1
|
Bana J, Warwar J, Bayer EA, Livnah O. Self-assembly of a dimeric avidin into unique higher-order oligomers. FEBS J 2023. [PMID: 36853192 DOI: 10.1111/febs.16764] [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: 11/09/2022] [Revised: 02/16/2023] [Accepted: 02/27/2023] [Indexed: 03/01/2023]
Abstract
The dimeric avidin family has been expanded in recent years to include many new members. All of them lack the intermonomeric Trp that plays a critical role in biotin-binding. Nevertheless, these new members of the avidins maintain the high affinity towards biotin. Additionally, all of the dimeric avidins share a very unique property: namely, the cylindrical oligomerization in the crystal structure. The newest member described here, agroavidin from the agrobacterium, Rhizobium sp. AAP43, shares their important structural features. However, the affinity of agroavidin towards biotin is lower than all other members of the avidin family, due to the presence of phenylalanine instead of a conserved tyrosine in the biotin-binding site. Mutating this phenylalanine into tyrosine regenerated the high affinity, which emphasizes the importance of this particular tyrosine residue. Another unique feature that distinguishes agroavidin from the other dimeric avidins is that it does not produce oligomers in its crystal structure. In order to understand the factors that promote oligomerization in dimeric avidins, we exchanged the C-terminal region of agroavidin with that of hoefavidin that produced octamers. This exchange resulted in a decamer rather than an octamer. This unusual outcome demonstrates the impact of the C-terminal region on the ability to produce oligomers. The decameric assembly of agroavidin expands the avidin-biotin toolbox even further and could well pave the path into new biotin-based technologies. Moreover, uncovering the factors that induce dimeric avidins into oligomeric assemblies may aid in better understanding the general molecular determinants that promote oligomerization.
Collapse
Affiliation(s)
- Juana Bana
- Department of Biological Chemistry, The Wolfson Centre for Applied Structural Biology, Alexander Silverman Institute of Life Sciences, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Israel
| | - Jessica Warwar
- Department of Biological Chemistry, The Wolfson Centre for Applied Structural Biology, Alexander Silverman Institute of Life Sciences, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Israel
| | - Edward A Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Oded Livnah
- Department of Biological Chemistry, The Wolfson Centre for Applied Structural Biology, Alexander Silverman Institute of Life Sciences, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Israel
| |
Collapse
|
2
|
Phan HT, Conrad U. Production of Influenza H5 Vaccine Oligomers in Plants. Methods Mol Biol 2022; 2465:97-107. [PMID: 35118617 DOI: 10.1007/978-1-0716-2168-4_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The transient expression of veterinary vaccines in plants is a promising tool because of its low cost connected with a practically unlimited scale-up. To achieve these goals, two major challenges, high immunogenicity of vaccines and minimal of down-stream processing cost, have to be overcome. Here we present and discuss protocols enabling to generate highly immunogenic H5 influenza candidate vaccines as H5 oligomers, by transient expression in Nicotiana benthamiana plants and to perform analytical experiments as Western blot, ELISA, and hemagglutination and hemagglutination inhibition assays.
Collapse
Affiliation(s)
- Hoang Trong Phan
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Udo Conrad
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany.
| |
Collapse
|
3
|
Avraham O, Bayer EA, Livnah O. Wilavidin* - a novel member of the avidin family that forms unique biotin-binding hexamers. FEBS J 2021; 289:1700-1714. [PMID: 34726340 DOI: 10.1111/febs.16259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 10/20/2021] [Accepted: 11/01/2021] [Indexed: 11/28/2022]
Abstract
Nature's optimization of protein functions is a highly intricate evolutionary process. In addition to optimal tertiary folding, the intramolecular recognition among the monomers that generate higher-order quaternary arrangements is driven by stabilizing interactions that have a pivotal role for ideal activity. Homotetrameric avidin and streptavidin are regularly utilized in many applications, whereby their ultra-high affinity toward biotin is dependent on their quaternary arrangements. In recent years, a new subfamily of avidins was discovered that comprises homodimers rather than tetramers, in which the high affinity toward biotin is maintained. Intriguingly, several of the respective dimers have been shown to assemble into higher-order cylindrical hexamers or octamers that dissociate into dimers upon biotin binding. Here, we present wilavidin, a newly discovered member of the dimeric subfamily, forming hexamers in the apo form, which are uniquely maintained upon biotin binding with six high-affinity binding sites. Removal of the short C-terminal segment of wilavidin resulted in the presence of the dimer only, thus emphasizing the role of this segment in stabilizing the hexamer. Utilization of a hexavalent biotin-binding form of avidin would be beneficial for expanding the biotechnological toolbox. Additionally, this unique family of dimeric avidins and their propensity to oligomerize to hexamers or octamers can serve as a basis for protein oligomerization and intermonomeric recognition as well as cumulative interactions that determine molecular assemblies.
Collapse
Affiliation(s)
- Orly Avraham
- The Wolfson Centre for Applied Structural Biology, Department of Biological Chemistry, Alexander Silverman Institute of Life Sciences, The Hebrew University of Jerusalem, Israel
| | - Edward A Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel.,Department of Life Sciences, National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Oded Livnah
- The Wolfson Centre for Applied Structural Biology, Department of Biological Chemistry, Alexander Silverman Institute of Life Sciences, The Hebrew University of Jerusalem, Israel
| |
Collapse
|
4
|
Jeon BJ, Kim S, Kim MS, Lee JH, Kim BS, Hwang KY. Insights into the structure of mature streptavidin C1 from Streptomyces cinnamonensis reveal the self-binding of the extension C-terminal peptide to biotin-binding sites. IUCRJ 2021; 8:168-177. [PMID: 33708394 PMCID: PMC7924230 DOI: 10.1107/s2052252520015675] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 11/30/2020] [Indexed: 06/12/2023]
Abstract
The members of the avidin protein family are well known for their high affinity towards d-biotin and their structural stability. These properties make avidins a valuable tool for various biotechnological applications. In the present study, two avidin-like biotin-binding proteins (named streptavidin C1 and C2) from Streptomyces cinnamonensis were newly identified while exploring antifungal proteins against Fusarium oxysporum f. sp. cucumerinum. Streptavidin C1 reveals a low correlation (a sequence identity of approximately 64%) with all known streptavidins, whereas streptavidin C2 shares a sequence identity of approximately 94% with other streptavidins. Here, the crystal structures of streptavidin C1 in the mature form and in complex with biotin at 2.1 and 2.5 Å resolution, respectively, were assessed. The overall structures present similar tetrameric features with D 2 symmetry to other (strept)avidin structures. Interestingly, the long C-terminal region comprises a short α-helix (C-Lid; residues 169-179) and an extension C-terminal peptide (ECP; residues 180-191) which stretches into the biotin-binding sites of the same monomer. This ECP sequence (-180VTSANPPAS188-) is a newly defined biotin-binding site, which reduces the ability to bind to (strept)avidin family proteins. The novel streptavidin C1 could help in the development of an engineered tetrameric streptavidin with reduced biotin-binding capacity as well as other biomaterial tools.
Collapse
Affiliation(s)
- Byeong Jun Jeon
- Department of Plant Biotechnology, School of Life Sciences and Biotechnology for BK21 PLUS, Institute of Life Science and Natural Resources, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, South Korea
| | - Sulhee Kim
- Department of Biotechnology, School of Life Sciences and Biotechnology for BK21 PLUS, Institute of Life Science and Natural Resources, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, South Korea
| | - Min-Seok Kim
- Department of Biotechnology, School of Life Sciences and Biotechnology for BK21 PLUS, Institute of Life Science and Natural Resources, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, South Korea
| | - Ji-Ho Lee
- Department of Biotechnology, School of Life Sciences and Biotechnology for BK21 PLUS, Institute of Life Science and Natural Resources, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, South Korea
| | - Beom Seok Kim
- Department of Plant Biotechnology, School of Life Sciences and Biotechnology for BK21 PLUS, Institute of Life Science and Natural Resources, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, South Korea
| | - Kwang Yeon Hwang
- Department of Biotechnology, School of Life Sciences and Biotechnology for BK21 PLUS, Institute of Life Science and Natural Resources, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, South Korea
| |
Collapse
|
5
|
Phan HT, Pham VT, Ho TT, Pham NB, Chu HH, Vu TH, Abdelwhab EM, Scheibner D, Mettenleiter TC, Hanh TX, Meister A, Gresch U, Conrad U. Immunization with Plant-Derived Multimeric H5 Hemagglutinins Protect Chicken against Highly Pathogenic Avian Influenza Virus H5N1. Vaccines (Basel) 2020; 8:E593. [PMID: 33050224 PMCID: PMC7712794 DOI: 10.3390/vaccines8040593] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/02/2020] [Accepted: 10/05/2020] [Indexed: 12/26/2022] Open
Abstract
Since 2003, H5N1 highly pathogenic avian influenza viruses (HPAIV) have not only caused outbreaks in poultry but were also transmitted to humans with high mortality rates. Vaccination is an efficient and economical means of increasing immunity against infections to decrease the shedding of infectious agents in immunized animals and to reduce the probability of further infections. Subunit vaccines from plants are the focus of modern vaccine developments. In this study, plant-made hemagglutinin (H5) trimers were purified from transiently transformed N. benthamiana plants. All chickens immunized with purified H5 trimers were fully protected against the severe HPAIV H5N1 challenge. We further developed a proof-of-principle approach by using disulfide bonds, homoantiparallel peptides or homodimer proteins to combine H5 trimers leading to production of H5 oligomers. Mice vaccinated with crude leaf extracts containing H5 oligomers induced neutralizing antibodies better than those induced by crude leaf extracts containing trimers. As a major result, eleven out of twelve chickens (92%) immunized with adjuvanted H5 oligomer crude extracts were protected from lethal disease while nine out of twelve chickens (75%) vaccinated with adjuvanted H5 trimer crude extracts survived. The solid protective immune response achieved by immunization with crude extracts and the stability of the oligomers form the basis for the development of inexpensive protective veterinary vaccines.
Collapse
Affiliation(s)
- Hoang Trong Phan
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466 Seeland OT Gatersleben, Germany; (A.M.); (U.G.)
| | - Van Thi Pham
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi 100000, Vietnam; (V.T.P.); (T.T.H.); (N.B.P.); (H.H.C.); (T.H.V.)
- Faculty of Biotechnology, Graduate University of Science and Technology (GUST), VAST, Hanoi 10000, Vietnam
| | - Thuong Thi Ho
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi 100000, Vietnam; (V.T.P.); (T.T.H.); (N.B.P.); (H.H.C.); (T.H.V.)
| | - Ngoc Bich Pham
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi 100000, Vietnam; (V.T.P.); (T.T.H.); (N.B.P.); (H.H.C.); (T.H.V.)
- Faculty of Biotechnology, Graduate University of Science and Technology (GUST), VAST, Hanoi 10000, Vietnam
| | - Ha Hoang Chu
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi 100000, Vietnam; (V.T.P.); (T.T.H.); (N.B.P.); (H.H.C.); (T.H.V.)
- Faculty of Biotechnology, Graduate University of Science and Technology (GUST), VAST, Hanoi 10000, Vietnam
| | - Trang Huyen Vu
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi 100000, Vietnam; (V.T.P.); (T.T.H.); (N.B.P.); (H.H.C.); (T.H.V.)
- Faculty of Biotechnology, Graduate University of Science and Technology (GUST), VAST, Hanoi 10000, Vietnam
| | - Elsayed M. Abdelwhab
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, D-17493 Greifswald-Insel Riems, Germany; (E.M.A.); (D.S.); (T.C.M.)
| | - David Scheibner
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, D-17493 Greifswald-Insel Riems, Germany; (E.M.A.); (D.S.); (T.C.M.)
| | - Thomas C. Mettenleiter
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, D-17493 Greifswald-Insel Riems, Germany; (E.M.A.); (D.S.); (T.C.M.)
| | - Tran Xuan Hanh
- National Veterinary Joint Stock Company (NAVETCO), 29 Nguyen Dinh Chieu, Dist 1, Ho Chi Minh City 700000, Vietnam;
| | - Armin Meister
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466 Seeland OT Gatersleben, Germany; (A.M.); (U.G.)
| | - Ulrike Gresch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466 Seeland OT Gatersleben, Germany; (A.M.); (U.G.)
| | - Udo Conrad
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466 Seeland OT Gatersleben, Germany; (A.M.); (U.G.)
| |
Collapse
|
6
|
Engineering a disulfide-gated switch in streptavidin enables reversible binding without sacrificing binding affinity. Sci Rep 2020; 10:12483. [PMID: 32719366 PMCID: PMC7385176 DOI: 10.1038/s41598-020-69357-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 07/08/2020] [Indexed: 11/09/2022] Open
Abstract
Although high affinity binding between streptavidin and biotin is widely exploited, the accompanying low rate of dissociation prevents its use in many applications where rapid ligand release is also required. To combine extremely tight and reversible binding, we have introduced disulfide bonds into opposite sides of a flexible loop critical for biotin binding, creating streptavidin muteins (M88 and M112) with novel disulfide-switchable binding properties. Crystal structures reveal how each disulfide exerts opposing effects on structure and function. Whereas the disulfide in M112 disrupts the closed conformation to increase koff, the disulfide in M88 stabilizes the closed conformation, decreasing koff 260-fold relative to streptavidin. The simple and efficient reduction of this disulfide increases koff 19,000-fold, thus creating a reversible redox-dependent switch with 70-fold faster dissociation kinetics than streptavidin. The facile control of disulfide formation in M88 will enable the development of many new applications requiring high affinity and reversible binding.
Collapse
|
7
|
Recent advances in the engineering and application of streptavidin-like molecules. Appl Microbiol Biotechnol 2019; 103:7355-7365. [DOI: 10.1007/s00253-019-10036-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 07/12/2019] [Accepted: 07/15/2019] [Indexed: 01/24/2023]
|
8
|
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
| |
Collapse
|
9
|
Wellig S, Hamm P. Solvation Layer of Antifreeze Proteins Analyzed with a Markov State Model. J Phys Chem B 2018; 122:11014-11022. [PMID: 29889528 DOI: 10.1021/acs.jpcb.8b04491] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Three structurally very different antifreeze proteins (AFPs) are studied, addressing the question as to what extent the hypothesized preordering-binding mechanism is still relevant in the second solvation layer of the protein and beyond. Assuming a two-state model of water, the solvation layers are analyzed with the help of molecular dynamics simulations together with a Markov state model, which investigates the local tedrahedrality of the water hydrogen-bond network around a given water molecule. It has been shown previously that this analysis can discriminate the high-entropy, high-density state of the liquid (HDL) from its more structured low-density state (LDL). All investigated proteins, regardless of whether they are an AFP or not, have a tendency to increase the amount of HDL in their second solvation layer. The ice binding site (IBS) of the antifreeze proteins counteracts that trend, with either a hole in the HDL layer or a true excess of LDL. The results correlate to a certain extent with recent experiments, which have observed ice-like vibrational (VSFG) spectra for the water atop the IBS of only a subset of antifreeze proteins. It is concluded that the preordering-binding mechanism indeed seems to play a role but is only part of the overall picture.
Collapse
Affiliation(s)
- Sebastian Wellig
- Department of Chemistry , University of Zurich , 8057 Zurich , Switzerland
| | - Peter Hamm
- Department of Chemistry , University of Zurich , 8057 Zurich , Switzerland
| |
Collapse
|
10
|
Manandhar M, Cronan JE. Pimelic acid, the first precursor of the Bacillus subtilis biotin synthesis pathway, exists as the free acid and is assembled by fatty acid synthesis. Mol Microbiol 2017; 104:595-607. [PMID: 28196402 PMCID: PMC5426962 DOI: 10.1111/mmi.13648] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Biotin synthetic pathways are readily separated into two stages, synthesis of the seven carbon α, ω-dicarboxylic acid pimelate moiety and assembly of the fused heterocyclic rings. The biotin pathway genes responsible for pimelate moiety synthesis vary widely among bacteria whereas the ring synthesis genes are highly conserved. Bacillus subtilis seems to have redundant genes, bioI and bioW, for generation of the pimelate intermediate. Largely consistent with previous genetic studies it was found that deletion of bioW caused a biotin auxotrophic phenotype whereas deletion of bioI did not. BioW is a pimeloyl-CoA synthetase that converts pimelic acid to pimeloyl-CoA. The essentiality of BioW for biotin synthesis indicates that the free form of pimelic acid is an intermediate in biotin synthesis although this is not the case in E. coli. Since the origin of pimelic acid in Bacillus subtilis is unknown, 13 C-NMR studies were carried out to decipher the pathway for its generation. The data provided evidence for the role of free pimelate in biotin synthesis and the involvement of fatty acid synthesis in pimelate production. Cerulenin, an inhibitor of the key fatty acid elongation enzyme, FabF, markedly decreased biotin production by B. subtilis resting cells whereas a strain having a cerulenin-resistant FabF mutant produced more biotin. In addition, supplementation with pimelic acid fully restored biotin production in cerulenin-treated cells. These results indicate that pimelic acid originating from fatty acid synthesis pathway is a bona fide precursor of biotin in B. subtilis.
Collapse
Affiliation(s)
- Miglena Manandhar
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - John E Cronan
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| |
Collapse
|
11
|
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.
Collapse
|
12
|
Jain A, Cheng K. The principles and applications of avidin-based nanoparticles in drug delivery and diagnosis. J Control Release 2017; 245:27-40. [PMID: 27865853 PMCID: PMC5222781 DOI: 10.1016/j.jconrel.2016.11.016] [Citation(s) in RCA: 143] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 11/07/2016] [Indexed: 01/04/2023]
Abstract
Avidin-biotin interaction is one of the strongest non-covalent interactions in the nature. Avidin and its analogues have therefore been extensively utilized as probes and affinity matrices for a wide variety of applications in biochemical assays, diagnosis, affinity purification, and drug delivery. Recently, there has been a growing interest in exploring this non-covalent interaction in nanoscale drug delivery systems for pharmaceutical agents, including small molecules, proteins, vaccines, monoclonal antibodies, and nucleic acids. Particularly, the ease of fabrication without losing the chemical and biological properties of the coupled moieties makes the avidin-biotin system a versatile platform for nanotechnology. In addition, avidin-based nanoparticles have been investigated as diagnostic systems for various tumors and surface antigens. In this review, we will highlight the various fabrication principles and biomedical applications of avidin-based nanoparticles in drug delivery and diagnosis. The structures and biochemical properties of avidin, biotin and their respective analogues will also be discussed.
Collapse
Affiliation(s)
- Akshay Jain
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Missouri Kansas City, Kansas City, MO 64108, United States
| | - Kun Cheng
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Missouri Kansas City, Kansas City, MO 64108, United States.
| |
Collapse
|
13
|
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]
|
14
|
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.
Collapse
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:
| |
Collapse
|
15
|
Fairhead M, Krndija D, Lowe ED, Howarth M. Plug-and-play pairing via defined divalent streptavidins. J Mol Biol 2014; 426:199-214. [PMID: 24056174 PMCID: PMC4047826 DOI: 10.1016/j.jmb.2013.09.016] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 09/07/2013] [Accepted: 09/12/2013] [Indexed: 11/29/2022]
Abstract
Streptavidin is one of the most important hubs for molecular biology, either multimerizing biomolecules, bridging one molecule to another, or anchoring to a biotinylated surface/nanoparticle. Streptavidin has the advantage of rapid ultra-stable binding to biotin. However, the ability of streptavidin to bind four biotinylated molecules in a heterogeneous manner is often limiting. Here, we present an efficient approach to isolate streptavidin tetramers with two biotin-binding sites in a precise arrangement, cis or trans. We genetically modified specific subunits with negatively charged tags, refolded a mixture of monomers, and used ion-exchange chromatography to resolve tetramers according to the number and orientation of tags. We solved the crystal structures of cis-divalent streptavidin to 1.4Å resolution and trans-divalent streptavidin to 1.6Å resolution, validating the isolation strategy and explaining the behavior of the Dead streptavidin variant. cis- and trans-divalent streptavidins retained tetravalent streptavidin's high thermostability and low off-rate. These defined divalent streptavidins enabled us to uncover how streptavidin binding depends on the nature of the biotin ligand. Biotinylated DNA showed strong negative cooperativity of binding to cis-divalent but not trans-divalent streptavidin. A small biotinylated protein bound readily to cis and trans binding sites. We also solved the structure of trans-divalent streptavidin bound to biotin-4-fluorescein, showing how one ligand obstructs binding to an adjacent biotin-binding site. Using a hexaglutamate tag proved a more powerful way to isolate monovalent streptavidin, for ultra-stable labeling without undesired clustering. These forms of streptavidin allow this key hub to be used with a new level of precision, for homogeneous molecular assembly.
Collapse
Affiliation(s)
- Michael Fairhead
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Denis Krndija
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Ed D Lowe
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Mark Howarth
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
| |
Collapse
|
16
|
Streptavidin–biotin technology: improvements and innovations in chemical and biological applications. Appl Microbiol Biotechnol 2013; 97:9343-53. [DOI: 10.1007/s00253-013-5232-z] [Citation(s) in RCA: 238] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 08/29/2013] [Accepted: 09/02/2013] [Indexed: 12/25/2022]
|
17
|
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.
Collapse
Affiliation(s)
- Daniel Demonte
- Department of Chemical and Biological Engineering, University at Buffalo, Buffalo, New York, 14260
| | | | | | | | | |
Collapse
|
18
|
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.
Collapse
Affiliation(s)
- Jenni Leppiniemi
- Institute of Biomedical Technology, University of Tampere and Tampere University Hospital, FI-33014, Tampere, Finland
| | | | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Lim KH, Huang H, Pralle A, Park S. Stable, high-affinity streptavidin monomer for protein labeling and monovalent biotin detection. Biotechnol Bioeng 2012; 110:57-67. [DOI: 10.1002/bit.24605] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Revised: 06/27/2012] [Accepted: 07/03/2012] [Indexed: 01/19/2023]
|