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Henning RW, Kosheleva I, Šrajer V, Kim IS, Zoellner E, Ranganathan R. BioCARS: Synchrotron facility for probing structural dynamics of biological macromolecules. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2024; 11:014301. [PMID: 38304444 PMCID: PMC10834067 DOI: 10.1063/4.0000238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 01/10/2024] [Indexed: 02/03/2024]
Abstract
A major goal in biomedical science is to move beyond static images of proteins and other biological macromolecules to the internal dynamics underlying their function. This level of study is necessary to understand how these molecules work and to engineer new functions and modulators of function. Stemming from a visionary commitment to this problem by Keith Moffat decades ago, a community of structural biologists has now enabled a set of x-ray scattering technologies for observing intramolecular dynamics in biological macromolecules at atomic resolution and over the broad range of timescales over which motions are functionally relevant. Many of these techniques are provided by BioCARS, a cutting-edge synchrotron radiation facility built under Moffat leadership and located at the Advanced Photon Source at Argonne National Laboratory. BioCARS enables experimental studies of molecular dynamics with time resolutions spanning from 100 ps to seconds and provides both time-resolved x-ray crystallography and small- and wide-angle x-ray scattering. Structural changes can be initiated by several methods-UV/Vis pumping with tunable picosecond and nanosecond laser pulses, substrate diffusion, and global perturbations, such as electric field and temperature jumps. Studies of dynamics typically involve subtle perturbations to molecular structures, requiring specialized computational techniques for data processing and interpretation. In this review, we present the challenges in experimental macromolecular dynamics and describe the current state of experimental capabilities at this facility. As Moffat imagined years ago, BioCARS is now positioned to catalyze the scientific community to make fundamental advances in understanding proteins and other complex biological macromolecules.
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Affiliation(s)
- Robert W. Henning
- BioCARS, Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, USA
| | - Irina Kosheleva
- BioCARS, Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, USA
| | - Vukica Šrajer
- BioCARS, Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, USA
| | - In-Sik Kim
- BioCARS, Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, USA
| | - Eric Zoellner
- BioCARS, Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, USA
| | - Rama Ranganathan
- BioCARS, Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, USA
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2
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Makowski EK, Schardt JS, Smith MD, Tessier PM. Mutational analysis of SARS-CoV-2 variants of concern reveals key tradeoffs between receptor affinity and antibody escape. PLoS Comput Biol 2022; 18:e1010160. [PMID: 35639784 PMCID: PMC9223403 DOI: 10.1371/journal.pcbi.1010160] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 06/23/2022] [Accepted: 05/02/2022] [Indexed: 11/18/2022] Open
Abstract
SARS-CoV-2 variants with enhanced transmissibility represent a serious threat to global health. Here we report machine learning models that can predict the impact of receptor-binding domain (RBD) mutations on receptor (ACE2) affinity, which is linked to infectivity, and escape from human serum antibodies, which is linked to viral neutralization. Importantly, the models predict many of the known impacts of RBD mutations in current and former Variants of Concern on receptor affinity and antibody escape as well as novel sets of mutations that strongly modulate both properties. Moreover, these models reveal key opposing impacts of RBD mutations on transmissibility, as many sets of RBD mutations predicted to increase antibody escape are also predicted to reduce receptor affinity and vice versa. These models, when used in concert, capture the complex impacts of SARS-CoV-2 mutations on properties linked to transmissibility and are expected to improve the development of next-generation vaccines and biotherapeutics. Machine learning is a powerful predictive tool that is well suited for diverse infectious disease applications. In this study, we apply machine learning to comprehensively predict the impact of mutations in the SARS-CoV-2 receptor-binding domain on both receptor affinity, which mediates viral infectivity, and escape from human serum antibodies, which mediates virus neutralization. These methods identify key mutations in current and former SARS-CoV-2 Variants of Concern, and predict novel high-risk variants that may warrant further consideration for vaccine and therapeutic development. Moreover, these models provide a valuable framework for future investigations aimed at understanding and mitigating COVID-19, especially as continued viral evolution remains a key global health threat.
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Affiliation(s)
- Emily K. Makowski
- Pharmaceutical Sciences, University of Michigan, Ann Arbor, Michigan, United States of America
- Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan, United States of America
| | - John S. Schardt
- Pharmaceutical Sciences, University of Michigan, Ann Arbor, Michigan, United States of America
- Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan, United States of America
- Chemical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Matthew D. Smith
- Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan, United States of America
- Chemical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Peter M. Tessier
- Pharmaceutical Sciences, University of Michigan, Ann Arbor, Michigan, United States of America
- Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan, United States of America
- Chemical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
- Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail:
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Abstract
Yeast surface display is a powerful protein engineering technology that is extensively used to improve various properties of proteins, including affinity, specificity, and stability or even to add novel functions (usually ligand binding). Apart from its robustness and versatility as an engineering tool, yeast display offers a further critical advantage: Once the selection campaign is finished, usually resulting in an oligoclonal pool, these enriched protein variants can be analyzed individually on the surface of yeast without the need for any sub-cloning, soluble expression, and purification. Here, we provide detailed protocols for determining both the affinity and the thermal stability of yeast displayed proteins. In addition, we discuss the advantages, challenges, and potential pitfalls associated with affinity and stability analysis using yeast surface display.
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Affiliation(s)
- Charlotte U Zajc
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Austria
- CD Laboratory for Next Generation CAR T Cells, Vienna, Austria
| | - Magdalena Teufl
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Austria
- CD Laboratory for Next Generation CAR T Cells, Vienna, Austria
| | - Michael W Traxlmayr
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Austria.
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Antioxidative Activity of Soy, Wheat and Pea Protein Isolates Characterized by Multi-Enzyme Hydrolysis. NANOMATERIALS 2021; 11:nano11061509. [PMID: 34200422 PMCID: PMC8227270 DOI: 10.3390/nano11061509] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/02/2021] [Accepted: 06/04/2021] [Indexed: 02/06/2023]
Abstract
Hydrolysis of protein by proteases produces small molecular weights (MWs) peptides as nanomaterials that are easily absorbed. This study investigated the physicochemical properties and antioxidant activity of three plant protein isolates (PIs) including soy, wheat and pea after multi-enzyme hydrolysis. The MWs, particle size and microstructure of PI hydrolysate (PIH) were determined by SDS-PAGE and MALDI-TOF-MS mass spectrometry, dynamic light scattering and transmission electron microscopy, respectively. Cell viability was determined in vitro using a mouse skeletal muscle cell line (C2C12) and crystal violet staining. The MWs and particle sizes of the three plant PIs were reduced after hydrolysis by three proteases (bromelain, Neutrase and Flavourzyme). The MWs of soy, wheat and pea PIH were 103.5–383.0 Da, 103.5–1146.5 Da and 103.1–1937.7 Da, respectively, and particle size distributions of 1.9–2.0 nm, 3.2–5.6 nm and 1.3–3.2 nm, respectively. All three plant PIHs appeared as aggregated nanoparticles. Soy PIH (100 μg/mL) provided better protection against H2O2-induced oxidative damage to C2C12 than wheat or pea PIH. In summary, soy PIH had the best antioxidant activity, and particle size than wheat PIH and pea PIH. Therefore, soy PIH might be a dietary supplement for healthy diet and medical applications.
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Affinity maturation: highlights in the application of in vitro strategies for the directed evolution of antibodies. Emerg Top Life Sci 2021; 5:601-608. [PMID: 33660765 PMCID: PMC8726058 DOI: 10.1042/etls20200331] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 02/16/2021] [Accepted: 02/23/2021] [Indexed: 01/04/2023]
Abstract
Affinity maturation is a key technique in protein engineering which is used to improve affinity and binding interactions in vitro, a process often required to fulfil the therapeutic potential of antibodies. There are many available display technologies and maturation methods developed over the years, which have been instrumental in the production of therapeutic antibodies. However, due to the inherent limitations in display capacity of these technologies, accommodation of expansive and complex library builds is still a challenge. In this article, we discuss our recent efforts in the affinity maturation of a difficult antibody lineage using an unbiased approach, which sought to explore a larger sequence space through the application of DNA recombination and shuffling techniques across the entire antibody region and selections using ribosome display. We also highlight the key features of several display technologies and diversification methods, and discuss the strategies devised by different groups in response to different challenges. Particular attention is drawn to examples which are aimed at the expansion of sequence, structural or experimental diversity through different means and approaches. Here, we provide our perspectives on these methodologies and the considerations involved in the design of effective strategies for the directed evolution of antibodies.
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Chang CY, Jin JD, Chang HL, Huang KC, Chiang YF, Hsia SM. Physicochemical and Antioxidative Characteristics of Potato Protein Isolate Hydrolysate. Molecules 2020; 25:molecules25194450. [PMID: 32998236 PMCID: PMC7583958 DOI: 10.3390/molecules25194450] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 09/25/2020] [Accepted: 09/25/2020] [Indexed: 01/08/2023] Open
Abstract
This study investigated the physicochemical characteristics of potato protein isolate hydrolysate (PPIH) and its antioxidant activity. Potato protein isolate (PPI) was hydrolyzed into PPIH by the proteases bromelain, Neutrase, and Flavourzyme. Compared with PPI, the resulting PPIH had a lower molecular weight (MW, from 103.5 to 422.7 Da) and smaller particle size (<50 nm), as well as a higher solubility rate (>70%) under acidic conditions (pH 3–6). PPIH presented good solubility (73%) across the tested pH range of 3–6. As the pH was increased, the zeta potential of PPIH decreased from −7.4 to −21.6. Using the 2,2′-azino-bis-3-ethylbenzthiazoline-6-sulfonic acid (ABTS) radical-scavenging assay, we determined that the half-maximal effective concentration (EC50) values of ascorbic acid, PPIH, and PPI were 0.01, 0.89, and >2.33 mg/mL, respectively. Furthermore, PPIH (50 μg/mL) protected C2C12 cells from H2O2 oxidation significantly better than PPI (10.5% higher viability rate; p < 0.01). These findings demonstrated the possible use of PPIH as an antioxidant in medical applications.
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Affiliation(s)
- Chiung-Yueh Chang
- School of Nutrition and Health Sciences, College of Nutrition, Taipei Medical University, Taipei 110, Taiwan; (C.-Y.C.); (K.-C.H.); (Y.-F.C.)
| | - Jinn-Der Jin
- GeneFerm Biotechnology Co., Ltd., Tainan 741, Taiwan; (J.-D.J.); (H.-L.C.)
| | - Hsiao-Li Chang
- GeneFerm Biotechnology Co., Ltd., Tainan 741, Taiwan; (J.-D.J.); (H.-L.C.)
| | - Ko-Chieh Huang
- School of Nutrition and Health Sciences, College of Nutrition, Taipei Medical University, Taipei 110, Taiwan; (C.-Y.C.); (K.-C.H.); (Y.-F.C.)
| | - Yi-Fen Chiang
- School of Nutrition and Health Sciences, College of Nutrition, Taipei Medical University, Taipei 110, Taiwan; (C.-Y.C.); (K.-C.H.); (Y.-F.C.)
| | - Shih-Min Hsia
- School of Nutrition and Health Sciences, College of Nutrition, Taipei Medical University, Taipei 110, Taiwan; (C.-Y.C.); (K.-C.H.); (Y.-F.C.)
- Graduate Institute of Metabolism and Obesity Sciences, College of Nutrition, Taipei Medical University, Taipei 110, Taiwan
- School of Food and Safety, Taipei Medical University, Taipei 110, Taiwan
- Nutrition Research Center, Taipei Medical University Hospital, Taipei 110, Taiwan
- Correspondence: ; Tel.: +886-2-2736-1661
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7
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Oh EJ, Liu R, Liang L, Freed EF, Eckert CA, Gill RT. Multiplex Evolution of Antibody Fragments Utilizing a Yeast Surface Display Platform. ACS Synth Biol 2020; 9:2197-2202. [PMID: 32551581 DOI: 10.1021/acssynbio.0c00159] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Advances in high-throughput synthetic biology technologies based on the CRISPR/Cas9 system have enabled a comprehensive assessment of mutations conferring desired phenotypes, as well as a better understanding of genotype-phenotype correlations in protein engineering. Engineering antibodies to enhance properties such as binding affinity and stability plays an essential role in therapeutic applications. Here we report a method, multiplex navigation of antibody structure (MINAS), that combines a CRISPR/Cas9-based trackable editing method and fluorescent-activated cell sorting (FACS) of yeast-displayed libraries. We designed mutations in all of the complementarity-determining and framework regions of a well-characterized scFv antibody and mapped the contribution of these regions to enhanced properties. We identified specific mutants that showed higher binding affinities up to 100-fold compared to the wild-type. This study expands the applicability of CRISPR/Cas9-based trackable protein engineering by combining it with a surface display platform.
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Affiliation(s)
- Eun Joong Oh
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Rongming Liu
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Liya Liang
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Emily F. Freed
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Carrie A. Eckert
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, Colorado 80303, United States
- National Renewable Energy Laboratory (NREL), Bioscience Center, Golden, Colorado 80401, United States
| | - Ryan T. Gill
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, Colorado 80303, United States
- Novo Nordisk Foundation Center for Biosustainability, Danish Technical University, Lyngby, Denmark
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8
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Tiller KE, Chowdhury R, Li T, Ludwig SD, Sen S, Maranas CD, Tessier PM. Facile Affinity Maturation of Antibody Variable Domains Using Natural Diversity Mutagenesis. Front Immunol 2017; 8:986. [PMID: 28928732 PMCID: PMC5591402 DOI: 10.3389/fimmu.2017.00986] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 08/02/2017] [Indexed: 11/13/2022] Open
Abstract
The identification of mutations that enhance antibody affinity while maintaining high antibody specificity and stability is a time-consuming and laborious process. Here, we report an efficient methodology for systematically and rapidly enhancing the affinity of antibody variable domains while maximizing specificity and stability using novel synthetic antibody libraries. Our approach first uses computational and experimental alanine scanning mutagenesis to identify sites in the complementarity-determining regions (CDRs) that are permissive to mutagenesis while maintaining antigen binding. Next, we mutagenize the most permissive CDR positions using degenerate codons to encode wild-type residues and a small number of the most frequently occurring residues at each CDR position based on natural antibody diversity. This mutagenesis approach results in antibody libraries with variants that have a wide range of numbers of CDR mutations, including antibody domains with single mutations and others with tens of mutations. Finally, we sort the modest size libraries (~10 million variants) displayed on the surface of yeast to identify CDR mutations with the greatest increases in affinity. Importantly, we find that single-domain (VHH) antibodies specific for the α-synuclein protein (whose aggregation is associated with Parkinson’s disease) with the greatest gains in affinity (>5-fold) have several (four to six) CDR mutations. This finding highlights the importance of sampling combinations of CDR mutations during the first step of affinity maturation to maximize the efficiency of the process. Interestingly, we find that some natural diversity mutations simultaneously enhance all three key antibody properties (affinity, specificity, and stability) while other mutations enhance some of these properties (e.g., increased specificity) and display trade-offs in others (e.g., reduced affinity and/or stability). Computational modeling reveals that improvements in affinity are generally not due to direct interactions involving CDR mutations but rather due to indirect effects that enhance existing interactions and/or promote new interactions between the antigen and wild-type CDR residues. We expect that natural diversity mutagenesis will be useful for efficient affinity maturation of a wide range of antibody fragments and full-length antibodies.
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Affiliation(s)
- Kathryn E Tiller
- Isermann Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - Ratul Chowdhury
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, United States
| | - Tong Li
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, United States
| | - Seth D Ludwig
- Isermann Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - Sabyasachi Sen
- Isermann Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - Costas D Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, United States
| | - Peter M Tessier
- Isermann Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States
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9
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Akiba H, Tsumoto K. Thermodynamics of antibody–antigen interaction revealed by mutation analysis of antibody variable regions. ACTA ACUST UNITED AC 2015; 158:1-13. [DOI: 10.1093/jb/mvv049] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 03/11/2015] [Indexed: 01/20/2023]
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10
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11
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Diem MD, Hyun L, Yi F, Hippensteel R, Kuhar E, Lowenstein C, Swift EJ, O'Neil KT, Jacobs SA. Selection of high-affinity Centyrin FN3 domains from a simple library diversified at a combination of strand and loop positions. Protein Eng Des Sel 2014; 27:419-29. [PMID: 24786107 DOI: 10.1093/protein/gzu016] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Alternative scaffold molecules represent a class of proteins important to the study of protein design and mechanisms of protein-protein interactions, as well as for the development of therapeutic proteins. Here, we describe the generation of a library built upon the framework of a consensus FN3 domain sequence resulting in binding proteins we call Centyrins. This new library employs diversified positions within the C-strand, CD-loop, F-strand and FG-loop of the FN3 domain. CIS display was used to select high-affinity Centyrin variants against three targets; c-MET, murine IL-17A and rat TNFα and scanning mutagenesis studies were used to define the positions of the library most important for target binding. Contributions from both the strand and loop positions were noted, although the pattern was different for each molecule. In addition, an affinity maturation scheme is described that resulted in a significant improvement in the affinity of one selected Centyrin variant. Together, this work provides important data contributing to our understanding of potential FN3 binding interfaces and a new tool for generating high-affinity scaffold molecules.
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Affiliation(s)
- Michael D Diem
- Janssen Research & Development, L.L.C., 1400 McKean Road, PO Box 776, Spring House, PA 19477, USA
| | - Linus Hyun
- Janssen Research & Development, L.L.C., 1400 McKean Road, PO Box 776, Spring House, PA 19477, USA
| | - Fang Yi
- Janssen Research & Development, L.L.C., 1400 McKean Road, PO Box 776, Spring House, PA 19477, USA
| | - Randi Hippensteel
- Janssen Research & Development, L.L.C., 1400 McKean Road, PO Box 776, Spring House, PA 19477, USA
| | - Elise Kuhar
- Janssen Research & Development, L.L.C., 1400 McKean Road, PO Box 776, Spring House, PA 19477, USA
| | - Cassandra Lowenstein
- Janssen Research & Development, L.L.C., 1400 McKean Road, PO Box 776, Spring House, PA 19477, USA
| | - Edward J Swift
- Janssen Research & Development, L.L.C., 1400 McKean Road, PO Box 776, Spring House, PA 19477, USA
| | - Karyn T O'Neil
- Janssen Research & Development, L.L.C., 1400 McKean Road, PO Box 776, Spring House, PA 19477, USA
| | - Steven A Jacobs
- Janssen Research & Development, L.L.C., 1400 McKean Road, PO Box 776, Spring House, PA 19477, USA
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12
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Design of peptide affinity ligands for S-protein: a comparison of combinatorial and de novo design strategies. Mol Divers 2013; 17:357-69. [DOI: 10.1007/s11030-013-9436-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Accepted: 03/11/2013] [Indexed: 12/11/2022]
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13
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Tillotson BJ, de Larrinoa IF, Skinner CA, Klavas DM, Shusta EV. Antibody affinity maturation using yeast display with detergent-solubilized membrane proteins as antigen sources. Protein Eng Des Sel 2013; 26:101-12. [PMID: 23109730 PMCID: PMC3542525 DOI: 10.1093/protein/gzs077] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Revised: 09/14/2012] [Accepted: 09/23/2012] [Indexed: 01/21/2023] Open
Abstract
Antigen preparations in the form of detergent-solubilized cell lysates could, in principle, render membrane proteins (MPs) compatible with in vitro antibody engineering technologies. To this end, detergent-solubilized cell lysates were coupled with the yeast surface display platform to affinity mature an anti-transferrin receptor (TfR) single-chain antibody (scFv). Lysates were generated from TfR-expressing HEK293 cells by solubilization with detergent-containing buffer after undergoing plasma membrane-restricted biotinylation. Lysate-resident TfR was then combined with a mutagenic anti-TfR scFv library in a competitive, dissociation rate screen, and scFvs were identified with up to 4-fold improved dissociation rates on the surface of yeast. Importantly, although the lysates contained a complex mixture of biotinylated proteins, the engineered scFvs retained their TfR binding specificity. When secreted by yeast as soluble proteins, mutant scFvs bound to cell surface TfR with 3-7-fold improvements in equilibrium binding affinity. Although a known MP antigen was targeted for purposes of this study, employing biotin tagging as a means of antigen detection makes the lysate-based approach particularly flexible. We have previously shown that yeast display can be used to identify lead antibodies using cell lysate-resident MP antigens, and combined with this work showing that antibodies can also be quantitatively engineered using cell lysates, these approaches may provide a high-throughput platform for generation and optimization of antibodies against MPs.
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Affiliation(s)
- Benjamin J. Tillotson
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Dr., Madison, WI 53706, USA
| | - Iñigo F. de Larrinoa
- Departamento de Quimica Aplicada, Universidad del País Vasco, P M. Lardizabal 3, San Sebastian 20018, Spain
| | - Colin A. Skinner
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Dr., Madison, WI 53706, USA
| | - Derek M. Klavas
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Dr., Madison, WI 53706, USA
| | - Eric V. Shusta
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Dr., Madison, WI 53706, USA
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14
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Hu X, Hortigüela MJ, Robin S, Lin H, Li Y, Moran AP, Wang W, Wall JG. Covalent and oriented immobilization of scFv antibody fragments via an engineered glycan moiety. Biomacromolecules 2012; 14:153-9. [PMID: 23215344 DOI: 10.1021/bm301518p] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Antibody-derived fragments have enormous potential application in solid-phase assays such as biomarker detection and protein purification. Controlled orientation of the immobilized antibody molecules is a critical requirement for the sensitivity and efficacy of such assays. We present an approach for covalent, correctly oriented attachment of scFv antibody fragments on solid supports. Glycosylated scFvs were expressed in Escherichia coli and the C-terminal, binding pocket-distal glycan tag was oxidized for covalent attachment to amine-functionalized beads. The glycosylated scFvs could be immobilized at salt concentrations that precluded nonspecific adsorption of unglycosylated molecules and the covalently attached antibody fragments exhibited 4-fold higher functional activity than ionically adsorbed scFvs. The glyco-tethered scFvs were stable in NaCl concentrations that removed greater than 90% of adsorbed scFvs and they exhibited improved stability of antigen binding over both adsorbed scFvs and soluble, nonimmobilized scFvs in accelerated degradation tests. The simple expression and immobilization approach reported is likely to find broad application in in vitro antibody tests.
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Affiliation(s)
- Xuejun Hu
- Medical College, Dalian University, Xuefu Avenue No.10, Dalian Economical and Technological Development Zone, Liaoning 116622, China.
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15
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Fukunishi H. Influence of ionization states of antigen on anti-fluorescein antibodies. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2012.08.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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16
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Fukunishi H, Yagi H, Kamijo K, Shimada J. Role of a Mutated Residue at the Entrance of the Substrate Access Channel in Cytochrome P450 Engineered for Vitamin D3 Hydroxylation Activity. Biochemistry 2011; 50:8302-10. [DOI: 10.1021/bi2006493] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Hiroaki Fukunishi
- Green Innovation Research Laboratories, NEC Corporation, 34, Miyukigaoka, Tsukuba, Ibaraki
305-8501, Japan
| | - Hirotaka Yagi
- VALWAY
Technology Center, NEC Soft, Ltd., 1-18-7,
Shinkiba, Koto-ku, Tokyo 136-8627,
Japan
| | - Ken’ichi Kamijo
- Green Innovation Research Laboratories, NEC Corporation, 34, Miyukigaoka, Tsukuba, Ibaraki
305-8501, Japan
| | - Jiro Shimada
- Green Innovation Research Laboratories, NEC Corporation, 34, Miyukigaoka, Tsukuba, Ibaraki
305-8501, Japan
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17
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Abstract
Recombinant antibody fragments, for example, the classic monovalent single-chain antibody (scFv), are emerging as credible alternatives to monoclonal antibody (mAb) products. scFv fragments maintain a diverse range of potential applications in biotechnology and can be implemented as powerful therapeutic and diagnostic agents. As such, a variety of hosts have been used to produce antibody fragments resulting in varying degrees of success. Yeast, Saccharomyces cerevisiae, is an attractive host due to quality control mechanisms of the secretory pathway that ensure secreted proteins are properly folded. However, the expression of a recombinant protein in yeast is not trivial; neither are the quality control mechanisms the cell initiates to respond to overwhelming stress, such as an increased protein load, simplistic. The endoplasmic reticulum (ER) is a dynamic organelle, capable of sensing and adjusting its folding capacity in response to increased demand. When protein abundance or terminally misfolded proteins overwhelm the ER's capacity, the unfolded protein response (UPR) is activated. In the guidelines presented here, we discuss varying aspects of quality control, its modulation, and ways to design appropriate constructs for yeast recombinant protein expression. Furthermore, we have provided protocols and methods to monitor intracellular protein expression and trafficking as well as evaluation of the UPR, with essential controls. The latter part of this chapter will review considerations for the experimental design of microarray and quantitative polymerase chain reaction (q-PCR) techniques while suggesting appropriate means of data analysis.
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Pierce BG, Haidar JN, Yu Y, Weng Z. Combinations of affinity-enhancing mutations in a T cell receptor reveal highly nonadditive effects within and between complementarity determining regions and chains. Biochemistry 2010; 49:7050-9. [PMID: 20681514 DOI: 10.1021/bi901969a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Understanding the energetic and structural response to multiple mutations in a protein-protein interface is a key aspect of rational protein design. Here we investigate the cooperativity of combinations of point mutations of a T cell receptor (TCR) that binds in vivo to HLA-A2 MHC and a viral peptide. The mutations were obtained from two sources: a structure-based design study on the TCR alpha chain (nine mutations) and an in vitro selection study on the TCR beta chain (four mutations). In addition to combining the highest-affinity variants from each chain, we tested other combinations of mutations within and among the chains, for a total of 23 TCR mutants that we measured for binding kinetics to the peptide and major histocompatibility complex. A wide range of binding affinities was observed, from 2- to 1000-fold binding improvement versus that of the wild type, with significant nonadditive effects observed within and between TCR chains. This included an amino acid-dependent cooperative interaction between CDR1 and CDR3 residues that are separated by more than 9 A in the wild-type complex. When analyzing the kinetics of the mutations, we found that the association rates were primarily responsible for the cooperativity, while the dissociation rates were responsible for the anticooperativity (less-than-additive energetics). On the basis of structural modeling of anticooperative mutants, we determined that side chain clash between proximal mutants likely led to nonadditive binding energies. These results highlight the complex nature of TCR association and binding and will be informative in future design efforts that combine multiple mutant residues.
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Affiliation(s)
- Brian G Pierce
- Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA
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19
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Chaparro-Riggers JF, Polizzi KM, Bommarius AS. Better library design: data-driven protein engineering. Biotechnol J 2007; 2:180-91. [PMID: 17183506 DOI: 10.1002/biot.200600170] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Data-driven protein engineering is increasingly used as an alternative to rational design and combinatorial engineering because it uses available knowledge to limit library size, while still allowing for the identification of unpredictable substitutions that lead to large effects. Recent advances in computational modeling and bioinformatics, as well as an increasing databank of experiments on functional variants, have led to new strategies to choose particular amino acid residues to vary in order to increase the chances of obtaining a variant protein with the desired property. Strategies for limiting diversity at each position, design of small sub-libraries, and the performance of scouting experiments, have also been developed or even automated, further reducing the library size.
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Affiliation(s)
- Javier F Chaparro-Riggers
- School of Chemical and Biomolecular Engineering, Parker H. Petit Institute of Bioengineering and Bioscience, Atlanta, GA, USA
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20
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Lippow SM, Wittrup KD, Tidor B. Computational design of antibody-affinity improvement beyond in vivo maturation. Nat Biotechnol 2007; 25:1171-6. [PMID: 17891135 PMCID: PMC2803018 DOI: 10.1038/nbt1336] [Citation(s) in RCA: 256] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2007] [Accepted: 08/09/2007] [Indexed: 11/10/2022]
Abstract
Antibodies are used extensively in diagnostics and as therapeutic agents. Achieving high-affinity binding is important for expanding detection limits, extending dissociation half-times, decreasing drug dosages and increasing drug efficacy. However, antibody-affinity maturation in vivo often fails to produce antibody drugs of the targeted potency, making further affinity maturation in vitro by directed evolution or computational design necessary. Here we present an iterative computational design procedure that focuses on electrostatic binding contributions and single mutants. By combining multiple designed mutations, a tenfold affinity improvement to 52 pM was engineered into the anti-epidermal growth factor receptor drug cetuximab (Erbitux), and a 140-fold improvement in affinity to 30 pM was obtained for the anti-lysozyme model antibody D44.1. The generality of the methods was further demonstrated through identification of known affinity-enhancing mutations in the therapeutic antibody bevacizumab (Avastin) and the model anti-fluorescein antibody 4-4-20. These results demonstrate computational capabilities for enhancing and accelerating the development of protein reagents and therapeutics.
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Affiliation(s)
- Shaun M Lippow
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
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21
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Lipovsek D, Lippow SM, Hackel BJ, Gregson MW, Cheng P, Kapila A, Wittrup KD. Evolution of an Interloop Disulfide Bond in High-Affinity Antibody Mimics Based on Fibronectin Type III Domain and Selected by Yeast Surface Display: Molecular Convergence with Single-Domain Camelid and Shark Antibodies. J Mol Biol 2007; 368:1024-41. [PMID: 17382960 DOI: 10.1016/j.jmb.2007.02.029] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2006] [Revised: 02/06/2007] [Accepted: 02/09/2007] [Indexed: 11/28/2022]
Abstract
The 10th human fibronectin type III domain ((10)Fn3) is one of several protein scaffolds used to design and select families of proteins that bind with high affinity and specificity to macromolecular targets. To date, the highest affinity (10)Fn3 variants have been selected by mRNA display of libraries generated by randomizing all three complementarity-determining region -like loops of the (10)Fn3 scaffold. The sub-nanomolar affinities of such antibody mimics have been attributed to the extremely large size of the library accessible by mRNA display (10(12) unique sequences). Here we describe the selection and affinity maturation of (10)Fn3-based antibody mimics with dissociation constants as low as 350 pM selected from significantly smaller libraries (10(7)-10(9) different sequences), which were constructed by randomizing only 14 (10)Fn3 residues. The finding that two adjacent loops in human (10)Fn3 provide a large enough variable surface area to select high-affinity antibody mimics is significant because a smaller deviation from wild-type (10)Fn3 sequence is associated with a higher stability of selected antibody mimics. Our results also demonstrate the utility of an affinity-maturation strategy that led to a 340-fold improvement in affinity by maximizing sampling of sequence space close to the original selected antibody mimic. A striking feature of the highest affinity antibody mimics selected against lysozyme is a pair of cysteines on adjacent loops, in positions 28 and 77, which are critical for the affinity of the (10)Fn3 variant for its target and are close enough to form a disulfide bond. The selection of this cysteine pair is structurally analogous to the natural evolution of disulfide bonds found in new antigen receptors of cartilaginous fish and in camelid heavy-chain variable domains. We propose that future library designs incorporating such an interloop disulfide will further facilitate the selection of high-affinity, highly stable antibody mimics from libraries accessible to phage and yeast surface display methods.
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Affiliation(s)
- Dasa Lipovsek
- Biological Engineering Division, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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22
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Subramanian S, Boder ET, Discher DE. Phylogenetic divergence of CD47 interactions with human signal regulatory protein alpha reveals locus of species specificity. Implications for the binding site. J Biol Chem 2006; 282:1805-18. [PMID: 17098740 DOI: 10.1074/jbc.m603923200] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Cell-cell interactions between ubiquitously expressed integrin-associated protein (CD47) and its counterreceptor signal regulatory protein (SIRPalpha) on phagocytes regulate a wide range of adhesive signaling processes, including the inhibition of phagocytosis as documented in mice. We show that CD47-SIRPalpha binding interactions are different between mice and humans, and we exploit phylogenetic divergence to identify the species-specific binding locus on the immunoglobulin domain of human CD47. All of the studies are conducted in the physiological context of membrane protein display on Chinese hamster ovary (CHO) cells. Novel quantitative flow cytometry analyses with CD47-green fluorescent protein and soluble human SIRPalpha as a probe show that neither human CD47 nor SIRPalpha requires glycosylation for interaction. Human CD47-expressing CHO cells spread rapidly on SIRPalpha-coated glass surfaces, correlating well with the spreading of primary human T cells. In contrast, CHO cells expressing mouse CD47 spread minimally and show equally weak binding to soluble human SIRPalpha. Further phylogenetic analyses and multisite substitutions of the CD47 Ig domain show that human to cow mutation of a cluster of seven residues on adjacent strands near the middle of the domain decreases the association constant for human SIRPalpha to about one-third that of human CD47. Direct tests of cell-cell adhesion between human monocytes and CD47-displaying CHO cells affirm the species specificity as well as the importance of the newly identified binding locus in cell-cell interactions.
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Affiliation(s)
- Shyamsundar Subramanian
- Biophysical Engineering Laboratory, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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