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Agrawal N, Lehtonen SI, Uusi-Mäkelä M, Jain P, Viitala S, Määttä JAE, Kähkönen N, Azizi L, Riihimäki TA, Kulomaa MS, Johnson MS, Hytönen VP, Airenne TT. Molecular features of steroid-binding antidins and their use for assaying serum progesterone. PLoS One 2019; 14:e0212339. [PMID: 30785944 PMCID: PMC6382169 DOI: 10.1371/journal.pone.0212339] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 01/31/2019] [Indexed: 11/23/2022] Open
Abstract
Chicken avidin (Avd) and streptavidin from Streptomyces avidinii are extensively used in bionanotechnology due to their extremely tight binding to biotin (Kd ~ 10−15 M for chicken Avd). We previously reported engineered Avds known as antidins, which have micro- to nanomolar affinities for steroids, non-natural ligands of Avd. Here, we report the 2.8 Å X-ray structure of the sbAvd-2 (I117Y) antidin co-crystallized with progesterone. We describe the creation of new synthetic phage display libraries and report the experimental as well as computational binding analysis of progesterone-binding antidins. We introduce a next-generation antidin with 5 nM binding affinity for progesterone, and demonstrate the use of antidins for measuring progesterone in serum samples. Our data give insights on how to engineer and alter the binding preferences of Avds and to develop better molecular tools for modern bionanotechnological applications.
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Affiliation(s)
- Nitin Agrawal
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Soili I. Lehtonen
- BioMediTech Institute and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Meri Uusi-Mäkelä
- BioMediTech Institute and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Purvi Jain
- BioMediTech Institute and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Sari Viitala
- University of Eastern Finland, School of Pharmacy, Kuopio, Finland
| | - Juha A. E. Määttä
- BioMediTech Institute and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Niklas Kähkönen
- BioMediTech Institute and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Latifeh Azizi
- BioMediTech Institute and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Tiina A. Riihimäki
- BioMediTech Institute and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Markku S. Kulomaa
- BioMediTech Institute and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Mark S. Johnson
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Vesa P. Hytönen
- BioMediTech Institute and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Fimlab Laboratories, Tampere, Finland
- * E-mail: (TTA); (VPH)
| | - Tomi T. Airenne
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
- * E-mail: (TTA); (VPH)
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Avraham O, Bayer EA, Livnah O. Crystal structure of afifavidin reveals common features of molecular assemblage in the bacterial dimeric avidins. FEBS J 2018; 285:4617-4630. [DOI: 10.1111/febs.14685] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 10/10/2018] [Accepted: 10/24/2018] [Indexed: 01/05/2023]
Affiliation(s)
- Orly Avraham
- Department of Biological Chemistry The Alexander Silverman Institute of Life Sciences The Wolfson Centre for Applied Structural Biology The Hebrew University of Jerusalem Israel
| | - Edward A. Bayer
- Department of Biological Chemistry The Weizmann Institute of Science Rehovot Israel
| | - Oded Livnah
- Department of Biological Chemistry The Alexander Silverman Institute of Life Sciences The Wolfson Centre for Applied Structural Biology The Hebrew University of Jerusalem Israel
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Abstract
Khoo and Pless examine new work that provides mechanistic insight into the role of the intrinsic ligand in KCNH ion channels.
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Affiliation(s)
- Keith K Khoo
- Department of Drug Design and Pharmacology, Center for Biopharmaceuticals, University of Copenhagen, Copenhagen, Denmark
| | - Stephan A Pless
- Department of Drug Design and Pharmacology, Center for Biopharmaceuticals, University of Copenhagen, Copenhagen, Denmark
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Structural characterization of core-bradavidin in complex with biotin. PLoS One 2017; 12:e0176086. [PMID: 28426764 PMCID: PMC5398887 DOI: 10.1371/journal.pone.0176086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 04/05/2017] [Indexed: 02/07/2023] Open
Abstract
Bradavidin is a tetrameric biotin-binding protein similar to chicken avidin and bacterial streptavidin, and was originally cloned from the nitrogen-fixing bacteria Bradyrhizobium diazoefficiens. We have previously reported the crystal structure of the full-length, wild-type (wt) bradavidin with 138 amino acids, where the C-terminal residues Gly129-Lys138 (“Brad-tag”) act as an intrinsic ligand (i.e. Gly129-Lys138 bind into the biotin-binding site of an adjacent subunit within the same tetramer) and has potential as an affinity tag for biotechnological purposes. Here, the X-ray structure of core-bradavidin lacking the C-terminal residues Gly114-Lys138, and hence missing the Brad-tag, was crystallized in complex with biotin at 1.60 Å resolution [PDB:4BBO]. We also report a homology model of rhodavidin, an avidin-like protein from Rhodopseudomonas palustris, and of an avidin-like protein from Bradyrhizobium sp. Ai1a-2, both of which have the Brad-tag sequence at their C-terminus. Moreover, core-bradavidin V1, an engineered variant of the original core-bradavidin, was also expressed at high levels in E. coli, as well as a double mutant (Cys39Ala and Cys69Ala) of core-bradavidin (CC mutant). Our data help us to further engineer the core-bradavidin–Brad-tag pair for biotechnological assays and chemical biology applications, and provide deeper insight into the biotin-binding mode of bradavidin.
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Avraham O, Meir A, Fish A, Bayer EA, Livnah O. Hoefavidin: A dimeric bacterial avidin with a C-terminal binding tail. J Struct Biol 2015; 191:139-48. [DOI: 10.1016/j.jsb.2015.06.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 06/22/2015] [Accepted: 06/24/2015] [Indexed: 11/30/2022]
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Demonte D, Drake EJ, Lim KH, Gulick AM, Park S. Structure-based engineering of streptavidin monomer with a reduced biotin dissociation rate. Proteins 2013; 81:1621-33. [PMID: 23670729 DOI: 10.1002/prot.24320] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 04/18/2013] [Accepted: 04/22/2013] [Indexed: 11/07/2022]
Abstract
We recently reported the engineering of monomeric streptavidin, mSA, corresponding to one subunit of wild type (wt) streptavidin tetramer. The monomer was designed by homology modeling, in which the streptavidin and rhizavidin sequences were combined to engineer a high affinity binding pocket containing residues from a single subunit only. Although mSA is stable and binds biotin with nanomolar affinity, its fast off rate (koff ) creates practical challenges during applications. We obtained a 1.9 Å crystal structure of mSA bound to biotin to understand their interaction in detail, and used the structure to introduce targeted mutations to improve its binding kinetics. To this end, we compared mSA to shwanavidin, which contains a hydrophobic lid containing F43 in the binding pocket and binds biotin tightly. However, the T48F mutation in mSA, which introduces a comparable hydrophobic lid, only resulted in a modest 20-40% improvement in the measured koff . On the other hand, introducing the S25H mutation near the bicyclic ring of bound biotin increased the dissociation half life (t½ ) from 11 to 83 min at 20°C. Molecular dynamics (MD) simulations suggest that H25 stabilizes the binding loop L3,4 by interacting with A47, and protects key intermolecular hydrogen bonds by limiting solvent entry into the binding pocket. Concurrent T48F or T48W mutation clashes with H25 and partially abrogates the beneficial effects of H25. Taken together, this study suggests that stabilization of the binding loop and solvation of the binding pocket are important determinants of the dissociation kinetics in mSA.
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Affiliation(s)
- Daniel Demonte
- Department of Chemical and Biological Engineering, University at Buffalo, Buffalo, New York, 14260
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Leppiniemi J, Meir A, Kähkönen N, Kukkurainen S, Määttä JA, Ojanen M, Jänis J, Kulomaa MS, Livnah O, Hytönen VP. The highly dynamic oligomeric structure of bradavidin II is unique among avidin proteins. Protein Sci 2013; 22:980-94. [PMID: 23661323 DOI: 10.1002/pro.2281] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Revised: 04/05/2013] [Accepted: 05/06/2013] [Indexed: 11/07/2022]
Abstract
Bradavidin II is a biotin-binding protein from Bradyrhizobium japonicum that resembles chicken avidin and bacterial streptavidin. A biophysical characterization was carried out using dynamic light scattering, native mass spectrometry, differential scanning calorimetry, and isothermal titration calorimetry combined with structural characterization using X-ray crystallography. These observations revealed that bradavidin II differs from canonical homotetrameric avidin protein family members in its quaternary structure. In contrast with the other avidins, bradavidin II appears to have a dynamic (transient) oligomeric state in solution. It is monomeric at low protein concentrations but forms higher oligomeric assemblies at higher concentrations. The crystal structure of bradavidin II revealed an important role for Phe42 in shielding the bound ligand from surrounding water molecules, thus functionally replacing the L7,8 loop essential for tight ligand binding in avidin and streptavidin. This bradavidin II characterization opens new avenues for oligomerization-independent biotin-binding protein development.
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Affiliation(s)
- Jenni Leppiniemi
- Institute of Biomedical Technology, University of Tampere and Tampere University Hospital, FI-33014, Tampere, Finland
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