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Rodrigues ÉF, Fachin AL, Marins M, Stabeli RG, Beleboni RO. Challenges in recombinant brain-derived neurotrophic factor production. Trends Biotechnol 2024; 42:522-525. [PMID: 38008688 DOI: 10.1016/j.tibtech.2023.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 11/05/2023] [Accepted: 11/06/2023] [Indexed: 11/28/2023]
Abstract
Brain-derived neurotrophic factor (BDNF) is a neurotrophin of marked commercial, scientific, diagnostic, and therapeutic interest. The preservation of its structural cystine-knot is the main challenge in its industrial production. A suitable expression system is critical to achieve the most efficient production of bioactive and stable BDNF for pharmaceutical purposes.
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Affiliation(s)
- Éllen F Rodrigues
- Biotechnology Unit, University of Ribeirão Preto/UNAERP, Ribeirão Preto, SP, Brazil
| | - Ana L Fachin
- Biotechnology Unit, University of Ribeirão Preto/UNAERP, Ribeirão Preto, SP, Brazil; Medicine School, University of Ribeirão Preto/UNAERP, Ribeirão Preto, SP, Brazil
| | - Mozart Marins
- Biotechnology Unit, University of Ribeirão Preto/UNAERP, Ribeirão Preto, SP, Brazil; Medicine School, University of Ribeirão Preto/UNAERP, Ribeirão Preto, SP, Brazil; Pharmacy School, University of Ribeirão Preto/UNAERP, Ribeirão Preto, SP, Brazil
| | - Rodrigo G Stabeli
- Oswaldo Cruz Foundation/Fiocruz-SP, Ribeirão Preto, SP, Brazil; Department of Medicine, Federal University of São Carlos, São Carlos, SP, Brazil
| | - Renê O Beleboni
- Biotechnology Unit, University of Ribeirão Preto/UNAERP, Ribeirão Preto, SP, Brazil; Medicine School, University of Ribeirão Preto/UNAERP, Ribeirão Preto, SP, Brazil; Pharmacy School, University of Ribeirão Preto/UNAERP, Ribeirão Preto, SP, Brazil.
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2
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Saisawang C, Priewkhiew S, Wongsantichon J, Reamtong O, Nopparat C, Mukda S, Ketterman AJ, Govitrapong P. Characterization of endotoxin free protein production of brain-derived neurotrophic factor (BDNF) for the study of Parkinson model in SH-SY5Y differentiated cells. Protein Expr Purif 2023; 203:106212. [PMID: 36481372 DOI: 10.1016/j.pep.2022.106212] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 11/29/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022]
Abstract
Human neuronal cells are a more appropriate cell model for neurological disease studies such as Alzheimer and Parkinson's disease. SH-SY5Y neuroblastoma cells have been widely used for differentiation into a mature neuronal cell phenotype. The cellular differentiation process begins with retinoic acid incubation, followed by incubation with brain-derived neurotrophic factor (BDNF), a recombinant protein produced in E. coli cells. Endotoxin or lipopolysaccharide (LPS) is the major component of the outer membrane of bacterial cells that triggers the activation of pro-inflammatory cytokines and ultimately cell death. Consequently, any endotoxin contamination of the recombinant BDNF used for cell culture experiments would impact on data interpretation. Therefore, in this study, we expressed the BDNF recombinant protein in bacterial endotoxin-free cells that were engineered to modify the oligosaccharide chain of LPS rendering the LPS unable to trigger the immune response of human cells. The expression of DCX and MAP-2 in differentiated cells indicate that in-house and commercial BDNF are equally effective in inducing differentiation. This suggests that our in-house BDNF protein can be used to differentiate SH-SY5Y neuroblastoma cells without the need for an endotoxin removal step.
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Affiliation(s)
- Chonticha Saisawang
- Molecular Medical Biosciences Cluster, Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhon Pathom, 73170, Thailand.
| | - Suphansa Priewkhiew
- Molecular Medical Biosciences Cluster, Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhon Pathom, 73170, Thailand
| | - Jantana Wongsantichon
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Onrapak Reamtong
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Chutikorn Nopparat
- Innovative Learning Center, Srinakharinwirot University, Sukhumvit 23, Bangkok, 10110, Thailand
| | - Sujira Mukda
- Research Center for Neuroscience, Institute of Molecular Biosciences, Mahidol University, 25/25 Putthamonthol Road 4, Salaya, Nakhon Pathom, 73170, Thailand
| | - Albert J Ketterman
- Molecular Medical Biosciences Cluster, Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhon Pathom, 73170, Thailand
| | - Piyarat Govitrapong
- Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok, 10210, Thailand
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3
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Heinzelman P, Romero PA. Directed evolution of angiotensin-converting enzyme 2 (ACE2) peptidase activity profiles for therapeutic applications. Protein Sci 2023; 32:e4597. [PMID: 36794431 PMCID: PMC10019445 DOI: 10.1002/pro.4597] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/19/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023]
Abstract
Angiotensin-Converting Enzyme 2 (ACE2) has been investigated for its ability to beneficially modulate the Angiotensin receptor (ATR) therapeutic axis to treat multiple human diseases. Its broad substrate scope and diverse physiological roles however, limit its potential as a therapeutic agent. In this work, we address this limitation by establishing a yeast display-based liquid chromatography screen that enabled use of directed evolution to discover ACE2 variants that possess both wildtype or greater Ang-II hydrolytic activity and improved specificity toward Ang-II relative to the off-target peptide substrate Apelin-13. To obtain these results, we screened ACE2 active site libraries to reveal three substitution-tolerant positions (M360, T371 and Y510) that can be mutated to enhance ACE2's activity profile and followed up on these hits with focused double mutant libraries to further improve the enzyme. Relative to wildtype ACE2, our top variant (T371L/Y510Ile) displayed a sevenfold increase in Ang-II turnover number (kcat ), a sixfold diminished catalytic efficiency (kcat /Km ) on Apelin-13, and an overall decreased activity on other ACE2 substrates that were not directly assayed in the directed evolution screen. At physiologically relevant substrate concentrations, T371L/Y510Ile hydrolyzes as much or more Ang-II than wildtype ACE2 with concomitant Ang-II:Apelin-13 specificity improvements reaching 30-fold. Our efforts have delivered ATR axis-acting therapeutic candidates with relevance to both established and unexplored ACE2 therapeutic applications and provide a foundation for further ACE2 engineering efforts. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Pete Heinzelman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Philip A Romero
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.,Department of Chemical & Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
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4
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Fay JM, Lim C, Finkelstein A, Batrakova EV, Kabanov AV. PEG-Free Polyion Complex Nanocarriers for Brain-Derived Neurotrophic Factor. Pharmaceutics 2022; 14:pharmaceutics14071391. [PMID: 35890287 PMCID: PMC9317007 DOI: 10.3390/pharmaceutics14071391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/29/2022] [Accepted: 06/29/2022] [Indexed: 12/10/2022] Open
Abstract
Many therapeutic formulations incorporate poly(ethylene glycol) (PEG) as a stealth component to minimize early clearance. However, PEG is immunogenic and susceptible to accelerated clearance after multiple administrations. Here, we present two novel reformulations of a polyion complex (PIC), originally composed of poly(ethylene glycol)113-b-poly(glutamic acid)50 (PEG-PLE) and brain-derived neurotrophic factor (BDNF), termed Nano-BDNF (Nano-BDNF PEG-PLE). We replace the PEG based block copolymer with two new polymers, poly(sarcosine)127-b-poly(glutamic acid)50 (PSR-PLE) and poly(methyl-2-oxazolines)38-b-poly(oxazolepropanoic acid)27-b-poly(methyl-2-oxazoline)38 (PMeOx-PPaOx-PMeOx), which are driven to association with BDNF via electrostatic interactions and hydrogen bonding to form a PIC. Formulation using a microfluidic mixer yields small and narrowly disperse nanoparticles which associate following similar principles. Additionally, we demonstrate that encapsulation does not inhibit access by the receptor kinase, which affects BDNF’s physiologic benefits. Finally, we investigate the formation of nascent nanoparticles through a series of characterization experiments and isothermal titration experiments which show the effects of pH in the context of particle self-assembly. Our findings indicate that thoughtful reformulation of PEG based, therapeutic PICs with non-PEG alternatives can be accomplished without compromising the self-assembly of the PIC.
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Affiliation(s)
- James M. Fay
- Center for Nanotechnology in Drug Delivery, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599-7362, USA; (J.M.F.); (C.L.); (E.V.B.)
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, NC 27599-7260, USA
| | - Chaemin Lim
- Center for Nanotechnology in Drug Delivery, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599-7362, USA; (J.M.F.); (C.L.); (E.V.B.)
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599-7260, USA
| | - Anna Finkelstein
- Center for Nanotechnology in Drug Delivery, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599-7362, USA; (J.M.F.); (C.L.); (E.V.B.)
| | - Elena V. Batrakova
- Center for Nanotechnology in Drug Delivery, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599-7362, USA; (J.M.F.); (C.L.); (E.V.B.)
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599-7260, USA
| | - Alexander V. Kabanov
- Center for Nanotechnology in Drug Delivery, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599-7362, USA; (J.M.F.); (C.L.); (E.V.B.)
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599-7260, USA
- Laboratory of Chemical Design of Bionanomaterials, Faculty of Chemistry, M.V. Lomonosov Moscow State University, 119992 Moscow, Russia
- Correspondence:
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Raeeszadeh-Sarmazdeh M, Boder ET. Yeast Surface Display: New Opportunities for a Time-Tested Protein Engineering System. Methods Mol Biol 2022; 2491:3-25. [PMID: 35482182 DOI: 10.1007/978-1-0716-2285-8_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Yeast surface display has proven to be a powerful tool for the discovery of antibodies and other novel binding proteins and for engineering the affinity and selectivity of existing proteins for their targets. In the decades since the first demonstrations of the approach, the range of yeast display applications has greatly expanded to include many different protein targets and has grown to encompass methods for rapid protein characterization. Here, we briefly summarize the development of yeast display methodologies and highlight several selected examples of recent applications to timely and challenging protein engineering and characterization problems.
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Affiliation(s)
| | - Eric T Boder
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN, USA.
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6
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Heinzelman P, Romero PA. Discovery of human ACE2 variants with altered recognition by the SARS-CoV-2 spike protein. PLoS One 2021; 16:e0251585. [PMID: 33979391 PMCID: PMC8115845 DOI: 10.1371/journal.pone.0251585] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 04/29/2021] [Indexed: 01/25/2023] Open
Abstract
Understanding how human ACE2 genetic variants differ in their recognition by SARS-CoV-2 can facilitate the leveraging of ACE2 as an axis for treating and preventing COVID-19. In this work, we experimentally interrogate thousands of ACE2 mutants to identify over one hundred human single-nucleotide variants (SNVs) that are likely to have altered recognition by the virus, and make the complementary discovery that ACE2 residues distant from the spike interface influence the ACE2-spike interaction. These findings illuminate new links between ACE2 sequence and spike recognition, and could find substantial utility in further fundamental research that augments epidemiological analyses and clinical trial design in the contexts of both existing strains of SARS-CoV-2 and novel variants that may arise in the future.
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Affiliation(s)
- Pete Heinzelman
- Department of Biochemistry, University of Wisconsin—Madison, Madison, WI, United States of America
| | - Philip A. Romero
- Department of Biochemistry, University of Wisconsin—Madison, Madison, WI, United States of America
- Department of Chemical & Biological Engineering, University of Wisconsin—Madison, Madison, WI, United States of America
- * E-mail:
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7
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Heinzelman P, Romero PA. Discovery of human ACE2 variants with altered recognition by the SARS-CoV-2 spike protein. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.09.17.301861. [PMID: 32995796 PMCID: PMC7523126 DOI: 10.1101/2020.09.17.301861] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Understanding how human ACE2 genetic variants differ in their recognition by SARS-CoV-2 can have a major impact in leveraging ACE2 as an axis for treating and preventing COVID-19. In this work, we experimentally interrogate thousands of ACE2 mutants to identify over one hundred human single-nucleotide variants (SNVs) that are likely to have altered recognition by the virus, and make the complementary discovery that ACE2 residues distant from the spike interface can have a strong influence upon the ACE2-spike interaction. These findings illuminate new links between ACE2 sequence and spike recognition, and will find wide-ranging utility in SARS-CoV-2 fundamental research, epidemiological analyses, and clinical trial design.
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Affiliation(s)
- Pete Heinzelman
- Department of Biochemistry, University of Wisconsin--Madison, Madison, WI, USA
| | - Philip A. Romero
- Department of Biochemistry, University of Wisconsin--Madison, Madison, WI, USA
- Department of Chemical & Biological Engineering, University of Wisconsin--Madison, Madison, WI, USA
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8
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Umlauf BJ, Clark PA, Lajoie JM, Georgieva JV, Bremner S, Herrin BR, Kuo JS, Shusta EV. Identification of variable lymphocyte receptors that can target therapeutics to pathologically exposed brain extracellular matrix. SCIENCE ADVANCES 2019; 5:eaau4245. [PMID: 31106264 PMCID: PMC6520025 DOI: 10.1126/sciadv.aau4245] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 04/02/2019] [Indexed: 05/21/2023]
Abstract
Diseases that lead to blood-brain barrier (BBB) disruption will pathologically expose normally inaccessible brain extracellular matrix (ECM) to circulating blood components. Therefore, we hypothesized that brain ECM-targeting moieties could specifically target the disrupted BBB and potentially deliver therapies. Variable lymphocyte receptors (VLRs) that preferentially associate with brain ECM were identified from an immune VLR library via yeast surface display biopanning coupled with a moderate throughput ECM screen. Brain ECM binding of VLR clones to murine and human brain tissue sections was confirmed. After systemic administration, P1C10, the lead brain ECM-targeting VLR candidate, specifically accumulated in brains with mannitol-disrupted BBB and at disrupted BBB regions in two different intracranial glioblastoma models. We also demonstrate P1C10's ability to deliver doxorubicin-loaded liposomes, leading to significantly improved survival in glioblastoma-bearing mice. Thus, VLRs can be used to selectively target pathologically exposed brain ECM and deliver drug payloads.
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Affiliation(s)
- Benjamin J. Umlauf
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Paul A. Clark
- Department of Neurological Surgery, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, USA
| | - Jason M. Lajoie
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Julia V. Georgieva
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Samantha Bremner
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | | | - John S. Kuo
- Department of Neurological Surgery, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, USA
- Carbone Cancer Center, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, USA
- Department of Neurosurgery, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
- Mulva Clinic for the Neurosciences, The University of Texas at Austin, Austin, TX, USA
- Corresponding author. (E.V.S.); (J.S.K.)
| | - Eric V. Shusta
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
- Carbone Cancer Center, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, USA
- Corresponding author. (E.V.S.); (J.S.K.)
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9
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Raeeszadeh-Sarmazdeh M, Patel N, Cruise S, Owen L, O'Neill H, Boder ET. Identifying Stable Fragments of Arabidopsis thaliana Cellulose Synthase Subunit 3 by Yeast Display. Biotechnol J 2018; 14:e1800353. [PMID: 30171735 DOI: 10.1002/biot.201800353] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 08/08/2018] [Indexed: 12/22/2022]
Abstract
Determining structures of large, complex proteins remains challenging, especially for transmembrane proteins, as the protein size increases. Arabidopsis thaliana cellulose synthesis complex is a large, multimeric complex located in the plant cell membrane that synthesizes cellulose microfibrils in the plant cell wall. Despite the biological and economic importance of cellulose and therefore cellulose synthesis, many aspects of the cellulase synthase complex (CSC) structure and function are still unknown. Here, yeast surface display (YSD) is used to determine the full-length expression of A. thaliana cellulose synthase 3 (AtCesA3) fragments. The level of stably-folded AtCesA3 fragments displayed on the yeast surface are determined using flow cytometric analysis of differential surface expression of epitopes flanking the AtCesA3 fragment. This technique provides a fast and simple method for examining folding and expression of protein domains and fragments of complex proteins.
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Affiliation(s)
- Maryam Raeeszadeh-Sarmazdeh
- Department of Chemical and Biomolecular Engineering, University of Tennessee at Knoxville, Knoxville, TN 37996
| | - Nikhil Patel
- Department of Chemical and Biomolecular Engineering, University of Tennessee at Knoxville, Knoxville, TN 37996
| | - Sarah Cruise
- Department of Chemical and Biomolecular Engineering, University of Tennessee at Knoxville, Knoxville, TN 37996
| | - Leila Owen
- Department of Chemical and Biomolecular Engineering, University of Tennessee at Knoxville, Knoxville, TN 37996
| | - Hugh O'Neill
- Center for Structural Molecular Biology and Neutron Scsattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
| | - Eric T Boder
- Department of Chemical and Biomolecular Engineering, University of Tennessee at Knoxville, Knoxville, TN 37996
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10
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Li D, Wang L, Maziuk BF, Yao X, Wolozin B, Cho YK. Directed evolution of a picomolar-affinity, high-specificity antibody targeting phosphorylated tau. J Biol Chem 2018; 293:12081-12094. [PMID: 29899114 PMCID: PMC6078456 DOI: 10.1074/jbc.ra118.003557] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 06/12/2018] [Indexed: 01/03/2023] Open
Abstract
Antibodies are essential biochemical reagents for detecting protein post-translational modifications (PTMs) in complex samples. However, recent efforts in developing PTM-targeting antibodies have reported frequent nonspecific binding and limited affinity of such antibodies. To address these challenges, we investigated whether directed evolution could be applied to improve the affinity of a high-specificity antibody targeting phosphothreonine 231 (pThr-231) of the human microtubule-associated protein tau. On the basis of existing structural information, we hypothesized that improving antibody affinity may come at the cost of loss in specificity. To test this hypothesis, we developed a novel approach using yeast surface display to quantify the specificity of PTM-targeting antibodies. When we affinity-matured the single-chain variable antibody fragment through directed evolution, we found that its affinity can be improved >20-fold over that of the WT antibody, reaching a picomolar range. We also discovered that most of the high-affinity variants exhibit cross-reactivity toward the nonphosphorylated target site but not to the phosphorylation site with a scrambled sequence. However, systematic quantification of the specificity revealed that such a tradeoff between the affinity and specificity did not apply to all variants and led to the identification of a picomolar-affinity variant that has a matching high specificity of the original phosphotau antibody. In cell- and tissue-imaging experiments, the high-affinity variant gave significantly improved signal intensity while having no detectable nonspecific binding. These results demonstrate that directed evolution is a viable approach for obtaining high-affinity PTM-specific antibodies and highlight the importance of assessing the specificity in the antibody engineering process.
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Affiliation(s)
- Dan Li
- Department of Biomedical Engineering, University of Connecticut, Storrs, Connecticut 06269
| | - Lei Wang
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269
| | - Brandon F Maziuk
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, Massachusetts 02118
| | - Xudong Yao
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269; Department of Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut 06269
| | - Benjamin Wolozin
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, Massachusetts 02118
| | - Yong Ku Cho
- Department of Biomedical Engineering, University of Connecticut, Storrs, Connecticut 06269; Department of Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut 06269; Department of Chemical and Biomolecular Engineering, University of Connecticut, Storrs, Connecticut 06269.
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11
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Umlauf BJ, Mix KA, Grosskopf VA, Raines RT, Shusta EV. Site-Specific Antibody Functionalization Using Tetrazine-Styrene Cycloaddition. Bioconjug Chem 2018; 29:1605-1613. [PMID: 29694034 DOI: 10.1021/acs.bioconjchem.8b00114] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Biologics, such as antibody-drug conjugates, are becoming mainstream therapeutics. Consequently, methods to functionalize biologics without disrupting their native properties are essential for identifying, characterizing, and translating candidate biologics from the bench to clinical practice. Here, we present a method for site-specific, carboxy-terminal modification of single-chain antibody fragments (scFvs). ScFvs displayed on the surface of yeast were isolated and functionalized by combining intein-mediated expressed protein ligation (EPL) with inverse electron-demand Diels-Alder (IEDDA) cycloaddition using a styrene-tetrazine pair. The high thiol concentration required to trigger EPL can hinder the subsequent chemoselective ligation reactions; therefore, the EPL reaction was used to append styrene to the scFv, limiting tetrazine exposure to damaging thiols. Subsequently, the styrene-functionalized scFv was reacted with tetrazine-conjugated compounds in an IEDDA cycloaddition to generate functionalized scFvs that retain their native binding activity. Rapid functionalization of yeast surface-derived scFv in a site-directed manner could find utility in many downstream laboratory and preclinical applications.
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12
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Medina-Cucurella AV, Zhu Y, Bowen SJ, Bergeron LM, Whitehead TA. Pro region engineering of nerve growth factor by deep mutational scanning enables a yeast platform for conformational epitope mapping of anti-NGF monoclonal antibodies. Biotechnol Bioeng 2018; 115:1925-1937. [PMID: 29663315 DOI: 10.1002/bit.26706] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 03/29/2018] [Accepted: 04/03/2018] [Indexed: 01/19/2023]
Abstract
Nerve growth factor (NGF) plays a central role in multiple chronic pain conditions. As such, anti-NGF monoclonal antibodies (mAbs) that function by antagonizing NGF downstream signaling are leading drug candidates for non-opioid pain relief. To evaluate anti-canine NGF (cNGF) mAbs we sought a yeast surface display platform of cNGF. Both mature cNGF and pro-cNGF displayed on the yeast surface but bound conformationally sensitive mAbs at most 2.5-fold in mean fluorescence intensity above background, suggesting that cNGF was mostly misfolded. To improve the amount of folded, displayed cNGF, we used comprehensive mutagenesis, FACS, and deep sequencing to identify point mutants in the pro-region of canine NGF that properly enhance the folded protein displayed on the yeast surface. Out of 1,737 tested single point mutants in the pro region, 49 increased the amount of NGF recognized by conformationally sensitive mAbs. These gain-of-function mutations cluster around residues A-61-P-26. Gain-of-function mutants were additive, and a construct containing three mutations increased amount of folded cNGF to 23-fold above background. Using this new cNGF construct, fine conformational epitopes for tanezumab and three anti-cNGF mAbs were evaluated. The epitope revealed by the yeast experiments largely overlapped with the tanezumab epitope previously determined by X-ray crystallography. The other mAbs showed site-specific differences with tanezumab. As the number of binding epitopes of functionally neutralizing anti-NGF mAbs on NGF are limited, subtle differences in the individual interacting residues on NGF that bind each mAb contribute to the understanding of each antibody and variations in its neutralizing activity. These results demonstrate the potential of deep sequencing-guided protein engineering to improve the production of folded surface-displayed protein, and the resulting cNGF construct provides a platform to map conformational epitopes for other anti-neurotrophin mAbs.
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Affiliation(s)
- Angélica V Medina-Cucurella
- Department of Chemical Engineering and Materials Science, Michigan State University Engineering Building, East Lansing, Michigan
| | - Yaqi Zhu
- Zoetis Global Therapeutic Research, Veterinary Medicine Research and Development, Kalamazoo, Michigan
| | - Scott J Bowen
- Zoetis Global Therapeutic Research, Veterinary Medicine Research and Development, Kalamazoo, Michigan
| | - Lisa M Bergeron
- Zoetis Global Therapeutic Research, Veterinary Medicine Research and Development, Kalamazoo, Michigan
| | - Timothy A Whitehead
- Department of Chemical Engineering and Materials Science, Michigan State University Engineering Building, East Lansing, Michigan.,Department of Biosystems and Agricultural Engineering, Michigan State University, East Lansing, Michigan.,Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, Michigan
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13
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VLR Recognition of TLR5 Expands the Molecular Characterization of Protein Antigen Binding by Non-Ig-based Antibodies. J Mol Biol 2018; 430:1350-1367. [PMID: 29596914 DOI: 10.1016/j.jmb.2018.03.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 03/20/2018] [Accepted: 03/20/2018] [Indexed: 01/24/2023]
Abstract
Variable lymphocyte receptors (VLRs) are unconventional adaptive immune receptors relatively recently discovered in the phylogenetically ancient jawless vertebrates, lamprey and hagfish. VLRs bind antigens using a leucine-rich repeat fold and are the only known adaptive immune receptors that do not utilize an immunoglobulin fold for antigen recognition. While immunoglobulin antibodies have been studied extensively, there are comparatively few studies on antigen recognition by VLRs, particularly for protein antigens. Here we report isolation, functional and structural characterization of three VLRs that bind the protein toll-like receptor 5 (TLR5) from zebrafish. Two of the VLRs block binding of TLR5 to its cognate ligand flagellin in functional assays using reporter cells. Co-crystal structures revealed that these VLRs bind to two different epitopes on TLR5, both of which include regions involved in flagellin binding. Our work here demonstrates that the lamprey adaptive immune system can be used to generate high-affinity VLR clones that recognize different epitopes and differentially impact natural ligand binding to a protein antigen.
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Jiang Y, Fay JM, Poon CD, Vinod N, Zhao Y, Bullock K, Qin S, Manickam DS, Yi X, Banks WA, Kabanov AV. Nanoformulation of Brain-Derived Neurotrophic Factor with Target Receptor-Triggered-Release in the Central Nervous System. ADVANCED FUNCTIONAL MATERIALS 2018; 28:1703982. [PMID: 29785179 PMCID: PMC5958903 DOI: 10.1002/adfm.201703982] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Brain-derived neurotrophic factor (BDNF) is identified as a potent neuroprotective and neuroregenerative agent for many neurological diseases. Regrettably, its delivery to the brain is hampered by poor serum stability and rapid brain clearance. Here, a novel nanoformulation is reported composed of a bio-compatible polymer, poly(ethylene glycol)-b-poly(L-glutamic acid) (PEG-PLE), that hosts the BDNF molecule in a nanoscale complex, termed here Nano-BDNF. Upon simple mixture, Nano-BDNF spontaneously forms uniform spherical particles with a core-shell structure. Molecular dynamics simulations suggest that binding between BDNF and PEG-PLE is mediated through electrostatic coupling as well as transient hydrogen bonding. The formation of Nano-BDNF complex stabilizes BDNF and protects it from nonspecific binding with common proteins in the body fluid, while allowing it to associate with its receptors. Following intranasal administration, the nanoformulation improves BDNF delivery throughout the brain and displays a more preferable regional distribution pattern than the native protein. Furthermore, intranasally delivered Nano-BDNF results in superior neuroprotective effects in the mouse brain with lipopolysaccharides-induced inflammation, indicating promise for further evaluation of this agent for the therapy of neurologic diseases.
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Affiliation(s)
| | - James M. Fay
- Center for Nanotechnology in Drug Delivery, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599-7362, USA
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, NC 27599-7260, USA
| | - Chi-Duen Poon
- Research Computer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Natasha Vinod
- Center for Nanotechnology in Drug Delivery, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599-7362, USA
- Joint UNC/NC State Department of Biomedical Engineering, University of North Carolina, Chapel Hill, NC 27599-7575, USA
| | - Yuling Zhao
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599-7362, USA
- Center for Nanotechnology in Drug Delivery, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599-7362, USA
| | - Kristin Bullock
- Geriatric Research Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, Seattle, WA 98108, USA
- Division of Gerontology and Geriatric Medicine, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98108, USA
| | - Si Qin
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599-7362, USA
- Center for Nanotechnology in Drug Delivery, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599-7362, USA
| | | | - Xiang Yi
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599-7362, USA
- Center for Nanotechnology in Drug Delivery, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599-7362, USA
| | - William A. Banks
- Geriatric Research Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, Seattle, WA 98108, USA
- Division of Gerontology and Geriatric Medicine, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98108, USA
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15
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Zorniak M, Clark PA, Umlauf BJ, Cho Y, Shusta EV, Kuo JS. Yeast display biopanning identifies human antibodies targeting glioblastoma stem-like cells. Sci Rep 2017; 7:15840. [PMID: 29158489 PMCID: PMC5696472 DOI: 10.1038/s41598-017-16066-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 11/07/2017] [Indexed: 01/01/2023] Open
Abstract
Glioblastoma stem-like cells (GSC) are hypothesized to evade current therapies and cause tumor recurrence, contributing to poor patient survival. Existing cell surface markers for GSC are developed from embryonic or neural stem cell systems; however, currently available GSC markers are suboptimal in sensitivity and specificity. We hypothesized that the GSC cell surface proteome could be mined with a yeast display antibody library to reveal novel immunophenotypes. We isolated an extensive collection of antibodies that were differentially selective for GSC. A single domain antibody VH-9.7 showed selectivity for five distinct patient-derived GSC lines and visualized orthotopic GBM xenografts in vivo after conjugation with a near-infrared dye. These findings demonstrate a previously unexplored high-throughput strategy for GSC-selective antibody discovery, to aid in GSC isolation, diagnostic imaging, and therapeutic targeting.
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Affiliation(s)
- Michael Zorniak
- Neuroscience Training Program, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53792-8660, USA.,Department of Neurological Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53792-8660, USA
| | - Paul A Clark
- Department of Neurological Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53792-8660, USA
| | - Benjamin J Umlauf
- Department of Chemical and Biological Engineering, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53792-8660, USA
| | - Yongku Cho
- Department of Chemical and Biological Engineering, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53792-8660, USA
| | - Eric V Shusta
- Department of Chemical and Biological Engineering, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53792-8660, USA. .,Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53792-8660, USA.
| | - John S Kuo
- Neuroscience Training Program, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53792-8660, USA. .,Department of Neurological Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53792-8660, USA. .,Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53792-8660, USA.
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16
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Collins BC, Gunn RJ, McKitrick TR, Cummings RD, Cooper MD, Herrin BR, Wilson IA. Structural Insights into VLR Fine Specificity for Blood Group Carbohydrates. Structure 2017; 25:1667-1678.e4. [PMID: 28988747 PMCID: PMC5677568 DOI: 10.1016/j.str.2017.09.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 08/16/2017] [Accepted: 09/01/2017] [Indexed: 12/28/2022]
Abstract
High-quality reagents to study and detect glycans with high specificity for research and clinical applications are severely lacking. Here, we structurally and functionally characterize several variable lymphocyte receptor (VLR)-based antibodies from lampreys immunized with O erythrocytes that specifically recognize the blood group H-trisaccharide type II antigen. Glycan microarray analysis and biophysical data reveal that these VLRs exhibit greater specificity for H-trisaccharide compared with the plant lectin UEA-1, which is widely used in blood typing. Among these antibodies, O13 exhibits superior specificity for H-trisaccharide, the basis for which is revealed by comparative analysis of high-resolution VLR:glycan crystal structures. Using a structure-guided approach, we designed an O13 mutant with further enhanced specificity for H-trisaccharide. These insights into glycan recognition by VLRs suggest that lampreys can produce highly specific glycan antibodies, and are a valuable resource for the production of next-generation glycan reagents for biological and biomedical research and as diagnostics and therapeutics.
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MESH Headings
- Amino Acid Sequence
- Animals
- Antibodies, Monoclonal/biosynthesis
- Antibodies, Monoclonal/chemistry
- Antibodies, Monoclonal/isolation & purification
- Antibody Specificity
- Binding Sites
- Blood Group Antigens/analysis
- Blood Group Antigens/immunology
- Blood Grouping and Crossmatching/methods
- Crystallography, X-Ray
- Erythrocytes/chemistry
- Erythrocytes/immunology
- Humans
- Immunization
- Lampreys/immunology
- Models, Molecular
- Plant Lectins/chemistry
- Plant Lectins/immunology
- Polysaccharides/chemistry
- Polysaccharides/immunology
- Polysaccharides/metabolism
- Protein Binding
- Protein Conformation
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Receptors, Antigen, T-Cell/chemistry
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Sequence Alignment
- Sequence Homology, Amino Acid
- Trisaccharides/chemistry
- Trisaccharides/immunology
- Trisaccharides/metabolism
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Affiliation(s)
- Bernard C Collins
- Department of Integrative Structural and Computational Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Robin J Gunn
- Department of Integrative Structural and Computational Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tanya R McKitrick
- National Center for Functional Glycomics, Beth Israel Deaconess Medical Center Department of Surgery, Harvard Medical School, 330 Brookline Avenue, Boston, MA 02215, USA
| | - Richard D Cummings
- National Center for Functional Glycomics, Beth Israel Deaconess Medical Center Department of Surgery, Harvard Medical School, 330 Brookline Avenue, Boston, MA 02215, USA
| | - Max D Cooper
- Emory Vaccine Center and Department of Pathology and Laboratory Medicine, Emory University, 1462 Clifton Road North-East, Atlanta, GA 30322, USA
| | - Brantley R Herrin
- Emory Vaccine Center and Department of Pathology and Laboratory Medicine, Emory University, 1462 Clifton Road North-East, Atlanta, GA 30322, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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17
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Angart PA, Carlson RJ, Thorwall S, Patrick Walton S. Use of Brevibacillus choshinensis for the production of biologically active brain-derived neurotrophic factor (BDNF). Appl Microbiol Biotechnol 2017; 101:5645-5652. [DOI: 10.1007/s00253-017-8273-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 03/09/2017] [Accepted: 03/23/2017] [Indexed: 01/08/2023]
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18
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Velásquez AC, Nomura K, Cooper MD, Herrin BR, He SY. Leucine-rich-repeat-containing variable lymphocyte receptors as modules to target plant-expressed proteins. PLANT METHODS 2017; 13:29. [PMID: 28428809 PMCID: PMC5395774 DOI: 10.1186/s13007-017-0180-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Accepted: 04/09/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND The ability to target and manipulate protein-based cellular processes would accelerate plant research; yet, the technology to specifically and selectively target plant-expressed proteins is still in its infancy. Leucine-rich repeats (LRRs) are ubiquitously present protein domains involved in mediating protein-protein interactions. LRRs confer the binding specificity to the highly diverse variable lymphocyte receptor (VLR) antibodies (including VLRA, VLRB and VLRC types) that jawless vertebrates make as the functional equivalents of jawed vertebrate immunoglobulin-based antibodies. RESULTS In this study, VLRBs targeting an effector protein from a plant pathogen, HopM1, were developed by immunizing lampreys and using yeast surface display to select for high-affinity VLRBs. HopM1-specific VLRBs (VLRM1) were expressed in planta in the cytosol, the trans-Golgi network, and the apoplast. Expression of VLRM1 was higher when the protein localized to an oxidizing environment that would favor disulfide bridge formation (when VLRM1 was not localized to the cytoplasm), as disulfide bonds are necessary for proper VLR folding. VLRM1 specifically interacted in planta with HopM1 but not with an unrelated bacterial effector protein while HopM1 failed to interact with a non-specific VLRB. CONCLUSIONS In the future, VLRs may be used as flexible modules to bind proteins or carbohydrates of interest in planta, with broad possibilities for their use by binding directly to their targets and inhibiting their action, or by creating chimeric proteins with new specificities in which endogenous LRR domains are replaced by those present in VLRs.
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Affiliation(s)
- André C. Velásquez
- DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824 USA
| | - Kinya Nomura
- DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824 USA
| | - Max D. Cooper
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30322 USA
| | - Brantley R. Herrin
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30322 USA
| | - Sheng Yang He
- DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824 USA
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824 USA
- Plant Resilience Institute, Michigan State University, East Lansing, MI 48824 USA
- Howard Hughes Medical Institute, Gordon and Betty Moore Foundation, Michigan State University, East Lansing, MI 48824 USA
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19
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Adams RM, Mora T, Walczak AM, Kinney JB. Measuring the sequence-affinity landscape of antibodies with massively parallel titration curves. eLife 2016; 5. [PMID: 28035901 PMCID: PMC5268739 DOI: 10.7554/elife.23156] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 12/27/2016] [Indexed: 11/30/2022] Open
Abstract
Despite the central role that antibodies play in the adaptive immune system and in biotechnology, much remains unknown about the quantitative relationship between an antibody’s amino acid sequence and its antigen binding affinity. Here we describe a new experimental approach, called Tite-Seq, that is capable of measuring binding titration curves and corresponding affinities for thousands of variant antibodies in parallel. The measurement of titration curves eliminates the confounding effects of antibody expression and stability that arise in standard deep mutational scanning assays. We demonstrate Tite-Seq on the CDR1H and CDR3H regions of a well-studied scFv antibody. Our data shed light on the structural basis for antigen binding affinity and suggests a role for secondary CDR loops in establishing antibody stability. Tite-Seq fills a large gap in the ability to measure critical aspects of the adaptive immune system, and can be readily used for studying sequence-affinity landscapes in other protein systems. DOI:http://dx.doi.org/10.7554/eLife.23156.001 Antibodies are proteins produced by cells of the immune system to tag or neutralize potential threats to the body, such as foreign substances and disease-causing microbes. Antibodies do this by binding to target molecules called antigens. An antibody’s ability to bind to an antigen depends on the sequence of amino acids – the building blocks of proteins – that make up the antibody. Through a process that randomizes this sequence of amino acids, the immune system generates a vast pool of antibodies that are able to target almost any foreign antigen that exists in nature. Currently, little is understood about how the sequence of amino acids in an antibody determines how strongly that antibody binds to its antigen target – a property referred to as the antibody’s binding affinity. Answering this fundamental question requires techniques that can measure the affinities of many different antibodies at the same time. However, previous high-throughput methods have been unable to provide quantitative measurements of binding affinities. These kinds of measurements are difficult because an antibody’s amino acid sequence governs more than just binding affinity: it also affects how easy it is to produce that antibody, and what fraction of antibody molecules work properly. Adams et al. now describe a new method, named “Tite-Seq”, that overcomes these issues. First, thousands of different antibodies are displayed on the surface of yeast cells, with each cell carrying a single kind of antibody. These cells are then incubated with fluorescently labeled antigen at a wide range of different concentrations. Next, the yeast cells are sorted based on how brightly they glow; brighter cells have more antigen bound to them, and so it is possible to calculate how much of the antigen is bound to each kind of antibody at each concentration. Plotting these data provides a “binding curve” for each antibody, which is then used to read off the antibody’s binding affinity in a way that is not affected by the factors that have plagued other high-throughput methods. Tite-Seq is thus able to measure the binding affinities for thousands of different antibodies at the same time. This will potentially allow researchers to address many fundamental and yet unanswered questions about how the immune system works. Tite-Seq can also be used to measure how amino acid sequence affects the binding affinity of proteins other than antibodies. DOI:http://dx.doi.org/10.7554/eLife.23156.002
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Affiliation(s)
- Rhys M Adams
- Laboratoire de Physique Théorique, UMR8549, CNRS, École Normale Supérieure, Paris, France.,Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
| | - Thierry Mora
- Laboratoire de Physique Statistique, UMR8550, CNRS, École Normale Supérieure, Paris, France
| | - Aleksandra M Walczak
- Laboratoire de Physique Théorique, UMR8549, CNRS, École Normale Supérieure, Paris, France
| | - Justin B Kinney
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
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20
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Kowalsky CA, Whitehead TA. Determination of binding affinity upon mutation for type I dockerin-cohesin complexes from Clostridium thermocellum and Clostridium cellulolyticum using deep sequencing. Proteins 2016; 84:1914-1928. [PMID: 27699856 DOI: 10.1002/prot.25175] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 09/05/2016] [Accepted: 09/27/2016] [Indexed: 12/27/2022]
Abstract
The comprehensive sequence determinants of binding affinity for type I cohesin toward dockerin from Clostridium thermocellum and Clostridium cellulolyticum was evaluated using deep mutational scanning coupled to yeast surface display. We measured the relative binding affinity to dockerin for 2970 and 2778 single point mutants of C. thermocellum and C. cellulolyticum, respectively, representing over 96% of all possible single point mutants. The interface ΔΔG for each variant was reconstructed from sequencing counts and compared with the three independent experimental methods. This reconstruction results in a narrow dynamic range of -0.8-0.5 kcal/mol. The computational software packages FoldX and Rosetta were used to predict mutations that disrupt binding by more than 0.4 kcal/mol. The area under the curve of receiver operator curves was 0.82 for FoldX and 0.77 for Rosetta, showing reasonable agreements between predictions and experimental results. Destabilizing mutations to core and rim positions were predicted with higher accuracy than support positions. This benchmark dataset may be useful for developing new computational prediction tools for the prediction of the mutational effect on binding affinities for protein-protein interactions. Experimental considerations to improve precision and range of the reconstruction method are discussed. Proteins 2016; 84:1914-1928. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Caitlin A Kowalsky
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan, 48824
| | - Timothy A Whitehead
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan, 48824
- Department of Biosystems and Agricultural Engineering, Michigan State University, East Lansing, Michigan, 48824
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21
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Burns ML, Malott TM, Metcalf KJ, Puguh A, Chan JR, Shusta EV. Pro-region engineering for improved yeast display and secretion of brain derived neurotrophic factor. Biotechnol J 2015; 11:425-36. [PMID: 26580314 DOI: 10.1002/biot.201500360] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 08/21/2015] [Accepted: 10/19/2015] [Indexed: 11/11/2022]
Abstract
Brain derived neurotrophic factor (BDNF) is a promising therapeutic candidate for a variety of neurological diseases. However, it is difficult to produce as a recombinant protein. In its native mammalian context, BDNF is first produced as a pro-protein with subsequent proteolytic removal of the pro-region to yield mature BDNF protein. Therefore, in an attempt to improve yeast as a host for heterologous BDNF production, the BDNF pro-region was first evaluated for its effects on BDNF surface display and secretion. Addition of the wild-type pro-region to yeast BDNF production constructs improved BDNF folding both as a surface-displayed and secreted protein in terms of binding its natural receptors TrkB and p75, but titers remained low. Looking to further enhance the chaperone-like functions provided by the pro-region, two rounds of directed evolution were performed, yielding mutated pro-regions that further improved the display and secretion properties of BDNF. Subsequent optimization of the protease recognition site was used to control whether the produced protein was in pro- or mature BDNF forms. Taken together, we have demonstrated an effective strategy for improving BDNF compatibility with yeast protein engineering and secretion platforms.
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Affiliation(s)
- Michael L Burns
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Thomas M Malott
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Kevin J Metcalf
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Arthya Puguh
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jonah R Chan
- Department of Neurology, Program in Neuroscience, University of California, San Francisco, San Francisco, California, USA
| | - Eric V Shusta
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA.
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22
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Comprehensive Analysis and Characterization of Linear Antigenic Domains on HN Protein from Genotype VII Newcastle Disease Virus Using Yeast Surface Display System. PLoS One 2015; 10:e0131723. [PMID: 26121247 PMCID: PMC4488241 DOI: 10.1371/journal.pone.0131723] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 06/04/2015] [Indexed: 11/19/2022] Open
Abstract
Circulation of genotype VII Newcastle disease virus (NDV) has posed a great threat for the poultry industry worldwide. Antibodies against Hemagglutinin-neuraminidase (HN), a membrane protein of NDV with critical roles in NDV infection, have been reported to provide chickens protection from NDV infection. In this study, we comprehensively analyzed the in vivo antibody responses against the linear antigenic domains of the HN protein from genotype VII NDV using a yeast surface display system. The results revealed four distinct regions of HN, P1 (1-52aa), P2 (53-192aa), P3 (193-302aa) and P4 (303-571aa), respectively, according to their antigenic potency. Analysis by FACS and ELISA assay indicated P2 to be the dominant linear antigenic domain, with the immunogenic potency to protect the majority of chickens from NDV challenge. In contrast, the P1, P3 and P4 domains showed weak antigenicity in vivo and could not protect chickens from NDV challenge. These results provide important insight into the characteristic of humoral immune responses elicited by HN of NDV in vivo.
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