1
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Anderson GP, Shriver-Lake LC, Liu JL, Goldman ER. Integrating Single Domain Antibodies into Field-Deployable Rapid Assays. Antibodies (Basel) 2022; 11:antib11040064. [PMID: 36278617 PMCID: PMC9624348 DOI: 10.3390/antib11040064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 09/25/2022] [Accepted: 10/08/2022] [Indexed: 12/03/2022] Open
Abstract
Single domain antibodies (sdAb) are the recombinant variable heavy domains derived from camelid heavy-chain antibodies. While they have binding affinities equivalent to conventional antibodies, sdAb are only one-tenth the size and possess numerous advantages such as excellent thermal stability with the ability to refold following denaturation, and inexpensive production in Escherichia coli or yeast. However, their small size does have drawbacks, one being that they can lose activity upon attachment or adsorption to surfaces, or may fail to adsorb efficiently, as they are highly soluble. This can make the transition from using conventional antibodies to sdAb nontrivial for assay development. Specifically, it is often necessary to re-optimize the protocols and tailor the recombinant sdAb through protein engineering to function efficiently in handheld assays, which currently are utilized for point of care testing and field applications. This work focuses on optimizing the integration of sdAb into rapid vertical flow assays. To achieve this goal, we engineered sdAb-based constructs and developed general protocols for the attachment of the sdAb to both gold nanoparticles and a support membrane. We achieved a limit of detection of 0.11 µg/mL for toxins staphylococcal enterotoxin B and ricin, both potential biothreat agents. Additionally, we demonstrated the ability to detect the nucleocapsid protein of SARS-CoV-2, a common target of antigen tests for COVID-19.
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2
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Liu JL, Webb EM, Zabetakis D, Burke CW, Gardner CL, Glass PJ, Legler PM, Weger-Lucarelli J, Anderson GP, Goldman ER. Stabilization of a Broadly Neutralizing Anti-Chikungunya Virus Single Domain Antibody. Front Med (Lausanne) 2021; 8:626028. [PMID: 33585527 PMCID: PMC7876468 DOI: 10.3389/fmed.2021.626028] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 01/04/2021] [Indexed: 12/31/2022] Open
Abstract
A single domain antibody (clone CC3) previously found to neutralize a vaccine strain of the chikungunya virus (PRNT50 = 2. 5 ng/mL) was found to be broadly neutralizing. Clone CC3 is not only able to neutralize a wild-type (WT) strain of chikungunya virus (CHIKV), but also neutralizes WT strains of Mayaro virus (MAYV) and Ross River virus (RRV); both arthralgic, Old World alphaviruses. Interestingly, CC3 also demonstrated a degree of neutralizing activity against the New World alphavirus, Venezuelan equine encephalitis virus (VEEV); albeit both the vaccine strain, TC-83, and the parental, WT Trinidad donkey strain had PRNT50 values ~1,000-fold higher than that of CHIKV. However, no neutralization activity was observed with Western equine encephalitis virus (WEEV). Ten CC3 variants designed to possess a range of isoelectric points, both higher and lower, were constructed. This approach successfully identified several lower pI mutants which possessed improved thermal stabilities by as much as 10°C over the original CC3 (Tm = 62°C), and excellent refolding abilities while maintaining their capacity to bind and neutralize CHIKV.
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Affiliation(s)
- Jinny L Liu
- U.S. Naval Research Laboratory, Center for BioMolecular Science and Engineering, Washington, DC, United States
| | - Emily M Webb
- Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Dan Zabetakis
- U.S. Naval Research Laboratory, Center for BioMolecular Science and Engineering, Washington, DC, United States
| | - Crystal W Burke
- Virology Division, U.S. Army Medical Research Institute for Infectious Diseases, Fort Detrick, MD, United States
| | - Christina L Gardner
- Virology Division, U.S. Army Medical Research Institute for Infectious Diseases, Fort Detrick, MD, United States
| | - Pamela J Glass
- Virology Division, U.S. Army Medical Research Institute for Infectious Diseases, Fort Detrick, MD, United States
| | - Patricia M Legler
- U.S. Naval Research Laboratory, Center for BioMolecular Science and Engineering, Washington, DC, United States
| | | | - George P Anderson
- U.S. Naval Research Laboratory, Center for BioMolecular Science and Engineering, Washington, DC, United States
| | - Ellen R Goldman
- U.S. Naval Research Laboratory, Center for BioMolecular Science and Engineering, Washington, DC, United States
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3
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Esparza TJ, Martin NP, Anderson GP, Goldman ER, Brody DL. High affinity nanobodies block SARS-CoV-2 spike receptor binding domain interaction with human angiotensin converting enzyme. Sci Rep 2020; 10:22370. [PMID: 33353972 PMCID: PMC7755911 DOI: 10.1038/s41598-020-79036-0] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 11/25/2020] [Indexed: 12/21/2022] Open
Abstract
There are currently few approved effective treatments for SARS-CoV-2, the virus responsible for the COVID-19 pandemic. Nanobodies are 12–15 kDa single-domain antibody fragments that can be delivered by inhalation and are amenable to relatively inexpensive large scale production compared to other biologicals. We have isolated nanobodies that bind to the SARS-CoV-2 spike protein receptor binding domain and block spike protein interaction with the angiotensin converting enzyme 2 (ACE2) with 1–5 nM affinity. The lead nanobody candidate, NIH-CoVnb-112, blocks SARS-CoV-2 spike pseudotyped lentivirus infection of HEK293 cells expressing human ACE2 with an EC50 of 0.3 µg/mL. NIH-CoVnb-112 retains structural integrity and potency after nebulization. Furthermore, NIH-CoVnb-112 blocks interaction between ACE2 and several high affinity variant forms of the spike protein. These nanobodies and their derivatives have therapeutic, preventative, and diagnostic potential.
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Affiliation(s)
- Thomas J Esparza
- Laboratory of Functional and Molecular Imaging, The National Institute of Neurological Disorders and Stroke Intramural Research Program, Bethesda, MD, 20892, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20892, USA
| | - Negin P Martin
- Viral Vector Core, National Institute of Environmental Health Sciences, NIH/DHHS, Research Triangle Park, NC, 27709, USA.,Neurobiology Laboratory, National Institute of Environmental Health Sciences, NIH/DHHS, Research Triangle Park, NC, 27709, USA
| | - George P Anderson
- Center for Biomolecular Science and Engineering, US Naval Research Laboratory, Washington, DC, 20375, USA
| | - Ellen R Goldman
- Center for Biomolecular Science and Engineering, US Naval Research Laboratory, Washington, DC, 20375, USA
| | - David L Brody
- Laboratory of Functional and Molecular Imaging, The National Institute of Neurological Disorders and Stroke Intramural Research Program, Bethesda, MD, 20892, USA. .,Department of Neurology, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA.
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4
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Liu JL, Zabetakis D, Breger JC, Anderson GP, Goldman ER. Multi-Enzyme Assembly on T4 Phage Scaffold. Front Bioeng Biotechnol 2020; 8:571. [PMID: 32671028 PMCID: PMC7327620 DOI: 10.3389/fbioe.2020.00571] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 05/12/2020] [Indexed: 01/11/2023] Open
Abstract
Over the past two decades, various scaffolds have been designed and synthesized to organize enzyme cascades spatially for enhanced enzyme activity based on the concepts of substrate channeling and enhanced stability. The most bio-compatible synthetic scaffolds known for enzyme immobilization are protein and DNA nanostructures. Herein, we examined the utility of the T4 phage capsid to serve as a naturally occurring protein scaffold for the immobilization of a three-enzyme cascade: Amylase, Maltase, and Glucokinase. Covalent constructs between each of the enzymes and the outer capsid protein Hoc were prepared through SpyTag-SpyCatcher pairing and assembled onto phage capsids in vitro with an estimated average of 90 copies per capsid. The capsid-immobilized Maltase has a fourfold higher initial rate relative to Maltase free in solution. Kinetic analysis also revealed that the immobilized three-enzyme cascade has an 18-fold higher converted number of NAD+ to NADH relative to the mixtures in solution. Our results demonstrate that the T4 phage capsid can act as a naturally occurring scaffold with substantial potential to enhance enzyme activity by spatially organizing enzymes on the capsid Hoc.
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Affiliation(s)
- Jinny L Liu
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, United States
| | - Daniel Zabetakis
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, United States
| | - Joyce C Breger
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, United States
| | - George P Anderson
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, United States
| | - Ellen R Goldman
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, United States
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5
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Shriver-Lake LC, Goldman ER, Dean SN, Liu JL, Davis TM, Anderson GP. Lipid-tagged single domain antibodies for improved enzyme-linked immunosorbent assays. J Immunol Methods 2020; 481-482:112790. [PMID: 32422135 DOI: 10.1016/j.jim.2020.112790] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 04/23/2020] [Accepted: 05/03/2020] [Indexed: 10/24/2022]
Abstract
Anti-Staphylococcal Enterotoxin B single domain antibodies were engineered to include the N-terminal peptide sequence of the major outer membrane lipoprotein from Escherichia coli, which directs the N-terminal addition of lipid to the single domain antibody. We produced and purified two different single domain antibodies as well as a variant and dimer construct of one of the two, all with and without the added lipid. Their ability to function as the capture antibody in standard enzyme-linked immunosorbent assays were evaluated, finding that coating polystyrene microtiter plates with the lipid-tagged single domain antibodies gave a 3-fold improvement in the observed limit of detection. This increase was likely due to an increased amount of single domain antibody adsorbed to the microtiter plate, which translated to improved limits of detection of Staphylococcal Enterotoxin B over using the same single domain antibody sans lipid-tag. However, improved orientation may also play a role. Regardless of the mechanism, the biosynthetic lipid-tagging of single domain antibodies represent a facile modality that can enhance their ability to be utilized as immunoassay capture reagent as well as facilitate their incorporation into liposome targeting applications in the future.
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Affiliation(s)
- Lisa C Shriver-Lake
- Naval Research Laboratory, Center for Biomolecular Science and Engineering, Washington, DC 20375, USA
| | - Ellen R Goldman
- Naval Research Laboratory, Center for Biomolecular Science and Engineering, Washington, DC 20375, USA
| | - Scott N Dean
- Naval Research Laboratory, Center for Biomolecular Science and Engineering, Washington, DC 20375, USA
| | - Jinny L Liu
- Naval Research Laboratory, Center for Biomolecular Science and Engineering, Washington, DC 20375, USA
| | - Tamiya M Davis
- Naval Research Laboratory, Center for Biomolecular Science and Engineering, Washington, DC 20375, USA; The Washington Center for Internships and Academic Seminars, 1333 16th Street N.W.,Washington, DC 20036, USA
| | - George P Anderson
- Naval Research Laboratory, Center for Biomolecular Science and Engineering, Washington, DC 20375, USA.
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6
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Zabetakis D, Shriver-Lake LC, Olson MA, Goldman ER, Anderson GP. Experimental evaluation of single-domain antibodies predicted by molecular dynamics simulations to have elevated thermal stability. Protein Sci 2019; 28:1909-1912. [PMID: 31342597 DOI: 10.1002/pro.3692] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 07/12/2019] [Accepted: 07/16/2019] [Indexed: 01/07/2023]
Abstract
Recently Bekker et al. [Bekker G-J et al. Protein Sci. 2019;28:429-438.] described a computational strategy of applying molecular-dynamics simulations to estimate the relative stabilities of single-domain antibodies, and utilized their method to design changes with the aim of increasing the stability of a single-domain antibody with a known crystal structure. The structure from which they generated potentially stabilizing mutations is an anti-cholera toxin single domain antibody selected from a naïve library which has relatively low thermal stability, reflected by a melting point of 48°C. Their work was purely theoretical, so to examine their predictions, we prepared the parental and predicted stabilizing mutant single domain antibodies and examined their thermal stability, ability to refold and affinity. We found that the mutation that improved stability the most (~7°C) was one which changed an amino acid in CDR1 from an asparagine to an aspartic acid. This change unfortunately was also accompanied by a reduction in affinity. Thus, while their modeling did appear to successfully predict stabilizing mutations, introducing mutations in the binding regions is problematic. Of further interest, the mutations selected via their high temperature simulations, did improve refolding, suggesting that they were successful in stabilizing the structure at high temperatures and thereby decrease aggregation. Our result should permit them to reassess and refine their model and may one day lead to a usefulin silico approach to protein stabilization.
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Affiliation(s)
- Dan Zabetakis
- Center for Biomolecular Science and Engineering, Naval Research Laboratory, Washington, District of Columbia
| | - Lisa C Shriver-Lake
- Center for Biomolecular Science and Engineering, Naval Research Laboratory, Washington, District of Columbia
| | - Mark A Olson
- Systems and Structural Biology Division, USAMRIID, Frederick, Maryland
| | - Ellen R Goldman
- Center for Biomolecular Science and Engineering, Naval Research Laboratory, Washington, District of Columbia
| | - George P Anderson
- Center for Biomolecular Science and Engineering, Naval Research Laboratory, Washington, District of Columbia
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7
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Anderson GP, Liu JL, Shriver-Lake LC, Zabetakis D, Sugiharto VA, Chen HW, Lee CR, Defang GN, Wu SJL, Venkateswaran N, Goldman ER. Oriented Immobilization of Single-Domain Antibodies Using SpyTag/SpyCatcher Yields Improved Limits of Detection. Anal Chem 2019; 91:9424-9429. [DOI: 10.1021/acs.analchem.9b02096] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- George P. Anderson
- Center for Biomolecular Science and Engineering, U.S. Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, D.C. 20375, United States
| | - Jinny L. Liu
- Center for Biomolecular Science and Engineering, U.S. Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, D.C. 20375, United States
| | - Lisa C. Shriver-Lake
- Center for Biomolecular Science and Engineering, U.S. Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, D.C. 20375, United States
| | - Dan Zabetakis
- Center for Biomolecular Science and Engineering, U.S. Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, D.C. 20375, United States
| | - Victor A. Sugiharto
- Viral and Rickettsial Diseases Department, Naval Medical Research Center, 503 Robert Grant Avenue, Silver Spring, Maryland 20910, United States
- Henry M. Jackson Foundation for the Advancement of Military Medicine, 6720A Rockledge Drive, Bethesda, Maryland 20817, United States
| | - Hua-Wei Chen
- Viral and Rickettsial Diseases Department, Naval Medical Research Center, 503 Robert Grant Avenue, Silver Spring, Maryland 20910, United States
- Henry M. Jackson Foundation for the Advancement of Military Medicine, 6720A Rockledge Drive, Bethesda, Maryland 20817, United States
| | - Cheng-Rei Lee
- Viral and Rickettsial Diseases Department, Naval Medical Research Center, 503 Robert Grant Avenue, Silver Spring, Maryland 20910, United States
- Henry M. Jackson Foundation for the Advancement of Military Medicine, 6720A Rockledge Drive, Bethesda, Maryland 20817, United States
| | - Gabriel N. Defang
- Viral and Rickettsial Diseases Department, Naval Medical Research Center, 503 Robert Grant Avenue, Silver Spring, Maryland 20910, United States
| | - Shuenn-Jue L. Wu
- Viral and Rickettsial Diseases Department, Naval Medical Research Center, 503 Robert Grant Avenue, Silver Spring, Maryland 20910, United States
| | - Neeraja Venkateswaran
- Tetracore, Inc., 9901 Belward Campus Drive, Suite 300, Rockville, Maryland 20850, United States
| | - Ellen R. Goldman
- Center for Biomolecular Science and Engineering, U.S. Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, D.C. 20375, United States
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8
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Olson MA, Legler PM, Zabetakis D, Turner KB, Anderson GP, Goldman ER. Sequence Tolerance of a Single-Domain Antibody with a High Thermal Stability: Comparison of Computational and Experimental Fitness Profiles. ACS Omega 2019; 4:10444-10454. [PMID: 31460140 PMCID: PMC6648363 DOI: 10.1021/acsomega.9b00730] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 05/09/2019] [Indexed: 06/10/2023]
Abstract
The sequence fitness of a llama single-domain antibody with an unusually high thermal stability is explored by a combined computational and experimental study. Starting with the X-ray crystallographic structure, RosettaBackrub simulations were applied to model sequence-structure tolerance profiles and identify key substitution sites. From the model calculations, an experimental site-directed mutagenesis was used to produce a panel of mutants, and their melting temperatures were determined by thermal denaturation. The results reveal a sequence fitness of an excess stability of approximately 12 °C, a value taken from a decrease in the melting temperature of an electrostatic charge-reversal substitution in the CRD3 without a deleterious effect on the binding affinity to the antigen. The tolerance for the disruption of antigen recognition without loss in the thermal stability was demonstrated by the introduction of a proline in place of a tyrosine in the CDR2, producing a mutant that eliminated binding. To further assist the sequence design and the selection of engineered single-domain antibodies, an assessment of different computational strategies is provided of their accuracy in the detection of substitution "hot spots" in the sequence tolerance landscape.
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Affiliation(s)
- Mark A. Olson
- Systems
and Structural Biology Division, USAMRIID, Frederick, Maryland 21702, United States
| | - Patricia M. Legler
- Center
for Bio/Molecular Science and Engineering, Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, District of Columbia 20375, United States
| | - Daniel Zabetakis
- Center
for Bio/Molecular Science and Engineering, Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, District of Columbia 20375, United States
| | - Kendrick B. Turner
- Center
for Bio/Molecular Science and Engineering, Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, District of Columbia 20375, United States
| | - George P. Anderson
- Center
for Bio/Molecular Science and Engineering, Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, District of Columbia 20375, United States
| | - Ellen R. Goldman
- Center
for Bio/Molecular Science and Engineering, Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, District of Columbia 20375, United States
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9
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Shriver-Lake LC, Liu JL, Zabetakis D, Sugiharto VA, Lee CR, Defang GN, Wu SJL, Anderson GP, Goldman ER. Selection and Characterization of Anti-Dengue NS1 Single Domain Antibodies. Sci Rep 2018; 8:18086. [PMID: 30591706 PMCID: PMC6308234 DOI: 10.1038/s41598-018-35923-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 11/13/2018] [Indexed: 01/13/2023] Open
Abstract
Reliable detection and diagnosis of dengue virus (DENV) is important for both patient care and epidemiological control. Starting with a llama immunized with a mixture of recombinant nonstructural protein 1 (NS1) antigen from the four DENV serotypes, a phage display immune library of single domain antibodies was constructed and binders selected which exhibited specificity and affinity for DENV NS1. Each of these single domain antibodies was evaluated for its binding affinity to NS1 from the four serotypes, and incorporated into a sandwich format for NS1 detection. An optimal pair was chosen that provided the best combination of sensitivity for all four DENV NS1 antigens spiked into 50% human serum while showing no cross reactivity to NS1 from Zika virus, yellow fever virus, tick-borne encephalitis virus, and minimal binding to NS1 from Japanese encephalitis virus and West Nile virus. These rugged and robust recombinant binding molecules offer attractive alternatives to conventional antibodies for implementation into immunoassays destined for resource limited locals.
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Affiliation(s)
- Lisa C Shriver-Lake
- Center for Biomolecular Science and Engineering, US Naval Research Laboratory, 4555 Overlook Ave SW, Washington, DC, 20375, USA
| | - Jinny L Liu
- Center for Biomolecular Science and Engineering, US Naval Research Laboratory, 4555 Overlook Ave SW, Washington, DC, 20375, USA
| | - Dan Zabetakis
- Center for Biomolecular Science and Engineering, US Naval Research Laboratory, 4555 Overlook Ave SW, Washington, DC, 20375, USA
| | - Victor A Sugiharto
- Viral and Rickettsial Diseases Department, Naval Medical Research Center, 503 Robert Grant Avenue, Silver Spring, MD, 20910, USA
| | - Cheng-Rei Lee
- Viral and Rickettsial Diseases Department, Naval Medical Research Center, 503 Robert Grant Avenue, Silver Spring, MD, 20910, USA
| | - Gabriel N Defang
- Viral and Rickettsial Diseases Department, Naval Medical Research Center, 503 Robert Grant Avenue, Silver Spring, MD, 20910, USA
| | - Shuenn-Jue L Wu
- Viral and Rickettsial Diseases Department, Naval Medical Research Center, 503 Robert Grant Avenue, Silver Spring, MD, 20910, USA
| | - George P Anderson
- Center for Biomolecular Science and Engineering, US Naval Research Laboratory, 4555 Overlook Ave SW, Washington, DC, 20375, USA
| | - Ellen R Goldman
- Center for Biomolecular Science and Engineering, US Naval Research Laboratory, 4555 Overlook Ave SW, Washington, DC, 20375, USA.
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10
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Liu JL, Shriver-Lake LC, Zabetakis D, Goldman ER, Anderson GP. Selection of Single-Domain Antibodies towards Western Equine Encephalitis Virus. Antibodies (Basel) 2018; 7:E44. [PMID: 31544894 PMCID: PMC6698954 DOI: 10.3390/antib7040044] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 12/12/2018] [Accepted: 12/12/2018] [Indexed: 12/21/2022] Open
Abstract
In this work, we describe the selection and characterization of single-domain antibodies (sdAb) towards the E2/E3E2 envelope protein of the Western equine encephalitis virus (WEEV). Our purpose was to identify novel recognition elements which could be used for the detection, diagnosis, and perhaps treatment of western equine encephalitis (WEE). To achieve this goal, we prepared an immune phage display library derived from the peripheral blood lymphocytes of a llama that had been immunized with an equine vaccine that includes killed WEEV (West Nile Innovator + VEWT). This library was panned against recombinant envelope (E2/E3E2) protein from WEEV, and seven representative sdAb from the five identified sequence families were characterized. The specificity, affinity, and melting point of each sdAb was determined, and their ability to detect the recombinant protein in a MagPlex sandwich immunoassay was confirmed. Thus, these new binders represent novel recognition elements for the E2/E3E2 proteins of WEEV that are available to the research community for further investigation into their applicability for use in the diagnosis or treatment of WEE.
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Affiliation(s)
- Jinny L Liu
- Naval Research Laboratory, Center for Biomolecular Science and Engineering, Washington, DC 20375, USA.
| | - Lisa C Shriver-Lake
- Naval Research Laboratory, Center for Biomolecular Science and Engineering, Washington, DC 20375, USA.
| | - Dan Zabetakis
- Naval Research Laboratory, Center for Biomolecular Science and Engineering, Washington, DC 20375, USA.
| | - Ellen R Goldman
- Naval Research Laboratory, Center for Biomolecular Science and Engineering, Washington, DC 20375, USA.
| | - George P Anderson
- Naval Research Laboratory, Center for Biomolecular Science and Engineering, Washington, DC 20375, USA.
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11
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Anderson GP, Shriver-Lake LC, Walper SA, Ashford L, Zabetakis D, Liu JL, Breger JC, Brozozog Lee PA, Goldman ER. Genetic Fusion of an Anti-BclA Single-Domain Antibody with Beta Galactosidase. Antibodies (Basel) 2018; 7:antib7040036. [PMID: 31544886 PMCID: PMC6698959 DOI: 10.3390/antib7040036] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 09/26/2018] [Accepted: 09/27/2018] [Indexed: 02/06/2023] Open
Abstract
The Bacillus collagen-like protein of anthracis (BclA), found in Bacillus anthracis spores, is an attractive target for immunoassays. Previously, using phage display we had selected llama-derived single-domain antibodies that bound to B. anthracis spore proteins including BclA. Single-domain antibodies (sdAbs), the recombinantly expressed heavy domains from the unique heavy-chain-only antibodies found in camelids, provide stable and well-expressed binding elements with excellent affinity. In addition, sdAbs offer the important advantage that they can be tailored for specific applications through protein engineering. A fusion of a BclA targeting sdAb with the enzyme Beta galactosidase (β-gal) would enable highly sensitive immunoassays with no need for a secondary reagent. First, we evaluated five anti-BclA sdAbs, including four that had been previously identified but not characterized. Each was tested to determine its binding affinity, melting temperature, producibility, and ability to function as both capture and reporter in sandwich assays for BclA. The sdAb with the best combination of properties was constructed as a fusion with β-gal and shown to enable sensitive detection. This fusion has the potential to be incorporated into highly sensitive assays for the detection of anthrax spores.
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Affiliation(s)
- George P Anderson
- Naval Research Laboratory, Center for Biomolecular Science and Engineering, Washington, DC 20375, USA.
| | - Lisa C Shriver-Lake
- Naval Research Laboratory, Center for Biomolecular Science and Engineering, Washington, DC 20375, USA.
| | - Scott A Walper
- Naval Research Laboratory, Center for Biomolecular Science and Engineering, Washington, DC 20375, USA.
| | - Lauryn Ashford
- The Washington Center for Internships and Academic Seminars, 1333 16th Street N.W., Washington, DC 20036, USA.
| | - Dan Zabetakis
- Naval Research Laboratory, Center for Biomolecular Science and Engineering, Washington, DC 20375, USA.
| | - Jinny L Liu
- Naval Research Laboratory, Center for Biomolecular Science and Engineering, Washington, DC 20375, USA.
| | - Joyce C Breger
- Naval Research Laboratory, Center for Biomolecular Science and Engineering, Washington, DC 20375, USA.
| | | | - Ellen R Goldman
- Naval Research Laboratory, Center for Biomolecular Science and Engineering, Washington, DC 20375, USA.
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12
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Raghu D, Christodoulides JA, Christophersen M, Liu JL, Anderson GP, Robitaille M, Byers JM, Raphael MP. Nanoplasmonic pillars engineered for single exosome detection. PLoS One 2018; 13:e0202773. [PMID: 30142169 PMCID: PMC6108516 DOI: 10.1371/journal.pone.0202773] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 08/08/2018] [Indexed: 11/18/2022] Open
Abstract
Exosomes are secreted nanovesicles which incorporate proteins and nucleic acids, thereby enabling multifunctional pathways for intercellular communication. There is an increasing appreciation of the critical role they play in fundamental processes such as development, wound healing and disease progression, yet because of their heterogeneous molecular content and low concentrations in vivo, their detection and characterization remains a challenge. In this work we combine nano- and microfabrication techniques for the creation of nanosensing arrays tailored toward single exosome detection. Elliptically–shaped nanoplasmonic sensors are fabricated to accommodate at most one exosome and individually imaged in real time, enabling the label-free recording of digital responses in a highly multiplexed geometry. This approach results in a three orders of magnitude sensitivity improvement over previously reported real-time, multiplexed platforms. Each nanosensor is elevated atop a quartz nanopillar, minimizing unwanted nonspecific substrate binding contributions. The approach is validated with the detection of exosomes secreted by MCF7 breast adenocarcinoma cells. We demonstrate the increasingly digital and stochastic nature of the response as the number of subsampled nanosensors is reduced from four hundred to one.
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Affiliation(s)
- Deepa Raghu
- Materials Science and Technology Division, Naval Research Laboratory, Washington, D.C., United States of America
| | - Joseph A. Christodoulides
- Materials Science and Technology Division, Naval Research Laboratory, Washington, D.C., United States of America
| | - Marc Christophersen
- Space Sciences Division, Naval Research Laboratory, Washington, D.C., United States of America
| | - Jinny L. Liu
- Center for Biomolecular Science & Engineering, Naval Research Laboratory, Washington, D.C., United States of America
| | - George P. Anderson
- Center for Biomolecular Science & Engineering, Naval Research Laboratory, Washington, D.C., United States of America
| | - Michael Robitaille
- Materials Science and Technology Division, Naval Research Laboratory, Washington, D.C., United States of America
| | - Jeff M. Byers
- Materials Science and Technology Division, Naval Research Laboratory, Washington, D.C., United States of America
| | - Marc P. Raphael
- Materials Science and Technology Division, Naval Research Laboratory, Washington, D.C., United States of America
- * E-mail:
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13
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Liu JL, Raghu D, Anderson GP, Goldman ER, Christodoulides JA, Raphael MP. Improving biosensing activity to carcinoembryonic antigen with orientated single domain antibodies. Heliyon 2017; 3:e00478. [PMID: 29423452 PMCID: PMC5772350 DOI: 10.1016/j.heliyon.2017.e00478] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 11/06/2017] [Accepted: 11/29/2017] [Indexed: 01/08/2023] Open
Abstract
Carcinoembryonic antigen (CEA), also referred as CEACAM5, is integral to the adhesion process during cancer invasion and metastasis and is one of the most widely used tumor markers for assisting the diagnosis of cancer recurrence and cancer metastasis. Antibodies against CEA molecules have been developed for detection and diagnostic applications following tumor removal. Single domain antibodies (sdAbs) against CEA isolated from dromedary and llama exhibited high specificity in binding to tumor cells. However, because these CEA sdAbs were not designed to be orientated when conjugated to surface sensors, there is potential for significant improvements in their activity and limit of detection. Herein we modified the CEA sdAbs with two different C-terminal fusions designed to aid with orientation by way of the tail’s charge and biotin binding. A fusion which incorporated the C-terminus addition of a positively charged tail (B5-GS3K) improved biosensor sensitivity to CEA while also retaining the sub-nanomolar binding affinity and thermal stability of the unmodified sdAb. Using our fabricated surfaces on bare gold chips and a multiplexed surface plasmon resonance imager (SPRi), we quantified the specific binding activities, defined as the percentage of bound epitopes to the total immobilized, of the sdAb fusions and anti-CEA mAb. Our results demonstrate that monovalent B5-GS3K exhibited significantly improved binding activity, approximately 3-fold higher than bivalent mAb.
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Affiliation(s)
- Jinny L Liu
- Center for Biomolecular Science & Engineering, Naval Research Laboratory, Washington, DC 20375, United States
| | - Deepa Raghu
- BioReliance, Sigma-Aldrich Corp, 14920 Broschart Road, Rockville, MD 20850, United States
| | - George P Anderson
- Center for Biomolecular Science & Engineering, Naval Research Laboratory, Washington, DC 20375, United States
| | - Ellen R Goldman
- Center for Biomolecular Science & Engineering, Naval Research Laboratory, Washington, DC 20375, United States
| | - Joseph A Christodoulides
- Materials Science and Technology Division, Naval Research Laboratory, Washington, DC 20375, United States
| | - Marc P Raphael
- Materials Science and Technology Division, Naval Research Laboratory, Washington, DC 20375, United States
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14
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Goldman ER, Broussard A, Anderson GP, Liu JL. Bglbrick strategy for the construction of single domain antibody fusions. Heliyon 2017; 3:e00474. [PMID: 29322100 PMCID: PMC5753753 DOI: 10.1016/j.heliyon.2017.e00474] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 11/07/2017] [Accepted: 11/27/2017] [Indexed: 11/30/2022] Open
Abstract
Single domain antibodies, recombinantly expressed variable domains derived from camelid heavy chain antibodies, are often expressed as multimers for detection and therapeutic applications. Constructs in which several single domain antibodies are genetically fused serially, as well as those in which single domain antibodies are genetically linked with domains that naturally form multimers, yield improvement in apparent binding affinity due to avidity. Here, using a single domain antibody that binds envelope protein from the Dengue virus, we demonstrated the construction of single domain antibody dimers using the Bglbrick cloning strategy. Constructing single domain antibodies and multimerization domains as Bglbrick parts enables the easy mixing and matching of parts. The dimeric constructs provided enhanced fluorescent signal in assays for detection of Dengue virus like particles over the monomeric single domain antibody.
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Affiliation(s)
- Ellen R Goldman
- US Naval Research Laboratory, Center for Biomolecular Science and Engineering, 4555 Overlook Ave SW, Washington DC 20375, USA
| | - Aeris Broussard
- US Naval Research Laboratory, Historically Black Colleges and Universities/Minority Institutions Summer Internship Program, 4555 Overlook Ave SW, Washington, DC 20375, USA
| | - George P Anderson
- US Naval Research Laboratory, Center for Biomolecular Science and Engineering, 4555 Overlook Ave SW, Washington DC 20375, USA
| | - Jinny L Liu
- US Naval Research Laboratory, Center for Biomolecular Science and Engineering, 4555 Overlook Ave SW, Washington DC 20375, USA
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15
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Liu JL, Shriver-Lake LC, Anderson GP, Zabetakis D, Goldman ER. Selection, characterization, and thermal stabilization of llama single domain antibodies towards Ebola virus glycoprotein. Microb Cell Fact 2017; 16:223. [PMID: 29233140 PMCID: PMC5726015 DOI: 10.1186/s12934-017-0837-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 11/28/2017] [Indexed: 12/26/2022] Open
Abstract
Background A key advantage of recombinant antibody technology is the ability to optimize and tailor reagents. Single domain antibodies (sdAbs), the recombinantly produced variable domains derived from camelid and shark heavy chain antibodies, provide advantages of stability and solubility and can be further engineered to enhance their properties. In this study, we generated sdAbs specific for Ebola virus envelope glycoprotein (GP) and increased their stability to expand their utility for use in austere locals. Ebola virus is extremely virulent and causes fatal hemorrhagic fever in ~ 50 percent of the cases. The viral GP binds to host cell receptors to facilitate viral entry and thus plays a critical role in pathogenicity. Results An immune phage display library containing more than 107 unique clones was developed from a llama immunized with a combination of killed Ebola virus and recombinantly produced GP. We panned the library to obtain GP binding sdAbs and isolated sdAbs from 5 distinct sequence families. Three GP binders with dissociation constants ranging from ~ 2 to 20 nM, and melting temperatures from ~ 57 to 72 °C were selected for protein engineering in order to increase their stability through a combination of consensus sequence mutagenesis and the addition of a non-canonical disulfide bond. These changes served to increase the melting temperatures of the sdAbs by 15–17 °C. In addition, fusion of a short positively charged tail to the C-terminus which provided ideal sites for the chemical modification of these sdAbs resulted in improved limits of detection of GP and Ebola virus like particles while serving as tracer antibodies. Conclusions SdAbs specific for Ebola GP were selected and their stability and functionality were improved utilizing protein engineering. Thermal stability of antibody reagents may be of particular importance when operating in austere locations that lack reliable refrigeration. Future efforts can evaluate the potential of these isolated sdAbs as candidates for diagnostic or therapeutic applications for Ebola. Electronic supplementary material The online version of this article (10.1186/s12934-017-0837-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jinny L Liu
- US Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, 4555 Overlook Ave SW, Washington, DC, 20375, USA
| | - Lisa C Shriver-Lake
- US Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, 4555 Overlook Ave SW, Washington, DC, 20375, USA
| | - George P Anderson
- US Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, 4555 Overlook Ave SW, Washington, DC, 20375, USA
| | - Dan Zabetakis
- US Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, 4555 Overlook Ave SW, Washington, DC, 20375, USA
| | - Ellen R Goldman
- US Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, 4555 Overlook Ave SW, Washington, DC, 20375, USA.
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16
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Malanoski AP, Breger JC, Brown CW, Deschamps JR, Susumu K, Oh E, Anderson GP, Walper SA, Medintz IL. Kinetic enhancement in high-activity enzyme complexes attached to nanoparticles. Nanoscale Horiz 2017; 2:241-252. [PMID: 32260679 DOI: 10.1039/c7nh00052a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Accumulating studies by many groups have found consistent enhancement in a wide variety of enzyme activities when they are displayed around nanoparticles. However, the underlying mechanism(s) that give rise to this phenomenon are still largely unknown. Herein, we develop a detailed reaction scheme that considers many of the various possible interactions between a substrate and a given enzyme-nanoparticle bioconjugate. The properties and some functional predictions that emanate from the reaction scheme were then tested using a model system where the homotetrameric beta-galactosidase enzyme complex was assembled with luminescent semiconductor nanocrystalline quantum dots displayed around its periphery. This type of assembly occurs as the ∼465 kDa enzyme complex is significantly larger than the 4.2 nm diameter green emitting quantum dots utilized. This unique architecture, in conjunction with the fact that this enzyme functions at or near the diffusion limit, provided a unique opportunity to selectively probe certain aspects of enzyme enhancement when attached to a nanoparticle with minimal potential perturbations to the native enzyme structure. Experimental assays were conducted where both free enzymes and quantum dot-decorated enzymes were compared directly in side-by-side samples and included formats where the kinetic processes were challenged with increasing viscosity and competitive inhibitors. The results strongly suggest that it is possible for there to be significant enhancements in an enzyme's catalytic rate or kcat after attachment to a nanoparticle even when it is apparently diffusion limited without requiring any gross changes to the enzyme's structure. A discussion of how this reaction scheme and model can be applied to other systems is provided.
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Affiliation(s)
- Anthony P Malanoski
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, USA.
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17
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Shriver-Lake LC, Zabetakis D, Goldman ER, Anderson GP. Evaluation of anti-botulinum neurotoxin single domain antibodies with additional optimization for improved production and stability. Toxicon 2017; 135:51-58. [DOI: 10.1016/j.toxicon.2017.06.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 06/01/2017] [Accepted: 06/02/2017] [Indexed: 01/27/2023]
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18
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Breger JC, Muttenthaler M, Delehanty JB, Thompson DA, Oh E, Susumu K, Deschamps JR, Anderson GP, Field LD, Walper SA, Dawson PE, Medintz IL. Nanoparticle cellular uptake by dendritic wedge peptides: achieving single peptide facilitated delivery. Nanoscale 2017; 9:10447-10464. [PMID: 28703833 DOI: 10.1039/c7nr03362a] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Significant efforts are being undertaken to optimize the cargo carrying capacity and especially the cellular delivery efficiency of functionalized nanoparticles for applications in biological research and pharmacological delivery. One approach to increasing nanoparticle surface cargo display capacity is to decrease the number of moieties required for mediating cellular delivery by improving their efficiency. We describe a series of multivalent cell penetrating peptide (CPP) dendrimers that facilitate rapid cellular delivery of prototypical nanoparticle-semiconductor quantum dots (QDs). The modular CPP dendrimers were assembled through an innovative convergent oxime ligation strategy between (Arg9)n motifs and a dendritic QD-coordination scaffold. Dendrimeric peptides sequentially incorporate a terminal (His)6 motif for metal-affinity QD coordination, a Pro9 spacer, a branching poly-lysine scaffold, and wedged display of (Arg9)n binding motifs with n = 1×, 2×, 4×, 8×, 16× multivalency. QD dendrimer display capacity was estimated using structural simulations and QD-(Arg9)1-16 conjugates characterized by dynamic light scattering along with surface plasmon resonance-based binding assays to heparan sulfate proteoglycan surfaces. Cellular uptake via endocytosis was confirmed and peptide delivery kinetics investigated as a function of QD-(Arg9)1-16 conjugate exposure time and QD assembly ratio where cellular viability assays reflected no overt cytotoxicity. The ability of single dendrimer conjugates to facilitate cellular uptake was confirmed for QD-(Arg9)2-16 repeats along with the ability to deliver >850 kDa of protein cargo per QD. Minimizing the number of CPPs required for cellular uptake is critical for expanding nanoparticle cargo carrying capacity and can allow for inclusion of additional sensors, therapeutics and contrast agents on their surface.
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Affiliation(s)
- Joyce C Breger
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, USA. and American Society for Engineering Education, Washington, DC 20036, USA
| | - Markus Muttenthaler
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA and Institute for Molecular Bioscience, The University of Queensland, 4072 St Lucia, Brisbane, Australia
| | - James B Delehanty
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, USA.
| | - Darren A Thompson
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA and University of Idaho, Coeur d'Alene, ID 83814, USA
| | - Eunkeu Oh
- Optical Sciences Division, Code 5600, U.S. Naval Research Laboratory, Washington, DC 20375, USA and Sotera Defense Solutions, Inc., Columbia, MD 21046, USA
| | - Kimihiro Susumu
- Optical Sciences Division, Code 5600, U.S. Naval Research Laboratory, Washington, DC 20375, USA and Sotera Defense Solutions, Inc., Columbia, MD 21046, USA
| | - Jeffrey R Deschamps
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, USA.
| | - George P Anderson
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, USA.
| | - Lauren D Field
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, USA. and Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
| | - Scott A Walper
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, USA.
| | - Philip E Dawson
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, USA.
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19
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Goldman ER, Liu JL, Zabetakis D, Anderson GP. Enhancing Stability of Camelid and Shark Single Domain Antibodies: An Overview. Front Immunol 2017; 8:865. [PMID: 28791022 PMCID: PMC5524736 DOI: 10.3389/fimmu.2017.00865] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Accepted: 07/07/2017] [Indexed: 11/13/2022] Open
Abstract
Single domain antibodies (sdAbs) are gaining a reputation as superior recognition elements as they combine the advantages of the specificity and affinity found in conventional antibodies with high stability and solubility. Melting temperatures (Tms) of sdAbs cover a wide range from below 50 to over 80°C. Many sdAbs have been engineered to increase their Tm, making them stable until exposed to extreme temperatures. SdAbs derived from the variable heavy chains of camelid and shark heavy chain-only antibodies are termed VHH and VNAR, respectively, and generally exhibit some ability to refold and bind antigen after heat denaturation. This ability to refold varies from 0 to 100% and is a property dependent on both intrinsic factors of the sdAb and extrinsic conditions such as the sample buffer ionic strength, pH, and sdAb concentration. SdAbs have also been engineered to increase their solubility and refolding ability, which enable them to function even after exposure to temperatures that exceed their melting point. In addition, efforts to improve their stability at extreme pH and in the presence of chemical denaturants or proteases have been undertaken. Multiple routes have been employed to engineer sdAbs with these enhanced stabilities. The methods utilized to achieve these goals include grafting complementarity-determining regions onto stable frameworks, introduction of non-canonical disulfide bonds, random mutagenesis combined with stringent selection, point mutations such as inclusion of negative charges, and genetic fusions. Increases of up to 20°C have been realized, pushing the Tm of some sdAbs to over 90°C. Herein, we present an overview of the work done to stabilize sdAbs derived from camelids and sharks. Utilizing these various strategies sdAbs have been stabilized without significantly compromising their affinity, thereby providing superior reagents for detection, diagnostic, and therapeutic applications.
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Affiliation(s)
- Ellen R Goldman
- Center for BioMolecular Science and Engineering, US Naval Research Laboratory, Washington, DC, United States
| | - Jinny L Liu
- Center for BioMolecular Science and Engineering, US Naval Research Laboratory, Washington, DC, United States
| | - Dan Zabetakis
- Center for BioMolecular Science and Engineering, US Naval Research Laboratory, Washington, DC, United States
| | - George P Anderson
- Center for BioMolecular Science and Engineering, US Naval Research Laboratory, Washington, DC, United States
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20
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Shriver-Lake LC, Goldman ER, Zabetakis D, Anderson GP. Improved production of single domain antibodies with two disulfide bonds by co-expression of chaperone proteins in the Escherichia coli periplasm. J Immunol Methods 2017; 443:64-67. [DOI: 10.1016/j.jim.2017.01.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 01/24/2017] [Accepted: 01/24/2017] [Indexed: 10/20/2022]
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21
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Shriver-Lake LC, Anderson GP, Taitt CR. Effect of Linker Length on Cell Capture by Poly(ethylene glycol)-Immobilized Antimicrobial Peptides. Langmuir 2017; 33:2878-2884. [PMID: 28253616 DOI: 10.1021/acs.langmuir.6b04481] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Development of antimicrobial peptide (AMP)-functionalized materials has renewed interest in using poly(ethylene glycol) (PEG)-mediated linking to minimize unwanted interactions while engendering the peptides with sufficient flexibility and freedom of movement to interact with the targeted cell types. While PEG-based linkers have been used in many AMP-based materials, the role of the tether length has been minimally explored. Here, we assess the impact of varying the length of PEG-based linkers on the binding of bacterial cells by surface-immobilized AMPs. While higher surface densities of immobilized AMPs were observed using shorter PEG linkers, the increased density was insufficient to fully account for the increased binding activity of peptides. Furthermore, effects were specific to both the peptide and cell type tested. These results suggest that simple alterations in linking strategies-such as changing tether length-may result in large differences in the surface properties of the immobilized AMPs that are not easily predictable.
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Affiliation(s)
- Lisa C Shriver-Lake
- Center for Biomolecular Science & Engineering, Naval Research Laboratory , 4555 Overlook Avenue, SW, Washington, DC 20375, United States
| | - George P Anderson
- Center for Biomolecular Science & Engineering, Naval Research Laboratory , 4555 Overlook Avenue, SW, Washington, DC 20375, United States
| | - Chris Rowe Taitt
- Center for Biomolecular Science & Engineering, Naval Research Laboratory , 4555 Overlook Avenue, SW, Washington, DC 20375, United States
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22
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Anderson GP, Liu JH, Zabetakis D, Liu JL, Goldman ER. Thermal stabilization of anti-α-cobratoxin single domain antibodies. Toxicon 2017; 129:68-73. [PMID: 28209480 DOI: 10.1016/j.toxicon.2017.02.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 02/09/2017] [Accepted: 02/11/2017] [Indexed: 10/20/2022]
Abstract
There is an unmet need for snake antivenoms that can be stored ready to use near the point of care. To address that need we have taken two anti-α-cobratoxin single domain antibodies and increased their thermal stability to improve their ambient temperature shelf-life. The anti-α-cobratoxin single domain antibodies C2 and C20 were first isolated, and demonstrated to be toxin neutralizing by Richard et al., 2013 (Richard, G., Meyers, A.J., McLean, M.D., Arbabi-Ghahroudi, M., MacKenzie, R., Hall, J.C., 2013. In vivo neutralization of alpha-cobratoxin with high-affinity llama single-domain antibodies (VHHs) and a VHH-Fc antibody. PLoS One 8, e69495). To thermal stabilize C2 and C20, we first made changes to their frame work 1 region that we had previously identified to be stabilizing, as well as reverted to the hallmark amino acids highly conserved in VHH domains; these changes improved their melting temperature (Tm) by 2 and 6 °C respectively. The further addition of a non-canonical disulfide bond raised the Tm an additional 13 and 9 °C respectively; giving final Tm values of 86 and 75 °C. Testing these mutants at 1 mg/mL at a range of elevated temperatures for an hour; we found that at 65 °C the wild type C2 and C20 had lost 35 and 95% of their binding activity respectively, while the mutants with the added disulfide bond retained nearly 100% of their initial binding activity. While significant work remains to formulate and field a shelf-stable antivenom, our results indicate such a product should be attainable in the near future.
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Affiliation(s)
- George P Anderson
- US Naval Research Laboratory, Center for Biomolecular Science and Engineering, 4555 Overlook Ave SW, Washington, DC, 20375, USA.
| | - Jessica H Liu
- Science and Engineering Apprenticeship Program, US Naval Research Laboratory, 4555, Overlook Ave SW, Washington, DC, USA
| | - Dan Zabetakis
- US Naval Research Laboratory, Center for Biomolecular Science and Engineering, 4555 Overlook Ave SW, Washington, DC, 20375, USA
| | - Jinny L Liu
- US Naval Research Laboratory, Center for Biomolecular Science and Engineering, 4555 Overlook Ave SW, Washington, DC, 20375, USA
| | - Ellen R Goldman
- US Naval Research Laboratory, Center for Biomolecular Science and Engineering, 4555 Overlook Ave SW, Washington, DC, 20375, USA
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23
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Liu JL, Zabetakis D, Goldman ER, Anderson GP. Selection and characterization of single domain antibodies against human CD20. Mol Immunol 2016; 78:146-154. [DOI: 10.1016/j.molimm.2016.09.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 09/07/2016] [Accepted: 09/10/2016] [Indexed: 01/25/2023]
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24
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Legler PM, Compton JR, Hale ML, Anderson GP, Olson MA, Millard CB, Goldman ER. Stability of isolated antibody-antigen complexes as a predictive tool for selecting toxin neutralizing antibodies. MAbs 2016; 9:43-57. [PMID: 27660893 PMCID: PMC5240650 DOI: 10.1080/19420862.2016.1236882] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Ricin is an A-B ribosome inactivating protein (RIP) toxin composed of an A-chain subunit (RTA) that contains a catalytic N-glycosidase and a B-chain (RTB) lectin domain that binds cell surface glycans. Ricin exploits retrograde transport to enter into the Golgi and the endoplasmic reticulum, and then dislocates into the cytoplasm where it can reach its substrate, the rRNA. A subset of isolated antibodies (Abs) raised against the RTA subunit protect against ricin intoxication, and RTA-based vaccine immunogens have been shown to provide long-lasting protective immunity against the holotoxin. Anti-RTA Abs are unlikely to cross a membrane and reach the cytoplasm to inhibit the enzymatic activity of the A-chain. Moreover, there is not a strict correlation between the apparent binding affinity (Ka) of anti-RTA Abs and their ability to successfully neutralize ricin toxicity. Some anti-RTA antibodies are toxin-neutralizing, whereas others are not. We hypothesize that neutralizing anti-RTA Abs may interfere selectively with conformational change(s) or partial unfolding required for toxin internalization. To test this hypothesis, we measured the melting temperatures (Tm) of neutralizing single-domain Ab (sdAb)-antigen (Ag) complexes relative to the Tm of the free antigen (Tm-shift = Tmcomplex – TmAg), and observed increases in the Tmcomplex of 9–20 degrees. In contrast, non-neutralizing sdAb-Ag complexes shifted the TmComplex by only 6–7 degrees. A strong linear correlation (r2 = 0.992) was observed between the magnitude of the Tm-shift and the viability of living cells treated with the sdAb and ricin holotoxin. The Tm-shift of the sdAb-Ag complex provided a quantitative biophysical parameter that could be used to predict and rank-order the toxin-neutralizing activities of Abs. We determined the first structure of an sdAb-RTA1-33/44-198 complex, and examined other sdAb-RTA complexes. We found that neutralizing sdAb bound to regions involved in the early stages of unfolding. These Abs likely interfere with steps preceding or following endocytosis that require conformational changes. This method may have utility for the characterization or rapid screening of other Ab that act to prevent conformational changes or unfolding as part of their mechanism of action.
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Affiliation(s)
| | | | - Martha L Hale
- c US Army Medical Research Institute of Infectious Diseases , Frederick , MD , USA
| | | | - Mark A Olson
- c US Army Medical Research Institute of Infectious Diseases , Frederick , MD , USA
| | - Charles B Millard
- c US Army Medical Research Institute of Infectious Diseases , Frederick , MD , USA
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25
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Anderson GP, Teichler DD, Zabetakis D, Shriver-Lake LC, Liu JL, Lonsdale SG, Goodchild SA, Goldman ER. Importance of Hypervariable Region 2 for Stability and Affinity of a Shark Single-Domain Antibody Specific for Ebola Virus Nucleoprotein. PLoS One 2016; 11:e0160534. [PMID: 27494523 PMCID: PMC4975481 DOI: 10.1371/journal.pone.0160534] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 07/20/2016] [Indexed: 12/18/2022] Open
Abstract
Single-domain antibodies derived from the unique New Antigen Receptor found in sharks have numerous potential applications, ranging from diagnostic reagents to therapeutics. Shark-derived single-domain antibodies possess the same characteristic ability to refold after heat denaturation found in single-domain antibodies derived from camelid heavy-chain-only antibodies. Recently, two shark derived single-domain antibodies specific for the nucleoprotein of Ebola virus were described. Our evaluation confirmed their high affinity for the nucleoprotein, but found their melting temperatures to be low relative to most single-domain antibodies. Our first approach towards improving their stability was grafting antigen-binding regions (complementarity determining regions) of one of these single-domain antibodies onto a high melting temperature shark single-domain antibody. This resulted in two variants: one that displayed excellent affinity with a low melting temperature, while the other had poor affinity but a higher melting temperature. These new proteins, however, differed in only 3 amino acids within the complementarity determining region 2 sequence. In shark single-domain antibodies, the complementarity determining region 2 is often referred to as hypervariable region 2, as this segment of the antibody domain is truncated compared to the sequence in camelid single-domain antibodies and conventional heavy chain variable domains. To elucidate which of the three amino acids or combinations thereof were responsible for the affinity and stability we made the 6 double and single point mutants that covered the intermediates between these two clones. We found a single amino acid change that achieved a 10°C higher melting temperature while maintaining sub nM affinity. This research gives insights into the impact of the shark sdAb hypervariable 2 region on both stability and affinity.
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Affiliation(s)
- George P. Anderson
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, United States of America
| | - Daniel D. Teichler
- Science and Engineering Apprenticeship Program, Naval Research Laboratory, Washington, DC, United States of America
| | - Dan Zabetakis
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, United States of America
| | - Lisa C. Shriver-Lake
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, United States of America
| | - Jinny L. Liu
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, United States of America
| | - Stephen G. Lonsdale
- Defence Science and Technology Laboratory, Porton Down, Salisbury, United Kingdom
| | - Sarah A. Goodchild
- Defence Science and Technology Laboratory, Porton Down, Salisbury, United Kingdom
| | - Ellen R. Goldman
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, United States of America
- * E-mail:
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Liu JL, Walper SA, Turner KB, Lee AB, Medintz IL, Susumu K, Oh E, Zabetakis D, Goldman ER, Anderson GP. Conjugation of biotin-coated luminescent quantum dots with single domain antibody-rhizavidin fusions. ACTA ACUST UNITED AC 2016; 10:56-65. [PMID: 28352525 PMCID: PMC5040863 DOI: 10.1016/j.btre.2016.03.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 02/29/2016] [Accepted: 03/01/2016] [Indexed: 12/28/2022]
Abstract
Single domain antibody—rhizavidin fusion bioconjugated biotin coated quantum dots. Provided facile and effective method to orient antibodies on QD surface. Accomplished improved production of His-tagged rhizavidin (RZh) in E. coli. Demonstrated utility of RZh as a replacement for tetrameric biotin binders.
Straightforward and effective methods are required for the bioconjugation of proteins to surfaces and particles. Previously we demonstrated that the fusion of a single domain antibody with the biotin binding molecule rhizavidin provided a facile method to coat biotin-modified surfaces with a highly active and oriented antibody. Here, we constructed similar single domain antibody—rhizavidin fusions as well as unfused rhizavidin with a His-tag. The unfused rhizavidin produced efficiently and its utility for assay development was demonstrated in surface plasmon resonance experiments. The single domain antibody-rhizavidin fusions were utilized to coat quantum dots that had been prepared with surface biotins. Preparation of antibody coated quantum dots by this means was found to be both easy and effective. The prepared single domain antibody-quantum dot reagent was characterized by surface plasmon resonance and applied to toxin detection in a fluoroimmunoassay sensing format.
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Affiliation(s)
- Jinny L Liu
- Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, 4555 Overlook Ave SW, Washington DC 20375, USA
| | - Scott A Walper
- Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, 4555 Overlook Ave SW, Washington DC 20375, USA
| | - Kendrick B Turner
- Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, 4555 Overlook Ave SW, Washington DC 20375, USA
| | | | - Igor L Medintz
- Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, 4555 Overlook Ave SW, Washington DC 20375, USA
| | - Kimihiro Susumu
- Sotera Defense Solutions, Inc., 7230 Lee Deforest Drive, Columbia, MD 21046, USA
| | - Eunkeu Oh
- Sotera Defense Solutions, Inc., 7230 Lee Deforest Drive, Columbia, MD 21046, USA
| | - Dan Zabetakis
- Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, 4555 Overlook Ave SW, Washington DC 20375, USA
| | - Ellen R Goldman
- Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, 4555 Overlook Ave SW, Washington DC 20375, USA
| | - George P Anderson
- Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, 4555 Overlook Ave SW, Washington DC 20375, USA
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Turner KB, Naciri J, Liu JL, Anderson GP, Goldman ER, Zabetakis D. Next-Generation Sequencing of a Single Domain Antibody Repertoire Reveals Quality of Phage Display Selected Candidates. PLoS One 2016; 11:e0149393. [PMID: 26895405 PMCID: PMC4760936 DOI: 10.1371/journal.pone.0149393] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 02/01/2016] [Indexed: 11/18/2022] Open
Abstract
Next-Generation Sequencing and bioinformatics are powerful tools for analyzing the large number of DNA sequences present in an immune library. In this work, we constructed a cDNA library of single domain antibodies from a llama immunized with staphylococcal enterotoxin B. The resulting library was sequenced, resulting in approximately 8.5 million sequences with 5.4 million representing intact, useful sequences. The sequenced library was interrogated using sequences of known SEB-binding single domain antibodies from the library obtained through phage display panning methods in a previous study. New antibodies were identified, produced, and characterized, and were shown to have affinities and melting temperatures comparable to those obtained by traditional panning methods. This demonstrates the utility of using NGS as a complementary tool to phage-displayed biopanning as a means for rapidly obtaining additional antibodies from an immune library. It also shows that phage display, using a library of high diversity, is able to select high quality antibodies even when they are low in frequency.
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Affiliation(s)
- Kendrick B. Turner
- American Society for Engineering Education, Postdoctoral Fellow at the US Naval Research Laboratory, Washington, DC, United States of America
| | - Jennifer Naciri
- American Society for Engineering Education, Science and Engineering Apprenticeship Participant at US Naval Research Laboratory, Washington, DC, United States of America
| | - Jinny L. Liu
- Center for Bio/molecular Science and Engineering, US Naval Research Laboratory, Washington, DC, United States of America
| | - George P. Anderson
- Center for Bio/molecular Science and Engineering, US Naval Research Laboratory, Washington, DC, United States of America
| | - Ellen R. Goldman
- Center for Bio/molecular Science and Engineering, US Naval Research Laboratory, Washington, DC, United States of America
| | - Dan Zabetakis
- Center for Bio/molecular Science and Engineering, US Naval Research Laboratory, Washington, DC, United States of America
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Taitt CR, Anderson GP, Ligler FS. Evanescent wave fluorescence biosensors: Advances of the last decade. Biosens Bioelectron 2016; 76:103-12. [PMID: 26232145 PMCID: PMC5012222 DOI: 10.1016/j.bios.2015.07.040] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 07/15/2015] [Accepted: 07/18/2015] [Indexed: 12/12/2022]
Abstract
Biosensor development has been a highly dynamic field of research and has progressed rapidly over the past two decades. The advances have accompanied the breakthroughs in molecular biology, nanomaterial sciences, and most importantly computers and electronics. The subfield of evanescent wave fluorescence biosensors has also matured dramatically during this time. Fundamentally, this review builds on our earlier 2005 review. While a brief mention of seminal early work will be included, this current review will focus on new technological developments as well as technology commercialized in just the last decade. Evanescent wave biosensors have found a wide array applications ranging from clinical diagnostics to biodefense to food testing; advances in those applications and more are described herein.
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Affiliation(s)
- Chris Rowe Taitt
- Center for Bio/Molecular Science and Engineering, US Naval Research Laboratory, 4555 Overlook Ave SW, Washington, DC 20375-5348, USA
| | - George P Anderson
- Center for Bio/Molecular Science and Engineering, US Naval Research Laboratory, 4555 Overlook Ave SW, Washington, DC 20375-5348, USA
| | - Frances S Ligler
- UNC-Chapel Hill and NC State University Department of Biomedical Engineering, 911 Oval Drive, Raleigh, NC 27695-7115, USA.
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29
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Duan M, Steinfort DP, Smallwood D, Hew M, Chen W, Ernst M, Irving LB, Anderson GP, Hibbs ML. CD11b immunophenotyping identifies inflammatory profiles in the mouse and human lungs. Mucosal Immunol 2016; 9:550-63. [PMID: 26422753 PMCID: PMC7101582 DOI: 10.1038/mi.2015.84] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 07/12/2015] [Indexed: 02/04/2023]
Abstract
The development of easily accessible tools for human immunophenotyping to classify patients into discrete disease endotypes is advancing personalized therapy. However, no systematic approach has been developed for the study of inflammatory lung diseases with often complex and highly heterogeneous disease etiologies. We have devised an internally standardized flow cytometry approach that can identify parallel inflammatory alveolar macrophage phenotypes in both the mouse and human lungs. In mice, lung innate immune cell alterations during endotoxin challenge, influenza virus infection, and in two genetic models of chronic obstructive lung disease could be segregated based on the presence or absence of CD11b alveolar macrophage upregulation and lung eosinophilia. Additionally, heightened alveolar macrophage CD11b expression was a novel feature of acute lung exacerbations in the SHIP-1(-/-) model of chronic obstructive lung disease, and anti-CD11b antibody administration selectively blocked inflammatory CD11b(pos) but not homeostatic CD11b(neg) alveolar macrophages in vivo. The identification of analogous profiles in respiratory disease patients highlights this approach as a translational avenue for lung disease endotyping and suggests that heterogeneous innate immune cell phenotypes are an underappreciated component of the human lung disease microenvironment.
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Affiliation(s)
- M Duan
- grid.1002.30000 0004 1936 7857Department of Immunology, Monash University, Alfred Medical Research and Education Precinct, Melbourne, Australia ,grid.1008.90000 0001 2179 088XDepartment of Surgery, University of Melbourne, Melbourne, Australia ,grid.482095.2Ludwig Institute for Cancer Research, Melbourne, Australia ,grid.1018.80000 0001 2342 0938Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - D P Steinfort
- grid.416153.40000 0004 0624 1200Department of Respiratory Medicine, Royal Melbourne Hospital, Parkville, Australia
| | - D Smallwood
- grid.416153.40000 0004 0624 1200Department of Respiratory Medicine, Royal Melbourne Hospital, Parkville, Australia
| | - M Hew
- grid.1623.60000 0004 0432 511XDepartment of Allergy, Immunology and Respiratory Medicine, Alfred Hospital, Parkville, Australia
| | - W Chen
- grid.1018.80000 0001 2342 0938Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - M Ernst
- grid.1042.7The Walter and Eliza Hall Institute for Medical Research, Parkville, Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, University of Melbourne, Melbourne, Australia ,grid.410678.cPresent Address: 10Present address: Olivia Newton-John Cancer Research Institute, Austin Health, Heidelberg, Victoria 3084, Australia., ,
| | - L B Irving
- grid.416153.40000 0004 0624 1200Department of Respiratory Medicine, Royal Melbourne Hospital, Parkville, Australia
| | - G P Anderson
- grid.1008.90000 0001 2179 088XDepartment of Pharmacology, University of Melbourne, Melbourne, Australia
| | - M L Hibbs
- grid.1002.30000 0004 1936 7857Department of Immunology, Monash University, Alfred Medical Research and Education Precinct, Melbourne, Australia
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Charles PT, Davis J, Adams AA, Anderson GP, Liu JL, Deschamps JR, Kusterbeck AW. Multi-channeled single chain variable fragment (scFv) based microfluidic device for explosives detection. Talanta 2015; 144:439-44. [DOI: 10.1016/j.talanta.2015.06.039] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 06/11/2015] [Accepted: 06/16/2015] [Indexed: 10/23/2022]
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Liu JL, Goldman ER, Zabetakis D, Walper SA, Turner KB, Shriver-Lake LC, Anderson GP. Enhanced production of a single domain antibody with an engineered stabilizing extra disulfide bond. Microb Cell Fact 2015; 14:158. [PMID: 26449768 PMCID: PMC4599338 DOI: 10.1186/s12934-015-0340-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 09/12/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Single domain antibodies derived from the variable region of the unique heavy chain antibodies found in camelids yield high affinity and regenerable recognition elements. Adding an additional disulfide bond that bridges framework regions is a proven method to increase their melting temperature, however often at the expense of protein production. To fulfill their full potential it is essential to achieve robust protein production of these stable binding elements. In this work, we tested the hypothesis that decreasing the isoelectric point of single domain antibody extra disulfide bond mutants whose production fell due to the incorporation of the extra disulfide bond would lead to recovery of the protein yield, while maintaining the favorable melting temperature and affinity. RESULTS Introduction of negative charges into a disulfide bond mutant of a single domain antibody specific for the L1 antigen of the vaccinia virus led to approximately 3.5-fold increase of protein production to 14 mg/L, while affinity and melting temperature was maintained. In addition, refolding following heat denaturation improved from 15 to 70 %. It also maintained nearly 100 % of its binding function after heating to 85 °C for an hour at 1 mg/mL. Disappointingly, the replacement of neutral or positively charged amino acids with negatively charged ones to lower the isoelectric point of two anti-toxin single domain antibodies stabilized with a second disulfide bond yielded only slight increases in protein production. Nonetheless, for one of these binders the charge change itself stabilized the structure equivalent to disulfide bond addition, thus providing an alternative route to stabilization which is not accompanied by loss in production. CONCLUSION The ability to produce high affinity, stable single domain antibodies is critical for their utility. While the addition of a second disulfide bond is a proven method for enhancing stability of single domain antibodies, it frequently comes at the cost of reduced yields. While decreasing the isoelectric point of double disulfide mutants of single domain antibodies may improve protein production, charge addition appears to consistently improve refolding and some charge changes can also improve thermal stability, thus providing a number of benefits making the examination of such mutations worth consideration.
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Affiliation(s)
- Jinny L Liu
- Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, Washington, DC, 20375, USA.
| | - Ellen R Goldman
- Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, Washington, DC, 20375, USA.
| | - Dan Zabetakis
- Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, Washington, DC, 20375, USA.
| | - Scott A Walper
- Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, Washington, DC, 20375, USA.
| | - Kendrick B Turner
- Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, Washington, DC, 20375, USA.
| | - Lisa C Shriver-Lake
- Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, Washington, DC, 20375, USA.
| | - George P Anderson
- Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, Washington, DC, 20375, USA.
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32
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Olson MA, Zabetakis D, Legler PM, Turner KB, Anderson GP, Goldman ER. Can template-based protein models guide the design of sequence fitness for enhanced thermal stability of single domain antibodies? Protein Eng Des Sel 2015; 28:395-402. [PMID: 26374895 DOI: 10.1093/protein/gzv047] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 08/14/2015] [Indexed: 12/18/2022] Open
Abstract
We investigate the practical use of comparative (template-based) protein models in replica-exchange simulations of single-domain antibody (sdAb) chains to evaluate if the models can correctly predict in rank order the thermal susceptibility to unfold relative to experimental melting temperatures. The baseline model system is the recently determined crystallographic structure of a llama sdAb (denoted as A3), which exhibits an unusually high thermal stability. An evaluation of the simulation results for the A3 comparative model and crystal structure shows that, despite the overall low Cα root-mean-square deviation between the two structures, the model contains misfolded regions that yields a thermal profile of unraveling at a lower temperature. Yet comparison of the simulations of four different comparative models for sdAb A3, C8, A3C8 and E9, where A3C8 is a design of swapping the sequence of the complementarity determining regions of C8 onto the A3 framework, discriminated among the sequences to detect the highest and lowest experimental melting transition temperatures. Further structural analysis of A3 for selected alanine substitutions by a combined computational and experimental study found unexpectedly that the comparative model performed admirably in recognizing substitution 'hot spots' when using a support-vector machine algorithm.
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Affiliation(s)
- Mark A Olson
- Department of Cell Biology and Biochemistry, Molecular and Translational Sciences Division, USAMRIID, Frederick, MD, USA
| | - Dan Zabetakis
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, DC, USA
| | - Patricia M Legler
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, DC, USA
| | - Kendrick B Turner
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, DC, USA
| | - George P Anderson
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, DC, USA
| | - Ellen R Goldman
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, DC, USA
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33
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Gaylord ST, Dinh TL, Goldman ER, Anderson GP, Ngan KC, Walt DR. Ultrasensitive Detection of Ricin Toxin in Multiple Sample Matrixes Using Single-Domain Antibodies. Anal Chem 2015; 87:6570-7. [DOI: 10.1021/acs.analchem.5b00322] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shonda T. Gaylord
- Department
of Chemistry, Tufts University, 62 Talbot Avenue, Medford, Massachusetts 02155, United States
| | - Trinh L. Dinh
- Department
of Chemistry, Tufts University, 62 Talbot Avenue, Medford, Massachusetts 02155, United States
| | - Ellen R. Goldman
- Center for Bio/Molecular
Science and Engineering, Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, DC 20375, United States
| | - George P. Anderson
- Center for Bio/Molecular
Science and Engineering, Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, DC 20375, United States
| | - Kevin C. Ngan
- Department
of Chemistry, Tufts University, 62 Talbot Avenue, Medford, Massachusetts 02155, United States
| | - David R. Walt
- Department
of Chemistry, Tufts University, 62 Talbot Avenue, Medford, Massachusetts 02155, United States
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Raphael MP, Christodoulides JA, Byers JM, Anderson GP, Liu JL, Turner KB, Goldman ER, Delehanty JB. Optimizing Nanoplasmonic Biosensor Sensitivity with Orientated Single Domain Antibodies. Plasmonics 2015; 10:1649-1655. [PMID: 26594135 PMCID: PMC4644190 DOI: 10.1007/s11468-015-9969-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 05/08/2015] [Indexed: 06/05/2023]
Abstract
Localized surface plasmon resonance (LSPR) spectroscopy and imaging are emerging biosensor technologies which tout label-free biomolecule detection at the nanoscale and ease of integration with standard microscopy setups. The applicability of these techniques can be limited by the restrictions that surface-conjugated ligands must be both sufficiently small and orientated to meet analyte sensitivity requirements. We demonstrate that orientated single domain antibodies (sdAb) can optimize nanoplasmonic sensitivity by comparing three anti-ricin sdAb constructs to biotin-neutravidin, a model system for small and highly orientated ligand studies. LSPR imaging of electrostatically orientated sdAb exhibited a ricin sensitivity equivalent to that of the biotinylated LSPR biosensors for neutravidin. These results, combined with the facts that sdAb are highly stable and readily produced in bacteria and yeast, build a compelling case for the increased utilization of sdAbs in nanoplasmonic applications.
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Affiliation(s)
- Marc P. Raphael
- />Bioelectronics and Sensing, Code 6363, Naval Research Laboratory, 4555 Overlook Ave SW, Washington, DC 20375 USA
| | - Joseph A. Christodoulides
- />Bioelectronics and Sensing, Code 6363, Naval Research Laboratory, 4555 Overlook Ave SW, Washington, DC 20375 USA
| | - Jeff M. Byers
- />Bioelectronics and Sensing, Code 6363, Naval Research Laboratory, 4555 Overlook Ave SW, Washington, DC 20375 USA
| | - George P. Anderson
- />Center for Bio/Molecular Science and Engineering, Code 6900, Naval Research Laboratory, 4555 Overlook Ave SW, Washington, DC 20375 USA
| | - Jinny L. Liu
- />Center for Bio/Molecular Science and Engineering, Code 6900, Naval Research Laboratory, 4555 Overlook Ave SW, Washington, DC 20375 USA
| | - Kendrick B. Turner
- />Center for Bio/Molecular Science and Engineering, Code 6900, Naval Research Laboratory, 4555 Overlook Ave SW, Washington, DC 20375 USA
| | - Ellen R. Goldman
- />Center for Bio/Molecular Science and Engineering, Code 6900, Naval Research Laboratory, 4555 Overlook Ave SW, Washington, DC 20375 USA
| | - James B. Delehanty
- />Center for Bio/Molecular Science and Engineering, Code 6900, Naval Research Laboratory, 4555 Overlook Ave SW, Washington, DC 20375 USA
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Abstract
Single-domain antibodies (sdAbs) derived from heavy-chain only antibodies produced in camelids are attractive immunoreagents due to their small size, high affinity, and ability to refold and retain binding activity after denaturation. It has been observed that some sdAbs, however, exhibit undesirable properties including reduced solubility when subjected to heating or upon long-term storage at production-relevant concentrations, which can limit their usefulness. Using a multi-step, rational design approach that included consensus-sequence driven sequence repairs, the alteration of net protein charge, and the introduction of non-native disulfide bonds, augmented solubility and increased melting temperatures were achieved. The improved sdAbs tolerated storage in solution at high concentration (10 mg/mL) and were able to withstand multiple cycles of heating to high temperature (70 °C). This work demonstrates a pathway for improving the biophysical characteristics of sdAbs which is essential for expanding their utility for both diagnostic as well as therapeutic applications.
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Affiliation(s)
- Kendrick B. Turner
- American Society for Engineering Education, Postdoctoral Fellow at the Naval Research Laboratory, Washington, DC 20375, USA
| | - Jinny L. Liu
- Center for Biomolecular Science and Engineering, Naval Research Laboratory, Washington, DC 20375, USA
| | - Dan Zabetakis
- Center for Biomolecular Science and Engineering, Naval Research Laboratory, Washington, DC 20375, USA
| | | | - George P. Anderson
- Center for Biomolecular Science and Engineering, Naval Research Laboratory, Washington, DC 20375, USA
| | - Ellen R. Goldman
- Center for Biomolecular Science and Engineering, Naval Research Laboratory, Washington, DC 20375, USA
- Corresponding author. Tel.: +1 202 404 6052
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36
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Walper SA, Liu JL, Zabetakis D, Anderson GP, Goldman ER. Development and evaluation of single domain antibodies for vaccinia and the L1 antigen. PLoS One 2014; 9:e106263. [PMID: 25211488 PMCID: PMC4161341 DOI: 10.1371/journal.pone.0106263] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 07/30/2014] [Indexed: 11/25/2022] Open
Abstract
There is ongoing interest to develop high affinity, thermal stable recognition elements to replace conventional antibodies in biothreat detection assays. As part of this effort, single domain antibodies that target vaccinia virus were developed. Two llamas were immunized with killed viral particles followed by boosts with the recombinant membrane protein, L1, to stimulate the immune response for envelope and membrane proteins of the virus. The variable domains of the induced heavy chain antibodies were selected from M13 phage display libraries developed from isolated RNA. Selection via biopanning on the L1 antigen produced single domain antibodies that were specific and had affinities ranging from 4×10−9 M to 7.0×10−10 M, as determined by surface plasmon resonance. Several showed good ability to refold after heat denaturation. These L1-binding single domain antibodies, however, failed to recognize the killed vaccinia antigen. Useful vaccinia binding single domain antibodies were isolated by a second selection using the killed virus as the target. The virus binding single domain antibodies were incorporated in sandwich assays as both capture and tracer using the MAGPIX system yielding limits of detection down to 4×105 pfu/ml, a four-fold improvement over the limit obtained using conventional antibodies. This work demonstrates the development of anti-vaccinia single domain antibodies and their incorporation into sandwich assays for viral detection. It also highlights the properties of high affinity and thermal stability that are hallmarks of single domain antibodies.
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Affiliation(s)
- Scott A. Walper
- Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, Washington, DC, United States of America
| | - Jinny L. Liu
- Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, Washington, DC, United States of America
| | - Daniel Zabetakis
- Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, Washington, DC, United States of America
| | - George P. Anderson
- Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, Washington, DC, United States of America
| | - Ellen R. Goldman
- Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, Washington, DC, United States of America
- * E-mail:
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37
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Turner KB, Zabetakis D, Legler P, Goldman ER, Anderson GP. Isolation and epitope mapping of staphylococcal enterotoxin B single-domain antibodies. Sensors (Basel) 2014; 14:10846-63. [PMID: 24949641 PMCID: PMC4118376 DOI: 10.3390/s140610846] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 06/09/2014] [Accepted: 06/10/2014] [Indexed: 12/22/2022]
Abstract
Single-domain antibodies (sdAbs), derived from the heavy chain only antibodies found in camelids such as llamas have the potential to provide rugged detection reagents with high affinities, and the ability to refold after denaturation. We have isolated and characterized sdAbs specific to staphylococcal enterotoxin B (SEB) which bind to two distinct epitopes and are able to function in a sandwich immunoassay for toxin detection. Characterization of these sdAbs revealed that each exhibited nanomolar binding affinities or better. Melting temperatures for the sdAbs ranged from approximately 60 °C to over 70 °C, with each demonstrating at least partial refolding after denaturation and several were able to completely refold. A first set of sdAbs was isolated by panning the library using adsorbed antigen, all of which recognized the same epitope on SEB. Epitope mapping suggested that these sdAbs bind to a particular fragment of SEB (VKSIDQFLYFDLIYSI) containing position L45 (underlined), which is involved in binding to the major histocompatibility complex (MHC). Differences in the binding affinities of the sdAbs to SEB and a less-toxic vaccine immunogen, SEBv (L45R/Y89A/Y94A) were also consistent with binding to this epitope. A sandwich panning strategy was utilized to isolate sdAbs which bind a second epitope. This epitope differed from the initial one obtained or from that recognized by previously isolated anti-SEB sdAb A3. Using SEB-toxin spiked milk we demonstrated that these newly isolated sdAbs could be utilized in sandwich-assays with each other, A3, and with various monoclonal antibodies.
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Affiliation(s)
- Kendrick B Turner
- American Society for Engineering Education, Postdoctoral Fellow at the Naval Research Laboratory, Washington, DC 20375, USA.
| | - Dan Zabetakis
- Center for Biomolecular Science and Engineering, Naval Research Laboratory, Washington, DC 20375, USA.
| | - Patricia Legler
- Center for Biomolecular Science and Engineering, Naval Research Laboratory, Washington, DC 20375, USA.
| | - Ellen R Goldman
- Center for Biomolecular Science and Engineering, Naval Research Laboratory, Washington, DC 20375, USA.
| | - George P Anderson
- Center for Biomolecular Science and Engineering, Naval Research Laboratory, Washington, DC 20375, USA.
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38
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Liu JL, Zabetakis D, Walper SA, Goldman ER, Anderson GP. Bioconjugates of rhizavidin with single domain antibodies as bifunctional immunoreagents. J Immunol Methods 2014; 411:37-42. [PMID: 24946086 DOI: 10.1016/j.jim.2014.06.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 05/09/2014] [Accepted: 06/04/2014] [Indexed: 11/18/2022]
Abstract
Use of the avidin-biotin binding interaction for immunoassay applications is widespread. One advantageous immunoreagent is the recombinant fusion of an antibody fragment with a biotin binding protein. These genetic fusions alleviate the need to prepare chemical conjugates to achieve molecules that combine target recognition with signal transduction or to facilitate the directional immobilization of the binding element. In order for such a fusion protein to be useful, however, it must be able to be produced in good yield. Unfortunately, recombinant production of avidin or streptavidin as well as bioconjugates derived thereof has been problematic. An alternative biotin binding molecule called rhizavidin has been described, which forms a homodimer instead of a tetramer, but it has not been evaluated in genetic fusions with antibody binding domains. Single domain antibodies, the variable domain derived from camelid heavy chain only antibodies, offer binding domains with high affinity, and solubility that are well expressed in Escherichia coli. In this work, we prepared an anti-ricin single domain antibody - rhizavidin bioconjugate and evaluated it on the basis of its production in E. coli and on its activity in comparison to a streptavidin core bioconjugate and unfused single domain antibody. The single domain antibody-rhizavidin bioconjugate produced much better than its streptavidin core counterparts, yielding an average of 14 mg/L, a 20-fold improvement. When used in assays the rhizavidin conjugate provided the same desirable characteristics as the streptavidin core fusion as both capture and detection reagents. Since rhizavidin and single domain antibodies both display impressive thermal stabilities their fusion provides a route to achieve robust bifunctional immunoreagents.
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Affiliation(s)
- Jinny L Liu
- Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, 4555 Overlook Ave. SW, Washington, DC 20375, USA
| | - Dan Zabetakis
- Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, 4555 Overlook Ave. SW, Washington, DC 20375, USA
| | - Scott A Walper
- Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, 4555 Overlook Ave. SW, Washington, DC 20375, USA
| | - Ellen R Goldman
- Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, 4555 Overlook Ave. SW, Washington, DC 20375, USA
| | - George P Anderson
- Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, 4555 Overlook Ave. SW, Washington, DC 20375, USA.
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Liu JL, Zabetakis D, Brown JC, Anderson GP, Goldman ER. Thermal stability and refolding capability of shark derived single domain antibodies. Mol Immunol 2014; 59:194-9. [DOI: 10.1016/j.molimm.2014.02.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 02/19/2014] [Accepted: 02/25/2014] [Indexed: 12/17/2022]
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Turner KB, Zabetakis D, Goldman ER, Anderson GP. Enhanced stabilization of a stable single domain antibody for SEB toxin by random mutagenesis and stringent selection. Protein Eng Des Sel 2014; 27:89-95. [PMID: 24488977 DOI: 10.1093/protein/gzu001] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Single domain antibodies, recombinant variable heavy domains derived from the unique heavy-chain only antibodies found in camelids and sharks, are exceptionally rugged due to their ability to refold following heat or chemical denaturation. In addition, a number of single domain antibodies have been found to possess high melting points which provide an even greater degree of stability; one of these, llama-derived A3, is a binder of Staphylococcal enterotoxin B and has a Tm of 83.5 °C. In this work, we utilized random mutagenesis and stringent selection in an effort to obtain variants of A3 with even higher melting points. This effort resulted in the selection of a double mutant, A3-T28I-S72I, which has a melting point of 90.0 °C and near wild-type affinity for the target antigen. We further characterized the mutations individually to determine that while both contributed to the thermal stabilization, the T28I mutation accounted for ∼ 4.1 °C of the 6.5 °C increase. This work demonstrates that by the addition of relatively subtle changes it is possible to further improve the melting temperature of single domain antibodies that are already remarkably stable.
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Affiliation(s)
- Kendrick B Turner
- American Society for Engineering Education Postdoctoral Fellow, Naval Research Laboratory, Washington, DC 20375, USA
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Goldman ER, Brozozog-Lee PA, Zabetakis D, Turner KB, Walper SA, Liu JL, Anderson GP. Negative tail fusions can improve ruggedness of single domain antibodies. Protein Expr Purif 2014; 95:226-32. [PMID: 24440507 DOI: 10.1016/j.pep.2014.01.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Revised: 01/06/2014] [Accepted: 01/08/2014] [Indexed: 12/31/2022]
Abstract
Single-domain antibodies (sdAbs), the recombinantly expressed binding domains derived from the heavy-chain-only antibodies found in camelids and sharks, are valued for their ability to refold after heat denaturation. However, some sdAbs are prone to aggregation on extended heating at high concentration. Additionally, sdAbs prepared cytoplasmically often lack the conserved disulfide bond found in variable heavy domains, which both decreases their melting point and can decrease their ability to refold. Genetic fusions of sdAbs with the acid tail of α-synuclein (ATS) resulted in constructs that had enhanced ability to resist aggregation. In addition, almost complete refolding was observed even in the absence of the disulfide bond. These sdAb-ATS fusions expand the utility of sdAbs. They provide sdAbs that are resistant to aggregation, and enable the production of re-foldable sdAbs in the reducing environment of the cytoplasm.
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Affiliation(s)
- Ellen R Goldman
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, 4555 Overlook Ave. SW, Washington, DC 20375, USA
| | | | - Dan Zabetakis
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, 4555 Overlook Ave. SW, Washington, DC 20375, USA
| | - Kendrick B Turner
- Science and Engineering Apprenticeship Program, American Society for Engineering Education, 4555 Overlook Ave. SW, Washington, DC 20375, USA
| | - Scott A Walper
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, 4555 Overlook Ave. SW, Washington, DC 20375, USA
| | - Jinny L Liu
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, 4555 Overlook Ave. SW, Washington, DC 20375, USA
| | - George P Anderson
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, 4555 Overlook Ave. SW, Washington, DC 20375, USA.
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Abstract
Immunoassays have been well established for many years as the cornerstone of detection technologies. These assays are sensitive, selective and, in general, highly resistant to interference from complex sample matrices when compared with nucleic acid-based tests. However, both antibody- and nucleic acid-based detection systems require a priori knowledge of the target and development of specific reagents; multiplexed assays can become increasingly problematic when attempting to detect a plethora of different targets, the identities of which are unknown. In an effort to circumvent many of the limitations inherent in these conventional assays, other recognition reagents are being explored as alternatives, or indeed as adjuncts, to antibodies for pathogen and toxin detection. This article will review a number of different recognition systems ranging in complexity from small molecules, such as nucleic-acid aptamers, carbohydrates and peptides, to systems as highly complicated as whole cells and organisms. All of these alternative systems have tremendous potential to achieve superior sensitivity, selectivity, and stability, but are also subject to their own limitations, which are also discussed. In short, while in its infancy, this field holds great promise for the development of rapid, fieldable assays that are highly complementary to existing antibody- and nucleic acid-based technologies.
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Affiliation(s)
- Miriam M Ngundi
- US Food and Drug Administration, N29 RM418 HFM-434 8800 Rockville Pike, Bethesda, MD 20892, USA.
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Liu JL, Zabetakis D, Lee AB, Goldman ER, Anderson GP. Single domain antibody–alkaline phosphatase fusion proteins for antigen detection — Analysis of affinity and thermal stability of single domain antibody. J Immunol Methods 2013; 393:1-7. [DOI: 10.1016/j.jim.2013.04.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Revised: 03/29/2013] [Accepted: 04/01/2013] [Indexed: 11/28/2022]
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Boeneman Gemmill K, Deschamps JR, Delehanty JB, Susumu K, Stewart MH, Glaven RH, Anderson GP, Goldman ER, Huston AL, Medintz IL. Optimizing protein coordination to quantum dots with designer peptidyl linkers. Bioconjug Chem 2013; 24:269-81. [PMID: 23379817 DOI: 10.1021/bc300644p] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Semiconductor quantum dots (QDs) demonstrate select optical properties that make them of particular use in biological imaging and biosensing. Controlled attachment of biomolecules such as proteins to the QD surface is thus critically necessary for development of these functional nanobiomaterials. QD surface coatings such as poly(ethylene glycol) impart colloidal stability to the QDs, making them usable in physiological environments, but can impede attachment of proteins due to steric interactions. While this problem is being partially addressed through the development of more compact QD ligands, here we present an alternative and complementary approach to this issue by engineering rigid peptidyl linkers that can be appended onto almost all expressed proteins. The linkers are specifically designed to extend a terminal polyhistidine sequence out from the globular protein structure and penetrate the QD ligand coating to enhance binding by metal-affinity driven coordination. α-Helical linkers of two lengths terminating in either a single or triple hexahistidine motif were fused onto a single-domain antibody; these were then self-assembled onto QDs to create a model immunosensor system targeted against the biothreat agent ricin. We utilized this system to systematically evaluate the peptidyl linker design in functional assays using QDs stabilized with four different types of coating ligands including poly(ethylene glycol). We show that increased linker length, but surprisingly not added histidines, can improve protein to QD attachment and sensor performance despite the surface ligand size with both custom and commercial QD preparations. Implications for these findings on the development of QD-based biosensors are discussed.
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Affiliation(s)
- Kelly Boeneman Gemmill
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, USA
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Legler PM, Zabetakis D, Anderson GP, Lam A, Hol WGJ, Goldman ER. Structure of a low-melting-temperature anti-cholera toxin: llama V(H)H domain. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:90-3. [PMID: 23385744 DOI: 10.1107/s1744309112050750] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Accepted: 12/13/2012] [Indexed: 01/29/2023]
Abstract
Variable heavy domains derived from the heavy-chain-only antibodies found in camelids (V(H)H domains) are known for their thermal stability. Here, the structure of A9, an anti-cholera toxin V(H)H domain (K(d) = 77 ± 5 nM) that has an unusually low melting temperature of 319.9 ± 1.6 K, is reported. The CDR3 residues of A9 form a β-hairpin that is directed away from the former V(H)-V(L) interfacial surface, exposing hydrophobic residues to the solvent. A DALI structural similarity search showed that this CDR3 conformation is uncommon.
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Affiliation(s)
- Patricia M Legler
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC 20375, USA.
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Anderson GP, Legler PM, Zabetakis D, Goldman ER. Comparison of Immunoreactivity of Staphylococcal Enterotoxin B Mutants for Use as Toxin Surrogates. Anal Chem 2012; 84:5198-203. [DOI: 10.1021/ac300864j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- George P. Anderson
- Center for
Bio/Molecular Science and Engineering, Naval Research Laboratory, 4555 Overlook Ave SW, Washington,
D.C. 20375, United States
| | - Patricia M. Legler
- Center for
Bio/Molecular Science and Engineering, Naval Research Laboratory, 4555 Overlook Ave SW, Washington,
D.C. 20375, United States
| | - Dan Zabetakis
- Center for
Bio/Molecular Science and Engineering, Naval Research Laboratory, 4555 Overlook Ave SW, Washington,
D.C. 20375, United States
| | - Ellen R. Goldman
- Center for
Bio/Molecular Science and Engineering, Naval Research Laboratory, 4555 Overlook Ave SW, Washington,
D.C. 20375, United States
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Swain MD, Anderson GP, Serrano-González J, Liu JL, Zabetakis D, Goldman ER. Immunodiagnostic reagents using llama single domain antibody–alkaline phosphatase fusion proteins. Anal Biochem 2011; 417:188-94. [DOI: 10.1016/j.ab.2011.06.012] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Revised: 06/02/2011] [Accepted: 06/08/2011] [Indexed: 01/22/2023]
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Taitt CR, Shriver-Lake LC, Anderson GP, Ligler FS. Surface modification and biomolecule immobilization on polymer spheres for biosensing applications. Methods Mol Biol 2011; 726:77-94. [PMID: 21424444 DOI: 10.1007/978-1-61779-052-2_6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Microspheres and nanospheres are being used in many of today's biosensing applications for automated sample processing, flow cytometry, signal amplification in microarrays, and labeling in multiplexed analyses. The surfaces of the spheres/particles need to be modified with proteins and other biomolecules to be used in these sensing applications. This chapter contains protocols to modify carboxyl- and amine-coated polymer spheres with proteins and peptides.
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Affiliation(s)
- Chris R Taitt
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory, Washington, DC, USA
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Anderson GP, Bernstein RD, Swain MD, Zabetakis D, Goldman ER. Binding kinetics of antiricin single domain antibodies and improved detection using a B chain specific binder. Anal Chem 2011; 82:7202-7. [PMID: 20687583 DOI: 10.1021/ac100961x] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Single domain antibodies are the recombinantly expressed binding fragments derived from heavy chain antibodies found in camels and llamas. These unique binding elements offer many desirable properties such as their small size ( approximately 15 kDa) and thermal stability, which makes them attractive alternatives to conventional monoclonal antibodies. We created a phage display library from llamas immunized with ricin toxoid and selected a number of single domain antibodies. Phage selected on ricin were found to bind to either ricin A chain or the intact molecule; no ricin B chain binders were identified. By panning on B chain, we identified binders and have characterized their binding to the ricin B chain. While they have a poorer affinity than the previously described A chain binders, it was found that they performed dramatically better as capture reagents for the detection of ricin, providing a limit of detection in enzyme linked immunosorbent assay (ELISA) below 100 pg/mL and excellent specificity for ricin versus the highly related RCA 120 (1 to 10 000). We also reevaluated the previously isolated antiricin single domain antibody binding kinetics using surface plasmon resonance and found their K(d)s matched closely to those previously obtained under equilibrium binding conditions measured using the Luminex flow cytometer.
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Affiliation(s)
- George P Anderson
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, DC 20375, USA
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Anderson GP, Moore M, Charles PT, Goldman ER. Bead-Based Fluid Array Detection of Pentaerythritol Tetranitrate: Comparison of Monoclonal vs. Llama Polyclonal Antibodies. ANAL LETT 2010. [DOI: 10.1080/00032711003763699] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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