1
|
Seo K, Hwang K, Nam KM, Kim MJ, Song YK, Kim CY. Nucleolin-Targeting AS1411 Aptamer-Conjugated Nanospheres for Targeted Treatment of Glioblastoma. Pharmaceutics 2024; 16:566. [PMID: 38675227 PMCID: PMC11055028 DOI: 10.3390/pharmaceutics16040566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 04/15/2024] [Accepted: 04/19/2024] [Indexed: 04/28/2024] Open
Abstract
Post-operative chemotherapy is still required for the treatment of glioblastoma (GBM), for which nanocarrier-based drug delivery has been identified as one of the most effective methods. However, the blood-brain barrier (BBB) and non-specific delivery to non-tumor tissues can significantly limit drug accumulation in tumor tissues and cause damage to nearby normal tissues. This study describes a targeted cancer therapy approach that uses AS1411 aptamer-conjugated nanospheres (100-300 nm in size) loaded with doxorubicin (Dox) to selectively identify tumor cells overexpressing nucleolin (NCL) proteins. The study demonstrates that the active target model, which employs aptamer-mediated drug delivery, is more effective than non-specific enhanced permeability and maintenance (EPR)-mediated delivery and passive drug delivery in improving drug penetration and maintenance in tumor cells. Additionally, the study reveals the potential for anti-cancer effects through 3D spheroidal and in vivo GBM xenograft models. The DNA-protein hybrid nanospheres utilized in this study offer numerous benefits, such as efficient synthesis, structural stability, high drug loading, dye labeling, biocompatibility, and biodegradability. When combined with nanospheres, the 1411 aptamer has been shown to be an effective drug delivery carrier allowing for the precise targeting of tumors. This combination has the potential to produce anti-tumor effects in the active targeted therapy of GBM.
Collapse
Affiliation(s)
- Kyeongjin Seo
- Department of Neurosurgery, Seoul National University Bundang Hospital, Seongnam-si 13620, Republic of Korea; (K.S.); (K.H.); (K.M.N.)
- Department of Health Science and Technology, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 08826, Republic of Korea
| | - Kihwan Hwang
- Department of Neurosurgery, Seoul National University Bundang Hospital, Seongnam-si 13620, Republic of Korea; (K.S.); (K.H.); (K.M.N.)
- Department of Neurosurgery, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Kyung Mi Nam
- Department of Neurosurgery, Seoul National University Bundang Hospital, Seongnam-si 13620, Republic of Korea; (K.S.); (K.H.); (K.M.N.)
| | - Min Ju Kim
- Astrogen Inc., 440, Hyeoksin-daero, Dong-gu, Daegu 41072, Republic of Korea;
| | - Yoon-Kyu Song
- Department of Applied Bioengineering, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 08826, Republic of Korea
- Advanced Institutes of Convergence Technology, Suwon-si 16229, Republic of Korea
| | - Chae-Yong Kim
- Department of Neurosurgery, Seoul National University Bundang Hospital, Seongnam-si 13620, Republic of Korea; (K.S.); (K.H.); (K.M.N.)
- Department of Neurosurgery, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| |
Collapse
|
2
|
Kim S, Cathey MVJ, Bounds BC, Scholl Z, Marszalek PE, Kim M. Ligand-Mediated Mechanical Enhancement in Protein Complexes at Nano- and Macro-Scale. ACS APPLIED MATERIALS & INTERFACES 2024; 16:272-280. [PMID: 38111156 DOI: 10.1021/acsami.3c14653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Protein self-assembly plays a vital role in a myriad of biological functions and in the construction of biomaterials. Although the physical association underlying these assemblies offers high specificity, the advantage often compromises the overall durability of protein complexes. To address this challenge, we propose a novel strategy that reinforces the molecular self-assembly of protein complexes mediated by their ligand. Known for their robust noncovalent interactions with biotin, streptavidin (SAv) tetramers are examined to understand how the ligand influences the mechanical strength of protein complexes at the nanoscale and macroscale, employing atomic force microscopy-based single-molecule force spectroscopy, rheology, and bioerosion analysis. Our study reveals that biotin binding enhances the mechanical strength of individual SAv tetramers at the nanoscale. This enhancement translates into improved shear elasticity and reduced bioerosion rates when SAv tetramers are utilized as cross-linking junctions within hydrogel. This approach, which enhances the mechanical strength of protein-based materials without compromising specificity, is expected to open new avenues for advanced biotechnological applications, including self-assembled, robust biomimetic scaffolds and soft robotics.
Collapse
Affiliation(s)
- Samuel Kim
- Department of Biomedical Engineering, University of Arizona, Tucson, Arizona 85721, United States
| | - Marcus V J Cathey
- Department of Biomedical Engineering, University of Arizona, Tucson, Arizona 85721, United States
| | - Brandon C Bounds
- Department of Biomedical Engineering, University of Arizona, Tucson, Arizona 85721, United States
| | - Zackary Scholl
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Piotr E Marszalek
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Minkyu Kim
- Department of Biomedical Engineering, University of Arizona, Tucson, Arizona 85721, United States
- Department of Materials Science and Engineering, University of Arizona, Tucson, Arizona 85721, United States
- BIO5 Institute, University of Arizona, Tucson, Arizona 85719, United States
| |
Collapse
|
3
|
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
|
4
|
Preparation of Temperature-Responsive Antibody–Nanoparticles by RAFT-Mediated Grafting from Polymerization. Polymers (Basel) 2022; 14:polym14214584. [DOI: 10.3390/polym14214584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/22/2022] [Accepted: 10/24/2022] [Indexed: 10/31/2022] Open
Abstract
Herein, we report the preparation of temperature-responsive antibody–nanoparticles by the direct polymerization of N-isopropylacrylamide (NIPAAm) from immunoglobulin G (IgG). To this end, a chain transfer agent (CTA) was introduced into IgG, followed by the precipitation polymerization of NIPAAm in an aqueous medium via reversible addition–fragmentation chain transfer polymerization above the lower critical solution temperature (LCST). Consequently, antibody–polymer particles with diameters of approximately 100–200 nm were formed. Owing to the entanglement of the grafted polymers via partial chemical crosslinking, the antibody–nanoparticles maintained their stability even at temperatures below the LCST. Further, the dispersed nanoparticles could be collected by thermal precipitation above the LCST. Additionally, the antibody–nanoparticles formulation could maintain its binding constant and exhibited a good resistance against enzymatic treatment. Thus, the proposed antibody–nanoparticles can be useful for maximizing the therapeutic potential of antibody–drug conjugates or efficacies of immunoassays and antibody recovery and recycling.
Collapse
|
5
|
Yeh SL, Deval P, Wu JG, Luo SC, Tsai WB. One-step electrochemical deposition of antifouling polymers with pyrogallol for biosensing applications. J Mater Chem B 2022; 10:2504-2511. [PMID: 35018937 DOI: 10.1039/d1tb02536h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electrochemical techniques are highly sensitive and label-free sensing methods for the detection of various biomarkers, toxins, or pathogens. An ideal sensing element should be electroconductive, nonfouling, and readily available for conjugation of ligands. In this work, we have developed a facile, one-step electrodeposition method based on pyrogallol polymerization for preparation of a nonfouling and biotinylated surface on indium tin oxide (ITO). A copolymer of sulfobetaine methacrylate and aminoethyl methacrylate (pSBAE) was synthesized and deposited on ITO in the presence of pyrogallol via cyclic voltammetry. The deposition took less than 15 minutes to sufficiently inhibit cell adhesion. Using biotinylated pSBAE, the modified surface resisted nonspecific protein adsorption from the fetal bovine serum solution and detected added avidin concentrations. The results show an efficient platform to fabricate an electrochemical biosensor for the detection of biomarkers. We expect that this facile one-step technology could be applied to conjugate various biosensing elements for nonfouling biosensors.
Collapse
Affiliation(s)
- Shang-Lin Yeh
- Department of Chemical Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 10617, Taiwan.
| | - Piyush Deval
- Department of Chemical Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 10617, Taiwan.
| | - Jhih-Guang Wu
- Department of Material Science and Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 10617, Taiwan
| | - Shyh-Chyang Luo
- Department of Material Science and Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 10617, Taiwan
| | - Wei-Bor Tsai
- Department of Chemical Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 10617, Taiwan.
| |
Collapse
|
6
|
Temperature Responsive Polymer Conjugate Prepared by "Grafting from" Proteins toward the Adsorption and Removal of Uremic Toxin. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27031051. [PMID: 35164316 PMCID: PMC8839407 DOI: 10.3390/molecules27031051] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 01/30/2022] [Accepted: 02/01/2022] [Indexed: 01/28/2023]
Abstract
In this study, temperature-responsive polymer-protein conjugate was synthesized using a “grafting from” concept by introducing a chain transfer agent (CTA) into bovine serum albumin (BSA). The BSA-CTA was used as a starting point for poly(N-isopropylacrylamide) (PNIPAAm) through reversible addition-fragmentation chain transfer polymerization. The research investigations suggest that the thermally responsive behavior of PNIPAAm was controlled by the monomer ratio to CTA, as well as the amount of CTA introduced to BSA. The study further synthesized the human serum albumin (HSA)-PNIPAAm conjugate, taking the advantage that HSA can specifically adsorb indoxyl sulfate (IS) as a uremic toxin. The HSA-PNIPAAm conjugate could capture IS and decreased the concentration by about 40% by thermal precipitation. It was also revealed that the protein activity was not impaired by the conjugation with PNIPAAm. The proposed strategy is promising in not only removal of uremic toxins but also enrichment of biomarkers for early diagnostic applications.
Collapse
|
7
|
Kojima K, Iizumi Y, Zhang M, Okazaki T. Streptavidin-Conjugated Oxygen-Doped Single-Walled Carbon Nanotubes as Near-Infrared Labels for Immunoassays. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:1509-1513. [PMID: 35029992 DOI: 10.1021/acs.langmuir.1c02824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Single-walled carbon nanotubes (CNTs) are promising candidates for near-infrared (NIR) fluorescent labels in diagnostic fields. We report a complex of oxygen-doped CNT (o-CNT) and streptavidin (SA) for preparing CNT-based NIR labels with a high reaction efficiency in immunoassays. This complex specifically binds to biotin molecules by conjugating a linker molecule of phospholipid polyethylene glycol (PL-PEG) to SA (o-CNT-SA). The immunoprecipitation reaction efficiency between o-CNT-SA and biotin reaches 79.3% when the surface of o-CNTs is uniformly covered with SA-conjugated PL-PEG. The strong affinity between SA and biotin is useful for preparing CNT-based sensitive NIR fluorescent labels.
Collapse
Affiliation(s)
- Keiko Kojima
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8577, Japan
- CNT-Application Research Center, National Institute of Advanced Industrial Science and Technology, Tsukuba 305-8565, Japan
| | - Yoko Iizumi
- CNT-Application Research Center, National Institute of Advanced Industrial Science and Technology, Tsukuba 305-8565, Japan
| | - Minfang Zhang
- CNT-Application Research Center, National Institute of Advanced Industrial Science and Technology, Tsukuba 305-8565, Japan
| | - Toshiya Okazaki
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8577, Japan
- CNT-Application Research Center, National Institute of Advanced Industrial Science and Technology, Tsukuba 305-8565, Japan
| |
Collapse
|
8
|
Yates EA, Estrella LA, So CR. High-Throughput Screening of Heterologous Functional Amyloids Using Escherichia coli. Methods Mol Biol 2022; 2538:131-144. [PMID: 35951298 DOI: 10.1007/978-1-0716-2529-3_10] [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: 06/15/2023]
Abstract
Escherichia coli remains one of the most widely used workhorse microorganisms for the expression of heterologous proteins. The large number of cloning vectors and mutant host strains available for E. coli yields an impressively wide array of folded globular proteins in the laboratory. However, applying modern functional screening approaches to interrogate insoluble protein aggregates such as amyloids requires the use of nonstandard expression pathways. In this chapter, we detail the use of the curli export pathway in E. coli to express a library of gene fragments and variants of a functional amyloid protein to screen sequence traits responsible for aggregation and the formation of nanoscale materials.
Collapse
Affiliation(s)
| | - Luis A Estrella
- Formerly Chemistry Division, US Naval Research Laboratory, Washington, DC, USA
| | - Christopher R So
- Chemistry Division, US Naval Research Laboratory, Washington, DC, USA.
| |
Collapse
|
9
|
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
|
10
|
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.
Collapse
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.
| |
Collapse
|
11
|
Schmidt TGM, Eichinger A, Schneider M, Bonet L, Carl U, Karthaus D, Theobald I, Skerra A. The Role of Changing Loop Conformations in Streptavidin Versions Engineered for High-affinity Binding of the Strep-tag II Peptide. J Mol Biol 2021; 433:166893. [PMID: 33639211 DOI: 10.1016/j.jmb.2021.166893] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/25/2021] [Accepted: 02/18/2021] [Indexed: 02/06/2023]
Abstract
The affinity system based on the artificial peptide ligand Strep-tag® II and engineered tetrameric streptavidin, known as Strep-Tactin®, offers attractive applications for the study of recombinant proteins, from detection and purification to functional immobilization. To further improve binding of the Strep-tag II to streptavidin we have subjected two protruding loops that shape its ligand pocket for the peptide - instead of D-biotin recognized by the natural protein - to iterative random mutagenesis. Sequence analyses of hits from functional screening assays revealed several unexpected structural motifs, such as a disulfide bridge at the base of one loop, replacement of the crucial residue Trp120 by Gly and a two-residue deletion in the second loop. The mutant m1-9 (dubbed Strep-Tactin XT) showed strongly enhanced affinity towards the Strep-tag II, which was further boosted in case of the bivalent Twin-Strep-tag®. Four representative streptavidin mutants were crystallized in complex with the Strep-tag II peptide and their X-ray structures were solved at high resolutions. In addition, the crystal structure of the complex between Strep-Tactin XT and the Twin-Strep-tag was elucidated, indicating a bivalent mode of binding and explaining the experimentally observed avidity effect. Our study illustrates the structural plasticity of streptavidin as a scaffold for ligand binding and reveals interaction modes that would have been difficult to predict. As result, Strep-Tactin XT offers a convenient reagent for the kinetically stable immobilization of recombinant proteins fused with the Twin-Strep-tag. The possibility of reversibly dissociating such complexes simply with D-biotin as a competing ligand enables functional studies in protein science as well as cell biology.
Collapse
Affiliation(s)
| | - Andreas Eichinger
- Lehrstuhl für Biologische Chemie, Technische Universität München, 85354 Freising, Germany
| | - Markus Schneider
- Lehrstuhl für Biologische Chemie, Technische Universität München, 85354 Freising, Germany
| | - Lidia Bonet
- IBA GmbH, Rudolf-Wissell-Str. 28, 37079 Göttingen, Germany
| | - Uwe Carl
- IBA GmbH, Rudolf-Wissell-Str. 28, 37079 Göttingen, Germany
| | | | - Ina Theobald
- Lehrstuhl für Biologische Chemie, Technische Universität München, 85354 Freising, Germany
| | - Arne Skerra
- Lehrstuhl für Biologische Chemie, Technische Universität München, 85354 Freising, Germany.
| |
Collapse
|
12
|
A magnetism/laser-auxiliary cascaded drug delivery to pulmonary carcinoma. Acta Pharm Sin B 2020; 10:1549-1562. [PMID: 32963949 PMCID: PMC7488357 DOI: 10.1016/j.apsb.2019.12.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 11/08/2019] [Accepted: 11/30/2019] [Indexed: 01/16/2023] Open
Abstract
Although high-efficiency targeted delivery is investigated for years, the efficiency of tumor targeting seems still a hard core to smash. To overcome this problem, we design a three-step delivery strategy based on streptavidin–biotin interaction with the help of c(RGDfK), magnetic fields and lasers. The ultrasmall superparamagnetic iron oxide nanoparticles (USIONPs) modified with c(RGDfK) and biotin are delivered at step 1, followed by streptavidin and the doxorubicin (Dox) loaded nanosystems conjugated with biotin at steps 2 and 3, respectively. The delivery systems were proved to be efficient on A549 cells. The co-localization of signal for each step revealed the targeting mechanism. The external magnetic field could further amplify the endocytosis of USPIONs based on c(RGDfK), and magnify the uptake distinctions among different test groups. Based on photoacoustic imaging, laser-heating treatment could enhance the permeability of tumor venous blood vessels and change the insufficient blood flow in cancer. Then, it was noticed in vivo that only three-step delivery with laser-heating and magnetic fields realized the highest tumor distribution of nanosystem. Finally, the magnetism/laser-auxiliary cascaded delivery exhibited the best antitumor efficacy. Generally, this study demonstrated the necessity of combining physical, biological and chemical means of targeting.
Collapse
|
13
|
L. Mpye K, Gildenhuys S, Mosebi S. The effects of temperature on streptavidin-biotin binding using affinity isothermal titration calorimetry. AIMS BIOPHYSICS 2020. [DOI: 10.3934/biophy.2020018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
|
14
|
Identification of Acinetobacter baumannii and its carbapenem-resistant gene bla OXA-23-like by multiple cross displacement amplification combined with lateral flow biosensor. Sci Rep 2019; 9:17888. [PMID: 31784652 PMCID: PMC6884502 DOI: 10.1038/s41598-019-54465-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Accepted: 11/14/2019] [Indexed: 12/25/2022] Open
Abstract
Acinetobacter baumannii is a frequent cause of the nosocomial infections. Herein, a novel isothermal amplification technique, multiple cross displacement amplification (MCDA) is employed for detecting all A. baumannii strains and identifying the strains harboring blaOXA-23-like gene. The duplex MCDA assay, which targets the pgaD and blaOXA-23-like genes, could identify the A. baumannii isolates and differentiate these isolates harboring blaOXA-23-like gene. The disposable lateral flow biosensors (LFB) were used for analyzing the MCDA products. A total of sixty-eight isolates, include fifty-three A. baumannii strains and fifteen non-A. baumannii strains, were employed to optimize MCDA methods and determine the sensitivity, specificity and feasibility. The optimal reaction condition is found to be 63 °C within 1 h, with limit of detection at 100 fg templates per tube for pgaD and blaOXA-23-like genes in pure cultures. The specificity of this assay is 100%. Moreover, the practical application of the duplex MCDA-LFB assay was evaluated using clinical samples, and the results obtained from duplex MCDA-LFB method were consistent with conventional culture-based technique. In sum, the duplex MCDA-LFB assay appears to be a reliable, rapid and specific technique to detect all A. baumannii strains and identify these strains harboring blaOXA-23-like gene for appropriate antibiotic therapy.
Collapse
|
15
|
Cooperativity of hydrogen bonding network in microsolvated biotin, the ligand of avidin class proteins. J Mol Model 2019; 25:361. [DOI: 10.1007/s00894-019-4253-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Accepted: 11/12/2019] [Indexed: 10/25/2022]
|
16
|
Thelu HVP, Atchimnaidu S, Perumal D, Harikrishnan KS, Vijayan S, Varghese R. Self-Assembly of an Aptamer-Decorated, DNA–Protein Hybrid Nanogel: A Biocompatible Nanocarrier for Targeted Cancer Therapy. ACS APPLIED BIO MATERIALS 2019; 2:5227-5234. [DOI: 10.1021/acsabm.9b00323] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Hari Veera Prasad Thelu
- School of Chemistry, Indian Institute of Science Education and Research (IISER) Thiruvananthapuram, Trivandrum, Kerala 695 551, India
| | - Siriki Atchimnaidu
- School of Chemistry, Indian Institute of Science Education and Research (IISER) Thiruvananthapuram, Trivandrum, Kerala 695 551, India
| | - Devanathan Perumal
- School of Chemistry, Indian Institute of Science Education and Research (IISER) Thiruvananthapuram, Trivandrum, Kerala 695 551, India
| | - Kaloor S. Harikrishnan
- School of Chemistry, Indian Institute of Science Education and Research (IISER) Thiruvananthapuram, Trivandrum, Kerala 695 551, India
| | - Shajesh Vijayan
- School of Chemistry, Indian Institute of Science Education and Research (IISER) Thiruvananthapuram, Trivandrum, Kerala 695 551, India
| | - Reji Varghese
- School of Chemistry, Indian Institute of Science Education and Research (IISER) Thiruvananthapuram, Trivandrum, Kerala 695 551, India
| |
Collapse
|
17
|
Xiao L, Sloan-Dennison S, Schultz ZD. Probing Membrane Receptors with Enhanced Raman Imaging. PROCEEDINGS OF SPIE--THE INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING 2018; 10726. [PMID: 30270964 DOI: 10.1117/12.2321300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Our lab has shown that nanoparticles functionalized with short peptides can selectively bind to receptor proteins in vitro. Our results indicate that the Raman signals observed from purified receptors in surface enhanced Raman scattering (SERS) experiments match those observed with tip-enhanced Raman scattering (TERS) experiments performed on membrane receptors in intact cell membranes. Analysis of the observed Raman signals suggest the signals arise from the amino-acids in the protein receptor responsible for binding and recognition of the ligand attached to the nanoparticle probe. Further experiments show the variance in the data correlates with affinity of the nanoparticle probe with a specific receptor. This result illustrates a new approach to studying membrane receptors.
Collapse
Affiliation(s)
- Lifu Xiao
- Department of Chemistry and Biochemistry, Ohio State University, W 18th Ave, Columbus, OH USA 43210
| | - Sian Sloan-Dennison
- Department of Chemistry and Biochemistry, Ohio State University, W 18th Ave, Columbus, OH USA 43210
| | - Zachary D Schultz
- Department of Chemistry and Biochemistry, Ohio State University, W 18th Ave, Columbus, OH USA 43210
| |
Collapse
|
18
|
Pang M, Liu HY, Li T, Wang D, Hu XY, Zhang XR, Yu BF, Guo R, Wang HL. Recombinant club cell protein 16 (CC16) ameliorates cigarette smoke‑induced lung inflammation in a murine disease model of COPD. Mol Med Rep 2018; 18:2198-2206. [PMID: 29956762 PMCID: PMC6072201 DOI: 10.3892/mmr.2018.9216] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 06/21/2018] [Indexed: 11/21/2022] Open
Abstract
Club cell protein (CC16) is expressed primarily by club cells possesses anti-inflammatory properties and is located in the bronchiolar epithelium. Previous studies have demonstrated that CC16 deficiency is associated with the progression of chronic obstructive pulmonary disease (COPD). In the present study, the therapeutic effects of recombinant rat CC16 protein in mice with COPD were examined and the underlying mechanisms investigated. A total of 30 adult male C57/BL6 mice were randomly divided into three groups (10 mice/group). A mouse COPD model was generated by exposing 20 mice to cigarette smoke (CS) for 24 weeks. A total of 10 mice were treated intranasally with rCC16 (2.5 µg/g body weight) and control mice were exposed to normal room air. Results indicated that rCC16 treatment ameliorated pathological damage in the lungs and reduced the production of tumor necrosis factor (TNF)-α, interleukin (IL)-6 and IL-8, which were induced by CS exposure. After rCC16 administration, endogenous CC16 was upregulated and the body weight of COPD mice was increased, whereas the opposite was observed in CS-exposed mice. Additionally, rCC16 treatment inhibited the DNA binding of NF-κB/p65 in lung tissues and reduced nuclear translocation of NF-κB/p65 in BALF and epithelial cells. Moreover, rCC16 treatment lead to a decrease in the total number of BALF cells, including macrophages, which was elevated in COPD mice. In conclusion, the present results demonstrate that rCC16 has therapeutic effects on COPD by downregulating pro-inflammatory factors via the NF-κB pathway.
Collapse
Affiliation(s)
- Min Pang
- Department of Respiratory Medicine, The First Hospital, Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
| | - Hong-Yan Liu
- School of Basic Medicine; Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
| | - Ting Li
- Department of Respiratory Medicine, The First Hospital, Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
| | - Dan Wang
- Department of Respiratory Medicine, The First Hospital, Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
| | - Xiao-Yun Hu
- Department of Respiratory Medicine, The First Hospital, Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
| | - Xin-Ri Zhang
- Department of Respiratory Medicine, The First Hospital, Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
| | - Bao-Feng Yu
- School of Basic Medicine; Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
| | - Rui Guo
- School of Basic Medicine; Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
| | - Hai-Long Wang
- School of Basic Medicine; Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
| |
Collapse
|
19
|
Imiołek M, Karunanithy G, Ng WL, Baldwin AJ, Gouverneur V, Davis BG. Selective Radical Trifluoromethylation of Native Residues in Proteins. J Am Chem Soc 2018; 140:1568-1571. [PMID: 29301396 PMCID: PMC5806083 DOI: 10.1021/jacs.7b10230] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Indexed: 12/20/2022]
Abstract
The incorporation of fluorine can not only significantly facilitate the study of proteins but also potentially modulate their function. Though some biosynthetic methods allow global residue-replacement, post-translational fluorine incorporation would constitute a fast and efficient alternative. Here, we reveal a mild method for direct protein radical trifluoromethylation at native residues as a strategy for symmetric-multifluorine incorporation on mg scales with high recoveries. High selectivity toward tryptophan residues enhanced the utility of this direct trifluoromethylation technique allowing ready study of fluorinated protein constructs using 19F-NMR.
Collapse
Affiliation(s)
- Mateusz Imiołek
- Chemistry Research Laboratory,
Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United
Kingdom
| | - Gogulan Karunanithy
- Chemistry Research Laboratory,
Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United
Kingdom
| | - Wai-Lung Ng
- Chemistry Research Laboratory,
Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United
Kingdom
| | - Andrew J. Baldwin
- Chemistry Research Laboratory,
Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United
Kingdom
| | - Véronique Gouverneur
- Chemistry Research Laboratory,
Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United
Kingdom
| | - Benjamin G. Davis
- Chemistry Research Laboratory,
Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United
Kingdom
| |
Collapse
|
20
|
Yuan X, Yang M, Chen X, Zhang X, Sukhadia S, Musolino N, Bao H, Chen T, Xu C, Wang Q, Santoro S, Ricklin D, Hu J, Lin R, Yang W, Li Z, Qin W, Zhao A, Scholler N, Coukos G. Correction to: Characterization of the first fully human anti-TEM1 scFv in models of solid tumor imaging and immunotoxin-based therapy. Cancer Immunol Immunother 2018; 67:329-339. [PMID: 29313073 PMCID: PMC11028179 DOI: 10.1007/s00262-017-2101-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Tumor endothelial marker 1 (TEM1) has been identified as a novel surface marker upregulated on the blood vessels and stroma in many solid tumors. We previously isolated a novel single-chain variable fragment (scFv) 78 against TEM1 from a yeast display scFv library. Here we evaluated the potential applications of scFv78 as a tool for tumor molecular imaging, immunotoxin-based therapy and nanotherapy. Epitope mapping, three-dimensional (3D) structure docking and affinity measurements indicated that scFv78 could bind to both human and murine TEM1, with equivalent affinity, at a well-conserved conformational epitope. The rapid internalization of scFv78 and scFv78-labeled nanoparticles was triggered after specific TEM1 binding. The scFv78-saporin immunoconjugate also exerted dose-dependent cytotoxicity with high specificity to TEM1-positive cells in vitro. Finally, specific and sensitive tumor localization of scFv78 was confirmed with optical imaging in a mouse tumor model that has highly endogenous mTEM1 expression in the vasculature. Our data indicate that scFv78, the first fully human anti-TEM1 recombinant antibody, recognizes both human and mouse TEM1 and has unique and favorable features that are advantageous for the development of imaging probes or antibody-toxin conjugates for a large spectrum of human TEM1-positive solid tumors.
Collapse
Affiliation(s)
- Xiaopeng Yuan
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
- Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangdong, China
| | - Mingjuan Yang
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Xiang Chen
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Xuhua Zhang
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Shrey Sukhadia
- Department of Chemistry and Biochemistry, University of the Sciences in Philadelphia, Philadelphia, PA, USA
| | - Najia Musolino
- Ludwig Institute for Cancer Research at CHUV, Rue du Bugnon 46-BH09-701, 1011, Lausanne, Switzerland
| | - Huijing Bao
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Tingtao Chen
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Chen Xu
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Qirui Wang
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Stephen Santoro
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Daniel Ricklin
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jia Hu
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Ruihe Lin
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Wei Yang
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Zhijun Li
- Department of Chemistry and Biochemistry, University of the Sciences in Philadelphia, Philadelphia, PA, USA
| | - Weijun Qin
- Department of Urology, Xijing Hospital, Fourth Military University, Xi'an, 710032, China.
| | - Aizhi Zhao
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Nathalie Scholler
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
- SRI International, Menlo Park, CA, USA
| | - George Coukos
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA.
- Ludwig Institute for Cancer Research at CHUV, Rue du Bugnon 46-BH09-701, 1011, Lausanne, Switzerland.
| |
Collapse
|
21
|
Jacobsen MT, Fairhead M, Fogelstrand P, Howarth M. Amine Landscaping to Maximize Protein-Dye Fluorescence and Ultrastable Protein-Ligand Interaction. Cell Chem Biol 2017; 24:1040-1047.e4. [PMID: 28757182 PMCID: PMC5563079 DOI: 10.1016/j.chembiol.2017.06.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 05/15/2017] [Accepted: 06/27/2017] [Indexed: 12/11/2022]
Abstract
Chemical modification of proteins provides great opportunities to control and visualize living systems. The most common way to modify proteins is reaction of their abundant amines with N-hydroxysuccinimide (NHS) esters. Here we explore the impact of amine number and positioning on protein-conjugate behavior using streptavidin-biotin, a central research tool. Dye-NHS modification of streptavidin severely damaged ligand binding, necessitating development of a new streptavidin-retaining ultrastable binding after labeling. Exploring the ideal level of dye modification, we engineered a panel bearing 1–6 amines per subunit: “amine landscaping.” Surprisingly, brightness increased as amine number decreased, revealing extensive quenching following conventional labeling. We ultimately selected Flavidin (fluorophore-friendly streptavidin), combining ultrastable ligand binding with increased brightness after conjugation. Flavidin enhanced fluorescent imaging, allowing more sensitive and specific cell labeling in tissues. Flavidin should have wide application in molecular detection, providing a general insight into how to optimize simultaneously the behavior of the biomolecule and the chemical probe. Labeling of streptavidin with small-molecule dyes impairs ligand binding K121R mutation rescues ligand stability after dye labeling Landscaping of protein amines optimizes brightness Fluorophore-friendly streptavidin improves imaging specificity and sensitivity
Collapse
Affiliation(s)
- Michael T Jacobsen
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Michael Fairhead
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Per Fogelstrand
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Mark Howarth
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
| |
Collapse
|
22
|
Ozawa M, Ozawa T, Nishio M, Ueda K. The role of CH/π interactions in the high affinity binding of streptavidin and biotin. J Mol Graph Model 2017; 75:117-124. [PMID: 28551501 DOI: 10.1016/j.jmgm.2017.05.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 04/27/2017] [Accepted: 05/02/2017] [Indexed: 11/28/2022]
Abstract
The streptavidin-biotin complex has an extraordinarily high affinity (Ka: 1015mol-1) and contains one of the strongest non-covalent interactions known. This strong interaction is widely used in biological tools, including for affinity tags, detection, and immobilization of proteins. Although hydrogen bond networks and hydrophobic interactions have been proposed to explain this high affinity, the reasons for it remain poorly understood. Inspired by the deceased affinity of biotin observed for point mutations of streptavidin at tryptophan residues, we hypothesized that a CH/π interaction may also contribute to the strong interaction between streptavidin and biotin. CH/π interactions were explored and analyzed at the biotin-binding site and at the interface of the subunits by the fragment molecular orbital method (FMO) and extended applications: PIEDA and FMO4. The results show that CH/π interactions are involved in the high affinity for biotin at the binding site of streptavidin. We further suggest that the involvement of CH/π interactions at the subunit interfaces and an extended CH/π network play more critical roles in determining the high affinity, rather than involvement at the binding site.
Collapse
Affiliation(s)
- Motoyasu Ozawa
- Central Research Laboratory, Kissei Pharmaceutical Co., Ltd., 4365-1 Hotakakashiwabara, Azumino, Nagano 399-8304, Japan.
| | - Tomonaga Ozawa
- Central Research Laboratory, Kissei Pharmaceutical Co., Ltd., 4365-1 Hotakakashiwabara, Azumino, Nagano 399-8304, Japan
| | | | - Kazuyoshi Ueda
- Graduate School of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya-Ku, Yokohama 240-8501, Japan
| |
Collapse
|
23
|
Dubacheva GV, Araya-Callis C, Geert Volbeda A, Fairhead M, Codée J, Howarth M, Richter RP. Controlling Multivalent Binding through Surface Chemistry: Model Study on Streptavidin. J Am Chem Soc 2017; 139:4157-4167. [PMID: 28234007 PMCID: PMC5364436 DOI: 10.1021/jacs.7b00540] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Indexed: 12/22/2022]
Abstract
Although multivalent binding to surfaces is an important tool in nanotechnology, quantitative information about the residual valency and orientation of surface-bound molecules is missing. To address these questions, we study streptavidin (SAv) binding to commonly used biotinylated surfaces such as supported lipid bilayers (SLBs) and self-assembled monolayers (SAMs). Stability and kinetics of SAv binding are characterized by quartz crystal microbalance with dissipation monitoring, while the residual valency of immobilized SAv is quantified using spectroscopic ellipsometry by monitoring binding of biotinylated probes. Purpose-designed SAv constructs having controlled valencies (mono-, di-, trivalent in terms of biotin-binding sites) are studied to rationalize the results obtained on regular (tetravalent) SAv. We find that divalent interaction of SAv with biotinylated surfaces is a strict requirement for stable immobilization, while monovalent attachment is reversible and, in the case of SLBs, leads to the extraction of biotinylated lipids from the bilayer. The surface density and lateral mobility of biotin, and the SAv surface coverage are all found to influence the average orientation and residual valency of SAv on a biotinylated surface. We demonstrate how the residual valency can be adjusted to one or two biotin binding sites per immobilized SAv by choosing appropriate surface chemistry. The obtained results provide means for the rational design of surface-confined supramolecular architectures involving specific biointeractions at tunable valency. This knowledge can be used for the development of well-defined bioactive coatings, biosensors and biomimetic model systems.
Collapse
Affiliation(s)
- Galina V. Dubacheva
- Biosurfaces
Lab, CIC biomaGUNE, Paseo Miramon 182, 20014 Donostia − San Sebastian, Spain
- PPSM
CNRS UMR8531, ENS Cachan, Université
Paris-Saclay, 61 Avenue du Président Wilson, 94235 Cachan, France
| | - Carolina Araya-Callis
- Biosurfaces
Lab, CIC biomaGUNE, Paseo Miramon 182, 20014 Donostia − San Sebastian, Spain
| | - Anne Geert Volbeda
- Leiden
Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Michael Fairhead
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Jeroen Codée
- Leiden
Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Mark Howarth
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Ralf P. Richter
- Biosurfaces
Lab, CIC biomaGUNE, Paseo Miramon 182, 20014 Donostia − San Sebastian, Spain
- School
of Biomedical Sciences and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, United Kingdom
- Laboratory
of Interdisciplinary Physics, University
Grenoble Alpes − CNRS, 140 Rue de la Physique, 38402 Saint Martin d’Hères, France
| |
Collapse
|
24
|
Yuan X, Yang M, Chen X, Zhang X, Sukhadia S, Musolino N, Bao H, Chen T, Xu C, Wang Q, Santoro S, Ricklin D, Hu J, Lin R, Yang W, Li Z, Qin W, Zhao A. Characterization of the first fully human anti-TEM1 scFv in models of solid tumor imaging and immunotoxin-based therapy. Cancer Immunol Immunother 2017; 66:367-378. [PMID: 27933426 PMCID: PMC11029759 DOI: 10.1007/s00262-016-1937-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 11/19/2016] [Indexed: 10/20/2022]
Abstract
Tumor endothelial marker 1 (TEM1) has been identified as a novel surface marker upregulated on the blood vessels and stroma in many solid tumors. We previously isolated a novel single-chain variable fragment (scFv) 78 against TEM1 from a yeast display scFv library. Here, we evaluated the potential applications of scFv78 as a tool for tumor molecular imaging, immunotoxin-based therapy and nanotherapy. Epitope mapping, three-dimensional structure docking and affinity measurements indicated that scFv78 could bind to both human and murine TEM1, with equivalent affinity, at a well-conserved conformational epitope. The rapid internalization of scFv78 and scFv78-labeled nanoparticles was triggered after specific TEM1 binding. The scFv78-saporin immunoconjugate also exerted dose-dependent cytotoxicity with high specificity to TEM1-positive cells in vitro. Finally, specific and sensitive tumor localization of scFv78 was confirmed with optical imaging in a tumor mouse model that has highly endogenous mTEM1 expression in the vasculature. Our data indicated that scFv78, the first fully human anti-TEM1 recombinant antibody, recognizes both human and mouse TEM1 and has unique and favorable features that are advantageous for the development of imaging probes or antibody-toxin conjugates for a large spectrum of human TEM1-positive solid tumors.
Collapse
Affiliation(s)
- Xiaopeng Yuan
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
- Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangdong, China
| | - Mingjuan Yang
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Xiang Chen
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Xuhua Zhang
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Shrey Sukhadia
- Department of Chemistry and Biochemistry, University of the Sciences in Philadelphia, Philadelphia, PA, USA
| | | | - Huijing Bao
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Tingtao Chen
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Chen Xu
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Qirui Wang
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Stephen Santoro
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Daniel Ricklin
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jia Hu
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Ruihe Lin
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Wei Yang
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Zhijun Li
- Department of Chemistry and Biochemistry, University of the Sciences in Philadelphia, Philadelphia, PA, USA
| | - Weijun Qin
- Department of Urology, Xijing Hospital, Fourth Military Medical University, Xi'an, 710032, China.
| | - Aizhi Zhao
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA.
- University City Science Center, Room 544, 3624 Market Street, Philadelphia, PA, 19104, USA.
| |
Collapse
|
25
|
Wu SC, Wang C, Hansen D, Wong SL. A simple approach for preparation of affinity matrices: Simultaneous purification and reversible immobilization of a streptavidin mutein to agarose matrix. Sci Rep 2017; 7:42849. [PMID: 28220817 PMCID: PMC5318860 DOI: 10.1038/srep42849] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 01/18/2017] [Indexed: 11/09/2022] Open
Abstract
SAVSBPM18 is an engineered streptavidin for affinity purification of both biotinylated biomolecules and recombinant proteins tagged with streptavidin binding peptide (SBP) tags. To develop a user-friendly approach for the preparation of the SAVSBPM18-based affinity matrices, a designer fusion protein containing SAVSBPM18 and a galactose binding domain was engineered. The galactose binding domain derived from the earthworm lectin EW29 was genetically modified to eliminate a proteolytic cleavage site located at the beginning of the domain. This domain was fused to the C-terminal end of SAVSBPM18. It allows the SAVSBPM18 fusions to bind reversibly to agarose and can serve as an affinity handle for purification of the fusion. Fluorescently labeled SAVSBPM18 fusions were found to be stably immobilized on Sepharose 6B-CL. The enhanced immobilization capability of the fusion to the agarose beads results from the avidity effect mediated by the tetrameric nature of SAVSBPM18. This approach allows the consolidation of purification and immobilization of SAVSBPM18 fusions to Sepharose 6B-CL in one step for affinity matrix preparation. The resulting affinity matrix has been successfully applied to purify both SBP tagged β-lactamase and biotinylated proteins. No significant reduction in binding capacity of the column was observed for at least six months.
Collapse
Affiliation(s)
- Sau-Ching Wu
- Department of Biological Sciences, University of Calgary, 2500 University Dr., N.W. Calgary, Alberta, T2N 1N4, Canada
| | - Chris Wang
- Department of Biological Sciences, University of Calgary, 2500 University Dr., N.W. Calgary, Alberta, T2N 1N4, Canada
| | - Dave Hansen
- Department of Biological Sciences, University of Calgary, 2500 University Dr., N.W. Calgary, Alberta, T2N 1N4, Canada
| | - Sui-Lam Wong
- Department of Biological Sciences, University of Calgary, 2500 University Dr., N.W. Calgary, Alberta, T2N 1N4, Canada
| |
Collapse
|
26
|
Lee M, Peterson BR. Quantification of Small Molecule-Protein Interactions using FRET between Tryptophan and the Pacific Blue Fluorophore. ACS OMEGA 2016; 1:1266-1276. [PMID: 28058293 PMCID: PMC5204206 DOI: 10.1021/acsomega.6b00356] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 12/06/2016] [Indexed: 05/14/2023]
Abstract
We report a new method to quantify the affinity of small molecules for proteins. This method is based on Förster resonance energy transfer (FRET) between endogenous tryptophan (Trp) residues and the coumarin-derived fluorophore Pacific Blue (PB). Tryptophan residues are frequently found in proteins near ligand-binding sites, making this approach potentially applicable to a wide range of systems. To improve access to PB, we developed a scalable multigram synthesis of this fluorophore, starting with inexpensive 2,3,4,5-tetrafluorobenzoic acid. This route was used to synthesize fluorescent derivatives of biotin, as well as lower affinity thiobiotin, iminobiotin, and imidazolidinethione analogues that bind the protein streptavidin. Compared with previously published FRET acceptors for tryptophan, PB proved to be superior in both sensitivity and efficiency. These unique properties of PB enabled direct quantification of dissociation constants (Kd) as well as competitive inhibition constants (Ki) in the micromolar to nanomolar range. In comparison to analogous binding studies using fluorescence polarization, fluorescence quenching, or fluorescence enhancement, affinities determined using Trp-FRET were more precise and accurate as validated using independent isothermal titration calorimetry studies. FRET between tryptophan and PB represents a new tool for the characterization of protein-ligand complexes.
Collapse
|
27
|
Smirnova DV, Rubtsova MY, Grigorenko VG, Ugarova NN. A Novel Streptavidin-luciferase Fusion Protein: Preparation, Properties and Application in Hybridization Analysis of DNA. Photochem Photobiol 2016; 93:541-547. [PMID: 27861953 DOI: 10.1111/php.12666] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 09/29/2016] [Indexed: 12/14/2022]
Abstract
A streptavidin-luciferase fusion protein comprising the thermostable mutant form of firefly luciferase Luciola mingrelica and minimal core streptavidin was constructed. The streptavidin-luciferase fusion was mainly produced in a tetrameric form with high luciferase and biotin-binding activities. It was shown that fusion has the same Km values for ATP and luciferin and the bioluminescence spectra as initial luciferase. The linear dependence of the bioluminescence signal on the content of the fusion was observed within the range of 10-18 -10-13 mol per well. Successful application of obtained fusion in a biospecific bioluminescence assay based on biotin-streptavidin interactions was demonstrated by the example of a specific DNA hybridization analysis. A DNA hybridization analysis for Escherichia coli cells identification was developed using unique for these cells gadB fragment encoding glutamate decarboxylase. The amplified biotinylated GadB fragments were hybridized with the immobilized oligonucleotide probes; then, the biotin in the DNA duplexes was detected using the streptavidin-luciferase fusion protein. To reach the high sensitivity of the assay, we optimized the conditions of the assay. It was shown that the use of Pluronic for plate modification resulted in a significant reduction in the DNA detection limit which finally was 0.4 ng per well.
Collapse
Affiliation(s)
- Daria V Smirnova
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia.,"Lumtek" LLC, Moscow, Russia
| | - Maya Y Rubtsova
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | | | - Natalia N Ugarova
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia.,"Lumtek" LLC, Moscow, Russia
| |
Collapse
|
28
|
Varga M. Targeting at the Nanoscale: A Novel S-Layer Fusion Protein Enabling Controlled Immobilization of Biotinylated Molecules. NANOMATERIALS (BASEL, SWITZERLAND) 2016; 6:E199. [PMID: 28335327 PMCID: PMC5245738 DOI: 10.3390/nano6110199] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 10/25/2016] [Accepted: 10/28/2016] [Indexed: 11/16/2022]
Abstract
With the aim of constructing an S-layer fusion protein that combines both excellent self-assembly and specific ligand i.e., biotin binding ability, streptavidin (aa 16-133) was fused to the S-layer protein of Sporosarcina ureae ATCC 13881 (SslA) devoid of its N-terminal 341 and C-terminal 172 amino acids. The genetically engineered chimeric protein could be successfully produced in E. coli, isolated, and purified via Ni affinity chromatography. In vitro recrystallisation experiments performed with the purified chimeric protein in solution and on a silicon wafer have demonstrated that fusion of the streptavidin domain does not interfere with the self-assembling properties of the S-layer part. The chimeric protein self-assembled into multilayers. More importantly, the streptavidin domain retained its full biotin-binding ability, a fact evidenced by experiments in which biotinylated quantum dots were coupled to the fusion protein monomers and adsorbed onto the in vitro recrystallised fusion protein template. In this way, this S-layer fusion protein can serve as a functional template for the controlled immobilization of biotinylated and biologically active molecules.
Collapse
Affiliation(s)
- Melinda Varga
- Electronics Packaging Laboratory, Department of Electrical Engineering and Information Technology, Technische Universität Dresden, Dresden 01069, Germany.
| |
Collapse
|
29
|
Library design and screening protocol for artificial metalloenzymes based on the biotin-streptavidin technology. Nat Protoc 2016; 11:835-52. [DOI: 10.1038/nprot.2016.019] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
|
30
|
Qiao YF, Guo WJ, Li L, Shao S, Qiao X, Shao JJ, Zhang Q, Li RS, Wang LH. Melatonin attenuates hypertension-induced renal injury partially through inhibiting oxidative stress in rats. Mol Med Rep 2015; 13:21-6. [PMID: 26531807 PMCID: PMC4686099 DOI: 10.3892/mmr.2015.4495] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 06/25/2015] [Indexed: 12/31/2022] Open
Abstract
The aim of the present study was to investigate the protective effects of melatonin (MLT) on hypertension-induced renal injury and identify its mechanism of action. Twenty-four healthy male Wistar rats were divided into a sham control group (n=8), which was subjected to sham operation and received vehicle treatment (physiological saline intraperitoneally at 0.1 ml/100 g), a vehicle group (n=8), which was subjected to occlusion of the left renal artery and vehicle treatment, and the MLT group (n=8), which was subjected to occlusion of the left renal artery and treated with MLT (10 mg/kg/day). Pathological features of the renal tissues were determined using hematoxylin and eosin staining and Masson staining. Urine protein, serum creatinine (Scr), superoxide dismutase (SOD) and malondialdehyde (MDA) were determined. Immunohistochemical analysis was performed to determine the expression of heme oxygenase-1 (HO-1), intercellular adhesion molecule-1 (ICAM-1), inducible nitric oxide synthase (iNOS) and endothelial nitric oxide synthase (eNOS). Furthermore, reverse transcription polymerase chain reaction was conducted to determine the mRNA expression of HO-1, ICAM-1, eNOS and iNOS. A marked decrease in blood pressure was noticed in the MLT group at week 4 compared with that of the vehicle group (P<0.01). Furthermore, MLT treatment attenuated the infiltration of inflammatory cells and oedema/atrophy of renal tubules. MLT attenuated hypertension-induced increases in urine protein excretion, serum creatinine and MDA as well as decreases in SOD activity in renal tissues. Furthermore, MLT attenuated hypertension-induced increases in iNOS and ICAM-1 as well as decreases in eNOS and HO-1 expression at the mRNA and protein level. In conclusion, the results of the present study indicated that MLT had protective roles in hypertension-induced renal injury. Its mechanism of action is, at least in part, associated with the inhibition of oxidative stress.
Collapse
Affiliation(s)
- Yu-Feng Qiao
- Department of Nephrology, Second Hospital of Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
| | - Wen-Juan Guo
- Department of Nephrology, Second Hospital of Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
| | - Lu Li
- Department of Nephrology, Baoding No. 1 Hospital, Baoding, Hebei 071000, P.R. China
| | - Shan Shao
- Department of Nephrology, Second Hospital of Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
| | - Xi Qiao
- Department of Nephrology, Second Hospital of Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
| | - Jin-Jin Shao
- Department of Nephrology, Second Hospital of Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
| | - Qiong Zhang
- Department of Nephrology, Shanxi People's Hospital, Taiyuan, Shanxi 030001, P.R. China
| | - Rong-Shan Li
- Department of Nephrology, Shanxi People's Hospital, Taiyuan, Shanxi 030001, P.R. China
| | - Li-Hua Wang
- Department of Nephrology, Second Hospital of Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
| |
Collapse
|
31
|
Shetty D, Khedkar JK, Park KM, Kim K. Can we beat the biotin-avidin pair?: cucurbit[7]uril-based ultrahigh affinity host-guest complexes and their applications. Chem Soc Rev 2015; 44:8747-61. [PMID: 26434388 DOI: 10.1039/c5cs00631g] [Citation(s) in RCA: 291] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The design of synthetic, monovalent host-guest molecular recognition pairs is still challenging and of particular interest to inquire into the limits of the affinity that can be achieved with designed systems. In this regard, cucurbit[7]uril (CB[7]), an important member of the host family cucurbit[n]uril (CB[n], n = 5-8, 10, 14), has attracted much attention because of its ability to form ultra-stable complexes with multiple guests. The strong hydrophobic effect between the host cavity and guests, ion-dipole and dipole-dipole interactions of guests with CB portals helps in cooperative and multiple noncovalent interactions that are essential for realizing such strong complexations. These highly selective, strong yet dynamic interactions can be exploited in many applications including affinity chromatography, biomolecule immobilization, protein isolation, biological catalysis, and sensor technologies. In this review, we summarize the progress in the development of high affinity guests for CB[7], factors affecting the stability of complexes, theoretical insights, and the utility of these high affinity pairs in different challenging applications.
Collapse
Affiliation(s)
- Dinesh Shetty
- Center for Self-assembly and Complexity (CSC), Institute for Basic Science (IBS), Pohang 37673, Republic of Korea.
| | | | | | | |
Collapse
|
32
|
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]
|
33
|
Paleček E, Tkáč J, Bartošík M, Bertók T, Ostatná V, Paleček J. Electrochemistry of nonconjugated proteins and glycoproteins. Toward sensors for biomedicine and glycomics. Chem Rev 2015; 115:2045-108. [PMID: 25659975 PMCID: PMC4360380 DOI: 10.1021/cr500279h] [Citation(s) in RCA: 214] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Indexed: 02/07/2023]
Affiliation(s)
- Emil Paleček
- Institute
of Biophysics Academy of Science of the Czech Republic, v.v.i., Královopolská
135, 612 65 Brno, Czech Republic
| | - Jan Tkáč
- Institute
of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38 Bratislava, Slovakia
| | - Martin Bartošík
- Regional
Centre for Applied Molecular Oncology, Masaryk
Memorial Cancer Institute, Žlutý kopec 7, 656 53 Brno, Czech Republic
| | - Tomáš Bertók
- Institute
of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38 Bratislava, Slovakia
| | - Veronika Ostatná
- Institute
of Biophysics Academy of Science of the Czech Republic, v.v.i., Královopolská
135, 612 65 Brno, Czech Republic
| | - Jan Paleček
- Central
European Institute of Technology, Masaryk
University, Kamenice
5, 625 00 Brno, Czech Republic
| |
Collapse
|
34
|
Kuo TC, Tsai CW, Lee PC, Chen WY. Revisiting the streptavidin-biotin binding by using an aptamer and displacement isothermal calorimetry titration. J Mol Recognit 2015; 28:125-8. [PMID: 25615849 DOI: 10.1002/jmr.2366] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 01/19/2014] [Accepted: 01/28/2014] [Indexed: 12/21/2022]
Abstract
The association constant of a well-known streptavidin-biotin binding has only been inferred from separately measured kinetic parameters. In a single experiment, we obtained Ka 1 × 10(12) M(-1) by using a streptavidin-binding aptamer and ligand-displacement isothermal titration calorimetry. This study explores the challenges of determining thermodynamic parameters and the derived equilibrium binding affinity of tight ligand-receptor binding.
Collapse
Affiliation(s)
- Tai-Chih Kuo
- Department of Biochemistry, Taipei Medical University, Taipei, Taiwan
| | | | | | | |
Collapse
|
35
|
Wu TC, Rahman M, Norton ML. From nonfinite to finite 1D arrays of origami tiles. Acc Chem Res 2014; 47:1750-8. [PMID: 24803094 DOI: 10.1021/ar400330y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
CONSPECTUS: DNA based nanotechnology provides a basis for high-resolution fabrication of objects almost without physical size limitations. However, the pathway to large-scale production of large objects is currently unclear. Operationally, one method forward is to use high information content, large building blocks, which can be generated with high yield and reproducibility. Although flat DNA origami naturally invites comparison to pixels in zero, one, and two dimensions and voxels in three dimensions and has provided an excellent mechanism for generating blocks of significant size and complexity and a multitude of shapes, the field is young enough that a single "brick" has not become the standard platform used by the majority of researchers in the field. In this Account, we highlight factors we considered that led to our adoption of a cross-shaped, non-space-filling origami species, designed by Dr. Liu of the Seeman laboratory, as the building block ideal for use in the fabrication of finite one-dimensional arrays. Three approaches that can be employed for uniquely coding origami-origami linkages are presented. Such coding not only provides the energetics for tethering the species but also uniquely designates the relative orientation of the origami building blocks. The strength of the coding approach implemented in our laboratory is demonstrated using examples of oligomers ranging from finite multimers composed of four, six, and eight origami structures to semi-infinite polymers (100mers). Two approaches to finite array design and the series of assembly steps that each requires are discussed. The process of AFM observation for array characterization is presented as a critical case study. For these soft species, the array images do not simply present the solution phase geometry projected onto a two-dimensional surface. There are additional perturbations associated with fluidic forces associated with sample preparation. At this time, reconstruction of the "true" or average solution structures for blocks is more readily achieved using computer models than using direct imaging methods. The development of scalable 1D-origami arrays composed of uniquely addressable components is a logical, if not necessary, step in the evolution of higher order fully addressable structures. Our research into the fabrication of arrays has led us to generate a listing of several important areas of future endeavor. Of high importance is the re-enforcement of the mechanical properties of the building blocks and the organization of multiple arrays on a surface of technological importance. While addressing this short list of barriers to progress will prove challenging, coherent development along each of these lines of inquiry will accelerate the appearance of commercial scale molecular manufacturing.
Collapse
Affiliation(s)
- Tsai Chin Wu
- Department of Chemistry, Marshall University, 1 John Marshall Drive, Huntingon, West Virginia 25755, United States
| | - Masudur Rahman
- Department of Chemistry, Marshall University, 1 John Marshall Drive, Huntingon, West Virginia 25755, United States
| | - Michael L. Norton
- Department of Chemistry, Marshall University, 1 John Marshall Drive, Huntingon, West Virginia 25755, United States
| |
Collapse
|
36
|
An amino acid depleted cell-free protein synthesis system for the incorporation of non-canonical amino acid analogs into proteins. J Biotechnol 2014; 178:12-22. [DOI: 10.1016/j.jbiotec.2014.02.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 02/08/2014] [Accepted: 02/14/2014] [Indexed: 11/19/2022]
|
37
|
Kim JH, Sumranjit J, Kang HJ, Chung SJ. Discovery of coumarin derivatives as fluorescence acceptors for intrinsic fluorescence resonance energy transfer of proteins. ACTA ACUST UNITED AC 2014; 10:30-3. [DOI: 10.1039/c3mb70323a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
|
38
|
Tamavidin 2-HOT, a highly thermostable biotin-binding protein. J Biotechnol 2013; 169:1-8. [PMID: 24211408 DOI: 10.1016/j.jbiotec.2013.10.034] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 10/17/2013] [Accepted: 10/25/2013] [Indexed: 11/22/2022]
Abstract
Tamavidin 2 is a fungal tetrameric protein that binds with high affinity to biotin, like avidin and streptavidin. We replaced asparagine-115, which lies in a subunit-subunit interface of tamavidin 2, with cysteine to generate the novel, highly thermostable protein tamavidin 2-HOT. Tamavidin 2-HOT retained more than 80% of its biotin-binding activity even after incubation at 99.9°C for 60min and was fully active in 70% dimethylsulfoxide for 30min, whereas in these harsh conditions, avidin, streptavidin, and tamavidin 2 lost their activities (less than 20% of their biotin-binding activities). The Tm in which the biotin-binding activity becomes half of tamavidin 2-HOT was 105°C, at least 20°C higher than those of avidin, streptavidin, and tamavidin 2. Because a reducing agent removed the thermal stability of tamavidin 2-HOT, the N115C mutation likely created disulfide bridges that stabilized inter-subunit associations. Tamavidin 2-HOT is efficiently produced in the soluble form by Escherichia coli for practical use. The isoelectric point of tamavidin 2-HOT (7.4) is sufficiently low to reduce the chance for non-specific binding of non-target molecules due to high positive charges. Therefore, tamavidin 2-HOT may be useful in diverse novel applications that take advantage of its high biotin-binding capability that can withstand harsh conditions.
Collapse
|
39
|
Purushotham U, Sastry GN. A comprehensive conformational analysis of tryptophan, its ionic and dimeric forms. J Comput Chem 2013; 35:595-610. [DOI: 10.1002/jcc.23482] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 10/08/2013] [Accepted: 10/13/2013] [Indexed: 01/21/2023]
Affiliation(s)
- Uppula Purushotham
- Center for Molecular Modeling, CSIR-Indian Institute of Chemical Technology; Tarnaka, Hyderabad 500607 Andhra Pradesh India
| | - G. Narahari Sastry
- Center for Molecular Modeling, CSIR-Indian Institute of Chemical Technology; Tarnaka, Hyderabad 500607 Andhra Pradesh India
| |
Collapse
|
40
|
Zhang Y, Deng L, Kitova EN, Klassen JS. Dissociation of multisubunit protein-ligand complexes in the gas phase. Evidence for ligand migration. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1573-1583. [PMID: 23943432 DOI: 10.1007/s13361-013-0712-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Revised: 06/19/2013] [Accepted: 06/27/2013] [Indexed: 06/02/2023]
Abstract
The results of collision-induced dissociation (CID) experiments performed on gaseous protonated and deprotonated ions of complexes of cholera toxin B subunit homopentamer (CTB5) with the pentasaccharide (β-D-Galp-(1→3)-β-D-GalpNAc-(1→4)[α-D-Neu5Ac-(2→3)]-β-D-Galp-(1→4)-β-D-Glcp (GM1)) and corresponding glycosphingolipid (β-D-Galp-(1→3)-β-D-GalpNAc-(1→4)[α-D-Neu5Ac-(2→3)]-β-D-Galp-(1→4)-β-D-Glcp-Cer (GM1-Cer)) ligands, and the homotetramer streptavidin (S4) with biotin (B) and 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine-N-(biotinyl) (Btl), are reported. The protonated (CTB5 + 5GM1)(n+) ions dissociated predominantly by the loss of a single subunit, with the concomitant migration of ligand to another subunit. The simultaneous loss of ligand and subunit was observed as a minor pathway. In contrast, the deprotonated (CTB5 + 5GM1)(n-) ions dissociated preferentially by the loss of deprotonated ligand; the loss of ligand-bound and ligand-free subunit were minor pathways. The presence of ceramide (Cer) promoted ligand migration and the loss of subunit. The main dissociation pathway for the protonated and deprotonated (S4 + 4B)(n+/-) ions, as well as for deprotonated (S4 + 4Btl)(n-) ions, was loss of the ligand. However, subunit loss from the (S4 + 4B)(n+) ions was observed as a minor pathway. The (S4 + 4Btl)(n+) ions dissociated predominantly by the loss of free and ligand-bound subunit. The charge state of the complex and the collision energy were found to have little effect on the relative contribution of the different dissociation channels. Thermally-driven ligand migration between subunits was captured in the results of molecular dynamics simulations performed on protonated (CTB5 + 5GM1)(15+) ions (with a range of charge configurations) at 800 K. Notably, the migration pathway was found to be highly dependent on the charge configuration of the ion. The main conclusion of this study is that the dissociation pathways of multisubunit protein-ligand complexes in the gas phase depend, not only on the native topology of the complex, but also on structural changes that occur upon collisional activation.
Collapse
Affiliation(s)
- Yixuan Zhang
- Department of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
| | | | | | | |
Collapse
|
41
|
Deng L, Kitova EN, Klassen JS. Mapping protein-ligand interactions in the gas phase using a functional group replacement strategy. Comparison of CID and BIRD activation methods. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:988-996. [PMID: 23702709 DOI: 10.1007/s13361-013-0651-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 04/09/2013] [Accepted: 04/09/2013] [Indexed: 06/02/2023]
Abstract
Intermolecular interactions in the gaseous ions of two protein-ligand complexes, a single chain antibody (scFv) and its trisaccharide ligand (α-D-Galp-(1→2)-[α-D-Abep-(1→3)]-α-Manp-OCH3, L1) and streptavidin homotetramer (S4) and biotin (B), were investigated using a collision-induced dissociation (CID)-functional group replacement (FGR) strategy. CID was performed on protonated ions of a series of structurally related complexes based on the (scFv + L1) and (S4 + 4B) complexes, at the +10 and +13 charge states, respectively. Intermolecular interactions were identified from decreases in the collision energy required to dissociate 50% of the reactant ion (Ec50) upon modification of protein residues or ligand functional groups. For the (scFv + L1)(10+) ion, it was found that deoxygenation of L1 (at Gal C3 and C6 and Man C4 and C6) or mutation of His101 (to Ala) resulted in a decrease in Ec50 values. These results suggest that the four hydroxyl groups and His101 participate in intermolecular H-bonds. These findings agree with those obtained using the blackbody infrared radiative dissociation (BIRD)-FGR method. However, the CID-FGR method failed to reveal the relative strengths of the intermolecular interactions or establish Man C4 OH and His101 as an H-bond donor/acceptor pair. The CID-FGR method correctly identified Tyr43, but not Ser27, Trp79, and Trp120, as a stabilizing contact in the (S4 + 4B)(13+) ion. In fact, mutation of Trp79 and Trp120 led to an increase in the Ec50 value. Taken together, these results suggest that the CID-FGR method, as implemented here, does not represent a reliable approach for identifying interactions in the gaseous protein-ligand complexes.
Collapse
Affiliation(s)
- Lu Deng
- Department of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
| | | | | |
Collapse
|
42
|
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
|
43
|
Saracino GAA, Gelain F. Modelling and analysis of early aggregation events of BMHP1-derived self-assembling peptides. J Biomol Struct Dyn 2013; 32:759-75. [PMID: 23730849 DOI: 10.1080/07391102.2013.790848] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Despite the increasing use and development of peptide-based scaffolds in different fields including that of regenerative medicine, the understanding of the factors governing the self-assembly process and the relationship between sequence and properties have not yet been fully understood. BMHP1-derived self-assembling peptides (SAPs) have been developed and characterized showing that biotinylation at the N-terminal cap corresponds to better performing assembly and scaffold biomechanics. In this study, the effects of biotinylation on the self-assembly dynamics of seven BMHP1-derived SAPs have been investigated by molecular dynamics simulations. We confirmed that these SAPs self-assemble into β-structures and that proline acts as a β-breaker of the assembled aggregates. In biotinylated peptides, the formation of ordered β-structured aggregates is triggered by both the establishment of a dense and dynamic H-bonds network and the formation of a 'hydrophobic wall' available to interact with other peptides. Such conditions result from the peculiar chemical composition of the biotinyl-cap, given by the synergic cooperation of the uracil function of the ureido ring with the high hydrophobic portion consisting of the thiophenyl ring and valeryl chain. The inbuilt propensity of biotinylated peptides towards the formation of ordered small aggregates makes them ideal precursors of higher hierarchically organized self-assembled nanostructures as experimentally observed.
Collapse
Affiliation(s)
- Gloria Anna Ada Saracino
- a Center of Nanomedicine and Tissue Engineering A. O. Ospedale Niguarda Ca' Granda , Milan , 20162 Italy
| | | |
Collapse
|
44
|
Le Trong I, Chu V, Xing Y, Lybrand TP, Stayton PS, Stenkamp RE. Structural consequences of cutting a binding loop: two circularly permuted variants of streptavidin. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:968-77. [PMID: 23695241 PMCID: PMC3663120 DOI: 10.1107/s0907444913003855] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Accepted: 02/08/2013] [Indexed: 11/10/2022]
Abstract
Circular permutation of streptavidin was carried out in order to investigate the role of a main-chain amide in stabilizing the high-affinity complex of the protein and biotin. Mutant proteins CP49/48 and CP50/49 were constructed to place new N-termini at residues 49 and 50 in a flexible loop involved in stabilizing the biotin complex. Crystal structures of the two mutants show that half of each loop closes over the binding site, as observed in wild-type streptavidin, while the other half adopts the open conformation found in the unliganded state. The structures are consistent with kinetic and thermodynamic data and indicate that the loop plays a role in enthalpic stabilization of the bound state via the Asn49 amide-biotin hydrogen bond. In wild-type streptavidin, the entropic penalties of immobilizing a flexible portion of the protein to enhance binding are kept to a manageable level by using a contiguous loop of medium length (six residues) which is already constrained by its anchorage to strands of the β-barrel protein. A molecular-dynamics simulation for CP50/49 shows that cleavage of the binding loop results in increased structural fluctuations for Ser45 and that these fluctuations destabilize the streptavidin-biotin complex.
Collapse
Affiliation(s)
- Isolde Le Trong
- Department of Biological Structure, University of Washington, Box 357420, Seattle, WA 98195-7420, USA
- Biomolecular Structure Center, University of Washington, Box 357742, Seattle, WA 98195-7742, USA
| | - Vano Chu
- Department of Bioengineering, University of Washington, Box 355061, Seattle, WA 98195-5061, USA
| | - Yi Xing
- Department of Biological Structure, University of Washington, Box 357420, Seattle, WA 98195-7420, USA
| | - Terry P. Lybrand
- Center for Structural Biology, Department of Chemistry, Vanderbilt University, 5142 Medical Research Building III, 465 21st Avenue South, Nashville, TN 37232-8725, USA
| | - Patrick S. Stayton
- Department of Bioengineering, University of Washington, Box 355061, Seattle, WA 98195-5061, USA
| | - Ronald E. Stenkamp
- Department of Biological Structure, University of Washington, Box 357420, Seattle, WA 98195-7420, USA
- Biomolecular Structure Center, University of Washington, Box 357742, Seattle, WA 98195-7742, USA
- Department of Biochemistry, University of Washington, Box 357430, Seattle, WA 98195-7430, USA
| |
Collapse
|
45
|
Takakura Y, Sofuku K, Tsunashima M. Tamavidin 2-REV: An engineered tamavidin with reversible biotin-binding capability. J Biotechnol 2013; 164:19-25. [DOI: 10.1016/j.jbiotec.2013.01.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 12/28/2012] [Accepted: 01/09/2013] [Indexed: 11/29/2022]
|
46
|
Kim KW, Song J, Kee JS, Liu Q, Lo GQ, Park MK. Label-free biosensor based on an electrical tracing-assisted silicon microring resonator with a low-cost broadband source. Biosens Bioelectron 2013; 46:15-21. [PMID: 23500471 DOI: 10.1016/j.bios.2013.02.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 01/25/2013] [Accepted: 02/02/2013] [Indexed: 10/27/2022]
Abstract
We present a novel biosensor based on an electrical tracing-assisted silicon dual-microring resonator sensor system. The dual-microring system comprises one microring resonator as a sensing element and the other microring resonator integrated with an electrical controller as a tracing element. The resonance wavelength shift of the sensing microring induced by the refractive index change due to antigen-ligand bindings is traced and determined by direct voltage applied to the electrical tunable tracing microring. The sensor system enables the use of a low-cost broadband light source instead of a bulky and expensive tunable laser, which allows the development of cost-effective point-of-care diagnostic devices by significantly reducing the device cost and increasing its portability. The sensing capability of the developed dual-microring sensor was investigated using biotin-streptavidin binding as a model system. We have demonstrated the quantitative detection of streptavidin over a broad range of concentrations down to 190 pM by monitoring the electrical power applied to the tracing ring. We have also validated the sensing principle of the dual-microring system by a direct comparison between the calculated and measured values for the resonance wavelength shift of the sensing microring. Furthermore, we have shown the quantitative and specific detection of a well-known breast cancer biomarker, human epidermal growth factor receptor 2 (HER2), in a bovine serum albumin solution using the antibody-modified dual-microring sensor system.
Collapse
Affiliation(s)
- Kyung Woo Kim
- Institute of Microelectronics, A*STAR (Agency for Science, Technology and Research), 11 Science Park Road, Singapore Science Park II, Singapore 117685, Singapore
| | | | | | | | | | | |
Collapse
|
47
|
Hong H, Chang YC, Bowie JU. Measuring transmembrane helix interaction strengths in lipid bilayers using steric trapping. Methods Mol Biol 2013; 1063:37-56. [PMID: 23975771 DOI: 10.1007/978-1-62703-583-5_3] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We have developed a method to measure strong transmembrane (TM) helix interaction affinities in lipid bilayers that are difficult to measure by traditional dilution methods. The method, called steric trapping, couples dissociation of biotinylated TM helices to a competitive binding by monovalent streptavidin (mSA), so that dissociation is driven by the affinity of mSA for biotin and mSA concentration. By adjusting the binding affinity of mSA through mutation, the method can obtain dissociation constants of TM helix dimers (K d,dimer) over a range of six orders of magnitudes. The K d,dimer limit of measurable target interaction is extended 3-4 orders of magnitude lower than possible by dilution methods. Thus, steric trapping opens up new opportunities to study the folding and assembly of α-helical membrane proteins in lipid bilayer environments. Here we provide detailed methods for applying steric trapping to a TM helix dimer.
Collapse
Affiliation(s)
- Heedeok Hong
- Department of Chemistry, Michigan State University, East Lansing, MI, USA
| | | | | |
Collapse
|
48
|
Deng L, Kitova EN, Klassen JS. Dissociation kinetics of the streptavidin-biotin interaction measured using direct electrospray ionization mass spectrometry analysis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:49-56. [PMID: 23247970 DOI: 10.1007/s13361-012-0533-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Revised: 10/31/2012] [Accepted: 11/02/2012] [Indexed: 06/01/2023]
Abstract
Dissociation rate constants (k (off)) for the model high affinity interaction between biotin (B) and the homotetramer of natural core streptavidin (S(4)) were measured at pH 7 and temperatures ranging from 15 to 45 °C using electrospray ionization mass spectrometry (ESI-MS). Two different approaches to data analysis were employed, one based on the initial rate of dissociation of the (S(4) + 4B) complex, the other involving nonlinear fitting of the time-dependent relative abundances of the (S(4) + iB) species. The two methods were found to yield k (off) values that are in good agreement, within a factor of two. The Arrhenius parameters for the dissociation of the biotin-streptavidin interaction in solution were established from the k (off) values determined by ESI-MS and compared with values measured using a radiolabeled biotin assay. Importantly, the dissociation activation energies determined by ESI-MS agree, within 1 kcal mol(-1), with the reported value. In addition to providing a quantitative measure of k (off), the results of the ESI-MS measurements revealed that the apparent cooperative distribution of (S(4) + iB) species observed at short reaction times is of kinetic origin and that sequential binding of B to S(4) occurs in a noncooperative fashion with the four ligand binding sites being kinetically and thermodynamically equivalent and independent.
Collapse
Affiliation(s)
- Lu Deng
- Department of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | | | | |
Collapse
|
49
|
Specific interactions between adenosine and streptavidin/avidin. Bioorg Med Chem Lett 2012; 22:7052-5. [PMID: 23084893 DOI: 10.1016/j.bmcl.2012.09.088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Revised: 09/18/2012] [Accepted: 09/25/2012] [Indexed: 11/22/2022]
Abstract
The screening of ligands against proteins plays important role in drug discovery and biological research. Using a dye labelled Streptavidin binding aptamer (SBA) as a competitive reporter probe, we found that adenosine bound to streptavidin specifically. Fluorescence spectral analysis showed that adenosine bound to both avidin and streptavidin with the K(ds) in the range of 0.1-0.2 mM, and these bindings can be blocked by biotin. Although streptavidin and avidin are well-known and widely used in bioanalysis, their biological role is still a riddle so far. Since adenosine is a ubiquitous physiological regulator present in cells, our finding provides new clues for the understanding of the functions of both proteins.
Collapse
|
50
|
Kinetic Stability of the Streptavidin–Biotin Interaction Enhanced in the Gas Phase. J Am Chem Soc 2012; 134:16586-96. [DOI: 10.1021/ja305213z] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
|