1
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Bonadio A, Wenig BL, Hockla A, Radisky ES, Shifman JM. Designed Loop Extension Followed by Combinatorial Screening Confers High Specificity to a Broad Matrix MetalloproteinaseInhibitor. J Mol Biol 2023; 435:168095. [PMID: 37068580 PMCID: PMC10312305 DOI: 10.1016/j.jmb.2023.168095] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 04/03/2023] [Accepted: 04/10/2023] [Indexed: 04/19/2023]
Abstract
Matrix metalloproteinases (MMPs) are key drivers of various diseases, including cancer. Development of probes and drugs capable of selectively inhibiting the individual members of the large MMP family remains a persistent challenge. The inhibitory N-terminal domain of tissue inhibitor of metalloproteinases-2 (N-TIMP2), a natural broad MMP inhibitor, can provide a scaffold for protein engineering to create more selective MMP inhibitors. Here, we pursued a unique approach harnessing both computational design and combinatorial screening to confer high binding specificity toward a target MMP in preference to an anti-target MMP. We designed a loop extension of N-TIMP2 to allow new interactions with the non-conserved MMP surface and generated an efficient focused library for yeast surface display, which was then screened for high binding to the target MMP-14 and low binding to anti-target MMP-3. Deep sequencing analysis identified the most promising variants, which were expressed, purified, and tested for selectivity of inhibition. Our best N-TIMP2 variant exhibited 29 pM binding affinity to MMP-14 and 2.4 µM affinity to MMP-3, revealing 7500-fold greater specificity than WT N-TIMP2. High-confidence structural models were obtained by including NGS data in the AlphaFold multiple sequence alignment. The modeling together with experimental mutagenesis validated our design predictions, demonstrating that the loop extension packs tightly against non-conserved residues on MMP-14 and clashes with MMP-3. This study demonstrates how introduction of loop extensions in a manner guided by target protein conservation data and loop design can offer an attractive strategy to achieve specificity in design of protein ligands.
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Affiliation(s)
- Alessandro Bonadio
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Israel
| | - Bernhard L Wenig
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, Florida, USA; Paracelsus Medical University, Salzburg, Austria
| | - Alexandra Hockla
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, Florida, USA
| | - Evette S Radisky
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, Florida, USA.
| | - Julia M Shifman
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Israel.
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2
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Lee SY, Cheah JS, Zhao B, Xu C, Roh H, Kim CK, Cho KF, Udeshi ND, Carr SA, Ting AY. Engineered allostery in light-regulated LOV-Turbo enables precise spatiotemporal control of proximity labeling in living cells. Nat Methods 2023; 20:908-917. [PMID: 37188954 PMCID: PMC10539039 DOI: 10.1038/s41592-023-01880-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 04/14/2023] [Indexed: 05/17/2023]
Abstract
The incorporation of light-responsive domains into engineered proteins has enabled control of protein localization, interactions and function with light. We integrated optogenetic control into proximity labeling, a cornerstone technique for high-resolution proteomic mapping of organelles and interactomes in living cells. Through structure-guided screening and directed evolution, we installed the light-sensitive LOV domain into the proximity labeling enzyme TurboID to rapidly and reversibly control its labeling activity with low-power blue light. 'LOV-Turbo' works in multiple contexts and dramatically reduces background in biotin-rich environments such as neurons. We used LOV-Turbo for pulse-chase labeling to discover proteins that traffic between endoplasmic reticulum, nuclear and mitochondrial compartments under cellular stress. We also showed that instead of external light, LOV-Turbo can be activated by bioluminescence resonance energy transfer from luciferase, enabling interaction-dependent proximity labeling. Overall, LOV-Turbo increases the spatial and temporal precision of proximity labeling, expanding the scope of experimental questions that can be addressed with proximity labeling.
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Affiliation(s)
- Song-Yi Lee
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Joleen S Cheah
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Boxuan Zhao
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Charles Xu
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Heegwang Roh
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Christina K Kim
- Department of Genetics, Stanford University, Stanford, CA, USA
- Center for Neuroscience and Department of Neurology, University of California, Davis, CA, USA
| | - Kelvin F Cho
- Department of Genetics, Stanford University, Stanford, CA, USA
- Amgen Research, South San Francisco, CA, USA
| | | | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alice Y Ting
- Department of Genetics, Stanford University, Stanford, CA, USA.
- Department of Biology, Stanford University, Stanford, CA, USA.
- Department of Chemistry, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub-San Francisco, San Francisco, CA, USA.
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3
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Vollmer L, Krah S, Zielonka S, Yanakieva D. A Two-Step Golden Gate Cloning Procedure for the Generation of Natively Paired YSD Fab Libraries. Methods Mol Biol 2023; 2681:161-173. [PMID: 37405648 DOI: 10.1007/978-1-0716-3279-6_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2023]
Abstract
In vitro antibody display libraries have emerged as powerful tools for a streamlined discovery of novel antibody binders. While in vivo antibody repertoires are matured and selected as a specific pair of variable heavy and light chains (VH and VL) with optimal specificity and affinity, during the recombinant generation of in vitro libraries, the native sequence pairing is not maintained. Here we describe a cloning method that combines the flexibility and versatility of in vitro antibody display with the advantages of natively paired VH-VL antibodies. In this regard, VH-VL amplicons are cloned via a two-step Golden Gate cloning procedure, allowing the display of Fab fragments on yeast cells.
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Affiliation(s)
- Lena Vollmer
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | - Simon Krah
- Protein Engineering and Antibody Technologies (PEAT), Merck Healthcare KGaA, Darmstadt, Germany
| | - Stefan Zielonka
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
- Protein Engineering and Antibody Technologies (PEAT), Merck Healthcare KGaA, Darmstadt, Germany
| | - Desislava Yanakieva
- Protein Engineering and Antibody Technologies (PEAT), Merck Healthcare KGaA, Darmstadt, Germany.
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4
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Cruz CJG, Kil R, Wong S, Dacquay LC, Mirano-Bascos D, Rivera PT, McMillen DR. Malarial Antibody Detection with an Engineered Yeast Agglutination Assay. ACS Synth Biol 2022; 11:2938-2946. [PMID: 35861604 DOI: 10.1021/acssynbio.2c00160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Malaria, a disease caused by the Plasmodium parasite carried by Anopheles mosquitoes, is commonly diagnosed by microscopy of peripheral blood smears and with rapid diagnostic tests. Both methods show limited detection of low parasitemia that may maintain transmission and hinder malaria elimination. We have developed a novel agglutination assay in which modified Saccharomyces cerevisiae cells act as antigen-displaying bead-like particles to capture malaria antibodies. The Epidermal Growth Factor-1 like domain (EGF1) of the Plasmodium falciparum merozoite surface protein-1 (PfMSP-119) was displayed on the yeast surface and shown to be capable of binding antimalaria antibodies. Mixed with a second yeast strain displaying the Z domain of Protein A from Staphylococcus aureus and allowed to settle in a round-bottomed well, the yeast produce a visually distinctive agglutination test result: a tight "button" at a low level of malarial antibodies, and a diffuse "sheet" when higher antibody levels are present. Positive agglutination results were observed in malaria-positive human serum to a serum dilution of 1:100 to 1:125. Since the yeast cells are inexpensive to produce, the test may be amenable to local production in regions seeking malaria surveillance information to guide their elimination programs.
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Affiliation(s)
- Criselda Jean G Cruz
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada.,College of Medicine, University of the Philippines Manila, Manila 1108, Philippines
| | - Richard Kil
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada.,Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Stanley Wong
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada.,Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Louis C Dacquay
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada.,Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S 3G5, Canada
| | - Denise Mirano-Bascos
- National Institute of Molecular Biology and Biotechnology, University of the Philippines Diliman, Quezon City 1101, Philippines
| | - Pilarita T Rivera
- College of Medicine, University of the Philippines Manila, Manila 1108, Philippines.,Department of Parasitology, College of Public Health, University of the Philippines Manila, Manila 1000, Philippines
| | - David R McMillen
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada.,Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada.,Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S 3G5, Canada
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5
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Linciano S, Wong EL, Mazzocato Y, Chinellato M, Scaravetti T, Caregnato A, Cacco V, Romanyuk Z, Angelini A. Guidelines, Strategies, and Principles for the Directed Evolution of Cross-Reactive Antibodies Using Yeast Surface Display Technology. Methods Mol Biol 2022; 2491:251-262. [PMID: 35482195 DOI: 10.1007/978-1-0716-2285-8_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The ability of cross-reactive antibodies to bind multiple related or unrelated targets derived from different species provides not only superior therapeutic efficacy but also a better assessment of treatment toxicity, thereby facilitating the transition from preclinical models to human clinical studies. This chapter provides some guidelines for the directed evolution of cross-reactive antibodies using yeast surface display technology. Cross-reactive antibodies are initially isolated from a naïve library by combining highly avid magnetic bead separations followed by multiple cycles of flow cytometry sorting. Once initial cross-reactive clones are identified, sequential rounds of mutagenesis and two-pressure selection strategies are applied to engineer cross-reactive antibodies with improved affinity and yet retained or superior cross-reactivity.
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Affiliation(s)
- Sara Linciano
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Mestre, Italy
| | - Ee Lin Wong
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Mestre, Italy
| | - Ylenia Mazzocato
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Mestre, Italy
| | - Monica Chinellato
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Mestre, Italy
- Department of Medicine (DIMED), University of Padua, Padua, Italy
| | - Tiziano Scaravetti
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Mestre, Italy
| | - Alberto Caregnato
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Mestre, Italy
| | - Veronica Cacco
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Mestre, Italy
| | - Zhanna Romanyuk
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Mestre, Italy
| | - Alessandro Angelini
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Mestre, Italy.
- European Centre for Living Technology (ECLT), Ca' Bottacin, Venice, Italy.
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6
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Abstract
Molecular display technologies have enabled the generation of synthetic binders with high affinities against a variety of antigens. However, engineering binders with high selectivity is still a challenging task. Here, we illustrate points to consider in developing highly selective binders against antigens of interest. We describe a systematic strategy for sorting selective binders using the yeast display technology. Using the approach described, our group has overcome molecular recognition challenges and developed a series of synthetic binders with exceptional selectivity against diverse antigens.
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Affiliation(s)
- Kai Wen Teng
- Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, USA
- Discovery Biologics, Merck & Co., Inc., Boston, MA, USA
| | - Akiko Koide
- Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, USA
- Department of Medicine, New York University School of Medicine, New York, NY, USA
| | - Shohei Koide
- Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, USA.
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA.
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7
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Zahradník J, Dey D, Marciano S, Kolářová L, Charendoff CI, Subtil A, Schreiber G. A Protein-Engineered, Enhanced Yeast Display Platform for Rapid Evolution of Challenging Targets. ACS Synth Biol 2021; 10:3445-3460. [PMID: 34809429 PMCID: PMC8689690 DOI: 10.1021/acssynbio.1c00395] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Indexed: 02/08/2023]
Abstract
Here, we enhanced the popular yeast display method by multiple rounds of DNA and protein engineering. We introduced surface exposure-tailored reporters, eUnaG2 and DnbALFA, creating a new platform of C and N terminal fusion vectors. The optimization of eUnaG2 resulted in five times brighter fluorescence and 10 °C increased thermostability than UnaG. The optimized DnbALFA has 10-fold the level of expression of the starting protein. Following this, different plasmids were developed to create a complex platform allowing a broad range of protein expression organizations and labeling strategies. Our platform showed up to five times better separation between nonexpressing and expressing cells compared with traditional pCTcon2 and c-myc labeling, allowing for fewer rounds of selection and achieving higher binding affinities. Testing 16 different proteins, the enhanced system showed consistently stronger expression signals over c-myc labeling. In addition to gains in simplicity, speed, and cost-effectiveness, new applications were introduced to monitor protein surface exposure and protein retention in the secretion pathway that enabled successful protein engineering of hard-to-express proteins. As an example, we show how we optimized the WD40 domain of the ATG16L1 protein for yeast surface and soluble bacterial expression, starting from a nonexpressing protein. As a second example, we show how using the here-presented enhanced yeast display method we rapidly selected high-affinity binders toward two protein targets, demonstrating the simplicity of generating new protein-protein interactions. While the methodological changes are incremental, it results in a qualitative enhancement in the applicability of yeast display for many applications.
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Affiliation(s)
- Jiří Zahradník
- Weizmann
Institute of Science, Herzl St. 234, Rehovot 7610001, Israel
| | - Debabrata Dey
- Weizmann
Institute of Science, Herzl St. 234, Rehovot 7610001, Israel
| | - Shir Marciano
- Weizmann
Institute of Science, Herzl St. 234, Rehovot 7610001, Israel
| | - Lucie Kolářová
- Institute
of Biotechnology, CAS v.v.i., Prumyslova 595, Vestec 252 50 Prague region, Czech Republic
| | - Chloé I. Charendoff
- Institut
Pasteur, Unité de Biologie cellulaire de l’infection
microbienne, 25 rue du Dr Roux, Paris 75015, France
| | - Agathe Subtil
- Institut
Pasteur, Unité de Biologie cellulaire de l’infection
microbienne, 25 rue du Dr Roux, Paris 75015, France
| | - Gideon Schreiber
- Weizmann
Institute of Science, Herzl St. 234, Rehovot 7610001, Israel
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8
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Casey GR, Zhou X, Lesiak L, Xu B, Fang Y, Becker DF, Stains CI. An Evolutionary Strategy for Identification of Higher Order, Green Fluorescent Host-Guest Pairs Compatible with Living Systems. Chemistry 2020; 26:16721-16726. [PMID: 32725914 DOI: 10.1002/chem.202002423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 07/26/2020] [Indexed: 11/09/2022]
Abstract
Engineered miniprotein host-small-molecule guest pairs could be utilized to design new processes within cells as well as investigate fundamental aspects of cell signaling mechanisms. However, the development of host-guest pairs capable of functioning in living systems has proven challenging. Moreover, few examples of host-guest pairs with stoichiometries other than 2:1 exist, significantly hindering the ability to study the influence of oligomerization state on signaling fidelity. Herein, we present an approach to identify host-guest systems for relatively small green fluorescent guests by incorporation into cyclic peptides. The optimal host-guest pair produced a 10-fold increase in green fluorescence signal upon binding. Biophysical characterization clearly demonstrated higher order supramolecular assembly, which could be visualized on the surface of living yeast cells using a turn-on fluorescence readout. This work further defines evolutionary design principles to afford host-guest pairs with stoichiometries other than 2:1 and enables the identification of spectrally orthogonal host-guest pairs.
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Affiliation(s)
- Garrett R Casey
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.,Department of Chemistry and Physics, Southeast Missouri State University, Cape Girardeau, MO, 63701, USA
| | - Xinqi Zhou
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Lauren Lesiak
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Bi Xu
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Yuan Fang
- Department of Chemistry, University of Virginia, Charlottesville, VA, 22904, USA
| | - Donald F Becker
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Cliff I Stains
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.,Department of Chemistry, University of Virginia, Charlottesville, VA, 22904, USA.,Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.,Cancer Genes and Molecular Regulation Program, Fred & Pamela Buffet Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA.,University of Virginia Cancer Center, University of Virginia, Charlottesville, VA, 22904, USA
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9
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Engineering Stem Cell Factor Ligands with Different c-Kit Agonistic Potencies. Molecules 2020; 25:molecules25204850. [PMID: 33096693 PMCID: PMC7588011 DOI: 10.3390/molecules25204850] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/14/2020] [Accepted: 10/19/2020] [Indexed: 11/17/2022] Open
Abstract
Receptor tyrosine kinases (RTKs) are major players in signal transduction, regulating cellular activities in both normal regeneration and malignancy. Thus, many RTKs, c-Kit among them, play key roles in the function of both normal and neoplastic cells, and as such constitute attractive targets for therapeutic intervention. We thus sought to manipulate the self-association of stem cell factor (SCF), the cognate ligand of c-Kit, and hence its suboptimal affinity and activation potency for c-Kit. To this end, we used directed evolution to engineer SCF variants having different c-Kit activation potencies. Our yeast-displayed SCF mutant (SCFM) library screens identified altered dimerization potential and increased affinity for c-Kit by specific SCF-variants. We demonstrated the delicate balance between SCF homo-dimerization, c-Kit binding, and agonistic potencies by structural studies, in vitro binding assays and a functional angiogenesis assay. Importantly, our findings showed that a monomeric SCF variant exhibited superior agonistic potency vs. the wild-type SCF protein and vs. other high-affinity dimeric SCF variants. Our data showed that action of the monomeric ligands in binding to the RTK monomers and inducing receptor dimerization and hence activation was superior to that of the wild-type dimeric ligand, which has a higher affinity to RTK dimers but a lower activation potential. The findings of this study on the binding and c-Kit activation of engineered SCF variants thus provides insights into the structure–function dynamics of ligands and RTKs.
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10
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Mehta N, Maddineni S, Kelly RL, Lee RB, Hunter SA, Silberstein JL, Parra Sperberg RA, Miller CL, Rabe A, Labanieh L, Cochran JR. An engineered antibody binds a distinct epitope and is a potent inhibitor of murine and human VISTA. Sci Rep 2020; 10:15171. [PMID: 32938950 PMCID: PMC7494997 DOI: 10.1038/s41598-020-71519-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 08/12/2020] [Indexed: 12/27/2022] Open
Abstract
V-domain immunoglobulin (Ig) suppressor of T cell activation (VISTA) is an immune checkpoint that maintains peripheral T cell quiescence and inhibits anti-tumor immune responses. VISTA functions by dampening the interaction between myeloid cells and T cells, orthogonal to PD-1 and other checkpoints of the tumor-T cell signaling axis. Here, we report the use of yeast surface display to engineer an anti-VISTA antibody that binds with high affinity to mouse, human, and cynomolgus monkey VISTA. Our anti-VISTA antibody (SG7) inhibits VISTA function and blocks purported interactions with both PSGL-1 and VSIG3 proteins. SG7 binds a unique epitope on the surface of VISTA, which partially overlaps with other clinically relevant antibodies. As a monotherapy, and to a greater extent as a combination with anti-PD1, SG7 slows tumor growth in multiple syngeneic mouse models. SG7 is a promising clinical candidate that can be tested in fully immunocompetent mouse models and its binding epitope can be used for future campaigns to develop species cross-reactive inhibitors of VISTA.
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Affiliation(s)
- Nishant Mehta
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | | | | | - Robert B Lee
- Department of Chemical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Sean A Hunter
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.,Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - John L Silberstein
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.,Immunology Program, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | | | - Caitlyn L Miller
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Amanda Rabe
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.,Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Louai Labanieh
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Jennifer R Cochran
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA. .,xCella Biosciences, Menlo Park, CA, 94025, USA. .,Department of Chemical Engineering, Stanford University, Stanford, CA, 94305, USA. .,Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, 94305, USA. .,Immunology Program, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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11
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Mehta N, Maddineni S, Mathews II, Andres Parra Sperberg R, Huang PS, Cochran JR. Structure and Functional Binding Epitope of V-domain Ig Suppressor of T Cell Activation. Cell Rep 2020; 28:2509-2516.e5. [PMID: 31484064 DOI: 10.1016/j.celrep.2019.07.073] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 06/13/2019] [Accepted: 07/19/2019] [Indexed: 12/20/2022] Open
Abstract
V-domain immunoglobulin (Ig) suppressor of T cell activation (VISTA) is an immune checkpoint protein that inhibits the T cell response against cancer. Similar to PD-1 and CTLA-4, a blockade of VISTA promotes tumor clearance by the immune system. Here, we report a 1.85 Å crystal structure of the elusive human VISTA extracellular domain, whose lack of homology necessitated a combinatorial MR-Rosetta approach for structure determination. We highlight features that make the VISTA immunoglobulin variable (IgV)-like fold unique among B7 family members, including two additional disulfide bonds and an extended loop region with an attached helix that we show forms a contiguous binding epitope for a clinically relevant anti-VISTA antibody. We propose an overlap of this antibody-binding region with the binding epitope for V-set and Ig domain containing 3 (VSIG3), a purported functional binding partner of VISTA. The structure and functional epitope presented here will help guide future drug development efforts against this important checkpoint target.
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Affiliation(s)
- Nishant Mehta
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | | | - Irimpan I Mathews
- Stanford Synchrotron Radiation Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | | | - Po-Ssu Huang
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
| | - Jennifer R Cochran
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA.
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12
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Zhao B, Tsai YC, Jin B, Wang B, Wang Y, Zhou H, Carpenter T, Weissman AM, Yin J. Protein Engineering in the Ubiquitin System: Tools for Discovery and Beyond. Pharmacol Rev 2020; 72:380-413. [PMID: 32107274 PMCID: PMC7047443 DOI: 10.1124/pr.118.015651] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Ubiquitin (UB) transfer cascades consisting of E1, E2, and E3 enzymes constitute a complex network that regulates a myriad of biologic processes by modifying protein substrates. Deubiquitinating enzymes (DUBs) reverse UB modifications or trim UB chains of diverse linkages. Additionally, many cellular proteins carry UB-binding domains (UBDs) that translate the signals encoded in UB chains to target proteins for degradation by proteasomes or in autophagosomes, as well as affect nonproteolytic outcomes such as kinase activation, DNA repair, and transcriptional regulation. Dysregulation of the UB transfer pathways and malfunctions of DUBs and UBDs play causative roles in the development of many diseases. A greater understanding of the mechanism of UB chain assembly and the signals encoded in UB chains should aid in our understanding of disease pathogenesis and guide the development of novel therapeutics. The recent flourish of protein-engineering approaches such as unnatural amino acid incorporation, protein semisynthesis by expressed protein ligation, and high throughput selection by phage and yeast cell surface display has generated designer proteins as powerful tools to interrogate cell signaling mediated by protein ubiquitination. In this study, we highlight recent achievements of protein engineering on mapping, probing, and manipulating UB transfer in the cell. SIGNIFICANCE STATEMENT: The post-translational modification of proteins with ubiquitin alters the fate and function of proteins in diverse ways. Protein engineering is fundamentally transforming research in this area, providing new mechanistic insights and allowing for the exploration of concepts that can potentially be applied to therapeutic intervention.
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Affiliation(s)
- Bo Zhao
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China (B.Z., B.J., B.W.); Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, China (Y.W.); Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland (Y.C.T., A.M.W.); and Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia (Y.W., H.Z., T.C., J.Y.)
| | - Yien Che Tsai
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China (B.Z., B.J., B.W.); Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, China (Y.W.); Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland (Y.C.T., A.M.W.); and Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia (Y.W., H.Z., T.C., J.Y.)
| | - Bo Jin
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China (B.Z., B.J., B.W.); Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, China (Y.W.); Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland (Y.C.T., A.M.W.); and Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia (Y.W., H.Z., T.C., J.Y.)
| | - Bufan Wang
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China (B.Z., B.J., B.W.); Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, China (Y.W.); Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland (Y.C.T., A.M.W.); and Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia (Y.W., H.Z., T.C., J.Y.)
| | - Yiyang Wang
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China (B.Z., B.J., B.W.); Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, China (Y.W.); Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland (Y.C.T., A.M.W.); and Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia (Y.W., H.Z., T.C., J.Y.)
| | - Han Zhou
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China (B.Z., B.J., B.W.); Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, China (Y.W.); Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland (Y.C.T., A.M.W.); and Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia (Y.W., H.Z., T.C., J.Y.)
| | - Tomaya Carpenter
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China (B.Z., B.J., B.W.); Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, China (Y.W.); Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland (Y.C.T., A.M.W.); and Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia (Y.W., H.Z., T.C., J.Y.)
| | - Allan M Weissman
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China (B.Z., B.J., B.W.); Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, China (Y.W.); Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland (Y.C.T., A.M.W.); and Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia (Y.W., H.Z., T.C., J.Y.)
| | - Jun Yin
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China (B.Z., B.J., B.W.); Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, China (Y.W.); Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland (Y.C.T., A.M.W.); and Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia (Y.W., H.Z., T.C., J.Y.)
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13
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Abstract
While antibody libraries are traditionally screened in phage, bacterial, or yeast display formats, they are produced in large scale for pharmaceutical and commercial use in mammalian cell lines. The simpler organisms used for screening have significantly different folding and glycosylation machinery than mammalian cells; consequently, clones resulting from these libraries may require further optimization for mammalian cell expression. To streamline the antibody discovery process, we developed a Chinese hamster ovary (CHO) cell-based selection system that allows for long-term display of antibody Fab fragments. This system is facilitated by a semi-stable Epi-CHO episomal platform to maintain antibody expression for up to 2 months and is compatible with standard PCR-based mutagenesis strategies. This protocol describes the simple and accessible use of CHO display coupled with flow cytometry to enrich for antibody variants with increased ligand-binding affinity from large libraries of ~106 variants, using HER2-binding antibodies as an example.
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Affiliation(s)
- Annalee W Nguyen
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA.
| | - Kevin Le
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Jennifer A Maynard
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
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14
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Wagner EK, Qerqez AN, Stevens CA, Nguyen AW, Delidakis G, Maynard JA. Human cytomegalovirus-specific T-cell receptor engineered for high affinity and soluble expression using mammalian cell display. J Biol Chem 2019; 294:5790-5804. [PMID: 30796163 PMCID: PMC6463697 DOI: 10.1074/jbc.ra118.007187] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 02/07/2019] [Indexed: 01/01/2023] Open
Abstract
T-cell receptors (TCR) have considerable potential as therapeutics and antibody-like reagents to monitor disease progression and vaccine efficacy. Whereas antibodies recognize only secreted and surface-bound proteins, TCRs recognize otherwise inaccessible disease-associated intracellular proteins when they are presented as processed peptides bound to major histocompatibility complexes (pMHC). TCRs have been primarily explored for cancer therapy applications but could also target infectious diseases such as cytomegalovirus (CMV). However, TCRs are more difficult to express and engineer than antibodies, and advanced methods are needed to enable their widespread use. Here, we engineered the human CMV-specific TCR RA14 for high-affinity and robust soluble expression. To achieve this, we adapted our previously reported mammalian display system to present TCR extracellular domains and used this to screen CDR3 libraries for clones with increased pMHC affinity. After three rounds of selection, characterized clones retained peptide specificity and activation when expressed on the surface of human Jurkat T cells. We obtained high yields of soluble, monomeric protein by fusing the TCR extracellular domains to antibody hinge and Fc constant regions, adding a stabilizing disulfide bond between the constant domains and disrupting predicted glycosylation sites. One variant exhibited 50 nm affinity for its cognate pMHC, as measured by surface plasmon resonance, and specifically stained cells presenting this pMHC. Our work has identified a human TCR with high affinity for the immunodominant CMV peptide and offers a new strategy to rapidly engineer soluble TCRs for biomedical applications.
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Affiliation(s)
- Ellen K Wagner
- From the McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712
| | - Ahlam N Qerqez
- From the McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712
| | - Christopher A Stevens
- From the McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712
| | - Annalee W Nguyen
- From the McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712
| | - George Delidakis
- From the McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712
| | - Jennifer A Maynard
- From the McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712.
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15
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Roth L, Grzeschik J, Hinz SC, Becker S, Toleikis L, Busch M, Kolmar H, Krah S, Zielonka S. Facile generation of antibody heavy and light chain diversities for yeast surface display by Golden Gate Cloning. Biol Chem 2018; 400:383-393. [DOI: 10.1515/hsz-2018-0347] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 11/11/2018] [Indexed: 01/03/2023]
Abstract
Abstract
Antibodies can be successfully engineered and isolated by yeast or phage display of combinatorial libraries. Still, generation of libraries comprising heavy chain as well as light chain diversities is a cumbersome process involving multiple steps. Within this study, we set out to compare the output of yeast display screening of antibody Fab libraries from immunized rodents that were generated by Golden Gate Cloning (GGC) with the conventional three-step method of individual heavy- and light-chain sub-library construction followed by chain combination via yeast mating (YM). We demonstrate that the GGC-based one-step process delivers libraries and antibodies from heavy- and light-chain diversities with similar quality to the traditional method while being significantly less complex and faster. Additionally, we show that this method can also be used to successfully screen and isolate chimeric chicken/human antibodies following avian immunization.
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Affiliation(s)
- Lukas Roth
- Institute for Organic Chemistry and Biochemistry , Technische Universität Darmstadt , Alarich-Weiss-Strasse 4 , D-64287 Darmstadt , Germany
| | - Julius Grzeschik
- Institute for Organic Chemistry and Biochemistry , Technische Universität Darmstadt , Alarich-Weiss-Strasse 4 , D-64287 Darmstadt , Germany
| | - Steffen C. Hinz
- Institute for Organic Chemistry and Biochemistry , Technische Universität Darmstadt , Alarich-Weiss-Strasse 4 , D-64287 Darmstadt , Germany
| | - Stefan Becker
- Protein Engineering and Antibody Technologies, Merck KGaA , Frankfurter Strasse 250 , D-64293 Darmstadt , Germany
| | - Lars Toleikis
- Protein Engineering and Antibody Technologies, Merck KGaA , Frankfurter Strasse 250 , D-64293 Darmstadt , Germany
| | - Michael Busch
- Discovery Pharmacology, Merck KGaA , Frankfurter Strasse 250 , D-64293 Darmstadt , Germany
| | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry , Technische Universität Darmstadt , Alarich-Weiss-Strasse 4 , D-64287 Darmstadt , Germany
| | - Simon Krah
- Protein Engineering and Antibody Technologies, Merck KGaA , Frankfurter Strasse 250 , D-64293 Darmstadt , Germany
| | - Stefan Zielonka
- Protein Engineering and Antibody Technologies, Merck KGaA , Frankfurter Strasse 250 , D-64293 Darmstadt , Germany
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16
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Branon TC, Bosch JA, Sanchez AD, Udeshi ND, Svinkina T, Carr SA, Feldman JL, Perrimon N, Ting AY. Efficient proximity labeling in living cells and organisms with TurboID. Nat Biotechnol 2018; 36:880-887. [PMID: 30125270 PMCID: PMC6126969 DOI: 10.1038/nbt.4201] [Citation(s) in RCA: 1007] [Impact Index Per Article: 167.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Accepted: 07/02/2018] [Indexed: 12/11/2022]
Abstract
Protein interaction networks and protein compartmentalization underlie all signaling and regulatory processes in cells. Enzyme-catalyzed proximity labeling (PL) has emerged as a new approach to study the spatial and interaction characteristics of proteins in living cells. However, current PL methods require over 18 h of labeling time or utilize chemicals with limited cell permeability or high toxicity. We used yeast display-based directed evolution to engineer two promiscuous mutants of biotin ligase, TurboID and miniTurbo, which catalyze PL with much greater efficiency than BioID or BioID2, and enable 10-min PL in cells with non-toxic and easily deliverable biotin. Furthermore, TurboID extends biotin-based PL to flies and worms.
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Affiliation(s)
- Tess C. Branon
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Departments of Genetics, Stanford University, Stanford, California, USA
- Departments of Chemistry, Stanford University, Stanford, California, USA
- Department of Biology, Stanford University, Stanford, California, USA
| | - Justin A. Bosch
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Ariana D. Sanchez
- Department of Biology, Stanford University, Stanford, California, USA
| | | | - Tanya Svinkina
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Steven A. Carr
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | | | - Norbert Perrimon
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Boston, Massachusetts, USA
| | - Alice Y. Ting
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Departments of Genetics, Stanford University, Stanford, California, USA
- Departments of Chemistry, Stanford University, Stanford, California, USA
- Department of Biology, Stanford University, Stanford, California, USA
- Howard Hughes Medical Institute, Boston, Massachusetts, USA
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17
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Lopez T, Chuan C, Ramirez A, Chen KHE, Lorenson MY, Benitez C, Mustafa Z, Pham H, Sanchez R, Walker AM, Ge X. Epitope-specific affinity maturation improved stability of potent protease inhibitory antibodies. Biotechnol Bioeng 2018; 115:2673-2682. [PMID: 30102763 DOI: 10.1002/bit.26814] [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: 04/23/2018] [Revised: 07/31/2018] [Accepted: 08/08/2018] [Indexed: 12/26/2022]
Abstract
Targeting effectual epitopes is essential for therapeutic antibodies to accomplish their desired biological functions. This study developed a competitive dual color fluorescence-activated cell sorting (FACS) to maturate a matrix metalloprotease 14 (MMP-14) inhibitory antibody. Epitope-specific screening was achieved by selection on MMP-14 during competition with N-terminal domain of tissue inhibitor of metalloproteinase-2 (TIMP-2) (nTIMP-2), a native inhibitor of MMP-14 binding strongly to its catalytic cleft. 3A2 variants with high potency, selectivity, and improved affinity and proteolytic stability were isolated from a random mutagenesis library. Binding kinetics indicated that the affinity improvements were mainly from slower dissociation rates. In vitro degradation tests suggested the isolated variants had half lives 6-11-fold longer than the wt. Inhibition kinetics suggested they were competitive inhibitors which showed excellent selectivity toward MMP-14 over highly homologous MMP-9. Alanine scanning revealed that they bound to the vicinity of MMP-14 catalytic cleft especially residues F204 and F260, suggesting that the desired epitope was maintained during maturation. When converted to immunoglobulin G, B3 showed 5.0 nM binding affinity and 6.5 nM inhibition potency with in vivo half-life of 4.6 days in mice. In addition to protease inhibitory antibodies, the competitive FACS described here can be applied for discovery and engineering biosimilars, and in general for other circumstances where epitope-specific modulation is needed.
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Affiliation(s)
- Tyler Lopez
- Department of Chemical and Environmental Engineering, Bourns College of Engineering, University of California Riverside, Riverside, California
| | - Chen Chuan
- Department of Chemical and Environmental Engineering, Bourns College of Engineering, University of California Riverside, Riverside, California
| | - Aaron Ramirez
- Department of Chemical and Environmental Engineering, Bourns College of Engineering, University of California Riverside, Riverside, California
| | - Kuan-Hui E Chen
- Division of Biomedical Sciences, School of Medicine, University of California Riverside, Riverside, California
| | - Mary Y Lorenson
- Division of Biomedical Sciences, School of Medicine, University of California Riverside, Riverside, California
| | - Chris Benitez
- Department of Chemical and Environmental Engineering, Bourns College of Engineering, University of California Riverside, Riverside, California
| | - Zahid Mustafa
- Department of Chemical and Environmental Engineering, Bourns College of Engineering, University of California Riverside, Riverside, California
| | - Henry Pham
- Department of Chemical and Environmental Engineering, Bourns College of Engineering, University of California Riverside, Riverside, California
| | - Ramon Sanchez
- Department of Chemical and Environmental Engineering, Bourns College of Engineering, University of California Riverside, Riverside, California
| | - Ameae M Walker
- Division of Biomedical Sciences, School of Medicine, University of California Riverside, Riverside, California
| | - Xin Ge
- Department of Chemical and Environmental Engineering, Bourns College of Engineering, University of California Riverside, Riverside, California
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18
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Yosef G, Arkadash V, Papo N. Targeting the MMP-14/MMP-2/integrin α vβ 3 axis with multispecific N-TIMP2-based antagonists for cancer therapy. J Biol Chem 2018; 293:13310-13326. [PMID: 29986882 DOI: 10.1074/jbc.ra118.004406] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Indexed: 12/27/2022] Open
Abstract
The pathophysiological functions of the signaling molecules matrix metalloproteinase-14 (MMP-14) and integrin αvβ3 in various types of cancer are believed to derive from their collaborative activity in promoting invasion, metastasis, and angiogenesis, as shown in vitro and in vivo The two effectors act in concert in a cell-specific manner through the localization of pro-MMP-2 to the cell surface, where it is processed to intermediate and matured MMP-2. The matured MMP-2 product is localized to the cell surface via its binding to integrin αvβ3 The MMP-14/MMP-2/integrin αvβ3 axis thus constitutes an attractive putative target for therapeutic interventions, but the development of inhibitors that target this axis remains an unfulfilled task. To address the lack of such multitarget inhibitors, we have established a combinatorial approach that is based on flow cytometry screening of a yeast-displayed N-TIMP2 (N-terminal domain variant of tissue inhibitor of metalloproteinase-2) mutant library. On the basis of this screening, we generated protein monomers and a heterodimer that contain monovalent and bivalent binding epitopes to MMP-14 and integrin αvβ3 Among these proteins, the bi-specific heterodimer, which bound strongly to both MMP-14 and integrin αvβ3, exhibited superior ability to inhibit MMP-2 activation and displayed the highest inhibitory activity in cell-based models of a MMP-14-, MMP-2-, and integrin αvβ3-dependent glioblastoma and of endothelial cell invasiveness and endothelial capillary tube formation. These assays enabled us to show the superiority of the combined target effects of the inhibitors and to investigate separately the role each of the three signaling molecules in various malignant processes.
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Affiliation(s)
- Gal Yosef
- From the Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Valeria Arkadash
- From the Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Niv Papo
- From the Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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19
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Miles TF, Spiess K, Jude KM, Tsutsumi N, Burg JS, Ingram JR, Waghray D, Hjorto GM, Larsen O, Ploegh HL, Rosenkilde MM, Garcia KC. Viral GPCR US28 can signal in response to chemokine agonists of nearly unlimited structural degeneracy. eLife 2018; 7:35850. [PMID: 29882741 PMCID: PMC5993540 DOI: 10.7554/elife.35850] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Accepted: 05/17/2018] [Indexed: 01/17/2023] Open
Abstract
Human cytomegalovirus has hijacked and evolved a human G-protein-coupled receptor into US28, which functions as a promiscuous chemokine 'sink’ to facilitate evasion of host immune responses. To probe the molecular basis of US28’s unique ligand cross-reactivity, we deep-sequenced CX3CL1 chemokine libraries selected on ‘molecular casts’ of the US28 active-state and find that US28 can engage thousands of distinct chemokine sequences, many of which elicit diverse signaling outcomes. The structure of a G-protein-biased CX3CL1-variant in complex with US28 revealed an entirely unique chemokine amino terminal peptide conformation and remodeled constellation of receptor-ligand interactions. Receptor signaling, however, is remarkably robust to mutational disruption of these interactions. Thus, US28 accommodates and functionally discriminates amongst highly degenerate chemokine sequences by sensing the steric bulk of the ligands, which distort both receptor extracellular loops and the walls of the ligand binding pocket to varying degrees, rather than requiring sequence-specific bonding chemistries for recognition and signaling.
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Affiliation(s)
- Timothy F Miles
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, United States.,Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
| | - Katja Spiess
- Laboratory for Molecular Pharmacology, Department of Biomedical Sciences, Faculty of Health and Medical Science, University of Copenhagen, Denmark, Europe
| | - Kevin M Jude
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, United States.,Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
| | - Naotaka Tsutsumi
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, United States.,Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
| | - John S Burg
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, United States.,Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
| | - Jessica R Ingram
- Department of Cancer Immunology and Virology, Dana Farber Cancer Institute, Boston, United States
| | - Deepa Waghray
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, United States.,Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
| | - Gertrud M Hjorto
- Laboratory for Molecular Pharmacology, Department of Biomedical Sciences, Faculty of Health and Medical Science, University of Copenhagen, Denmark, Europe
| | - Olav Larsen
- Laboratory for Molecular Pharmacology, Department of Biomedical Sciences, Faculty of Health and Medical Science, University of Copenhagen, Denmark, Europe
| | - Hidde L Ploegh
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, United States
| | - Mette M Rosenkilde
- Laboratory for Molecular Pharmacology, Department of Biomedical Sciences, Faculty of Health and Medical Science, University of Copenhagen, Denmark, Europe
| | - K Christopher Garcia
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, United States.,Department of Structural Biology, Stanford University School of Medicine, Stanford, United States.,Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, United States
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20
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Sirois AR, Deny DA, Baierl SR, George KS, Moore SJ. Fn3 proteins engineered to recognize tumor biomarker mesothelin internalize upon binding. PLoS One 2018; 13:e0197029. [PMID: 29738555 PMCID: PMC5940182 DOI: 10.1371/journal.pone.0197029] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 03/20/2018] [Indexed: 11/19/2022] Open
Abstract
Mesothelin is a cell surface protein that is overexpressed in numerous cancers, including breast, ovarian, lung, liver, and pancreatic tumors. Aberrant expression of mesothelin has been shown to promote tumor progression and metastasis through interaction with established tumor biomarker CA125. Therefore, molecules that specifically bind to mesothelin have potential therapeutic and diagnostic applications. However, no mesothelin-targeting molecules are currently approved for routine clinical use. While antibodies that target mesothelin are in development, some clinical applications may require a targeting molecule with an alternative protein fold. For example, non-antibody proteins are more suitable for molecular imaging and may facilitate diverse chemical conjugation strategies to create drug delivery complexes. In this work, we engineered variants of the fibronectin type III domain (Fn3) non-antibody protein scaffold to bind to mesothelin with high affinity, using directed evolution and yeast surface display. Lead engineered Fn3 variants were solubly produced and purified from bacterial culture at high yield. Upon specific binding to mesothelin on human cancer cell lines, the engineered Fn3 proteins internalized and co-localized to early endosomes. To our knowledge, this is the first report of non-antibody proteins engineered to bind mesothelin. The results validate that non-antibody proteins can be engineered to bind to tumor biomarker mesothelin, and encourage the continued development of engineered variants for applications such as targeted diagnostics and therapeutics.
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Affiliation(s)
- Allison R. Sirois
- Molecular and Cellular Biology Program, University of Massachusetts, Amherst, Amherst, Massachusetts, United States of America
- Picker Engineering Program, Smith College, Northampton, Massachusetts, United States of America
| | - Daniela A. Deny
- Department of Biochemistry, Smith College, Northampton, Massachusetts, United States of America
| | - Samantha R. Baierl
- Picker Engineering Program, Smith College, Northampton, Massachusetts, United States of America
| | - Katia S. George
- Department of Biochemistry, Smith College, Northampton, Massachusetts, United States of America
| | - Sarah J. Moore
- Molecular and Cellular Biology Program, University of Massachusetts, Amherst, Amherst, Massachusetts, United States of America
- Picker Engineering Program, Smith College, Northampton, Massachusetts, United States of America
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, United States of America
- * E-mail:
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21
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A cell surface display fluorescent biosensor for measuring MMP14 activity in real-time. Sci Rep 2018; 8:5916. [PMID: 29651043 PMCID: PMC5897415 DOI: 10.1038/s41598-018-24080-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 03/23/2018] [Indexed: 01/16/2023] Open
Abstract
Despite numerous recent advances in imaging technologies, one continuing challenge for cell biologists and microscopists is the visualization and measurement of endogenous proteins as they function within living cells. Achieving this goal will provide a tool that investigators can use to associate cellular outcomes with the behavior and activity of many well-studied target proteins. Here, we describe the development of a plasmid-based fluorescent biosensor engineered to measure the location and activity of matrix metalloprotease-14 (MMP14). The biosensor design uses fluorogen-activating protein technology coupled with a MMP14-selective protease sequence to generate a binary, “switch-on” fluorescence reporter capable of measuring MMP14 location, activity, and temporal dynamics. The MMP14-fluorogen activating protein biosensor approach is applicable to both short and long-term imaging modalities and contains an adaptable module that can be used to study many membrane-bound proteases. This MMP14 biosensor promises to serve as a tool for the advancement of a broad range of investigations targeting MMP14 activity during cell migration in health and disease.
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22
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D'Angelo S, Ferrara F, Naranjo L, Erasmus MF, Hraber P, Bradbury ARM. Many Routes to an Antibody Heavy-Chain CDR3: Necessary, Yet Insufficient, for Specific Binding. Front Immunol 2018; 9:395. [PMID: 29568296 PMCID: PMC5852061 DOI: 10.3389/fimmu.2018.00395] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 02/13/2018] [Indexed: 12/11/2022] Open
Abstract
Because of its great potential for diversity, the immunoglobulin heavy-chain complementarity-determining region 3 (HCDR3) is taken as an antibody molecule’s most important component in conferring binding activity and specificity. For this reason, HCDR3s have been used as unique identifiers to investigate adaptive immune responses in vivo and to characterize in vitro selection outputs where display systems were employed. Here, we show that many different HCDR3s can be identified within a target-specific antibody population after in vitro selection. For each identified HCDR3, a number of different antibodies bearing differences elsewhere can be found. In such selected populations, all antibodies with the same HCDR3 recognize the target, albeit at different affinities. In contrast, within unselected populations, the majority of antibodies with the same HCDR3 sequence do not bind the target. In one HCDR3 examined in depth, all target-specific antibodies were derived from the same VDJ rearrangement, while non-binding antibodies with the same HCDR3 were derived from many different V and D gene rearrangements. Careful examination of previously published in vivo datasets reveals that HCDR3s shared between, and within, different individuals can also originate from rearrangements of different V and D genes, with up to 26 different rearrangements yielding the same identical HCDR3 sequence. On the basis of these observations, we conclude that the same HCDR3 can be generated by many different rearrangements, but that specific target binding is an outcome of unique rearrangements and VL pairing: the HCDR3 is necessary, albeit insufficient, for specific antibody binding.
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Affiliation(s)
| | | | | | | | - Peter Hraber
- Los Alamos National Laboratory, Los Alamos, NM, United States
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23
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Salema V, Fernández LÁ. Escherichia coli surface display for the selection of nanobodies. Microb Biotechnol 2017; 10:1468-1484. [PMID: 28772027 PMCID: PMC5658595 DOI: 10.1111/1751-7915.12819] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 07/12/2017] [Accepted: 07/13/2017] [Indexed: 12/29/2022] Open
Abstract
Nanobodies (Nbs) are the smallest functional antibody fragments known in nature and have multiple applications in biomedicine or environmental monitoring. Nbs are derived from the variable segment of camelid heavy chain-only antibodies, known as VHH. For selection, libraries of VHH gene segments from naïve, immunized animals or of synthetic origin have been traditionally cloned in E. coli phage display or yeast display systems, and clones binding the target antigen recovered, usually from plastic surfaces with the immobilized antigen (phage display) or using fluorescence-activated cell sorting (FACS; yeast display). This review briefly describes these conventional approaches and focuses on the distinct properties of an E. coli display system developed in our laboratory, which combines the benefits of both phage display and yeast display systems. We demonstrate that E. coli display using an N-terminal domain of intimin is an effective platform for the surface display of VHH libraries enabling selection of high-affinity Nbs by magnetic cell sorting and direct selection on live mammalian cells displaying the target antigen on their surface. Flow cytometry analysis of E. coli bacteria displaying the Nbs on their surface allows monitoring of the selection process, facilitates screening, characterization of antigen-binding clones, specificity, ligand competition and estimation of the equilibrium dissociation constant (KD ).
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Affiliation(s)
- Valencio Salema
- Department of Microbial BiotechnologyCentro Nacional de Biotecnología (CNB)Consejo Superior de Investigaciones Científicas (CSIC)MadridSpain
| | - Luis Ángel Fernández
- Department of Microbial BiotechnologyCentro Nacional de Biotecnología (CNB)Consejo Superior de Investigaciones Científicas (CSIC)MadridSpain
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24
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Parola C, Neumeier D, Reddy ST. Integrating high-throughput screening and sequencing for monoclonal antibody discovery and engineering. Immunology 2017; 153:31-41. [PMID: 28898398 DOI: 10.1111/imm.12838] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 09/06/2017] [Accepted: 09/06/2017] [Indexed: 12/14/2022] Open
Abstract
Monoclonal antibody discovery and engineering is a field that has traditionally been dominated by high-throughput screening platforms (e.g. hybridomas and surface display). In recent years the emergence of high-throughput sequencing has made it possible to obtain large-scale information on antibody repertoire diversity. Additionally, it has now become more routine to perform high-throughput sequencing on antibody repertoires to also directly discover antibodies. In this review, we provide an overview of the progress in this field to date and show how high-throughput screening and sequencing are converging to deliver powerful new workflows for monoclonal antibody discovery and engineering.
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Affiliation(s)
- Cristina Parola
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.,Life Science Zurich Graduate School, Systems Biology, ETH Zurich, University of Zurich, Zurich, Switzerland
| | - Daniel Neumeier
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
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25
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Chang HJ, Voyvodic PL, Zúñiga A, Bonnet J. Microbially derived biosensors for diagnosis, monitoring and epidemiology. Microb Biotechnol 2017; 10:1031-1035. [PMID: 28771944 PMCID: PMC5609271 DOI: 10.1111/1751-7915.12791] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 07/04/2017] [Indexed: 11/27/2022] Open
Abstract
Living cells have evolved to detect and process various signals and can self-replicate, presenting an attractive platform for engineering scalable and affordable biosensing devices. Microbes are perfect candidates: they are inexpensive and easy to manipulate and store. Recent advances in synthetic biology promise to streamline the engineering of microbial biosensors with unprecedented capabilities. Here we review the applications of microbially-derived biosensors with a focus on environmental monitoring and healthcare applications. We also identify critical challenges that need to be addressed in order to translate the potential of synthetic microbial biosensors into large-scale, real-world applications.
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Affiliation(s)
- Hung-Ju Chang
- Centre de Biochimie Structurale, INSERM U1054, CNRS UMR5048, University of Montpellier, Montpellier, France
| | - Peter L Voyvodic
- Centre de Biochimie Structurale, INSERM U1054, CNRS UMR5048, University of Montpellier, Montpellier, France
| | - Ana Zúñiga
- Centre de Biochimie Structurale, INSERM U1054, CNRS UMR5048, University of Montpellier, Montpellier, France
| | - Jérôme Bonnet
- Centre de Biochimie Structurale, INSERM U1054, CNRS UMR5048, University of Montpellier, Montpellier, France
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26
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Banerjee V, Oren O, Ben-Zeev E, Taube R, Engel S, Papo N. A computational combinatorial approach identifies a protein inhibitor of superoxide dismutase 1 misfolding, aggregation, and cytotoxicity. J Biol Chem 2017; 292:15777-15788. [PMID: 28768772 DOI: 10.1074/jbc.m117.789610] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 07/21/2017] [Indexed: 12/12/2022] Open
Abstract
Molecular agents that specifically bind and neutralize misfolded and toxic superoxide dismutase 1 (SOD1) mutant proteins may find application in attenuating the disease progression of familial amyotrophic lateral sclerosis. However, high structural similarities between the wild-type and mutant SOD1 proteins limit the utility of this approach. Here we addressed this challenge by converting a promiscuous natural human IgG-binding domain, the hyperthermophilic variant of protein G (HTB1), into a highly specific aggregation inhibitor (designated HTB1M) of two familial amyotrophic lateral sclerosis-linked SOD1 mutants, SOD1G93A and SOD1G85R We utilized a computational algorithm for mapping protein surfaces predisposed to HTB1 intermolecular interactions to construct a focused HTB1 library, complemented with an experimental platform based on yeast surface display for affinity and specificity screening. HTB1M displayed high binding specificity toward SOD1 mutants, inhibited their amyloid aggregation in vitro, prevented the accumulation of misfolded proteins in living cells, and reduced the cytotoxicity of SOD1G93A expressed in motor neuron-like cells. Competition assays and molecular docking simulations suggested that HTB1M binds to SOD1 via both its α-helical and β-sheet domains at the native dimer interface that becomes exposed upon mutated SOD1 misfolding and monomerization. Our results demonstrate the utility of computational mapping of the protein-protein interaction potential for designing focused protein libraries to be used in directed evolution. They also provide new insight into the mechanism of conversion of broad-spectrum immunoglobulin-binding proteins, such as HTB1, into target-specific proteins, thereby paving the way for the development of new selective drugs targeting the amyloidogenic proteins implicated in a variety of human diseases.
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Affiliation(s)
- Victor Banerjee
- From the Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Ofek Oren
- From the Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel.,the Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel, and
| | - Efrat Ben-Zeev
- the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovoth 76100, Israel
| | - Ran Taube
- the Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel, and
| | - Stanislav Engel
- the Department of Clinical Biochemistry and Pharmacology and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Niv Papo
- From the Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel,
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27
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Kapur S, Silverman AP, Ye AZ, Papo N, Jindal D, Blumenkranz MS, Cochran JR. Engineered ligand-based VEGFR antagonists with increased receptor binding affinity more effectively inhibit angiogenesis. Bioeng Transl Med 2017; 2:81-91. [PMID: 28516164 PMCID: PMC5412928 DOI: 10.1002/btm2.10051] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Revised: 12/04/2016] [Accepted: 12/11/2016] [Indexed: 12/22/2022] Open
Abstract
Pathologic angiogenesis is mediated by the coordinated action of the vascular endothelial growth factor (VEGF)/vascular endothelial growth factor receptor 2 (VEGFR2) signaling axis, along with crosstalk contributed by other receptors, notably αvβ3 integrin. We build on earlier work demonstrating that point mutations can be introduced into the homodimeric VEGF ligand to convert it into an antagonist through disruption of binding to one copy of VEGFR2. This inhibitor has limited potency, however, due to loss of avidity effects from bivalent VEGFR2 binding. Here, we used yeast surface display to engineer a variant with VEGFR2 binding affinity approximately 40‐fold higher than the parental antagonist, and 14‐fold higher than the natural bivalent VEGF ligand. Increased VEGFR2 binding affinity correlated with the ability to more effectively inhibit VEGF‐mediated signaling, both in vitro and in vivo, as measured using VEGFR2 phosphorylation and Matrigel implantation assays. High affinity mutations found in this variant were then incorporated into a dual‐specific antagonist that we previously designed to simultaneously bind to and inhibit VEGFR2 and αvβ3 integrin. The resulting dual‐specific protein bound to human and murine endothelial cells with relative affinities of 120 ± 10 pM and 360 ± 50 pM, respectively, which is at least 30‐fold tighter than wild‐type VEGF (3.8 ± 0.5 nM). Finally, we demonstrated that this engineered high‐affinity dual‐specific protein could inhibit angiogenesis in a murine corneal neovascularization model. Taken together, these data indicate that protein engineering strategies can be combined to generate unique antiangiogenic candidates for further clinical development.
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Affiliation(s)
- Shiven Kapur
- Dept. of Bioengineering Stanford University Stanford CA 94303
| | | | - Anne Z Ye
- Dept. of Bioengineering Stanford University Stanford CA 94303
| | - Niv Papo
- Dept. of Bioengineering Stanford University Stanford CA 94303
| | - Darren Jindal
- Dept. of Bioengineering Stanford University Stanford CA 94303
| | - Mark S Blumenkranz
- Dept. of Ophthalmology Byers Eye Institute, Stanford University Stanford CA 94303
| | - Jennifer R Cochran
- Dept. of Bioengineering Stanford University Stanford CA 94303.,Dept. of Chemical Engineering Stanford University Stanford CA 94303.,Stanford Cancer Institute Stanford University Stanford CA 94303
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28
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Traxlmayr MW, Shusta EV. Directed Evolution of Protein Thermal Stability Using Yeast Surface Display. Methods Mol Biol 2017; 1575:45-65. [PMID: 28255874 DOI: 10.1007/978-1-4939-6857-2_4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Yeast surface display is a powerful protein engineering technology that has been used for many applications including engineering protein stability. Direct screening for improved thermal stability can be accomplished by heat shock of yeast displayed protein libraries. Thermally stable protein variants retain binding to conformationally specific ligands, and this binding event can be detected by flow cytometry, facilitating recovery of yeast clones displaying stabilized protein variants. In early efforts, the major limitation of this approach was the viability threshold of the yeast cells, precluding the application of significantly elevated heat shock temperatures (>50 °C) and therefore limited to the engineering of intrinsically unstable proteins. More recently, however, techniques for stability mutant gene recovery between sorting rounds have obviated the need for yeast growth amplification of improved mutant pools. The resultant methods allow significantly higher denaturation temperatures (up to 85 °C), thereby enabling the engineering of a broader range of protein substrates. In this chapter, a detailed protocol for this stability engineering approach is presented.
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Affiliation(s)
- Michael W Traxlmayr
- Department of Chemistry, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria.
| | - Eric V Shusta
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
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29
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Carlin KB, Cruz-Teran CA, Kumar JP, Gomes C, Rao BM. Combinatorial Pairwise Assembly Efficiently Generates High Affinity Binders and Enables a "Mix-and-Read" Detection Scheme. ACS Synth Biol 2016; 5:1348-1354. [PMID: 27268028 DOI: 10.1021/acssynbio.6b00034] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We show that a combinatorial library constructed by random pairwise assembly of low affinity binders can efficiently generate binders with increased affinity. Such a library based on the Sso7d scaffold, from a pool of low affinity binders subjected to random mutagenesis, contained putative high affinity clones for a model target (lysozyme) at higher frequency than a library of monovalent mutants generated by random mutagenesis alone. Increased binding affinity was due to intramolecular avidity generated by linking binders targeting nonoverlapping epitopes; individual binders of KD ∼ 1.3 μM and 250 nM produced a bivalent binder with apparent KD ∼ 2 nM. Furthermore, the bivalent protein retained thermal stability (TM = 84.5 °C) and high recombinant expression yields in E. coli. Finally, when binders comprising the bivalent protein are fused to two of the three fragments of tripartite split-green fluorescent protein (GFP), target-dependent reconstitution of fluorescence occurs, thereby enabling a "mix-and-read" assay for target quantification.
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Affiliation(s)
- Kevin B. Carlin
- Department of Chemical
and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Carlos A. Cruz-Teran
- Department of Chemical
and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Jay Prakash Kumar
- Institute of Stem Cell Biology and Regenerative Medicine, NCBS-TIFR, Bangalore 560065, Karnataka, India
- School of Chemical & Biotechnology, SASTRA University, Thanjavur 613401, Tamil Nadu, India
| | - Catherina Gomes
- Department of Chemical
and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Balaji M. Rao
- Department of Chemical
and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
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30
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Hunter SA, Cochran JR. Cell-Binding Assays for Determining the Affinity of Protein-Protein Interactions: Technologies and Considerations. Methods Enzymol 2016; 580:21-44. [PMID: 27586327 PMCID: PMC6067677 DOI: 10.1016/bs.mie.2016.05.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Determining the equilibrium-binding affinity (Kd) of two interacting proteins is essential not only for the biochemical study of protein signaling and function but also for the engineering of improved protein and enzyme variants. One common technique for measuring protein-binding affinities uses flow cytometry to analyze ligand binding to proteins presented on the surface of a cell. However, cell-binding assays require specific considerations to accurately quantify the binding affinity of a protein-protein interaction. Here we will cover the basic assumptions in designing a cell-based binding assay, including the relevant equations and theory behind determining binding affinities. Further, two major considerations in measuring binding affinities-time to equilibrium and ligand depletion-will be discussed. As these conditions have the potential to greatly alter the Kd, methods through which to avoid or minimize them will be provided. We then outline detailed protocols for performing direct- and competitive-binding assays against proteins displayed on the surface of yeast or mammalian cells that can be used to derive accurate Kd values. Finally, a comparison of cell-based binding assays to other types of binding assays will be presented.
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Affiliation(s)
- S A Hunter
- Stanford University, Stanford, CA, United States
| | - J R Cochran
- Stanford University, Stanford, CA, United States.
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31
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Martell JD, Yamagata M, Deerinck TJ, Phan S, Kwa CG, Ellisman MH, Sanes JR, Ting AY. A split horseradish peroxidase for the detection of intercellular protein-protein interactions and sensitive visualization of synapses. Nat Biotechnol 2016; 34:774-80. [PMID: 27240195 PMCID: PMC4942342 DOI: 10.1038/nbt.3563] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 04/07/2016] [Indexed: 12/26/2022]
Abstract
Intercellular protein-protein interactions (PPIs) enable communication between cells in diverse biological processes, including cell proliferation, immune responses, infection, and synaptic transmission, but they are challenging to visualize because existing techniques have insufficient sensitivity and/or specificity. Here we report a split horseradish peroxidase (sHRP) as a sensitive and specific tool for the detection of intercellular PPIs. The two sHRP fragments, engineered through screening of 17 cut sites in HRP followed by directed evolution, reconstitute into an active form when driven together by an intercellular PPI, producing bright fluorescence or contrast for electron microscopy. Fusing the sHRP fragments to the proteins neurexin (NRX) and neuroligin (NLG), which bind each other across the synaptic cleft, enabled sensitive visualization of synapses between specific sets of neurons, including two classes of synapses in the mouse visual system. sHRP should be widely applicable to studying mechanisms of communication between a variety of cell types.
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Affiliation(s)
- Jeffrey D Martell
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Masahito Yamagata
- Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, Massachusetts, USA
| | - Thomas J Deerinck
- National Center for Microscopy and Imaging Research, Center for Research on Biological Systems, University of California at San Diego, La Jolla, San Diego, California, USA
| | - Sébastien Phan
- National Center for Microscopy and Imaging Research, Center for Research on Biological Systems, University of California at San Diego, La Jolla, San Diego, California, USA
| | - Carolyn G Kwa
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Mark H Ellisman
- National Center for Microscopy and Imaging Research, Center for Research on Biological Systems, University of California at San Diego, La Jolla, San Diego, California, USA
- Department of Neurosciences, University of California at San Diego, La Jolla, San Diego, California, USA
- Salk Institute for Biological Studies, La Jolla, San Diego, California, USA
| | - Joshua R Sanes
- Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, Massachusetts, USA
| | - Alice Y Ting
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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32
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Generation of Fluorogen-Activating Designed Ankyrin Repeat Proteins (FADAs) as Versatile Sensor Tools. J Mol Biol 2016; 428:1272-1289. [PMID: 26812208 DOI: 10.1016/j.jmb.2016.01.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 01/12/2016] [Accepted: 01/15/2016] [Indexed: 11/21/2022]
Abstract
Fluorescent probes constitute a valuable toolbox to address a variety of biological questions and they have become irreplaceable for imaging methods. Commonly, such probes consist of fluorescent proteins or small organic fluorophores coupled to biological molecules of interest. Recently, a novel class of fluorescence-based probes, fluorogen-activating proteins (FAPs), has been reported. These binding proteins are based on antibody single-chain variable fragments and activate fluorogenic dyes, which only become fluorescent upon activation and do not fluoresce when free in solution. Here we present a novel class of fluorogen activators, termed FADAs, based on the very robust designed ankyrin repeat protein scaffold, which also readily folds in the reducing environment of the cytoplasm. The FADA generated in this study was obtained by combined selections with ribosome display and yeast surface display. It enhances the fluorescence of malachite green (MG) dyes by a factor of more than 11,000 and thus activates MG to a similar extent as FAPs based on single-chain variable fragments. As shown by structure determination and in vitro measurements, this FADA was evolved to form a homodimer for the activation of MG dyes. Exploiting the favorable properties of the designed ankyrin repeat protein scaffold, we created a FADA biosensor suitable for imaging of proteins on the cell surface, as well as in the cytosol. Moreover, based on the requirement of dimerization for strong fluorogen activation, a prototype FADA biosensor for in situ detection of a target protein and protein-protein interactions was developed. Therefore, FADAs are versatile fluorescent probes that are easily produced and suitable for diverse applications and thus extend the FAP technology.
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33
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Xu B, Zhou X, Stains CI. An improved miniprotein host for fluorogenic supramolecular assembly on the surface of living cells. RSC Adv 2016. [DOI: 10.1039/c6ra01215a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
A new host–guest pair produces a significant increase in the brightness of supramolecular complexes on the surface of living cells.
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Affiliation(s)
- Bi Xu
- Department of Chemistry
- University of Nebraska – Lincoln
- Lincoln
- USA
| | - Xinqi Zhou
- Department of Chemistry
- University of Nebraska – Lincoln
- Lincoln
- USA
| | - Cliff I. Stains
- Department of Chemistry
- University of Nebraska – Lincoln
- Lincoln
- USA
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34
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Min WK, Kim SG, Seo JH. Affinity maturation of single-chain variable fragment specific for aflatoxin B1 using yeast surface display. Food Chem 2015; 188:604-11. [DOI: 10.1016/j.foodchem.2015.04.117] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Revised: 04/23/2015] [Accepted: 04/25/2015] [Indexed: 12/31/2022]
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35
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Xu B, Zhou X, Stains CI. Supramolecular Assembly of an Evolved Miniprotein Host and Fluorogenic Guest Pair. J Am Chem Soc 2015; 137:14252-5. [DOI: 10.1021/jacs.5b09494] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Bi Xu
- Department of Chemistry, University of Nebraska—Lincoln, Lincoln, Nebraska 68588, United States
| | - Xinqi Zhou
- Department of Chemistry, University of Nebraska—Lincoln, Lincoln, Nebraska 68588, United States
| | - Cliff I. Stains
- Department of Chemistry, University of Nebraska—Lincoln, Lincoln, Nebraska 68588, United States
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36
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Rosenfeld L, Shirian J, Zur Y, Levaot N, Shifman JM, Papo N. Combinatorial and Computational Approaches to Identify Interactions of Macrophage Colony-stimulating Factor (M-CSF) and Its Receptor c-FMS. J Biol Chem 2015; 290:26180-93. [PMID: 26359491 PMCID: PMC4646268 DOI: 10.1074/jbc.m115.671271] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 09/06/2015] [Indexed: 01/06/2023] Open
Abstract
The molecular interactions between macrophage colony-stimulating factor (M-CSF) and the tyrosine kinase receptor c-FMS play a key role in the immune response, bone metabolism, and the development of some cancers. Because no x-ray structure is available for the human M-CSF · c-FMS complex, the binding epitope for this complex is largely unknown. Our goal was to identify the residues that are essential for binding of the human M-CSF to c-FMS. For this purpose, we used a yeast surface display (YSD) approach. We expressed a combinatorial library of monomeric M-CSF (M-CSFM) single mutants and screened this library to isolate variants with reduced affinity for c-FMS using FACS. Sequencing yielded a number of single M-CSFM variants with mutations both in the direct binding interface and distant from the binding site. In addition, we used computational modeling to map the identified mutations onto the M-CSFM structure and to classify the mutations into three groups as follows: those that significantly decrease protein stability; those that destroy favorable intermolecular interactions; and those that decrease affinity through allosteric effects. To validate the YSD and computational data, M-CSFM and three variants were produced as soluble proteins; their affinity and structure were analyzed; and very good correlations with both YSD data and computational predictions were obtained. By identifying the M-CSFM residues critical for M-CSF · c-FMS interactions, we have laid down the basis for a deeper understanding of the M-CSF · c-FMS signaling mechanism and for the development of target-specific therapeutic agents with the ability to sterically occlude the M-CSF·c-FMS binding interface.
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Affiliation(s)
- Lior Rosenfeld
- From the Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, and
| | - Jason Shirian
- the Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Yuval Zur
- From the Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, and the Department of Physiology and Cell Biology, Ben-Gurion University of the Negev, Beer-Sheva 8410501 and
| | - Noam Levaot
- the Department of Physiology and Cell Biology, Ben-Gurion University of the Negev, Beer-Sheva 8410501 and
| | - Julia M Shifman
- the Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Niv Papo
- From the Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, and
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37
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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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38
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Burg JS, Ingram JR, Venkatakrishnan AJ, Jude KM, Dukkipati A, Feinberg EN, Angelini A, Waghray D, Dror RO, Ploegh HL, Garcia KC. Structural biology. Structural basis for chemokine recognition and activation of a viral G protein-coupled receptor. Science 2015; 347:1113-7. [PMID: 25745166 DOI: 10.1126/science.aaa5026] [Citation(s) in RCA: 225] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Chemokines are small proteins that function as immune modulators through activation of chemokine G protein-coupled receptors (GPCRs). Several viruses also encode chemokines and chemokine receptors to subvert the host immune response. How protein ligands activate GPCRs remains unknown. We report the crystal structure at 2.9 angstrom resolution of the human cytomegalovirus GPCR US28 in complex with the chemokine domain of human CX3CL1 (fractalkine). The globular body of CX3CL1 is perched on top of the US28 extracellular vestibule, whereas its amino terminus projects into the central core of US28. The transmembrane helices of US28 adopt an active-state-like conformation. Atomic-level simulations suggest that the agonist-independent activity of US28 may be due to an amino acid network evolved in the viral GPCR to destabilize the receptor's inactive state.
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Affiliation(s)
- John S Burg
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA. Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA. Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jessica R Ingram
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - A J Venkatakrishnan
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA. Department of Computer Science, Stanford University, Stanford, CA 94305, USA. Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Kevin M Jude
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA. Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA. Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Abhiram Dukkipati
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA. Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA. Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Evan N Feinberg
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA. Department of Computer Science, Stanford University, Stanford, CA 94305, USA. Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Alessandro Angelini
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Deepa Waghray
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA. Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA. Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ron O Dror
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA. Department of Computer Science, Stanford University, Stanford, CA 94305, USA. Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Hidde L Ploegh
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - K Christopher Garcia
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA. Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA. Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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39
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Venkatesh AG, Sun A, Brickner H, Looney D, Hall DA, Aronoff-Spencer E. Yeast dual-affinity biobricks: Progress towards renewable whole-cell biosensors. Biosens Bioelectron 2015; 70:462-8. [PMID: 25863344 DOI: 10.1016/j.bios.2015.03.044] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 03/17/2015] [Accepted: 03/19/2015] [Indexed: 12/13/2022]
Abstract
Point-of-care (POC) diagnostic biosensors offer a promising solution to improve healthcare, not only in developed parts of the world, but also in resource limited areas that lack adequate medical infrastructure and trained technicians. However, in remote and resource limited settings, cost and storage of traditional POC immunoassays often limit actual deployment. Synthetically engineered biological components ("BioBricks") provide an avenue to reduce costs and simplify assay procedures. In this article, the design and development of an ultra-low cost, whole-cell "renewable" capture reagent for use in POC diagnostic applications is described. Yeast cells were genetically modified to display both single chain variable fragment (scFv) antibodies and gold-binding peptide (GBP) on their surfaces for simple one step enrichment and surface functionalization. Electrochemical impedance spectroscopy (EIS) and fluorescent imaging were used to verify and characterize the binding of cells to gold electrodes. A complete electrochemical detection assay was then performed on screen-printed electrodes fixed with yeast displaying scFv directed to Salmonella outer membrane protein D (OmpD). Electrochemical assays were optimized and cross-validated with established fluorescence techniques. Nanomolar detection limits were observed for both formats.
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Affiliation(s)
- A G Venkatesh
- Department of Electrical and Computer Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Alexander Sun
- Department of Electrical and Computer Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Howard Brickner
- School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - David Looney
- VA San Diego Healthcare System, 3350 La Jolla Village Drive, San Diego, CA 92161, USA; School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Drew A Hall
- Department of Electrical and Computer Engineering, University of California, San Diego, La Jolla, CA 92093, USA
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40
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Abstract
Biofuel cells are electrochemical devices which convert chemical energy to electricity using biochemical pathways and redox enzymes. In enzymatic fuel cells purified redox enzymes catalyze the reactions in the anode and cathode compartments whereas in microbial fuel cells (MFCs) the entire metabolism of the microorganisms is exploited. Here, a hybrid biofuel cell concept is presented, which is based on yeast surface display (YSD) of redox enzymes to catalyze the different cell reactions.
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Affiliation(s)
- Alon Szczupak
- Department of Life Sciences and Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, 653, Beer-Sheva, 84105, Israel
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41
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Zhang K, Bhuripanyo K, Wang Y, Yin J. Coupling Binding to Catalysis: Using Yeast Cell Surface Display to Select Enzymatic Activities. Methods Mol Biol 2015; 1319:245-60. [PMID: 26060080 PMCID: PMC4648535 DOI: 10.1007/978-1-4939-2748-7_14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We find yeast cell surface display can be used to engineer enzymes by selecting the enzyme library for high affinity binding to reaction intermediates. Here we cover key steps of enzyme engineering on the yeast cell surface including library design, construction, and selection based on magnetic and fluorescence-activated cell sorting.
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Affiliation(s)
- Keya Zhang
- Department of Chemistry, University of Chicago, 929 E57th Street, Chicago, IL 60637 (USA)
| | - Karan Bhuripanyo
- Department of Chemistry, University of Chicago, 929 E57th Street, Chicago, IL 60637 (USA)
| | - Yiyang Wang
- Department of Chemistry, Georgia State University, 50 Decatur Street SE, Atlanta, GA 30303 (USA)
| | - Jun Yin
- Department of Chemistry, Georgia State University, 50 Decatur Street SE, Atlanta, GA 30303 (USA)
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42
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Lam SS, Martell JD, Kamer KJ, Deerinck TJ, Ellisman MH, Mootha VK, Ting AY. Directed evolution of APEX2 for electron microscopy and proximity labeling. Nat Methods 2015; 12:51-4. [PMID: 25419960 PMCID: PMC4296904 DOI: 10.1038/nmeth.3179] [Citation(s) in RCA: 888] [Impact Index Per Article: 98.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 10/15/2014] [Indexed: 12/12/2022]
Abstract
APEX is an engineered peroxidase that functions as an electron microscopy tag and a promiscuous labeling enzyme for live-cell proteomics. Because limited sensitivity precludes applications requiring low APEX expression, we used yeast-display evolution to improve its catalytic efficiency. APEX2 is far more active in cells, enabling the use of electron microscopy to resolve the submitochondrial localization of calcium uptake regulatory protein MICU1. APEX2 also permits superior enrichment of endogenous mitochondrial and endoplasmic reticulum membrane proteins.
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Affiliation(s)
- Stephanie S Lam
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jeffrey D Martell
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Kimberli J Kamer
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Thomas J Deerinck
- National Center for Microscopy and Imaging Research, University of California at San Diego, La Jolla, California, USA
| | - Mark H Ellisman
- 1] National Center for Microscopy and Imaging Research, University of California at San Diego, La Jolla, California, USA. [2] Department of Neurosciences, University of California at San Diego, La Jolla, California, USA
| | - Vamsi K Mootha
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Alice Y Ting
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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43
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Doolan KM, Colby DW. Conformation-dependent epitopes recognized by prion protein antibodies probed using mutational scanning and deep sequencing. J Mol Biol 2014; 427:328-40. [PMID: 25451031 DOI: 10.1016/j.jmb.2014.10.024] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 10/23/2014] [Accepted: 10/24/2014] [Indexed: 11/24/2022]
Abstract
Prion diseases are caused by a structural rearrangement of the cellular prion protein, PrP(C), into a disease-associated conformation, PrP(Sc), which may be distinguished from one another using conformation-specific antibodies. We used mutational scanning by cell-surface display to screen 1341 PrP single point mutants for attenuated interaction with four anti-PrP antibodies, including several with conformational specificity. Single-molecule real-time gene sequencing was used to quantify enrichment of mutants, returning 26,000 high-quality full-length reads for each screened population on average. Relative enrichment of mutants correlated to the magnitude of the change in binding affinity. Mutations that diminished binding of the antibody ICSM18 represented the core of contact residues in the published crystal structure of its complex. A similarly located binding site was identified for D18, comprising discontinuous residues in helix 1 of PrP, brought into close proximity to one another only when the alpha helix is intact. The specificity of these antibodies for the normal form of PrP likely arises from loss of this conformational feature after conversion to the disease-associated form. Intriguingly, 6H4 binding was found to depend on interaction with the same residues, among others, suggesting that its ability to recognize both forms of PrP depends on a structural rearrangement of the antigen. The application of mutational scanning and deep sequencing provides residue-level resolution of positions in the protein-protein interaction interface that are critical for binding, as well as a quantitative measure of the impact of mutations on binding affinity.
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Affiliation(s)
- Kyle M Doolan
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA
| | - David W Colby
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA.
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44
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Directed evolution of brain-derived neurotrophic factor for improved folding and expression in Saccharomyces cerevisiae. Appl Environ Microbiol 2014; 80:5732-42. [PMID: 25015885 DOI: 10.1128/aem.01466-14] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Brain-derived neurotrophic factor (BDNF) plays an important role in nervous system function and has therapeutic potential. Microbial production of BDNF has resulted in a low-fidelity protein product, often in the form of large, insoluble aggregates incapable of binding to cognate TrkB or p75 receptors. In this study, employing Saccharomyces cerevisiae display and secretion systems, it was found that BDNF was poorly expressed and partially inactive on the yeast surface and that BDNF was secreted at low levels in the form of disulfide-bonded aggregates. Thus, for the purpose of increasing the compatibility of yeast as an expression host for BDNF, directed-evolution approaches were employed to improve BDNF folding and expression levels. Yeast surface display was combined with two rounds of directed evolution employing random mutagenesis and shuffling to identify BDNF mutants that had 5-fold improvements in expression, 4-fold increases in specific TrkB binding activity, and restored p75 binding activity, both as displayed proteins and as secreted proteins. Secreted BDNF mutants were found largely in the form of soluble homodimers that could stimulate TrkB phosphorylation in transfected PC12 cells. Site-directed mutagenesis studies indicated that a particularly important mutational class involved the introduction of cysteines proximal to the native cysteines that participate in the BDNF cysteine knot architecture. Taken together, these findings show that yeast is now a viable alternative for both the production and the engineering of BDNF.
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45
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Jha RK, Gaiotto T, Bradbury ARM, Strauss CEM. An improved Protein G with higher affinity for human/rabbit IgG Fc domains exploiting a computationally designed polar network. Protein Eng Des Sel 2014; 27:127-34. [PMID: 24632761 DOI: 10.1093/protein/gzu005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Protein G is an IgG binding protein that has been widely exploited for biotechnological purposes. Rosetta protein modeling identified a set of favorable polar mutations in Protein G, at its binding interface with the Fc domain of Immunoglobulin G, that were predicted to increase the stability and tighten the binding relative to native Protein G, with only a minor perturbation of the binding mode seen in the crystal structure. This triple mutant was synthesized and evaluated experimentally. Relative to the native protein G, the mutant showed a 3.5-fold enhancement in display level on the surface of yeast and a 5-fold tighter molar affinity for rabbit and human IgG. We attribute the improved affinity to a network of hydrogen bonds exploiting specific polar groups on human and rabbit Fc. The relative specificity increased as well since there was little affinity enhancement for goat and mouse Fc, while the affinity for rat Fc was poorer by half. This designed Protein G will be useful in biotechnological applications as a recombinant protein, where its improved affinity, display and specificity will increase antibody capture sensitivity and capacity. Furthermore, the display of this protein on the surface of yeast introduces the concept of the use of yeast as an affinity matrix.
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Affiliation(s)
- Ramesh K Jha
- Bioscience Division, MS M888, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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46
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Butz M, Kast P, Hilvert D. Affinity maturation of a computationally designed binding protein affords a functional but disordered polypeptide. J Struct Biol 2014; 185:168-77. [DOI: 10.1016/j.jsb.2013.03.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2013] [Revised: 03/08/2013] [Accepted: 03/18/2013] [Indexed: 10/27/2022]
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47
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Yeast surface display for antibody isolation: library construction, library screening, and affinity maturation. Methods Mol Biol 2014; 1131:151-81. [PMID: 24515465 DOI: 10.1007/978-1-62703-992-5_10] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Antibodies play key roles as reagents, diagnostics, and therapeutics in numerous biological and biomedical research settings. Although many antibodies are commercially available, oftentimes, specific applications require the development of antibodies with customized properties. Yeast surface display is a robust, versatile, and quantitative method for generating these antibodies and is accessible to single-investigator laboratories. This protocol details the key aspects of yeast surface display library construction and screening.
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48
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Szent-Gyorgyi C, Stanfield RL, Andreko S, Dempsey A, Ahmed M, Capek S, Waggoner AS, Wilson IA, Bruchez MP. Malachite green mediates homodimerization of antibody VL domains to form a fluorescent ternary complex with singular symmetric interfaces. J Mol Biol 2013; 425:4595-613. [PMID: 23978698 DOI: 10.1016/j.jmb.2013.08.014] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 08/15/2013] [Accepted: 08/16/2013] [Indexed: 01/19/2023]
Abstract
We report that a symmetric small-molecule ligand mediates the assembly of antibody light chain variable domains (VLs) into a correspondent symmetric ternary complex with novel interfaces. The L5* fluorogen activating protein is a VL domain that binds malachite green (MG) dye to activate intense fluorescence. Crystallography of liganded L5* reveals a 2:1 protein:ligand complex with inclusive C2 symmetry, where MG is almost entirely encapsulated between an antiparallel arrangement of the two VL domains. Unliganded L5* VL domains crystallize as a similar antiparallel VL/VL homodimer. The complementarity-determining regions are spatially oriented to form novel VL/VL and VL/ligand interfaces that tightly constrain a propeller conformer of MG. Binding equilibrium analysis suggests highly cooperative assembly to form a very stable VL/MG/VL complex, such that MG behaves as a strong chemical inducer of dimerization. Fusion of two VL domains into a single protein tightens MG binding over 1000-fold to low picomolar affinity without altering the large binding enthalpy, suggesting that bonding interactions with ligand and restriction of domain movements make independent contributions to binding. Fluorescence activation of a symmetrical fluorogen provides a selection mechanism for the isolation and directed evolution of ternary complexes where unnatural symmetric binding interfaces are favored over canonical antibody interfaces. As exemplified by L5*, these self-reporting complexes may be useful as modulators of protein association or as high-affinity protein tags and capture reagents.
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Affiliation(s)
- Chris Szent-Gyorgyi
- Molecular Biosensor and Imaging Center, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
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49
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Demonte D, Drake EJ, Lim KH, Gulick AM, Park S. Structure-based engineering of streptavidin monomer with a reduced biotin dissociation rate. Proteins 2013; 81:1621-33. [PMID: 23670729 DOI: 10.1002/prot.24320] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 04/18/2013] [Accepted: 04/22/2013] [Indexed: 11/07/2022]
Abstract
We recently reported the engineering of monomeric streptavidin, mSA, corresponding to one subunit of wild type (wt) streptavidin tetramer. The monomer was designed by homology modeling, in which the streptavidin and rhizavidin sequences were combined to engineer a high affinity binding pocket containing residues from a single subunit only. Although mSA is stable and binds biotin with nanomolar affinity, its fast off rate (koff ) creates practical challenges during applications. We obtained a 1.9 Å crystal structure of mSA bound to biotin to understand their interaction in detail, and used the structure to introduce targeted mutations to improve its binding kinetics. To this end, we compared mSA to shwanavidin, which contains a hydrophobic lid containing F43 in the binding pocket and binds biotin tightly. However, the T48F mutation in mSA, which introduces a comparable hydrophobic lid, only resulted in a modest 20-40% improvement in the measured koff . On the other hand, introducing the S25H mutation near the bicyclic ring of bound biotin increased the dissociation half life (t½ ) from 11 to 83 min at 20°C. Molecular dynamics (MD) simulations suggest that H25 stabilizes the binding loop L3,4 by interacting with A47, and protects key intermolecular hydrogen bonds by limiting solvent entry into the binding pocket. Concurrent T48F or T48W mutation clashes with H25 and partially abrogates the beneficial effects of H25. Taken together, this study suggests that stabilization of the binding loop and solvation of the binding pocket are important determinants of the dissociation kinetics in mSA.
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Affiliation(s)
- Daniel Demonte
- Department of Chemical and Biological Engineering, University at Buffalo, Buffalo, New York, 14260
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50
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White KA, Zegelbone PM. Directed evolution of a probe ligase with activity in the secretory pathway and application to imaging intercellular protein-protein interactions. Biochemistry 2013; 52:3728-39. [PMID: 23614685 DOI: 10.1021/bi400268m] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Previously, we reported a new method for intracellular protein labeling in living cells called PRIME (probe incorporation mediated by enzymes). PRIME uses a mutant of Escherichia coli lipoic acid ligase (LplA) to catalyze covalent probe ligation onto a 13-amino acid peptide recognition sequence. While our first demonstration labeled proteins with a coumarin fluorophore, subsequent engineering produced alkyl azide and trans-cyclooctene ligases as well as an interaction-dependent form of the coumarin PRIME method (ID-PRIME). One major limitation of the PRIME methodologies is that LplA mutants have very low activity in the secretory pathway. Here, we extend PRIME labeling to oxidizing compartments such as the endoplasmic reticulum and the cell surface. We used yeast-display evolution and four rounds of selection to isolate LplA mutants with improved picolyl azide ligation activity. Then we compared the ligation activities of the evolved mutants both in vitro and on the mammalian cell surface. We characterized the picolyl azide ligation activity of the most active LplA variant in vitro, in the endoplasmic reticulum, and at the mammalian cell surface. Finally, we used the optimized LplA variant to label neurexin and neuroligin interactions at the mammalian cell surface in just 5 min. Compared to another method for imaging these protein-protein interactions (GFP recomplementation across synapses), our optimized ID-PRIME ligase is faster, more sensitive, and does not trap interacting proteins in a complex (nontrapping).
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Affiliation(s)
- Katharine A White
- Department of Chemistry, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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