The highly dynamic oligomeric structure of bradavidin II is unique among avidin proteins

Leppiniemi, Jenni; Meir, Amit; Kähkönen, Niklas; Kukkurainen, Sampo; Määttä, Juha; Ojanen, Markus; Jänis, Janne; Kulomaa, Markku S.; Livnah, Oded; Hytönen, Vesa P.

doi:10.1002/pro.2281

Cited by 16 publications

(19 citation statements)

References 41 publications

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“…In contrast, the two dimers in the asymmetric unit of both afifavidin constructs do not form the canonical dimer of dimers and are merely the outcome of crystal packing. A similar case was observed for bradavidin II, where four monomers were present in the asymmetric unit, yet failed to form any interactions resembling those of other avidin dimers or tetramers .…”

Section: Resultssupporting

confidence: 68%

“…4B). Remarkably, as in shwanavidin and bradavidin II, its absence is compensated by Phe50 from the L3,4 loop, where its position is almost identical to that of the critical Trp in tetrameric avidins (Figs 4B and 5) [21,24].…”

Section: The Structures Of the Apo Form And Biotin Complex Of Short Amentioning

confidence: 85%

“…In the respective biotin complexes, the crystal packing is more diverse with limited indications of higher oligomeric states. In addition to the oligomeric assembly observed for the dimeric avidins, bradavidin II, another bacterial avidin, was also reported and displays a dynamic or even inconclusive oligomeric state .…”

Section: Introductionmentioning

confidence: 90%

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Crystal structure of afifavidin reveals common features of molecular assemblage in the bacterial dimeric avidins

2018

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The subfamily of bacterial dimeric avidins is being extended through the discovery of additional members originating from diverse sources. All of these newly discovered dimeric avidin forms exhibit high affinity towards biotin, despite their lack of critical Trp in the classical tetrameric forms. The common feature of forming cylinder‐like multimers (hexamers and octamers) seems to be more than a random occurrence, which generally characterizes their apo forms in the crystalline state and also in some cases in solution. Afifavidin from the Gram‐negative α‐proteobacterium Afifella pfennigii is the fourth member of the subfamily of dimers, which, in the intact apo form, also congregates into octamers both in the solution and in the crystalline state, whereby the C‐terminal extended segments stretch into the biotin‐binding sites of adjacent non‐canonical monomers. The intact apo afifavidin molecule self‐assembles into toroid‐shaped nanostructures that dissociate into the inherent dimers upon binding biotin. On removal of the C‐terminal regions, the short‐form of afifavidin forms dimers both in the solution and in the crystalline states. The high affinity of the dimeric forms of afifavidin towards biotin is maintained, due to the conserved disulfide bridge between L3,4 and L5,6 and the presence of Phe50 in L3,4 that compensate for the lack of the critical Trp in the tetrameric avidins. These cyclic multimeric‐avidin assemblies may be exploited in the future to further diversify biotin‐based nanotechnology or to serve as building blocks in the construction of bio‐inspired materials. Database Structural data are available in the PDB databases under the accession numbers: http://www.rcsb.org/pdb/search/structidSearch.do?structureId=6HDV, http://www.rcsb.org/pdb/search/structidSearch.do?structureId=6HDS, http://www.rcsb.org/pdb/search/structidSearch.do?structureId=6HDT.

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Section: Resultssupporting

confidence: 68%

Section: The Structures Of the Apo Form And Biotin Complex Of Short Amentioning

confidence: 85%

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Crystal structure of afifavidin reveals common features of molecular assemblage in the bacterial dimeric avidins

2018

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“…in 10 mM ammonium acetate buffer). Bradavidin II has been found to form oligomers as a function of protein concentration, but no clearly defined oligomeric states were observed and biotin had no effect on the oligomeric state [66]. However, transient oligomerisation was observed for mutant avidins.…”

Section: Discussionmentioning

confidence: 99%

Zebavidin - An Avidin-Like Protein from Zebrafish

Taskinen

Zmurko

Ojanen³

et al. 2013

PLoS ONE

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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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“…The structures of biotin-binding proteins are obtained from the Protein Data Bank (PDB) with following accession codes: Avidin (2avi), 52 Streptavidin (1stp), 53 Brabavidin II (4GGZ), 54 and Rhizavidin (3EW2). 55 The binding conformation of each protein on the biotin binding surface of gold nanoparticle is determined according to the biotin binding sites provided at PDB entries.…”

Section: Plasmonic-molecular Performance Characterizationmentioning

confidence: 99%

A quasi-static continuum model describing interactions between plasmons and non-absorbing biomolecules

Salary

Mosallaei

2015

Journal of Applied Physics

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Interactions between the plasmons of noble metal nanoparticles and non-absorbing biomolecules forms the basis of the plasmonic sensors, which have received much attention. Studying these interactions can help to exploit the full potentials of plasmonic sensors in quantification and analysis of biomolecules. Here, a quasi-static continuum model is adopted for this purpose. We present a boundary-element method for computing the optical response of plasmonic particles to the molecular binding events by solving the Poisson equation. The model represents biomolecules with their molecular surfaces, thus accurately accounting for the influence of exact binding conformations as well as structural differences between different proteins on the response of plasmonic nanoparticles. The linear systems arising in the method are solved iteratively with Krylov generalized minimum residual algorithm, and the acceleration is achieved by applying precorrected-Fast Fourier Transformation technique. We apply the developed method to investigate interactions of biotinylated gold nanoparticles (nanosphere and nanorod) with four different types of biotin-binding proteins. The interactions are studied at both ensemble and single-molecule level. Computational results demonstrate the ability of presented model for analyzing realistic nanoparticle-biomolecule configurations. The method can provide comprehensive study for wide variety of applications, including protein structures, monitoring structural and conformational transitions, and quantification of protein concentrations. In addition, it is suitable for design and optimization of the nano-plasmonic sensors.

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The highly dynamic oligomeric structure of bradavidin II is unique among avidin proteins

Cited by 16 publications

References 41 publications

Crystal structure of afifavidin reveals common features of molecular assemblage in the bacterial dimeric avidins

Crystal structure of afifavidin reveals common features of molecular assemblage in the bacterial dimeric avidins

Zebavidin - An Avidin-Like Protein from Zebrafish

A quasi-static continuum model describing interactions between plasmons and non-absorbing biomolecules

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