DARPin). Structural analysis indicated that in the progenitor DARPin the C-terminal capping repeat (C-cap) undergoes a 25° rotation to avoid a clash with tubulin upon binding. Additionally, the C-cap appears to be involved in electrostatic repulsion with tubulin. Biochemical and structural characterizations demonstrated that the evolved mutants achieved a gain in affinity through destabilization of the C-cap, which relieves the need of a DARPin conformational change upon tubulin binding and removes unfavorable interactions in the complex. Therefore, this specific case of an order-to-disorder transition led to a 100-fold tighter complex with a subnanomolar equilibrium dissociation constant, remarkably associated with a 30% decrease of the binding surface.
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Affiliation(s)
- Shoeb Ahmad
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Ludovic Pecqueur
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Birgit Dreier
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Djemel Hamdane
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
| | - Magali Aumont-Nicaise
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Marcel Knossow
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Benoît Gigant
- 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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23
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Huet S, Gorre H, Perrocheau A, Picot J, Cinier M. Use of the Nanofitin Alternative Scaffold as a GFP-Ready Fusion Tag. PLoS One 2015; 10:e0142304. [PMID: 26539718 PMCID: PMC4634965 DOI: 10.1371/journal.pone.0142304] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 10/19/2015] [Indexed: 11/26/2022] Open
Abstract
With the continuous diversification of recombinant DNA technologies, the possibilities for new tailor-made protein engineering have extended on an on-going basis. Among these strategies, the use of the green fluorescent protein (GFP) as a fusion domain has been widely adopted for cellular imaging and protein localization. Following the lead of the direct head-to-tail fusion of GFP, we proposed to provide additional features to recombinant proteins by genetic fusion of artificially derived binders. Thus, we reported a GFP-ready fusion tag consisting of a small and robust fusion-friendly anti-GFP Nanofitin binding domain as a proof-of-concept. While limiting steric effects on the carrier, the GFP-ready tag allows the capture of GFP or its blue (BFP), cyan (CFP) and yellow (YFP) alternatives. Here, we described the generation of the GFP-ready tag from the selection of a Nanofitin variant binding to the GFP and its spectral variants with a nanomolar affinity, while displaying a remarkable folding stability, as demonstrated by its full resistance upon thermal sterilization process or the full chemical synthesis of Nanofitins. To illustrate the potential of the Nanofitin-based tag as a fusion partner, we compared the expression level in Escherichia coli and activity profile of recombinant human tumor necrosis factor alpha (TNFα) constructs, fused to a SUMO or GFP-ready tag. Very similar expression levels were found with the two fusion technologies. Both domains of the GFP-ready tagged TNFα were proved fully active in ELISA and interferometry binding assays, allowing the simultaneous capture by an anti-TNFα antibody and binding to the GFP, and its spectral mutants. The GFP-ready tag was also shown inert in a L929 cell based assay, demonstrating the potent TNFα mediated apoptosis induction by the GFP-ready tagged TNFα. Eventually, we proposed the GFP-ready tag as a versatile capture and labeling system in addition to expected applications of anti-GFP Nanofitins (as illustrated with previously described state-of-the-art anti-GFP binders applied to living cells and in vitro applications). Through a single fusion domain, the GFP-ready tagged proteins benefit from subsequent customization within a wide range of fluorescence spectra upon indirect binding of a chosen GFP variant.
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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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