1
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Büchl A, Kopperger E, Vogt M, Langecker M, Simmel FC, List J. Energy landscapes of rotary DNA origami devices determined by fluorescence particle tracking. Biophys J 2022; 121:4849-4859. [PMID: 36071662 PMCID: PMC9808541 DOI: 10.1016/j.bpj.2022.08.046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/12/2022] [Accepted: 08/30/2022] [Indexed: 01/07/2023] Open
Abstract
Biomolecular nanomechanical devices are of great interest as tools for the processing and manipulation of molecules, thereby mimicking the function of nature's enzymes. DNA nanotechnology provides the capability to build molecular analogs of mechanical machine elements such as joints and hinges via sequence-programmable self-assembly, which are otherwise known from traditional mechanical engineering. Relative to their size, these molecular machine elements typically do not reach the same relative precision and reproducibility that we know from their macroscopic counterparts; however, as they are scaled down to molecular sizes, physical effects typically not considered by mechanical engineers such as Brownian motion, intramolecular forces, and the molecular roughness of the devices begin to dominate their behavior. In order to investigate the effect of different design choices on the roughness of the mechanical energy landscapes of DNA nanodevices in greater detail, we here study an exemplary DNA origami-based structure, a modularly designed rotor-stator arrangement, which resembles a rotatable nanorobotic arm. Using fluorescence tracking microscopy, we follow the motion of individual rotors and record their corresponding energy landscapes. We then utilize the modular construction of the device to exchange its constituent parts individually and systematically test the effect of different design variants on the movement patterns. This allows us to identify the design parameters that most strongly affect the shape of the energy landscapes of the systems. Taking into account these insights, we are able to create devices with significantly flatter energy landscapes, which translates to mechanical nanodevices with improved performance and behaviors more closely resembling those of their macroscopic counterparts.
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Affiliation(s)
- Adrian Büchl
- Physics Department E14, Technical University of Munich, Garching, Germany
| | - Enzo Kopperger
- Physics Department E14, Technical University of Munich, Garching, Germany
| | - Matthias Vogt
- Physics Department E14, Technical University of Munich, Garching, Germany
| | - Martin Langecker
- Physics Department E14, Technical University of Munich, Garching, Germany
| | - Friedrich C Simmel
- Physics Department E14, Technical University of Munich, Garching, Germany.
| | - Jonathan List
- Physics Department E14, Technical University of Munich, Garching, Germany.
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2
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Laitinen OH, Kuusela TP, Kukkurainen S, Nurminen A, Sinkkonen A, Hytönen VP. Bacterial avidins are a widely distributed protein family in Actinobacteria, Proteobacteria and Bacteroidetes. BMC Ecol Evol 2021; 21:53. [PMID: 33836663 PMCID: PMC8033661 DOI: 10.1186/s12862-021-01784-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 03/30/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Avidins are biotin-binding proteins commonly found in the vertebrate eggs. In addition to streptavidin from Streptomyces avidinii, a growing number of avidins have been characterized from divergent bacterial species. However, a systematic research concerning their taxonomy and ecological role has never been done. We performed a search for avidin encoding genes among bacteria using available databases and classified potential avidins according to taxonomy and the ecological niches utilized by host bacteria. RESULTS Numerous avidin-encoding genes were found in the phyla Actinobacteria and Proteobacteria. The diversity of protein sequences was high and several new variants of genes encoding biotin-binding avidins were found. The living strategies of bacteria hosting avidin encoding genes fall mainly into two categories. Human and animal pathogens were overrepresented among the found bacteria carrying avidin genes. The other widespread category were bacteria that either fix nitrogen or live in root nodules/rhizospheres of plants hosting nitrogen-fixing bacteria. CONCLUSIONS Bacterial avidins are a taxonomically and ecologically diverse group mainly found in Actinobacteria, Proteobacteria and Bacteroidetes, associated often with plant invasiveness. Avidin encoding genes in plasmids hint that avidins may be horizontally transferred. The current survey may be used as a basis in attempts to understand the ecological significance of biotin-binding capacity.
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Affiliation(s)
- Olli H Laitinen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Tanja P Kuusela
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Sampo Kukkurainen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Anssi Nurminen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Aki Sinkkonen
- Horticulture Technologies, Natural Resources Institute Finland, Turku, Finland
| | - Vesa P Hytönen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland. .,Fimlab Laboratories, Tampere, Finland.
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3
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Delgadillo RF, Mueser TC, Zaleta-Rivera K, Carnes KA, González-Valdez J, Parkhurst LJ. Detailed characterization of the solution kinetics and thermodynamics of biotin, biocytin and HABA binding to avidin and streptavidin. PLoS One 2019; 14:e0204194. [PMID: 30818336 PMCID: PMC6394990 DOI: 10.1371/journal.pone.0204194] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Accepted: 02/01/2019] [Indexed: 01/02/2023] Open
Abstract
The high affinity (KD ~ 10−15 M) of biotin for avidin and streptavidin is the essential component in a multitude of bioassays with many experiments using biotin modifications to invoke coupling. Equilibration times suggested for these assays assume that the association rate constant (kon) is approximately diffusion limited (109 M-1s-1) but recent single molecule and surface binding studies indicate that they are slower than expected (105 to 107 M-1s-1). In this study, we asked whether these reactions in solution are diffusion controlled, which reaction model and thermodynamic cycle describes the complex formation, and if there are any functional differences between avidin and streptavidin. We have studied the biotin association by two stopped-flow methodologies using labeled and unlabeled probes: I) fluorescent probes attached to biotin and biocytin; and II) unlabeled biotin and HABA, 2-(4’-hydroxyazobenzene)-benzoic acid. Both native avidin and streptavidin are homo-tetrameric and the association data show no cooperativity between the binding sites. The kon values of streptavidin are faster than avidin but slower than expected for a diffusion limited reaction in both complexes. Moreover, the Arrhenius plots of the kon values revealed strong temperature dependence with large activation energies (6–15 kcal/mol) that do not correspond to a diffusion limited process (3–4 kcal/mol). Accordingly, we propose a simple reaction model with a single transition state for non-immobilized reactants whose forward thermodynamic parameters complete the thermodynamic cycle, in agreement with previously reported studies. Our new understanding and description of the kinetics, thermodynamics, and spectroscopic parameters for these complexes will help to improve purification efficiencies, molecule detection, and drug screening assays or find new applications.
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Affiliation(s)
- Roberto F. Delgadillo
- Department of Chemistry, University of Nebraska—Lincoln, Lincoln, Nebraska, United States of America
- * E-mail: (RFD); (LJP)
| | - Timothy C. Mueser
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, Ohio, United States of America
| | - Kathia Zaleta-Rivera
- Department of Bioengineering, University of California San Diego, San Diego, California, United States of America
| | - Katie A. Carnes
- GlaxoSmithKline, Medicinal Science and Technology, R&D, King of Prussia, Pennsylvania, United States of America
| | - José González-Valdez
- Tecnologico de Monterrey, School of Engineering and Science, NL, Monterrey, Mexico
| | - Lawrence J. Parkhurst
- Department of Chemistry, University of Nebraska—Lincoln, Lincoln, Nebraska, United States of America
- * E-mail: (RFD); (LJP)
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4
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Kawato T, Mizohata E, Meshizuka T, Doi H, Kawamura T, Matsumura H, Yumura K, Tsumoto K, Kodama T, Inoue T, Sugiyama A. Crystal structure of streptavidin mutant with low immunogenicity. J Biosci Bioeng 2015; 119:642-7. [DOI: 10.1016/j.jbiosc.2014.10.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 10/26/2014] [Indexed: 12/21/2022]
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5
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Kawato T, Mizohata E, Shimizu Y, Meshizuka T, Yamamoto T, Takasu N, Matsuoka M, Matsumura H, Kodama T, Kanai M, Doi H, Inoue T, Sugiyama A. Structure-based design of a streptavidin mutant specific for an artificial biotin analogue. J Biochem 2015; 157:467-75. [PMID: 25645976 DOI: 10.1093/jb/mvv004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Accepted: 12/10/2014] [Indexed: 01/03/2023] Open
Abstract
For a multistep pre-targeting method using antibodies, a streptavidin mutant with low immunogenicity, termed low immunogenic streptavidin mutant No. 314 (LISA-314), was produced previously as a drug delivery tool. However, endogenous biotins (BTNs) with high affinity (Kd < 10(-10) M) for the binding pocket of LISA-314 prevents access of exogenous BTN-labelled anticancer drugs. In this study, we improve the binding pocket of LISA-314 to abolish its affinity for endogenous BTN species, therefore ensuring that the newly designed LISA-314 binds only artificial BTN analogue. The replacement of three amino acid residues was performed in two steps to develop a mutant termed V212, which selectively binds to 6-(5-((3aS,4S,6aR)-2-iminohexahydro-1H-thieno[3,4-d]imidazol-4-yl)pentanamido)hexanoic acid (iminobiotin long tail, IMNtail). Surface plasmon resonance results showed that V212 has a Kd value of 5.9 × 10(-7) M towards IMNtail, but no binding affinity for endogenous BTN species. This V212/IMNtail system will be useful as a novel delivery tool for anticancer therapy.
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Affiliation(s)
- Tatsuya Kawato
- Division of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan; and Radioisotope Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Eiichi Mizohata
- Division of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan; and Radioisotope Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Yohei Shimizu
- Division of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan; and Radioisotope Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Tomohiro Meshizuka
- Division of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan; and Radioisotope Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Tomohiro Yamamoto
- Division of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan; and Radioisotope Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Noriaki Takasu
- Division of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan; and Radioisotope Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Masahiro Matsuoka
- Division of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan; and Radioisotope Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Hiroyoshi Matsumura
- Division of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan; and Radioisotope Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Tatsuhiko Kodama
- Division of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan; and Radioisotope Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Motomu Kanai
- Division of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan; and Radioisotope Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Hirofumi Doi
- Division of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan; and Radioisotope Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Tsuyoshi Inoue
- Division of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan; and Radioisotope Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Akira Sugiyama
- Division of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan; and Radioisotope Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
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6
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Taskinen B, Airenne TT, Jänis J, Rahikainen R, Johnson MS, Kulomaa MS, Hytönen VP. A novel chimeric avidin with increased thermal stability using DNA shuffling. PLoS One 2014; 9:e92058. [PMID: 24632863 PMCID: PMC3954883 DOI: 10.1371/journal.pone.0092058] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 02/18/2014] [Indexed: 11/19/2022] Open
Abstract
Avidins are a family of proteins widely employed in biotechnology. We have previously shown that functional chimeric mutant proteins can be created from avidin and avidin-related protein 2 using a methodology combining random mutagenesis by recombination and selection by a tailored biopanning protocol (phage display). Here, we report the crystal structure of one of the previously selected and characterized chimeric avidin forms, A/A2-1. The structure was solved at 1.8 Å resolution and revealed that the protein fold was not affected by the shuffled sequences. The structure also supports the previously observed physicochemical properties of the mutant. Furthermore, we improved the selection and screening methodology to select for chimeric avidins with slower dissociation rate from biotin than were selected earlier. This resulted in the chimeric mutant A/A2-B, which showed increased thermal stability as compared to A/A2-1 and the parental proteins. The increased stability was especially evident at conditions of extreme pH as characterized using differential scanning calorimetry. In addition, amino acid sequence and structural comparison of the chimeric mutants and the parental proteins led to the rational design of A/A2-B I109K. This mutation further decreased the dissociation rate from biotin and yielded an increase in the thermal stability.
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Affiliation(s)
- Barbara Taskinen
- BioMediTech, University of Tampere, Tampere, Finland
- Fimlab Laboratories, Pirkanmaa Hospital District, Tampere, Finland
| | - Tomi T. Airenne
- Department of Biosciences, Åbo Akademi University, Turku, Finland
| | - Janne Jänis
- Department of Chemistry, University of Eastern Finland, Joensuu, Finland
| | - Rolle Rahikainen
- BioMediTech, University of Tampere, Tampere, Finland
- Fimlab Laboratories, Pirkanmaa Hospital District, Tampere, Finland
| | - Mark S. Johnson
- Department of Biosciences, Åbo Akademi University, Turku, Finland
| | - Markku S. Kulomaa
- BioMediTech, University of Tampere, Tampere, Finland
- Tampere University Hospital, Tampere, Finland
| | - Vesa P. Hytönen
- BioMediTech, University of Tampere, Tampere, Finland
- Fimlab Laboratories, Pirkanmaa Hospital District, Tampere, Finland
- * E-mail:
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7
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Nogueira ES, Schleier T, Dürrenberger M, Ballmer-Hofer K, Ward TR, Jaussi R. High-level secretion of recombinant full-length streptavidin in Pichia pastoris and its application to enantioselective catalysis. Protein Expr Purif 2013; 93:54-62. [PMID: 24184946 DOI: 10.1016/j.pep.2013.10.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Revised: 08/22/2013] [Accepted: 10/24/2013] [Indexed: 11/28/2022]
Abstract
Artificial metalloenzymes result from the incorporation of a catalytically competent biotinylated organometallic moiety into full-length (i.e. mature) streptavidin. With large-scale industrial biotechnology applications in mind, large quantities of recombinant streptavidin are required. Herein we report our efforts to produce wild-type mature and biotin-free streptavidin using the yeast Pichia pastoris expression system. The streptavidin gene was inserted into the expression vector pPICZαA in frame with the Saccharomyces cerevisiae α-mating factor secretion signal. In a fed-batch fermentation using a minimal medium supplemented with trace amounts of biotin, functional streptavidin was secreted at approximately 650mg/L of culture supernatant. This yield is approximately threefold higher than that from Escherichia coli, and although the overall expression process takes longer (ten days vs. two days), the downstream processing is simplified by eliminating denaturing/refolding steps. The purified streptavidin bound ∼3.2molecules of biotin per tetramer. Upon incorporation of a biotinylated piano-stool catalyst, the secreted streptavidin displayed identical properties to streptavidin produced in E. coli by showing activity as artificial imine reductase.
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Affiliation(s)
- Elisa S Nogueira
- Department of Chemistry, University of Basel, Spitalstrasse 51, CH-4056 Basel, Switzerland
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8
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Taskinen B, Zmurko J, Ojanen M, Kukkurainen S, Parthiban M, Määttä JAE, Leppiniemi J, Jänis J, Parikka M, Turpeinen H, Rämet M, Pesu M, Johnson MS, Kulomaa MS, Airenne TT, Hytönen VP. Zebavidin--an avidin-like protein from zebrafish. PLoS One 2013; 8:e77207. [PMID: 24204770 PMCID: PMC3811995 DOI: 10.1371/journal.pone.0077207] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 09/06/2013] [Indexed: 01/27/2023] Open
Abstract
The avidin protein family members are well known for their high affinity towards D-biotin and high structural stability. These properties make avidins valuable tools for a wide range of biotechnology applications. We have identified a new member of the avidin family in the zebrafish (Danio rerio) genome, hereafter called zebavidin. The protein is highly expressed in the gonads of both male and female zebrafish and in the gills of male fish, but our data suggest that zebavidin is not crucial for the developing embryo. Biophysical and structural characterisation of zebavidin revealed distinct properties not found in any previously characterised avidins. Gel filtration chromatography and native mass spectrometry suggest that the protein forms dimers in the absence of biotin at low ionic strength, but assembles into tetramers upon binding biotin. Ligand binding was analysed using radioactive and fluorescently labelled biotin and isothermal titration calorimetry. Moreover, the crystal structure of zebavidin in complex with biotin was solved at 2.4 Å resolution and unveiled unique ligand binding and subunit interface architectures; the atomic-level details support our physicochemical observations.
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Affiliation(s)
- Barbara Taskinen
- Institute of Biomedical Technology, University of Tampere, BioMediTech, Tampere, Finland
- Fimlab Laboratories, Pirkanmaa Hospital District, Tampere, Finland
| | - Joanna Zmurko
- Institute of Biomedical Technology, University of Tampere, BioMediTech, Tampere, Finland
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Markus Ojanen
- Institute of Biomedical Technology, University of Tampere, BioMediTech, Tampere, Finland
| | - Sampo Kukkurainen
- Institute of Biomedical Technology, University of Tampere, BioMediTech, Tampere, Finland
- Fimlab Laboratories, Pirkanmaa Hospital District, Tampere, Finland
| | - Marimuthu Parthiban
- Department of Biosciences, Biochemistry, Åbo Akademi University, Turku, Finland
| | - Juha A. E. Määttä
- Institute of Biomedical Technology, University of Tampere, BioMediTech, Tampere, Finland
- Fimlab Laboratories, Pirkanmaa Hospital District, Tampere, Finland
| | - Jenni Leppiniemi
- Institute of Biomedical Technology, University of Tampere, BioMediTech, Tampere, Finland
- Tampere University Hospital, Tampere, Finland
| | - Janne Jänis
- Department of Chemistry, University of Eastern Finland, Joensuu, Finland
| | - Mataleena Parikka
- Institute of Biomedical Technology, University of Tampere, BioMediTech, Tampere, Finland
| | - Hannu Turpeinen
- Institute of Biomedical Technology, University of Tampere, BioMediTech, Tampere, Finland
| | - Mika Rämet
- Institute of Biomedical Technology, University of Tampere, BioMediTech, Tampere, Finland
- Tampere University Hospital, Tampere, Finland
| | - Marko Pesu
- Institute of Biomedical Technology, University of Tampere, BioMediTech, Tampere, Finland
- Fimlab Laboratories, Pirkanmaa Hospital District, Tampere, Finland
| | - Mark S. Johnson
- Department of Biosciences, Biochemistry, Åbo Akademi University, Turku, Finland
| | - Markku S. Kulomaa
- Institute of Biomedical Technology, University of Tampere, BioMediTech, Tampere, Finland
- Tampere University Hospital, Tampere, Finland
| | - Tomi T. Airenne
- Department of Biosciences, Biochemistry, Åbo Akademi University, Turku, Finland
| | - Vesa P. Hytönen
- Institute of Biomedical Technology, University of Tampere, BioMediTech, Tampere, Finland
- Fimlab Laboratories, Pirkanmaa Hospital District, Tampere, Finland
- * E-mail:
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9
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Intestinal receptor targeting for peptide delivery: an expert's personal perspective on reasons for failure and new opportunities. Ther Deliv 2012; 2:1575-93. [PMID: 22833983 DOI: 10.4155/tde.11.129] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The technology has been available more than 25 years that would enable the oral delivery of vaccines, proteins and peptides, thus avoiding the need for injection. To this day, injection is still the mode of delivery, yet not the main mode of choice. This review focuses on several of the potential modes for oral delivery of peptides, proteins and vaccines. Additionally, the review will provide the reader with an insight into the problems and potential solutions for several of these modes of oral delivery of peptides and proteins.
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10
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Smith RD, Engdahl AL, Dunbar JB, Carlson HA. Biophysical limits of protein-ligand binding. J Chem Inf Model 2012; 52:2098-106. [PMID: 22713103 DOI: 10.1021/ci200612f] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In classic work, Kuntz et al. (Proc. Nat. Acad. Sci. USA 1999, 96, 9997-10002) introduced the concept of ligand efficiency. Though that study focused primarily on drug-like molecules, it also showed that metal binding led to the greatest ligand efficiencies. Here, the physical limits of binding are examined across the wide variety of small molecules in the Binding MOAD database. The complexes with the greatest ligand efficiencies share the trait of being small, charged ligands bound in highly charged, well buried binding sites. The limit of ligand efficiency is -1.75 kcal/mol·atom for the protein-ligand complexes within Binding MOAD, and 95% of the set have efficiencies below a "soft limit" of -0.83 kcal/mol·atom. On the basis of buried molecular surface area, the hard limit of ligand efficiency is -117 cal/mol·Å(2), which is in surprising agreement with the limit of macromolecule-protein binding. Close examination of the most efficient systems reveals their incredibly high efficiency is dictated by tight contacts between the charged groups of the ligand and the pocket. In fact, a misfit of 0.24 Å in the average contacts inherently decreases the maximum possible efficiency by at least 0.1 kcal/mol·atom.
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Affiliation(s)
- Richard D Smith
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1065, USA
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11
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Niederhauser B, Siivonen J, Määttä JA, Jänis J, Kulomaa MS, Hytönen VP. DNA family shuffling within the chicken avidin protein family – A shortcut to more powerful protein tools. J Biotechnol 2012; 157:38-49. [DOI: 10.1016/j.jbiotec.2011.10.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Revised: 09/30/2011] [Accepted: 10/30/2011] [Indexed: 10/15/2022]
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12
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Russell-Jones G, McTavish K, McEwan J. Preliminary studies on the selective accumulation of vitamin-targeted polymers within tumors. J Drug Target 2010; 19:133-9. [PMID: 20446757 DOI: 10.3109/10611861003734027] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Many different cancer types have previously been found to show increased uptake of the vitamins folate, vitamin B12, and biotin; however, it is not known whether these tumor lines show increased uptake of one or more of the vitamins. The current study was designed to examine the relative uptake of the three vitamins in 10 different types of cell lines. Rhodamine-labeled hydroxypropyl-methacrylamide (HPMA) was targeted with vitamin B(12), folate, or biotin, and the uptake of the labeled polymer was compared both in in vitro cell cultures and in mice-bearing tumors from a variety of tumor cell lines. Fluorescent microscopy of cell cultures and histological examination of tumor sections showed greatly increased uptake of the fluorescently labeled polymer in many tumors when the polymer was targeted with folate, biotin, or vitamin B(12). Tumors with enhanced uptake of vitamin B(12)- or folate-targeted rhodamine-HPMA also showed increased uptake of biotin-Rho-HPMA. In contrast, tumors with increased uptake of folate-Rho-HPMA did not show increased uptake of vitamin B12 (VB(12))-HPMA and vice versa. These findings suggest that vitamin-targeted polymers may greatly increase the uptake of drug-polymer complexes in certain tumors, which may result in an increased efficacy of antitumor agents, and which may allow for easier imaging of both the primary and metastatic tumors.
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Affiliation(s)
- Gregory Russell-Jones
- Formerly of Access Pharmaceuticals Australia Pty Ltd, Roseville, New South Wales, Australia
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Määttä JAE, Helppolainen SH, Hytönen VP, Johnson MS, Kulomaa MS, Airenne TT, Nordlund HR. Structural and functional characteristics of xenavidin, the first frog avidin from Xenopus tropicalis. BMC STRUCTURAL BIOLOGY 2009; 9:63. [PMID: 19788720 PMCID: PMC2761383 DOI: 10.1186/1472-6807-9-63] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2008] [Accepted: 09/29/2009] [Indexed: 11/10/2022]
Abstract
Background Avidins are proteins with extraordinarily high ligand-binding affinity, a property which is used in a wide array of life science applications. Even though useful for biotechnology and nanotechnology, the biological function of avidins is not fully understood. Here we structurally and functionally characterise a novel avidin named xenavidin, which is to our knowledge the first reported avidin from a frog. Results Xenavidin was identified from an EST sequence database for Xenopus tropicalis and produced in insect cells using a baculovirus expression system. The recombinant xenavidin was found to be homotetrameric based on gel filtration analysis. Biacore sensor analysis, fluorescently labelled biotin and radioactive biotin were used to evaluate the biotin-binding properties of xenavidin - it binds biotin with high affinity though less tightly than do chicken avidin and bacterial streptavidin. X-ray crystallography revealed structural conservation around the ligand-binding site, while some of the loop regions have a unique design. The location of structural water molecules at the entrance and/or within the ligand-binding site may have a role in determining the characteristic biotin-binding properties of xenavidin. Conclusion The novel data reported here provide information about the biochemically and structurally important determinants of biotin binding. This information may facilitate the discovery of novel tools for biotechnology.
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Affiliation(s)
- Juha A E Määttä
- Institute of Medical Technology, Biokatu 6, FI-33014 University of Tampere and Tampere University Hospital, Tampere, Finland.
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Meir A, Helppolainen SH, Podoly E, Nordlund HR, Hytönen VP, Määttä JA, Wilchek M, Bayer EA, Kulomaa MS, Livnah O. Crystal Structure of Rhizavidin: Insights into the Enigmatic High-Affinity Interaction of an Innate Biotin-Binding Protein Dimer. J Mol Biol 2009; 386:379-90. [DOI: 10.1016/j.jmb.2008.11.061] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2008] [Revised: 11/25/2008] [Accepted: 11/26/2008] [Indexed: 10/21/2022]
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Helppolainen SH, Määttä JAE, Halling KK, Slotte JP, Hytönen VP, Jänis J, Vainiotalo P, Kulomaa MS, Nordlund HR. Bradavidin II from Bradyrhizobium japonicum: a new avidin-like biotin-binding protein. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1784:1002-10. [PMID: 18486632 DOI: 10.1016/j.bbapap.2008.04.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2007] [Revised: 03/31/2008] [Accepted: 04/07/2008] [Indexed: 11/19/2022]
Abstract
A gene encoding an avidin-like protein was discovered in the genome of B. japonicum. The gene was cloned to an expression vector and a protein, named bradavidin II, was produced in E. coli. Bradavidin II has an identity of 20-30% and a similarity of 30-40% with previously discovered bradavidin and other avidin-like proteins. It has biochemical characteristics close to those of avidin and streptavidin and binds biotin tightly. In contrast to other tetrameric avidin-like proteins studied to date, bradavidin II has no tryptophan analogous to the W110 in avidin (W120 in streptavidin), thought to be one of the most essential residues for tight biotin-binding. Homology modeling suggests that a proline residue may function analogously to tryptophan in this particular position. Structural elements of bradavidin II such as an interface residue pattern or biotin contact residues could be used as such or transferred to engineered avidin forms to improve or create new tools for biotechnological applications.
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Affiliation(s)
- Satu H Helppolainen
- Institute of Medical Technology, Biokatu 6, FI-33014 University of Tampere and Tampere University Hospital, Finland
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