51
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Hughes DJ, Tiede C, Penswick N, Tang AAS, Trinh CH, Mandal U, Zajac KZ, Gaule T, Howell G, Edwards TA, Duan J, Feyfant E, McPherson MJ, Tomlinson DC, Whitehouse A. Generation of specific inhibitors of SUMO-1- and SUMO-2/3-mediated protein-protein interactions using Affimer (Adhiron) technology. Sci Signal 2017; 10:10/505/eaaj2005. [PMID: 29138295 DOI: 10.1126/scisignal.aaj2005] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Because protein-protein interactions underpin most biological processes, developing tools that target them to understand their function or to inform the development of therapeutics is an important task. SUMOylation is the posttranslational covalent attachment of proteins in the SUMO family (SUMO-1, SUMO-2, or SUMO-3), and it regulates numerous cellular pathways. SUMOylated proteins are recognized by proteins with SUMO-interaction motifs (SIMs) that facilitate noncovalent interactions with SUMO. We describe the use of the Affimer system of peptide display for the rapid isolation of synthetic binding proteins that inhibit SUMO-dependent protein-protein interactions mediated by SIMs both in vitro and in cells. Crucially, these synthetic proteins did not prevent SUMO conjugation either in vitro or in cell-based systems, enabling the specific analysis of SUMO-mediated protein-protein interactions. Furthermore, through structural analysis and molecular modeling, we explored the molecular mechanisms that may underlie their specificity in interfering with either SUMO-1-mediated interactions or interactions mediated by either SUMO-2 or SUMO-3. Not only will these reagents enable investigation of the biological roles of SUMOylation, but the Affimer technology used to generate these synthetic binding proteins could also be exploited to design or validate reagents or therapeutics that target other protein-protein interactions.
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Affiliation(s)
- David J Hughes
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK. .,Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews KY16 9ST, UK
| | - Christian Tiede
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,BioScreening Technology Group, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Natalie Penswick
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Anna Ah-San Tang
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,BioScreening Technology Group, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Chi H Trinh
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Upasana Mandal
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,BioScreening Technology Group, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Katarzyna Z Zajac
- BioScreening Technology Group, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Thembaninskosi Gaule
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Gareth Howell
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Thomas A Edwards
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | | | | | - Michael J McPherson
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,BioScreening Technology Group, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Darren C Tomlinson
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK. .,BioScreening Technology Group, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Adrian Whitehouse
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK. .,Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
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52
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Salzman GS, Ackerman SD, Ding C, Koide A, Leon K, Luo R, Stoveken HM, Fernandez CG, Tall GG, Piao X, Monk KR, Koide S, Araç D. Structural Basis for Regulation of GPR56/ADGRG1 by Its Alternatively Spliced Extracellular Domains. Neuron 2017; 91:1292-1304. [PMID: 27657451 DOI: 10.1016/j.neuron.2016.08.022] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2016] [Revised: 06/15/2016] [Accepted: 07/25/2016] [Indexed: 11/18/2022]
Abstract
Adhesion G protein-coupled receptors (aGPCRs) play critical roles in diverse neurobiological processes including brain development, synaptogenesis, and myelination. aGPCRs have large alternatively spliced extracellular regions (ECRs) that likely mediate intercellular signaling; however, the precise roles of ECRs remain unclear. The aGPCR GPR56/ADGRG1 regulates both oligodendrocyte and cortical development. Accordingly, human GPR56 mutations cause myelination defects and brain malformations. Here, we determined the crystal structure of the GPR56 ECR, the first structure of any complete aGPCR ECR, in complex with an inverse-agonist monobody, revealing a GPCR-Autoproteolysis-Inducing domain and a previously unidentified domain that we term Pentraxin/Laminin/neurexin/sex-hormone-binding-globulin-Like (PLL). Strikingly, PLL domain deletion caused increased signaling and characterizes a GPR56 splice variant. Finally, we show that an evolutionarily conserved residue in the PLL domain is critical for oligodendrocyte development in vivo. Thus, our results suggest that the GPR56 ECR has unique and multifaceted regulatory functions, providing novel insights into aGPCR roles in neurobiology.
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Affiliation(s)
- Gabriel S Salzman
- Biophysical Sciences Program, The University of Chicago, Chicago, IL 60637, USA; Medical Scientist Training Program, The University of Chicago, Chicago, IL 60637, USA; Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Sarah D Ackerman
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Chen Ding
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Akiko Koide
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Katherine Leon
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Rong Luo
- Division of Newborn Medicine, Department of Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Hannah M Stoveken
- Departments of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Celia G Fernandez
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Gregory G Tall
- Departments of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Xianhua Piao
- Division of Newborn Medicine, Department of Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Kelly R Monk
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Shohei Koide
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA.
| | - Demet Araç
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA.
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53
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Zhang S, Geryak R, Geldmeier J, Kim S, Tsukruk VV. Synthesis, Assembly, and Applications of Hybrid Nanostructures for Biosensing. Chem Rev 2017; 117:12942-13038. [DOI: 10.1021/acs.chemrev.7b00088] [Citation(s) in RCA: 206] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Shuaidi Zhang
- School of Materials Science
and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0245, United States
| | - Ren Geryak
- School of Materials Science
and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0245, United States
| | - Jeffrey Geldmeier
- School of Materials Science
and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0245, United States
| | - Sunghan Kim
- School of Materials Science
and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0245, United States
| | - Vladimir V. Tsukruk
- School of Materials Science
and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0245, United States
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54
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Wong ML, Murphy J, Harrington E, Gower CM, Jain RK, Schirle M, Thomas JR. Examining the influence of specificity ligands and ATP-competitive ligands on the overall effectiveness of bivalent kinase inhibitors. Proteome Sci 2017; 15:17. [PMID: 28725163 PMCID: PMC5513037 DOI: 10.1186/s12953-017-0125-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 07/03/2017] [Indexed: 01/02/2023] Open
Abstract
Background Identifying selective kinase inhibitors remains a major challenge. The design of bivalent inhibitors provides a rational strategy for accessing potent and selective inhibitors. While bivalent kinase inhibitors have been successfully designed, no comprehensive assessment of affinity and selectivity for a series of bivalent inhibitors has been performed. Here, we present an evaluation of the structure activity relationship for bivalent kinase inhibitors targeting ABL1. Methods Various SNAPtag constructs bearing different specificity ligands were expressed in vitro. Bivalent inhibitor formation was accomplished by synthesizing individual ATP-competitive kinase inhibitors containing a SNAPtag targeting moiety, enabling the spontaneous self-assembly of the bivalent inhibitor. Assembled bivalent inhibitors were incubated with K562 lysates, and then subjected to affinity enrichment using various ATP-competitive inhibitors immobilized to sepharose beads. Resulting eluents were analyzed using Tandem Mass Tag (TMT) labeling and two-dimensional liquid chromatography-tandem mass spectrometry (2D–LC-MS/MS). Relative binding affinity of the bivalent inhibitor was determined by calculating the concentration at which 50% of a given kinase remained bound to the affinity matrix. Results The profiling of three parental ATP-competitive inhibitors and nine SNAPtag conjugates led to the identification of 349 kinase proteins. In all cases, the bivalent inhibitors exhibited enhanced binding affinity and selectivity for ABL1 when compared to the parental compound conjugated to SNAPtag alone. While the rank order of binding affinity could be predicted by considering the binding affinities of the individual specificity ligands, the resulting affinity of the assembled bivalent inhibitor was not predictable. The results from this study suggest that as the potency of the ATP-competitive ligand increases, the contribution of the specificity ligand towards the overall binding affinity of the bivalent inhibitor decreases. However, the affinity of the specificity components in its interaction with the target is essential for achieving selectivity. Conclusion Through comprehensive chemical proteomic profiling, this work provides the first insight into the influence of ATP-competitive and specificity ligands binding to their intended target on a proteome-wide scale. The resulting data suggest a subtle interplay between the ATP-competitive and specificity ligands that cannot be accounted for by considering the specificity or affinity of the individual components alone. Electronic supplementary material The online version of this article (doi:10.1186/s12953-017-0125-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Margaret L Wong
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139 USA
| | - Jason Murphy
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139 USA
| | - Edmund Harrington
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139 USA
| | - Carrie M Gower
- Departments of Chemistry, University of Washington, Seattle, WA 98195 USA
| | - Rishi K Jain
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139 USA
| | - Markus Schirle
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139 USA
| | - Jason R Thomas
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139 USA
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55
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Tiede C, Bedford R, Heseltine SJ, Smith G, Wijetunga I, Ross R, AlQallaf D, Roberts APE, Balls A, Curd A, Hughes RE, Martin H, Needham SR, Zanetti-Domingues LC, Sadigh Y, Peacock TP, Tang AA, Gibson N, Kyle H, Platt GW, Ingram N, Taylor T, Coletta LP, Manfield I, Knowles M, Bell S, Esteves F, Maqbool A, Prasad RK, Drinkhill M, Bon RS, Patel V, Goodchild SA, Martin-Fernandez M, Owens RJ, Nettleship JE, Webb ME, Harrison M, Lippiat JD, Ponnambalam S, Peckham M, Smith A, Ferrigno PK, Johnson M, McPherson MJ, Tomlinson DC. Affimer proteins are versatile and renewable affinity reagents. eLife 2017; 6:e24903. [PMID: 28654419 PMCID: PMC5487212 DOI: 10.7554/elife.24903] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 06/07/2017] [Indexed: 12/11/2022] Open
Abstract
Molecular recognition reagents are key tools for understanding biological processes and are used universally by scientists to study protein expression, localisation and interactions. Antibodies remain the most widely used of such reagents and many show excellent performance, although some are poorly characterised or have stability or batch variability issues, supporting the use of alternative binding proteins as complementary reagents for many applications. Here we report on the use of Affimer proteins as research reagents. We selected 12 diverse molecular targets for Affimer selection to exemplify their use in common molecular and cellular applications including the (a) selection against various target molecules; (b) modulation of protein function in vitro and in vivo; (c) labelling of tumour antigens in mouse models; and (d) use in affinity fluorescence and super-resolution microscopy. This work shows that Affimer proteins, as is the case for other alternative binding scaffolds, represent complementary affinity reagents to antibodies for various molecular and cell biology applications.
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Affiliation(s)
- Christian Tiede
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Robert Bedford
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Sophie J Heseltine
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Gina Smith
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Imeshi Wijetunga
- Leeds Institute of Cancer Studies and Pathology, University of Leeds, Leeds, United Kingdom
| | - Rebecca Ross
- Leeds Institute of Cancer Studies and Pathology, University of Leeds, Leeds, United Kingdom
| | - Danah AlQallaf
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | | | - Alexander Balls
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Alistair Curd
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Ruth E Hughes
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Heather Martin
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Sarah R Needham
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Didcot, United Kingdom
| | - Laura C Zanetti-Domingues
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Didcot, United Kingdom
| | | | | | - Anna A Tang
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Naomi Gibson
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Hannah Kyle
- Avacta Life Sciences, Wetherby, United Kingdom
| | | | - Nicola Ingram
- Leeds Institute of Cancer Studies and Pathology, University of Leeds, Leeds, United Kingdom
| | - Thomas Taylor
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Louise P Coletta
- Leeds Institute of Cancer Studies and Pathology, University of Leeds, Leeds, United Kingdom
| | - Iain Manfield
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Margaret Knowles
- Leeds Institute of Cancer Studies and Pathology, University of Leeds, Leeds, United Kingdom
| | - Sandra Bell
- Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, Leeds, United Kingdom
| | - Filomena Esteves
- Leeds Institute of Cancer Studies and Pathology, University of Leeds, Leeds, United Kingdom
| | - Azhar Maqbool
- Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, United Kingdom
| | - Raj K Prasad
- Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, United Kingdom
| | - Mark Drinkhill
- Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, United Kingdom
| | - Robin S Bon
- Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, United Kingdom
| | | | | | - Marisa Martin-Fernandez
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Didcot, United Kingdom
| | - Ray J Owens
- Oxford Protein Production Facility UK, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Didcot, United Kingdom
| | - Joanne E Nettleship
- Oxford Protein Production Facility UK, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Didcot, United Kingdom
| | - Michael E Webb
- School of Chemistry, University of Leeds, Leeds, United Kingdom
| | - Michael Harrison
- School of Biomedical Sciences, University of Leeds, Leeds, United Kingdom
| | - Jonathan D Lippiat
- School of Biomedical Sciences, University of Leeds, Leeds, United Kingdom
| | - Sreenivasan Ponnambalam
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Michelle Peckham
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, United Kingdom
| | | | | | | | - Michael J McPherson
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Darren Charles Tomlinson
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, United Kingdom
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56
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Fulcher LJ, Hutchinson LD, Macartney TJ, Turnbull C, Sapkota GP. Targeting endogenous proteins for degradation through the affinity-directed protein missile system. Open Biol 2017; 7:170066. [PMID: 28490657 PMCID: PMC5451546 DOI: 10.1098/rsob.170066] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 04/19/2017] [Indexed: 12/18/2022] Open
Abstract
Targeted proteolysis of endogenous proteins is desirable as a research toolkit and in therapeutics. CRISPR/Cas9-mediated gene knockouts are irreversible and often not feasible for many genes. Similarly, RNA interference approaches necessitate prolonged treatments, can lead to incomplete knockdowns and are often associated with off-target effects. Targeted proteolysis can overcome these limitations. In this report, we describe an affinity-directed protein missile (AdPROM) system that harbours the von Hippel-Lindau (VHL) protein, the substrate receptor of the Cullin2 (CUL2) E3 ligase complex, tethered to polypeptide binders that selectively bind and recruit endogenous target proteins to the CUL2-E3 ligase complex for ubiquitination and proteasomal degradation. By using synthetic monobodies that selectively bind the protein tyrosine phosphatase SHP2 and a camelid-derived VHH nanobody that selectively binds the human ASC protein, we demonstrate highly efficient AdPROM-mediated degradation of endogenous SHP2 and ASC in human cell lines. We show that AdPROM-mediated loss of SHP2 in cells impacts SHP2 biology. This study demonstrates for the first time that small polypeptide binders that selectively recognize endogenous target proteins can be exploited for AdPROM-mediated destruction of the target proteins.
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Affiliation(s)
- Luke J Fulcher
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, Dundee, UK
| | - Luke D Hutchinson
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, Dundee, UK
| | - Thomas J Macartney
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, Dundee, UK
| | - Craig Turnbull
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, Dundee, UK
| | - Gopal P Sapkota
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, Dundee, UK
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57
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Kükenshöner T, Schmit NE, Bouda E, Sha F, Pojer F, Koide A, Seeliger M, Koide S, Hantschel O. Selective Targeting of SH2 Domain-Phosphotyrosine Interactions of Src Family Tyrosine Kinases with Monobodies. J Mol Biol 2017; 429:1364-1380. [PMID: 28347651 PMCID: PMC5417323 DOI: 10.1016/j.jmb.2017.03.023] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 03/20/2017] [Accepted: 03/20/2017] [Indexed: 12/17/2022]
Abstract
The binding of Src-homology 2 (SH2) domains to phosphotyrosine (pY) sites is critical for the autoinhibition and substrate recognition of the eight Src family kinases (SFKs). The high sequence conservation of the 120 human SH2 domains poses a significant challenge to selectively perturb the interactions of even the SFK SH2 family against the rest of the SH2 domains. We have developed synthetic binding proteins, termed monobodies, for six of the SFK SH2 domains with nanomolar affinity. Most of these monobodies competed with pY ligand binding and showed strong selectivity for either the SrcA (Yes, Src, Fyn, Fgr) or SrcB subgroup (Lck, Lyn, Blk, Hck). Interactome analysis of intracellularly expressed monobodies revealed that they bind SFKs but no other SH2-containing proteins. Three crystal structures of monobody-SH2 complexes unveiled different and only partly overlapping binding modes, which rationalized the observed selectivity and enabled structure-based mutagenesis to modulate inhibition mode and selectivity. In line with the critical roles of SFK SH2 domains in kinase autoinhibition and T-cell receptor signaling, monobodies binding the Src and Hck SH2 domains selectively activated respective recombinant kinases, whereas an Lck SH2-binding monobody inhibited proximal signaling events downstream of the T-cell receptor complex. Our results show that SFK SH2 domains can be targeted with unprecedented potency and selectivity using monobodies. They are excellent tools for dissecting SFK functions in normal development and signaling and to interfere with aberrant SFK signaling networks in cancer cells.
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Affiliation(s)
- Tim Kükenshöner
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École polytechnique fédérale de Lausanne (EPFL), Station 19, 1015 Lausanne, Switzerland
| | - Nadine Eliane Schmit
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École polytechnique fédérale de Lausanne (EPFL), Station 19, 1015 Lausanne, Switzerland
| | - Emilie Bouda
- Department of Pharmacological Sciences, Stony Brook University, BST 8-140, Stony Brook, NY 11794-8651, USA
| | - Fern Sha
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Florence Pojer
- Protein Crystallography Core Facility, School of Life Sciences, École polytechnique fédérale de Lausanne, Station 19, 1015 Lausanne, Switzerland
| | - Akiko Koide
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA; Laura and Isaac Perlmutter Cancer Center, New York University Langone Medical Center, 430 East 29th Street, New York, NY 10016, USA; Department of Medicine, New York University School of Medicine, 430 East 29th Street, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 430 East 29th Street, New York, NY 10016, USA
| | - Markus Seeliger
- Department of Pharmacological Sciences, Stony Brook University, BST 8-140, Stony Brook, NY 11794-8651, USA
| | - Shohei Koide
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA; Laura and Isaac Perlmutter Cancer Center, New York University Langone Medical Center, 430 East 29th Street, New York, NY 10016, USA; Department of Medicine, New York University School of Medicine, 430 East 29th Street, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 430 East 29th Street, New York, NY 10016, USA.
| | - Oliver Hantschel
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École polytechnique fédérale de Lausanne (EPFL), Station 19, 1015 Lausanne, Switzerland.
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58
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Sha F, Salzman G, Gupta A, Koide S. Monobodies and other synthetic binding proteins for expanding protein science. Protein Sci 2017; 26:910-924. [PMID: 28249355 PMCID: PMC5405424 DOI: 10.1002/pro.3148] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 02/20/2017] [Accepted: 02/21/2017] [Indexed: 01/20/2023]
Abstract
Synthetic binding proteins are constructed using nonantibody molecular scaffolds. Over the last two decades, in‐depth structural and functional analyses of synthetic binding proteins have improved combinatorial library designs and selection strategies, which have resulted in potent platforms that consistently generate binding proteins to diverse targets with affinity and specificity that rival those of antibodies. Favorable attributes of synthetic binding proteins, such as small size, freedom from disulfide bond formation and ease of making fusion proteins, have enabled their unique applications in protein science, cell biology and beyond. Here, we review recent studies that illustrate how synthetic binding proteins are powerful probes that can directly link structure and function, often leading to new mechanistic insights. We propose that synthetic proteins will become powerful standard tools in diverse areas of protein science, biotechnology and medicine.
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Affiliation(s)
- Fern Sha
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, 60637
| | - Gabriel Salzman
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, 60637
| | - Ankit Gupta
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, 60637.,Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, 10016
| | - Shohei Koide
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, 60637.,Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, 10016.,Department of Biochemistry and Molecular Pharmacology New York University School of Medicine, New York, NY, 10016
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59
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Woldring DR, Holec PV, Stern LA, Du Y, Hackel BJ. A Gradient of Sitewise Diversity Promotes Evolutionary Fitness for Binder Discovery in a Three-Helix Bundle Protein Scaffold. Biochemistry 2017; 56:1656-1671. [PMID: 28248518 DOI: 10.1021/acs.biochem.6b01142] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Engineered proteins provide clinically and industrially impactful molecules and utility within fundamental research, yet inefficiencies in discovering lead variants with new desired functionality, while maintaining stability, hinder progress. Improved function, which can result from a few strategic mutations, is fundamentally separate from discovering novel function, which often requires large leaps in sequence space. While a highly diverse combinatorial library covering immense sequence space would empower protein discovery, the ability to sample only a minor subset of sequence space and the typical destabilization of random mutations preclude this strategy. A balance must be reached. At library scale, compounding several destabilizing mutations renders many variants unable to properly fold and devoid of function. Broadly searching sequence space while reducing the level of destabilization may enhance evolution. We exemplify this balance with affibody, a three-helix bundle protein scaffold. Using natural ligand data sets, stability and structural computations, and deep sequencing of thousands of binding variants, a protein library was designed on a sitewise basis with a gradient of mutational levels across 29% of the protein. In direct competition of biased and uniform libraries, both with 1 × 109 variants, for discovery of 6 × 104 ligands (5 × 103 clusters) toward seven targets, biased amino acid frequency increased ligand discovery 13 ± 3-fold. Evolutionarily favorable amino acids, both globally and site-specifically, are further elucidated. The sitewise amino acid bias aids evolutionary discovery by reducing the level of mutant destabilization as evidenced by a midpoint of denaturation (62 ± 4 °C) 15 °C higher than that of unbiased mutants (47 ± 11 °C; p < 0.001). Sitewise diversification, identified by high-throughput evolution and rational library design, improves discovery efficiency.
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Affiliation(s)
- Daniel R Woldring
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities , 421 Washington Avenue Southeast, Minneapolis, Minnesota 55455, United States
| | - Patrick V Holec
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities , 421 Washington Avenue Southeast, Minneapolis, Minnesota 55455, United States
| | - Lawrence A Stern
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities , 421 Washington Avenue Southeast, Minneapolis, Minnesota 55455, United States
| | - Yang Du
- Molecular and Cellular Physiology, Stanford University , 279 Campus Drive, Stanford, California 94305, United States
| | - Benjamin J Hackel
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities , 421 Washington Avenue Southeast, Minneapolis, Minnesota 55455, United States
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Abstract
The Src Homology 2 (SH2) domain is the prototypical protein interaction module that lies at the heart of phosphotyrosine signaling. Since its serendipitous discovery, there has been a tremendous advancement in technologies and an array of techniques available for studying SH2 domains and phosphotyrosine signaling. In this chapter, we provide a glimpse of the history of SH2 domains and describe many of the tools and techniques that have been developed along the way and discuss future directions for SH2 domain studies. We highlight the gist of each chapter in this volume in the context of: the structural biology and phosphotyrosine binding; characterizing SH2 specificity and generating prediction models; systems biology and proteomics; SH2 domains in signal transduction; and SH2 domains in disease, diagnostics, and therapeutics. Many of the individual chapters provide an in-depth approach that will allow scientists to interrogate the function and role of SH2 domains.
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Affiliation(s)
- Bernard A Liu
- Broad Institute of Harvard and MIT, 415 Main St., 5175 JJ, Cambridge, MA, 02142, USA.
| | - Kazuya Machida
- Raymond and Beverly Sackler Laboratory of Genetics and Molecular Medicine, Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, 400 Farmington Ave., Farmington, CT, 06030, USA.
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Leenheer D, ten Dijke P, Hipolito CJ. A current perspective on applications of macrocyclic-peptide-based high-affinity ligands. Biopolymers 2016; 106:889-900. [PMID: 27352774 PMCID: PMC5132055 DOI: 10.1002/bip.22900] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Revised: 05/24/2016] [Accepted: 05/31/2016] [Indexed: 01/05/2023]
Abstract
Monoclonal antibodies can bind with high affinity and high selectivity to their targets. As a tool in therapeutics or diagnostics, however, their large size (∼150 kDa) reduces penetration into tissue and prevents passive cellular uptake. To overcome these and other problems, minimized protein scaffolds have been chosen or engineered, with care taken to not compromise binding affinity or specificity. An alternate approach is to begin with a minimal non-antibody scaffold and select functional ligands from a de novo library. We will discuss the structure, production, applications, strengths, and weaknesses of several classes of antibody-derived ligands, that is, antibodies, intrabodies, and nanobodies, and nonantibody-derived ligands, that is, monobodies, affibodies, and macrocyclic peptides. In particular, this review is focussed on macrocyclic peptides produced by the Random non-standard Peptides Integrated Discovery (RaPID) system that are small in size (typically ∼2 kDa), but are able to perform tasks typically handled by larger proteinaceous ligands.
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Affiliation(s)
- Daniël Leenheer
- Ph.D. Program in Human Biology, School of Integrative and Global MajorsUniversity of TsukubaTsukubaIbarakiJapan
| | - Peter ten Dijke
- Leiden University Medical Center, Department of Molecular Cell BiologyLeidenSouth HollandThe Netherlands
- Cancer Signaling, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of TsukubaTsukubaIbarakiJapan
| | - Christopher John Hipolito
- Cancer Signaling, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of TsukubaTsukubaIbarakiJapan
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62
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Schulze JO, Saladino G, Busschots K, Neimanis S, Süß E, Odadzic D, Zeuzem S, Hindie V, Herbrand AK, Lisa MN, Alzari PM, Gervasio FL, Biondi RM. Bidirectional Allosteric Communication between the ATP-Binding Site and the Regulatory PIF Pocket in PDK1 Protein Kinase. Cell Chem Biol 2016; 23:1193-1205. [PMID: 27693059 DOI: 10.1016/j.chembiol.2016.06.017] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 06/06/2016] [Accepted: 06/30/2016] [Indexed: 01/10/2023]
Abstract
Allostery is a phenomenon observed in many proteins where binding of a macromolecular partner or a small-molecule ligand at one location leads to specific perturbations at a site not in direct contact with the region where the binding occurs. The list of proteins under allosteric regulation includes AGC protein kinases. AGC kinases have a conserved allosteric site, the phosphoinositide-dependent protein kinase 1 (PDK1)-interacting fragment (PIF) pocket, which regulates protein ATP-binding, activity, and interaction with substrates. In this study, we identify small molecules that bind to the ATP-binding site and affect the PIF pocket of AGC kinase family members, PDK1 and Aurora kinase. We describe the mechanistic details and show that although PDK1 and Aurora kinase inhibitors bind to the conserved ATP-binding site, they differentially modulate physiological interactions at the PIF-pocket site. Our work outlines a strategy for developing bidirectional small-molecule allosteric modulators of protein kinases and other signaling proteins.
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Affiliation(s)
- Jörg O Schulze
- Research Group PhosphoSites, Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Giorgio Saladino
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK
| | - Katrien Busschots
- Research Group PhosphoSites, Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Sonja Neimanis
- Research Group PhosphoSites, Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Evelyn Süß
- Research Group PhosphoSites, Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Dalibor Odadzic
- Research Group PhosphoSites, Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Stefan Zeuzem
- Research Group PhosphoSites, Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Valerie Hindie
- Research Group PhosphoSites, Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Amanda K Herbrand
- Research Group PhosphoSites, Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - María-Natalia Lisa
- Structural Biochemistry Unit, Pasteur Institute, Rue du Docteur Roux 25, 75724 Paris, France
| | - Pedro M Alzari
- Structural Biochemistry Unit, Pasteur Institute, Rue du Docteur Roux 25, 75724 Paris, France
| | - Francesco L Gervasio
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK; Research Department of Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK.
| | - Ricardo M Biondi
- Research Group PhosphoSites, Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany; German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
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63
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Liu D, Cowburn D. Combining biophysical methods to analyze the disulfide bond in SH2 domain of C-terminal Src kinase. BIOPHYSICS REPORTS 2016; 2:33-43. [PMID: 27819029 PMCID: PMC5071372 DOI: 10.1007/s41048-016-0025-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 04/21/2016] [Indexed: 12/02/2022] Open
Abstract
The Src Homology 2 (SH2) domain is a structurally conserved protein domain that typically binds to a phosphorylated tyrosine in a peptide motif from the target protein. The SH2 domain of C-terminal Src kinase (Csk) contains a single disulfide bond, which is unusual for most SH2 domains. Although the global motion of SH2 domain regulates Csk function, little is known about the relationship between the disulfide bond and binding of the ligand. In this study, we combined X-ray crystallography, solution NMR, and other biophysical methods to reveal the interaction network in Csk. Denaturation studies have shown that disulfide bond contributes significantly to the stability of SH2 domain, and crystal structures of the oxidized and C122S mutant showed minor conformational changes. We further investigated the binding of SH2 domain to a phosphorylated peptide from Csk-binding protein upon reduction and oxidation using both NMR and fluorescence approaches. This work employed NMR, X-ray cryptography, and other biophysical methods to study a disulfide bond in Csk SH2 domain. In addition, this work provides in-depth understanding of the structural dynamics of Csk SH2 domain.
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Affiliation(s)
- Dongsheng Liu
- iHuman Institute, ShanghaiTech University, Shanghai, 201203 China ; Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | - David Cowburn
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461 USA
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64
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Rabideau AE, Pentelute BL. Delivery of Non-Native Cargo into Mammalian Cells Using Anthrax Lethal Toxin. ACS Chem Biol 2016; 11:1490-501. [PMID: 27055654 DOI: 10.1021/acschembio.6b00169] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The intracellular delivery of peptide and protein therapeutics is a major challenge due to the plasma membrane, which acts as a barrier between the extracellular environment and the intracellular milieu. Over the past two decades, a nontoxic PA/LFN delivery platform derived from anthrax lethal toxin has been developed for the transport of non-native cargo into the cytosol of cells in order to understand the translocation process through a protective antigen (PA) pore and to probe intracellular biological functions. Enzyme-mediated ligation using sortase A and native chemical ligation are two facile methods used to synthesize these non-native conjugates, inaccessible by recombinant technology. Cargo molecules that translocate efficiently include enzymes from protein toxins, antibody mimic proteins, and peptides of varying lengths and non-natural amino acid compositions. The PA pore has been found to effectively convey over 30 known cargos other than native lethal factor (LF; i.e., non-native) with diverse sequences and functionalities on the LFN transporter protein. All together these studies demonstrated that non-native cargos must adopt an unfolded or extended conformation and contain a suitable charge composition in order to efficiently pass through the PA pore. This review provides insight into design parameters for the efficient delivery of new cargos using PA and LFN.
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Affiliation(s)
- Amy E. Rabideau
- Massachusetts Institute of Technology, Department of Chemistry, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Bradley Lether Pentelute
- Massachusetts Institute of Technology, Department of Chemistry, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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65
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Continuous evolution of Bacillus thuringiensis toxins overcomes insect resistance. Nature 2016; 533:58-63. [PMID: 27120167 PMCID: PMC4865400 DOI: 10.1038/nature17938] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Accepted: 03/23/2016] [Indexed: 12/17/2022]
Abstract
The Bacillus thuringiensis δ-endotoxins (Bt toxins) are widely used insecticidal proteins in engineered crops that provide agricultural, economic, and environmental benefits. The development of insect resistance to Bt toxins endangers their long-term effectiveness. Here we have developed a phage-assisted continuous evolution selection that rapidly evolves high-affinity protein-protein interactions, and applied this system to evolve variants of the Bt toxin Cry1Ac that bind a cadherin-like receptor from the insect pest Trichoplusia ni (TnCAD) that is not natively bound by wild-type Cry1Ac. The resulting evolved Cry1Ac variants bind TnCAD with high affinity (dissociation constant Kd = 11-41 nM), kill TnCAD-expressing insect cells that are not susceptible to wild-type Cry1Ac, and kill Cry1Ac-resistant T. ni insects up to 335-fold more potently than wild-type Cry1Ac. Our findings establish that the evolution of Bt toxins with novel insect cell receptor affinity can overcome insect Bt toxin resistance and confer lethality approaching that of the wild-type Bt toxin against non-resistant insects.
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66
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Rosenfeld L, Heyne M, Shifman JM, Papo N. Protein Engineering by Combined Computational and In Vitro Evolution Approaches. Trends Biochem Sci 2016; 41:421-433. [PMID: 27061494 DOI: 10.1016/j.tibs.2016.03.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 02/29/2016] [Accepted: 03/09/2016] [Indexed: 12/30/2022]
Abstract
Two alternative strategies are commonly used to study protein-protein interactions (PPIs) and to engineer protein-based inhibitors. In one approach, binders are selected experimentally from combinatorial libraries of protein mutants that are displayed on a cell surface. In the other approach, computational modeling is used to explore an astronomically large number of protein sequences to select a small number of sequences for experimental testing. While both approaches have some limitations, their combination produces superior results in various protein engineering applications. Such applications include the design of novel binders and inhibitors, the enhancement of affinity and specificity, and the mapping of binding epitopes. The combination of these approaches also aids in the understanding of the specificity profiles of various PPIs.
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Affiliation(s)
- Lior Rosenfeld
- Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Michael Heyne
- Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel; Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Julia M Shifman
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Niv Papo
- 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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67
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Banerjee Y, Santos RD, Al-Rasadi K, Rizzo M. Targeting PCSK9 for therapeutic gains: Have we addressed all the concerns? Atherosclerosis 2016; 248:62-75. [PMID: 26987067 DOI: 10.1016/j.atherosclerosis.2016.02.018] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 01/28/2016] [Accepted: 02/16/2016] [Indexed: 02/08/2023]
Abstract
Proprotein Convertase Subtilisin/Kexin Type 9 (PCSK9) regulates the expression of low-density lipoprotein (LDL)-receptors, through reducing their recycling by binding to the receptor along with LDL and targeting it for lysosomal destruction. PCSK9 also enhances the degradation of very-low-density-lipoprotein receptor (VLDLR) and lipoprotein receptor-related protein 1 (LRP-1) in a LDL-receptor independent manner. This role in lipid homeostasis presents PCSK9 as an attractive target for the therapeutic management of familial hypercholesterolemia as well as other refractory dyslipidaemias. However, PCSK9 mediates multifarious functions independent of its role in lipid homeostasis, which can be grouped under "pleiotropic functions" of the protein. This includes PCSK9's role in: trafficking of epithelial sodium channel; hepatic regeneration; pancreatic integrity and glucose homeostasis; antiviral activity; antimalarial activity; regulation of different cell signalling pathways; cortical neural differentiation; neuronal apoptosis and Alzheimer's disease. The question that needs to be investigated in depth is "How will the pleotropic functions of PCSK9, be affected by the therapeutic intervention of the protease's LDL-receptor lowering activity?" In this review, we appraise the different lipid lowering strategies targeting PCSK9 in light of the protein's different pleiotropic functions. Additionally, we delineate the key areas that require further examination, to ensure the long-term safety of the above lipid-lowering strategies.
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Affiliation(s)
- Yajnavalka Banerjee
- Department of Biochemistry, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman.
| | - Raul D Santos
- Lipid Clinic Heart Institute (InCor), University of Sao Paulo Medical School Hospital, Sao Paulo, Brazil
| | - Khalid Al-Rasadi
- Department of Clinical Biochemistry, Sultan Qaboos University Hospital, Muscat, Oman
| | - Manfredi Rizzo
- Department of Internal Medicine and Medical Specialties, University of Palermo, Italy; Euro-Mediterranean Institute of Science and Technology, Italy
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68
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Wojcik J, Lamontanara AJ, Grabe G, Koide A, Akin L, Gerig B, Hantschel O, Koide S. Allosteric Inhibition of Bcr-Abl Kinase by High Affinity Monobody Inhibitors Directed to the Src Homology 2 (SH2)-Kinase Interface. J Biol Chem 2016; 291:8836-47. [PMID: 26912659 DOI: 10.1074/jbc.m115.707901] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Indexed: 12/22/2022] Open
Abstract
Bcr-Abl is a constitutively active kinase that causes chronic myelogenous leukemia. We have shown that a tandem fusion of two designed binding proteins, termed monobodies, directed to the interaction interface between the Src homology 2 (SH2) and kinase domains and to the phosphotyrosine-binding site of the SH2 domain, respectively, inhibits the Bcr-Abl kinase activity. Because the latter monobody inhibits processive phosphorylation by Bcr-Abl and the SH2-kinase interface is occluded in the active kinase, it remained undetermined whether targeting the SH2-kinase interface alone was sufficient for Bcr-Abl inhibition. To address this question, we generated new, higher affinity monobodies with single nanomolar KD values targeting the kinase-binding surface of SH2. Structural and mutagenesis studies revealed the molecular underpinnings of the monobody-SH2 interactions. Importantly, the new monobodies inhibited Bcr-Abl kinase activity in vitro and in cells, and they potently induced cell death in chronic myelogenous leukemia cell lines. This work provides strong evidence for the SH2-kinase interface as a pharmacologically tractable site for allosteric inhibition of Bcr-Abl.
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Affiliation(s)
- John Wojcik
- From the Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637
| | - Allan Joaquim Lamontanara
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, École polytechnique fédérale de Lausanne, 1015 Lausanne, Switzerland, and
| | - Grzegorz Grabe
- From the Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - Akiko Koide
- From the Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637
| | - Louesa Akin
- From the Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637
| | - Barbara Gerig
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, École polytechnique fédérale de Lausanne, 1015 Lausanne, Switzerland, and
| | - Oliver Hantschel
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, École polytechnique fédérale de Lausanne, 1015 Lausanne, Switzerland, and
| | - Shohei Koide
- From the Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637,
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69
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Gower CM, Thomas JR, Harrington E, Murphy J, Chang MEK, Cornella-Taracido I, Jain RK, Schirle M, Maly DJ. Conversion of a Single Polypharmacological Agent into Selective Bivalent Inhibitors of Intracellular Kinase Activity. ACS Chem Biol 2016; 11:121-31. [PMID: 26505072 DOI: 10.1021/acschembio.5b00847] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Loss-of-function studies are valuable for elucidating kinase function and the validation of new drug targets. While genetic techniques, such as RNAi and genetic knockouts, are highly specific and easy to implement, in many cases post-translational perturbation of kinase activity, specifically pharmacological inhibition, is preferable. However, due to the high degree of structural similarity between kinase active sites and the large size of the kinome, identification of pharmacological agents that are sufficiently selective to probe the function of a specific kinase of interest is challenging, and there is currently no systematic method for accomplishing this goal. Here, we present a modular chemical genetic strategy that uses antibody mimetics as highly selective targeting components of bivalent kinase inhibitors. We demonstrate that it is possible to confer high kinase selectivity to a promiscuous ATP-competitive inhibitor by tethering it to an antibody mimetic fused to the self-labeling protein SNAPtag. With this approach, a potent bivalent inhibitor of the tyrosine kinase Abl was generated. Profiling in complex cell lysates, with competition-based quantitative chemical proteomics, revealed that this bivalent inhibitor possesses greatly enhanced selectivity for its target, BCR-Abl, in K562 cells. Importantly, we show that both components of the bivalent inhibitor can be assembled in K562 cells to block the ability of BCR-Abl to phosphorylate a direct cellular substrate. Finally, we demonstrate the generality of using antibody mimetics as components of bivalent inhibitors by generating a reagent that is selective for the activated state of the serine/threonine kinase ERK2.
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Affiliation(s)
| | - Jason R. Thomas
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Edmund Harrington
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Jason Murphy
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | | | - Ivan Cornella-Taracido
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Rishi K. Jain
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Markus Schirle
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
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70
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Lee S, Kaku Y, Inoue S, Nagamune T, Kawahara M. Growth signalobody selects functional intrabodies in the mammalian cytoplasm. Biotechnol J 2016; 11:565-73. [PMID: 26647155 DOI: 10.1002/biot.201500364] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 09/03/2015] [Accepted: 12/08/2015] [Indexed: 12/18/2022]
Abstract
A versatile strategy to inhibit protein functions in the cytoplasmic environment is eagerly anticipated for drug discovery. In this study, we demonstrate a novel system to directly select functional intrabodies from a library in the mammalian cytoplasm. In this system, a target homo-oligomeric antigen is expressed together with a single-chain Fv (scFv) library that is linked to the cytoplasmic domain of a receptor tyrosine kinase (RTK) in the cytoplasm of murine interleukin-3 (IL-3)-dependent cells. As the tyrosine kinase is activated by dimerization, only scFv-RTK clones that can bind to the target antigen would be oligomerized and transduce a growth signal under the IL-3-deprived condition, which leads to selection of functional intrabodies. To demonstrate this system, we used rabies virus phosphoprotein (RV-P) that forms dimers in the cytoplasm as a target antigen. As a result, functional intrabodies were selected using our system from a naïve scFv library as well as from a pre-selected anti-RV-P library generated by phage display. This system may be applied for screening intrabodies that can prevent progression of various severe diseases.
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Affiliation(s)
- Songhee Lee
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Yoshihiro Kaku
- Department of Veterinary Science, National Institute of Infectious Diseases, Tokyo, Japan
| | - Satoshi Inoue
- Department of Veterinary Science, National Institute of Infectious Diseases, Tokyo, Japan
| | - Teruyuki Nagamune
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Masahiro Kawahara
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan.
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71
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Huang R, Fang P, Hao Z, Kay BK. Directed Evolution of a Highly Specific FN3 Monobody to the SH3 Domain of Human Lyn Tyrosine Kinase. PLoS One 2016; 11:e0145872. [PMID: 26731115 PMCID: PMC4701441 DOI: 10.1371/journal.pone.0145872] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Accepted: 12/09/2015] [Indexed: 11/26/2022] Open
Abstract
Affinity reagents of high affinity and specificity are very useful for studying the subcellular locations and quantities of individual proteins. To generate high-quality affinity reagents for human Lyn tyrosine kinase, a phage display library of fibronectin type III (FN3) monobodies was affinity selected with a recombinant form of the Lyn SH3 domain. While a highly specific monobody, TA8, was initially isolated, we chose to improve its affinity through directed evolution. A secondary library of 1.2 × 109 variants was constructed and screened by affinity selection, yielding three variants, two of which have affinities of ~ 40 nM, a 130-fold increase over the original TA8 monobody. One of the variants, 2H7, displayed high specificity to the Lyn SH3 domain, as shown by ELISA and probing arrays of 150 SH3 domains. Furthermore, the 2H7 monobody was able to pull down endogenous Lyn from a lysate of Burkitt's lymphoma cells, thereby demonstrating its utility as an affinity reagent for detecting Lyn in a complex biological mixture.
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Affiliation(s)
- Renhua Huang
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, United States of America
- * E-mail: (RH); (BK)
| | - Pete Fang
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Zengping Hao
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Brian K. Kay
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, United States of America
- * E-mail: (RH); (BK)
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72
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Bieli D, Alborelli I, Harmansa S, Matsuda S, Caussinus E, Affolter M. Development and Application of Functionalized Protein Binders in Multicellular Organisms. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 325:181-213. [DOI: 10.1016/bs.ircmb.2016.02.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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73
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Nady N, Gupta A, Ma Z, Swigut T, Koide A, Koide S, Wysocka J. ETO family protein Mtgr1 mediates Prdm14 functions in stem cell maintenance and primordial germ cell formation. eLife 2015; 4:e10150. [PMID: 26523391 PMCID: PMC4749557 DOI: 10.7554/elife.10150] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 11/01/2015] [Indexed: 01/15/2023] Open
Abstract
Prdm14 is a sequence-specific transcriptional regulator of embryonic stem cell (ESC) pluripotency and primordial germ cell (PGC) formation. It exerts its function, at least in part, through repressing genes associated with epigenetic modification and cell differentiation. Here, we show that this repressive function is mediated through an ETO-family co-repressor Mtgr1, which tightly binds to the pre-SET/SET domains of Prdm14 and co-occupies its genomic targets in mouse ESCs. We generated two monobodies, synthetic binding proteins, targeting the Prdm14 SET domain and demonstrate their utility, respectively, in facilitating crystallization and structure determination of the Prdm14-Mtgr1 complex, or as genetically encoded inhibitor of the Prdm14-Mtgr1 interaction. Structure-guided point mutants and the monobody abrogated the Prdm14-Mtgr1 association and disrupted Prdm14's function in mESC gene expression and PGC formation in vitro. Altogether, our work uncovers the molecular mechanism underlying Prdm14-mediated repression and provides renewable reagents for studying and controlling Prdm14 functions. DOI:http://dx.doi.org/10.7554/eLife.10150.001 In animals, there are many different types of cells that perform different roles. For example, stem cells divide to produce new cells that may then become other types of cells such as muscle or skin cells. Most stem cells can only produce a limited range of other cell types, except for a subset known as ‘pluripotent’ stem cells that can give rise to cells of any type in the body. A protein called Prdm14 helps to keep stem cells in a pluripotent state. In mouse embryos, Prdm14 binds to and represses particular genes that promote a process by which the stem cells can change into other cell types. If Prdm14 is missing from pluripotent stem cells, these cells become more sensitive to signals that encourage them to become other types of cells, which can lead to the loss of pluripotency. Prdm14 contains a region called the SET domain. In other proteins, this domain can alter how DNA is packaged to help switch particular genes on or off. However, such activity has not been found for the SET domain of Prdm14, raising questions about how it actually works. Here, Nady, Gupta et al. show that Prdm14 tightly interacts with a protein called Mtgr1, which belongs to a family of proteins known to be involved in leukemia. The loss of Mtgr1 also leads to the loss of pluripotency in mouse stem cells and disrupts the formation of reproductive stem cells. Furthermore, Mtgr1 binds to the same genes as Prdm14. Next, Nady, Gupta et al. made synthetic proteins, termed monobodies, that bind to the Prdm14 SET domain. One such monobody enabled the authors to determine the three-dimensional structure of Prdm1 and Mtgr1, which revealed that the SET domain of Prdm14 has many points of contact with Mtgr1. Importantly, interaction between the two partners is crucial for these proteins to maintain pluripotency and promote the production of reproductive stem cells. Altogether, these findings identify Mtgr1 as a key binding partner of Prdm14 in pluripotent stem cells and uncover a role for the SET domain in this interaction. A future challenge will be to understand the roles of these proteins in leukemia and other diseases. DOI:http://dx.doi.org/10.7554/eLife.10150.002
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Affiliation(s)
- Nataliya Nady
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, United States
| | - Ankit Gupta
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States
| | - Ziyang Ma
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, United States
| | - Tomek Swigut
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, United States
| | - Akiko Koide
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States
| | - Shohei Koide
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, United States.,National Institute of Environmental Health Sciences, , United States.,Department of Developmental Biology, Stanford University School of Medicine, Stanford, United States.,Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, United States
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74
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Guntas G, Lewis SM, Mulvaney KM, Cloer EW, Tripathy A, Lane TR, Major MB, Kuhlman B. Engineering a genetically encoded competitive inhibitor of the KEAP1-NRF2 interaction via structure-based design and phage display. Protein Eng Des Sel 2015; 29:1-9. [PMID: 26489878 DOI: 10.1093/protein/gzv055] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 09/24/2015] [Indexed: 12/31/2022] Open
Abstract
In its basal state, KEAP1 binds the transcription factor NRF2 (Kd = 5 nM) and promotes its degradation by ubiquitylation. Changes in the redox environment lead to modification of key cysteines within KEAP1, resulting in NRF2 protein accumulation and the transcription of genes important for restoring the cellular redox state. Using phage display and a computational loop grafting protocol, we engineered a monobody (R1) that is a potent competitive inhibitor of the KEAP1-NRF2 interaction. R1 bound to KEAP1 with a Kd of 300 pM and in human cells freed NRF2 from KEAP1 resulting in activation of the NRF2 promoter. Unlike cysteine-reactive small molecules that lack protein specificity, R1 is a genetically encoded, reversible inhibitor designed specifically for KEAP1. R1 should prove useful for studying the role of the KEAP1-NRF2 interaction in several disease states. The structure-based phage display strategy employed here is a general approach for engineering high-affinity binders that compete with naturally occurring interactions.
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Affiliation(s)
| | | | - Kathleen M Mulvaney
- Department of Cell Biology and Physiology Lineberger Comprehensive Cancer Center, University of North Carolina, 120 Mason Farm Road, Genetic Medicine Building 3010, Chapel Hill, NC 27599-7260, USA
| | - Erica W Cloer
- Department of Cell Biology and Physiology Lineberger Comprehensive Cancer Center, University of North Carolina, 120 Mason Farm Road, Genetic Medicine Building 3010, Chapel Hill, NC 27599-7260, USA
| | | | | | - Michael B Major
- Department of Cell Biology and Physiology Lineberger Comprehensive Cancer Center, University of North Carolina, 120 Mason Farm Road, Genetic Medicine Building 3010, Chapel Hill, NC 27599-7260, USA
| | - Brian Kuhlman
- Department of Cell Biology and Physiology Lineberger Comprehensive Cancer Center, University of North Carolina, 120 Mason Farm Road, Genetic Medicine Building 3010, Chapel Hill, NC 27599-7260, USA
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75
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Huang R, Gorman KT, Vinci CR, Dobrovetsky E, Gräslund S, Kay BK. Streamlining the Pipeline for Generation of Recombinant Affinity Reagents by Integrating the Affinity Maturation Step. Int J Mol Sci 2015; 16:23587-603. [PMID: 26437402 PMCID: PMC4632715 DOI: 10.3390/ijms161023587] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 09/18/2015] [Accepted: 09/23/2015] [Indexed: 12/26/2022] Open
Abstract
Often when generating recombinant affinity reagents to a target, one singles out an individual binder, constructs a secondary library of variants, and affinity selects a tighter or more specific binder. To enhance the throughput of this general approach, we have developed a more integrated strategy where the "affinity maturation" step is part of the phage-display pipeline, rather than a follow-on process. In our new schema, we perform two rounds of affinity selection, followed by error-prone PCR on the pools of recovered clones, generation of secondary libraries, and three additional rounds of affinity selection, under conditions of off-rate competition. We demonstrate the utility of this approach by generating low nanomolar fibronectin type III (FN3) monobodies to five human proteins: ubiquitin-conjugating enzyme E2 R1 (CDC34), COP9 signalosome complex subunit 5 (COPS5), mitogen-activated protein kinase kinase 5 (MAP2K5), Splicing factor 3A subunit 1 (SF3A1) and ubiquitin carboxyl-terminal hydrolase 11 (USP11). The affinities of the resulting monobodies are typically in the single-digit nanomolar range. We demonstrate the utility of two binders by pulling down the targets from a spiked lysate of HeLa cells. This integrated approach should be applicable to directed evolution of any phage-displayed affinity reagent scaffold.
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Affiliation(s)
- Renhua Huang
- Department of Biological Sciences, University of Illinois at Chicago, 900 S. Ashland Ave., Chicago, IL 60607, USA.
| | - Kevin T Gorman
- Department of Biological Sciences, University of Illinois at Chicago, 900 S. Ashland Ave., Chicago, IL 60607, USA.
| | - Chris R Vinci
- Department of Biological Sciences, University of Illinois at Chicago, 900 S. Ashland Ave., Chicago, IL 60607, USA.
| | - Elena Dobrovetsky
- Structural Genomics Consortium, University of Toronto, 101 College St., Toronto, ON M5G1L7, Canada.
| | - Susanne Gräslund
- Structural Genomics Consortium, University of Toronto, 101 College St., Toronto, ON M5G1L7, Canada.
| | - Brian K Kay
- Department of Biological Sciences, University of Illinois at Chicago, 900 S. Ashland Ave., Chicago, IL 60607, USA.
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76
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Woldring DR, Holec PV, Zhou H, Hackel BJ. High-Throughput Ligand Discovery Reveals a Sitewise Gradient of Diversity in Broadly Evolved Hydrophilic Fibronectin Domains. PLoS One 2015; 10:e0138956. [PMID: 26383268 PMCID: PMC4575168 DOI: 10.1371/journal.pone.0138956] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 09/04/2015] [Indexed: 12/25/2022] Open
Abstract
Discovering new binding function via a combinatorial library in small protein scaffolds requires balance between appropriate mutations to introduce favorable intermolecular interactions while maintaining intramolecular integrity. Sitewise constraints exist in a non-spatial gradient from diverse to conserved in evolved antibody repertoires; yet non-antibody scaffolds generally do not implement this strategy in combinatorial libraries. Despite the fact that biased amino acid distributions, typically elevated in tyrosine, serine, and glycine, have gained wider use in synthetic scaffolds, these distributions are still predominantly applied uniformly to diversified sites. While select sites in fibronectin domains and DARPins have shown benefit from sitewise designs, they have not been deeply evaluated. Inspired by this disparity between diversity distributions in natural libraries and synthetic scaffold libraries, we hypothesized that binders resulting from discovery and evolution would exhibit a non-spatial, sitewise gradient of amino acid diversity. To identify sitewise diversities consistent with efficient evolution in the context of a hydrophilic fibronectin domain, >105 binders to six targets were evolved and sequenced. Evolutionarily favorable amino acid distributions at 25 sites reveal Shannon entropies (range: 0.3-3.9; median: 2.1; standard deviation: 1.1) supporting the diversity gradient hypothesis. Sitewise constraints in evolved sequences are consistent with complementarity, stability, and consensus biases. Implementation of sitewise constrained diversity enables direct selection of nanomolar affinity binders validating an efficient strategy to balance inter- and intra-molecular interaction demands at each site.
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Affiliation(s)
- Daniel R. Woldring
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN, United States of America
| | - Patrick V. Holec
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN, United States of America
| | - Hong Zhou
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN, United States of America
| | - Benjamin J. Hackel
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN, United States of America
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77
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Tanaka SI, Takahashi T, Koide A, Ishihara S, Koikeda S, Koide S. Monobody-mediated alteration of enzyme specificity. Nat Chem Biol 2015; 11:762-4. [PMID: 26322825 DOI: 10.1038/nchembio.1896] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 07/11/2015] [Indexed: 12/16/2022]
Abstract
Current methods for engineering enzymes modify enzymes themselves and require a detailed mechanistic understanding or a high-throughput assay. Here, we describe a new approach where catalytic properties are modulated with synthetic binding proteins, termed monobodies, directed to an unmodified enzyme. Using the example of a β-galactosidase from Bacillus circulans, we efficiently identified monobodies that restricted its substrates for its transgalactosylation reaction and selectively enhanced the production of small oligosaccharide prebiotics.
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Affiliation(s)
- Shun-Ichi Tanaka
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, USA.,Frontier Research Department, Gifu R&D Center, Amano Enzyme, Inc., Gifu, Japan
| | - Tetsuya Takahashi
- Frontier Research Department, Gifu R&D Center, Amano Enzyme, Inc., Gifu, Japan
| | - Akiko Koide
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, USA
| | - Satoru Ishihara
- Frontier Research Department, Gifu R&D Center, Amano Enzyme, Inc., Gifu, Japan
| | - Satoshi Koikeda
- Frontier Research Department, Gifu R&D Center, Amano Enzyme, Inc., Gifu, Japan
| | - Shohei Koide
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, USA
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78
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Helma J, Cardoso MC, Muyldermans S, Leonhardt H. Nanobodies and recombinant binders in cell biology. J Cell Biol 2015; 209:633-44. [PMID: 26056137 PMCID: PMC4460151 DOI: 10.1083/jcb.201409074] [Citation(s) in RCA: 158] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Antibodies are key reagents to investigate cellular processes. The development of recombinant antibodies and binders derived from natural protein scaffolds has expanded traditional applications, such as immunofluorescence, binding arrays, and immunoprecipitation. In addition, their small size and high stability in ectopic environments have enabled their use in all areas of cell research, including structural biology, advanced microscopy, and intracellular expression. Understanding these novel reagents as genetic modules that can be integrated into cellular pathways opens up a broad experimental spectrum to monitor and manipulate cellular processes.
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Affiliation(s)
- Jonas Helma
- Department of Biology II, Ludwig Maximilians University Munich and Center for Integrated Protein Science Munich, 82152 Planegg-Martinsried, Germany
| | - M Cristina Cardoso
- Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - Serge Muyldermans
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Heinrich Leonhardt
- Department of Biology II, Ludwig Maximilians University Munich and Center for Integrated Protein Science Munich, 82152 Planegg-Martinsried, Germany
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79
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Application guide for omics approaches to cell signaling. Nat Chem Biol 2015; 11:387-97. [DOI: 10.1038/nchembio.1809] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 03/31/2015] [Indexed: 01/18/2023]
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80
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Iacob RE, Krystek SR, Huang RYC, Wei H, Tao L, Lin Z, Morin PE, Doyle ML, Tymiak AA, Engen JR, Chen G. Hydrogen/deuterium exchange mass spectrometry applied to IL-23 interaction characteristics: potential impact for therapeutics. Expert Rev Proteomics 2015; 12:159-69. [PMID: 25711416 DOI: 10.1586/14789450.2015.1018897] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
IL-23 is an important therapeutic target for the treatment of inflammatory diseases. Adnectins are targeted protein therapeutics that are derived from domain III of human fibronectin and have a similar protein scaffold to antibodies. Adnectin 2 was found to bind to IL-23 and compete with the IL-23/IL-23R interaction, posing a potential protein therapeutic. Hydrogen/deuterium exchange mass spectrometry and computational methods were applied to probe the binding interactions between IL-23 and Adnectin 2 and to determine the correlation between the two orthogonal methods. This review summarizes the current structural knowledge about IL-23 and focuses on the applicability of hydrogen/deuterium exchange mass spectrometry to investigate the higher order structure of proteins, which plays an important role in the discovery of new and improved biotherapeutics.
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Affiliation(s)
- Roxana E Iacob
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
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81
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Abstract
Monobodies are small recombinant proteins designed to bind with high affinity to target proteins. Monobodies have been generated to mimic the SIM [SUMO (small ubiquitin-like modifier)-interacting motif] present in many SUMO target proteins, but their properties have not been determined in cells. In the present study we characterize the properties of two SUMO1-specific monobodies (hS1MB4 and hS1MB5) in HEK (human embyronic kidney)-293 and HeLa cells and examine their ability to purify SUMO substrates from cell lines and rat brain. Both hS1MB4 and hS1MB5 compared favourably with commercially available antibodies and were highly selective for binding to SUMO1 over SUMO2/3 in pull-down assays against endogenous and overexpressed SUMO and SUMOylated proteins. Monobodies expressed in HeLa cells displayed a nuclear and cytosolic distribution that overlaps with SUMO1. Expression of the monobodies effectively inhibited protein SUMOylation by SUMO1 and, surprisingly, by SUMO2/3, but were not cytotoxic for at least 36 h. We attribute the effects on SUMO2/3 to the role of SUMO1 in chain termination and/or monobody inhibition of the SUMO-conjugating E1 enzyme complex. Taken together, these data provide the first demonstration that monobodies represent useful new tools both to isolate SUMO conjugates and to probe cell SUMOylation pathways in vivo.
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82
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Iacob RE, Chen G, Ahn J, Houel S, Wei H, Mo J, Tao L, Cohen D, Xie D, Lin Z, Morin PE, Doyle ML, Tymiak AA, Engen JR. The influence of adnectin binding on the extracellular domain of epidermal growth factor receptor. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:2093-2102. [PMID: 25223306 PMCID: PMC4224629 DOI: 10.1007/s13361-014-0973-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 07/29/2014] [Accepted: 08/03/2014] [Indexed: 06/03/2023]
Abstract
The precise and unambiguous elucidation and characterization of interactions between a high affinity recognition entity and its cognate protein provides important insights for the design and development of drugs with optimized properties and efficacy. In oncology, one important target protein has been shown to be the epidermal growth factor receptor (EGFR) through the development of therapeutic anticancer antibodies that are selective inhibitors of EGFR activity. More recently, smaller protein derived from the 10th type III domain of human fibronectin termed an adnectin has also been shown to inhibit EGFR in clinical studies. The mechanism of EGFR inhibition by either an adnectin or an antibody results from specific binding of the high affinity protein to the extracellular portion of EGFR (exEGFR) in a manner that prevents phosphorylation of the intracellular kinase domain of the receptor and thereby blocks intracellular signaling. Here, the structural changes induced upon binding were studied by probing the solution conformations of full length exEGFR alone and bound to a cognate adnectin through hydrogen/deuterium exchange mass spectrometry (HDX MS). The effects of binding in solution were identified and compared with the structure of a bound complex determined by X-ray crystallography.ᅟ
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Affiliation(s)
- Roxana E. Iacob
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA USA
| | - Guodong Chen
- Bioanalytical and Discovery Analytical Sciences, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Joomi Ahn
- Waters Corporation, Milford, MA, USA
| | | | - Hui Wei
- Bioanalytical and Discovery Analytical Sciences, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Jingjie Mo
- Bioanalytical and Discovery Analytical Sciences, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Li Tao
- Biologics Manufacturing and Process Development, Global Manufacturing and Supply, Bristol-Myers Squibb Company, Hopewell, NJ, USA
| | - Daniel Cohen
- Protein Science, Research and Development, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Dianlin Xie
- Protein Science, Research and Development, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Zheng Lin
- Protein Science, Research and Development, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Paul E. Morin
- Protein Science, Research and Development, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Michael L. Doyle
- Protein Science, Research and Development, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Adrienne A. Tymiak
- Bioanalytical and Discovery Analytical Sciences, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - John R. Engen
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA USA
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83
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Yan Y, Chen G, Wei H, Huang RYC, Mo J, Rempel DL, Tymiak AA, Gross ML. Fast photochemical oxidation of proteins (FPOP) maps the epitope of EGFR binding to adnectin. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:2084-92. [PMID: 25267085 PMCID: PMC4224620 DOI: 10.1007/s13361-014-0993-x] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 08/15/2014] [Accepted: 08/21/2014] [Indexed: 05/11/2023]
Abstract
Epitope mapping is an important tool for the development of monoclonal antibodies, mAbs, as therapeutic drugs. Recently, a class of therapeutic mAb alternatives, adnectins, has been developed as targeted biologics. They are derived from the 10th type III domain of human fibronectin ((10)Fn3). A common approach to map the epitope binding of these therapeutic proteins to their binding partners is X-ray crystallography. Although the crystal structure is known for Adnectin 1 binding to human epidermal growth factor receptor (EGFR), we seek to determine complementary binding in solution and to test the efficacy of footprinting for this purpose. As a relatively new tool in structural biology and complementary to X-ray crystallography, protein footprinting coupled with mass spectrometry is promising for protein-protein interaction studies. We report here the use of fast photochemical oxidation of proteins (FPOP) coupled with MS to map the epitope of EGFR-Adnectin 1 at both the peptide and amino-acid residue levels. The data correlate well with the previously determined epitopes from the crystal structure and are consistent with HDX MS data, which are presented in an accompanying paper. The FPOP-determined binding interface involves various amino-acid and peptide regions near the N terminus of EGFR. The outcome adds credibility to oxidative labeling by FPOP for epitope mapping and motivates more applications in the therapeutic protein area as a stand-alone method or in conjunction with X-ray crystallography, NMR, site-directed mutagenesis, and other orthogonal methods.
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Affiliation(s)
- Yuetian Yan
- Center for Biomedical and Bioorganic Mass Spectrometry, Department of Chemistry, Washington University in St. Louis, St. Louis, MO, 63130-4899, USA
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84
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Liao X, Rabideau AE, Pentelute BL. Delivery of antibody mimics into mammalian cells via anthrax toxin protective antigen. Chembiochem 2014; 15:2458-66. [PMID: 25250705 PMCID: PMC4498471 DOI: 10.1002/cbic.201402290] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Indexed: 11/06/2022]
Abstract
Antibody mimics have significant scientific and therapeutic utility for the disruption of protein-protein interactions inside cells; however, their delivery to the cell cytosol remains a major challenge. Here we show that protective antigen (PA), a component of anthrax toxin, efficiently transports commonly used antibody mimics to the cytosol of mammalian cells when conjugated to the N-terminal domain of LF (LFN). In contrast, a cell-penetrating peptide (CPP) was not able to deliver any of these antibody mimics into the cell cytosol. The refolding and binding of a transported tandem monobody to Bcr-Abl (its protein target) in chronic myeloid leukemia cells were confirmed by co-immunoprecipitation. We also observed inhibition of Bcr-Abl kinase activity and induction of apoptosis caused by the monobody. In a separate case, we show disruption of key interactions in the MAPK signaling pathway after PA-mediated delivery of an affibody binder that targets hRaf-1. We show for the first time that PA can deliver bioactive antibody mimics to disrupt intracellular protein-protein interactions. This technology adds a useful tool to expand the applications of these modern agents to the intracellular milieu.
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Affiliation(s)
- Xiaoli Liao
- Department of Chemistry, Massachusetts Institute of Technology77 Massachusetts Avenue 18-596, Cambridge, MA 02193 (USA) E-mail:
| | - Amy E Rabideau
- Department of Chemistry, Massachusetts Institute of Technology77 Massachusetts Avenue 18-596, Cambridge, MA 02193 (USA) E-mail:
| | - Bradley L Pentelute
- Department of Chemistry, Massachusetts Institute of Technology77 Massachusetts Avenue 18-596, Cambridge, MA 02193 (USA) E-mail:
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85
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Zheng H, Bi J, Krendel M, Loh SN. Converting a binding protein into a biosensing conformational switch using protein fragment exchange. Biochemistry 2014; 53:5505-14. [PMID: 25084233 PMCID: PMC4151334 DOI: 10.1021/bi500758u] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
![]()
Biosensors
can be used in applications ranging from identifying
disease biomarkers to detecting spatial and temporal distributions
of specific molecules in living cells. A major challenge facing biosensor
development is how to functionally couple a biological recognition
domain to an output module so that the binding event can be transduced
to a visible and quantifiable signal [e.g., Förster resonance
energy transfer (FRET)]. Most designs achieve
coupling by means of a binding protein that changes conformation upon
interacting with its target. This approach is limited by the fact
that few proteins possess such natural allosteric mechanisms, and
for those that do, the conformational change is frequently not extensive
enough to produce a large change in distance between FRET donor and
acceptor groups. Here, we introduce protein fragment exchange (FREX)
to address both problems. FREX employs two components: a folded binding
protein and a fragment duplicated from it, the latter of which can
be chosen from many possible fragments. The system is rationally tuned
so that addition of ligand induces a conformational change in which
the fragment exchanges positions with the corresponding segment of
the binding protein. Placing fluorescent donor and acceptor groups
on the binding protein and fragment reduces the background level of
FRET of the unbound sensor, resulting in a ratiometric FRET response
that is expected to be strong and reproducible from protein to protein.
FREX is demonstrated using fibronectin III, a monobody binding scaffold
that has been tailored to recognize multiple targets. Sensors labeled
with Alexa FRET pairs exhibit ratiometric FRET changes of up to 8.6-fold
and perform equally well in buffer and serum. A genetically
encoded variant of this sensor is shown to be functional
in cell lysates and in mammalian cell cultures.
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Affiliation(s)
- Huimei Zheng
- Department of Biochemistry and Molecular Biology and ‡Department of Cell and Developmental Biology, State University of New York Upstate Medical University , 750 East Adams Street, Syracuse, New York 13210, United States
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86
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Jost C, Plückthun A. Engineered proteins with desired specificity: DARPins, other alternative scaffolds and bispecific IgGs. Curr Opin Struct Biol 2014; 27:102-12. [PMID: 25033247 DOI: 10.1016/j.sbi.2014.05.011] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Revised: 05/13/2014] [Accepted: 05/23/2014] [Indexed: 12/22/2022]
Abstract
Specific binding proteins have become essential for diagnostic and therapeutic applications, and traditionally these have been antibodies. Nowadays an increasing number of alternative scaffolds have joined these ranks. These additional folds have raised a lot of interest and expectations within the last decade. It appears that they have come of age and caught up with antibodies in many fields of applications. The last years have seen an exploration of possibilities in research, diagnostics and therapy. Some scaffolds have received further improvements broadening their fields of application, while others have started to occupy their respective niche. Protein engineering, the prerequisite for the advent of all alternative scaffolds, remains the driving force in this process, for both non-immunoglobulins and immunoglobulins alike.
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Affiliation(s)
- Christian Jost
- Department of Biochemistry, University of Zürich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland
| | - Andreas Plückthun
- Department of Biochemistry, University of Zürich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland.
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87
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Mitchell T, Chao G, Sitkoff D, Lo F, Monshizadegan H, Meyers D, Low S, Russo K, DiBella R, Denhez F, Gao M, Myers J, Duke G, Witmer M, Miao B, Ho SP, Khan J, Parker RA. Pharmacologic profile of the Adnectin BMS-962476, a small protein biologic alternative to PCSK9 antibodies for low-density lipoprotein lowering. J Pharmacol Exp Ther 2014; 350:412-24. [PMID: 24917546 DOI: 10.1124/jpet.114.214221] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Proprotein convertase subtilisin kexin-9 (PCSK9) is an important pharmacological target for decreasing low-density lipoprotein (LDL) in cardiovascular disease, although seemingly inaccessible to small molecule approaches. Compared with therapeutic IgG antibodies currently in development, targeting circulating PCSK9 with smaller molecular scaffolds could offer different profiles and reduced dose burdens. This inspired genesis of PCSK9-binding Adnectins, a protein family derived from human fibronectin-10th-type III-domain and engineered for high-affinity target binding. BMS-962476, an ∼11-kDa polypeptide conjugated to polyethylene glycol to enhance pharmacokinetics, binds with subnanomolar affinity to human. The X-ray cocrystal structure of PCSK9 with a progenitor Adnectin shows ∼910 Å(2) of PCSK9 surface covered next to the LDL receptor binding site, largely by residues of a single loop of the Adnectin. In hypercholesterolemic, overexpressing human PCSK9 transgenic mice, BMS-962476 rapidly lowered cholesterol and free PCSK9 levels. In genomic transgenic mice, BMS-962476 potently reduced free human PCSK9 (ED50 ∼0.01 mg/kg) followed by ∼2-fold increases in total PCSK9 before return to baseline. Treatment of cynomolgus monkeys with BMS-962476 rapidly suppressed free PCSK9 >99% and LDL-cholesterol ∼55% with subsequent 6-fold increase in total PCSK9, suggesting reduced clearance of circulating complex. Liver sterol response genes were consequently downregulated, following which LDL and total PCSK9 returned to baseline. These studies highlight the rapid dynamics of PCSK9 control over LDL and liver cholesterol metabolism and characterize BMS-962476 as a potent and efficacious PCSK9 inhibitor.
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Affiliation(s)
- Tracy Mitchell
- Molecular Discovery Technologies (T.M., G.C., D.S., S.L., K.R., R.D., F.D., M.G., J.M., G.D., M.W., J.K.), Applied Genomics (S.P.H.), and Cardiovascular Discovery Biology (F.L., H.M., D.M., B.M., R.A.P.), Bristol-Myers Squibb Research and Development, Princeton, New Jersey
| | - Ginger Chao
- Molecular Discovery Technologies (T.M., G.C., D.S., S.L., K.R., R.D., F.D., M.G., J.M., G.D., M.W., J.K.), Applied Genomics (S.P.H.), and Cardiovascular Discovery Biology (F.L., H.M., D.M., B.M., R.A.P.), Bristol-Myers Squibb Research and Development, Princeton, New Jersey
| | - Doree Sitkoff
- Molecular Discovery Technologies (T.M., G.C., D.S., S.L., K.R., R.D., F.D., M.G., J.M., G.D., M.W., J.K.), Applied Genomics (S.P.H.), and Cardiovascular Discovery Biology (F.L., H.M., D.M., B.M., R.A.P.), Bristol-Myers Squibb Research and Development, Princeton, New Jersey
| | - Fred Lo
- Molecular Discovery Technologies (T.M., G.C., D.S., S.L., K.R., R.D., F.D., M.G., J.M., G.D., M.W., J.K.), Applied Genomics (S.P.H.), and Cardiovascular Discovery Biology (F.L., H.M., D.M., B.M., R.A.P.), Bristol-Myers Squibb Research and Development, Princeton, New Jersey
| | - Hossain Monshizadegan
- Molecular Discovery Technologies (T.M., G.C., D.S., S.L., K.R., R.D., F.D., M.G., J.M., G.D., M.W., J.K.), Applied Genomics (S.P.H.), and Cardiovascular Discovery Biology (F.L., H.M., D.M., B.M., R.A.P.), Bristol-Myers Squibb Research and Development, Princeton, New Jersey
| | - Daniel Meyers
- Molecular Discovery Technologies (T.M., G.C., D.S., S.L., K.R., R.D., F.D., M.G., J.M., G.D., M.W., J.K.), Applied Genomics (S.P.H.), and Cardiovascular Discovery Biology (F.L., H.M., D.M., B.M., R.A.P.), Bristol-Myers Squibb Research and Development, Princeton, New Jersey
| | - Simon Low
- Molecular Discovery Technologies (T.M., G.C., D.S., S.L., K.R., R.D., F.D., M.G., J.M., G.D., M.W., J.K.), Applied Genomics (S.P.H.), and Cardiovascular Discovery Biology (F.L., H.M., D.M., B.M., R.A.P.), Bristol-Myers Squibb Research and Development, Princeton, New Jersey
| | - Katie Russo
- Molecular Discovery Technologies (T.M., G.C., D.S., S.L., K.R., R.D., F.D., M.G., J.M., G.D., M.W., J.K.), Applied Genomics (S.P.H.), and Cardiovascular Discovery Biology (F.L., H.M., D.M., B.M., R.A.P.), Bristol-Myers Squibb Research and Development, Princeton, New Jersey
| | - Rose DiBella
- Molecular Discovery Technologies (T.M., G.C., D.S., S.L., K.R., R.D., F.D., M.G., J.M., G.D., M.W., J.K.), Applied Genomics (S.P.H.), and Cardiovascular Discovery Biology (F.L., H.M., D.M., B.M., R.A.P.), Bristol-Myers Squibb Research and Development, Princeton, New Jersey
| | - Fabienne Denhez
- Molecular Discovery Technologies (T.M., G.C., D.S., S.L., K.R., R.D., F.D., M.G., J.M., G.D., M.W., J.K.), Applied Genomics (S.P.H.), and Cardiovascular Discovery Biology (F.L., H.M., D.M., B.M., R.A.P.), Bristol-Myers Squibb Research and Development, Princeton, New Jersey
| | - Mian Gao
- Molecular Discovery Technologies (T.M., G.C., D.S., S.L., K.R., R.D., F.D., M.G., J.M., G.D., M.W., J.K.), Applied Genomics (S.P.H.), and Cardiovascular Discovery Biology (F.L., H.M., D.M., B.M., R.A.P.), Bristol-Myers Squibb Research and Development, Princeton, New Jersey
| | - Joseph Myers
- Molecular Discovery Technologies (T.M., G.C., D.S., S.L., K.R., R.D., F.D., M.G., J.M., G.D., M.W., J.K.), Applied Genomics (S.P.H.), and Cardiovascular Discovery Biology (F.L., H.M., D.M., B.M., R.A.P.), Bristol-Myers Squibb Research and Development, Princeton, New Jersey
| | - Gerald Duke
- Molecular Discovery Technologies (T.M., G.C., D.S., S.L., K.R., R.D., F.D., M.G., J.M., G.D., M.W., J.K.), Applied Genomics (S.P.H.), and Cardiovascular Discovery Biology (F.L., H.M., D.M., B.M., R.A.P.), Bristol-Myers Squibb Research and Development, Princeton, New Jersey
| | - Mark Witmer
- Molecular Discovery Technologies (T.M., G.C., D.S., S.L., K.R., R.D., F.D., M.G., J.M., G.D., M.W., J.K.), Applied Genomics (S.P.H.), and Cardiovascular Discovery Biology (F.L., H.M., D.M., B.M., R.A.P.), Bristol-Myers Squibb Research and Development, Princeton, New Jersey
| | - Bowman Miao
- Molecular Discovery Technologies (T.M., G.C., D.S., S.L., K.R., R.D., F.D., M.G., J.M., G.D., M.W., J.K.), Applied Genomics (S.P.H.), and Cardiovascular Discovery Biology (F.L., H.M., D.M., B.M., R.A.P.), Bristol-Myers Squibb Research and Development, Princeton, New Jersey
| | - Siew P Ho
- Molecular Discovery Technologies (T.M., G.C., D.S., S.L., K.R., R.D., F.D., M.G., J.M., G.D., M.W., J.K.), Applied Genomics (S.P.H.), and Cardiovascular Discovery Biology (F.L., H.M., D.M., B.M., R.A.P.), Bristol-Myers Squibb Research and Development, Princeton, New Jersey
| | - Javed Khan
- Molecular Discovery Technologies (T.M., G.C., D.S., S.L., K.R., R.D., F.D., M.G., J.M., G.D., M.W., J.K.), Applied Genomics (S.P.H.), and Cardiovascular Discovery Biology (F.L., H.M., D.M., B.M., R.A.P.), Bristol-Myers Squibb Research and Development, Princeton, New Jersey
| | - Rex A Parker
- Molecular Discovery Technologies (T.M., G.C., D.S., S.L., K.R., R.D., F.D., M.G., J.M., G.D., M.W., J.K.), Applied Genomics (S.P.H.), and Cardiovascular Discovery Biology (F.L., H.M., D.M., B.M., R.A.P.), Bristol-Myers Squibb Research and Development, Princeton, New Jersey
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88
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Gifford SM, Liu W, Mader CC, Halo TL, Machida K, Boggon TJ, Koleske AJ. Two amino acid residues confer different binding affinities of Abelson family kinase SRC homology 2 domains for phosphorylated cortactin. J Biol Chem 2014; 289:19704-13. [PMID: 24891505 DOI: 10.1074/jbc.m114.556480] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The closely related Abl family kinases, Arg and Abl, play important non-redundant roles in the regulation of cell morphogenesis and motility. Despite similar N-terminal sequences, Arg and Abl interact with different substrates and binding partners with varying affinities. This selectivity may be due to slight differences in amino acid sequence leading to differential interactions with target proteins. We report that the Arg Src homology (SH) 2 domain binds two specific phosphotyrosines on cortactin, a known Abl/Arg substrate, with over 10-fold higher affinity than the Abl SH2 domain. We show that this significant affinity difference is due to the substitution of arginine 161 and serine 187 in Abl to leucine 207 and threonine 233 in Arg, respectively. We constructed Abl SH2 domains with R161L and S187T mutations alone and in combination and find that these substitutions are sufficient to convert the low affinity Abl SH2 domain to a higher affinity "Arg-like" SH2 domain in binding to a phospho-cortactin peptide. We crystallized the Arg SH2 domain for structural comparison to existing crystal structures of the Abl SH2 domain. We show that these two residues are important determinants of Arg and Abl SH2 domain binding specificity. Finally, we expressed Arg containing an "Abl-like" low affinity mutant Arg SH2 domain (L207R/T233S) and find that this mutant, although properly localized to the cell periphery, does not support wild type levels of cell edge protrusion. Together, these observations indicate that these two amino acid positions confer different binding affinities and cellular functions on the distinct Abl family kinases.
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Affiliation(s)
| | | | | | | | - Kazuya Machida
- the Department of Genetics and Developmental Biology, Raymond and Beverly Sackler Laboratory of Genetics and Molecular Medicine, University of Connecticut Health Center, Farmington, Conneticut 06030
| | | | - Anthony J Koleske
- From the Departments of Molecular Biophysics and Biochemistry, the Yale Cancer Center, Interdepartmental Neuroscience Program, and Department of Neurobiology, Yale University, New Haven, Connecticut 06520 and
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89
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Taussig MJ, Schmidt R, Cook EA, Stoevesandt O. Development of proteome-wide binding reagents for research and diagnostics. Proteomics Clin Appl 2014; 7:756-66. [PMID: 24178846 DOI: 10.1002/prca.201300060] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2013] [Revised: 09/09/2013] [Accepted: 09/10/2013] [Indexed: 01/11/2023]
Abstract
Alongside MS, antibodies and other specific protein-binding molecules have a special place in proteomics as affinity reagents in a toolbox of applications for determining protein location, quantitative distribution and function (affinity proteomics). The realisation that the range of research antibodies available, while apparently vast is nevertheless still very incomplete and frequently of uncertain quality, has stimulated projects with an objective of raising comprehensive, proteome-wide sets of protein binders. With progress in automation and throughput, a remarkable number of recent publications refer to the practical possibility of selecting binders to every protein encoded in the genome. Here we review the requirements of a pipeline of production of protein binders for the human proteome, including target prioritisation, antigen design, 'next generation' methods, databases and the approaches taken by ongoing projects in Europe and the USA. While the task of generating affinity reagents for all human proteins is complex and demanding, the benefits of well-characterised and quality-controlled pan-proteome binder resources for biomedical research, industry and life sciences in general would be enormous and justify the effort. Given the technical, personnel and financial resources needed to fulfil this aim, expansion of current efforts may best be addressed through large-scale international collaboration.
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Affiliation(s)
- Michael J Taussig
- Protein Technology Group, The Babraham Institute, Cambridge, UK; Cambridge Protein Arrays Ltd, Babraham Research Campus, Cambridge, UK
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90
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Correa A, Pacheco S, Mechaly AE, Obal G, Béhar G, Mouratou B, Oppezzo P, Alzari PM, Pecorari F. Potent and specific inhibition of glycosidases by small artificial binding proteins (affitins). PLoS One 2014; 9:e97438. [PMID: 24823716 PMCID: PMC4019568 DOI: 10.1371/journal.pone.0097438] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2014] [Accepted: 04/17/2014] [Indexed: 01/05/2023] Open
Abstract
Glycosidases are associated with various human diseases. The development of efficient and specific inhibitors may provide powerful tools to modulate their activity. However, achieving high selectivity is a major challenge given that glycosidases with different functions can have similar enzymatic mechanisms and active-site architectures. As an alternative approach to small-chemical compounds, proteinaceous inhibitors might provide a better specificity by involving a larger surface area of interaction. We report here the design and characterization of proteinaceous inhibitors that specifically target endoglycosidases representative of the two major mechanistic classes; retaining and inverting glycosidases. These inhibitors consist of artificial affinity proteins, Affitins, selected against the thermophilic CelD from Clostridium thermocellum and lysozyme from hen egg. They were obtained from libraries of Sac7d variants, which involve either the randomization of a surface or the randomization of a surface and an artificially-extended loop. Glycosidase binders exhibited affinities in the nanomolar range with no cross-recognition, with efficient inhibition of lysozyme (Ki = 45 nM) and CelD (Ki = 95 and 111 nM), high expression yields in Escherichia coli, solubility, and thermal stabilities up to 81.1°C. The crystal structures of glycosidase-Affitin complexes validate our library designs. We observed that Affitins prevented substrate access by two modes of binding; covering or penetrating the catalytic site via the extended loop. In addition, Affitins formed salt-bridges with residues essential for enzymatic activity. These results lead us to propose the use of Affitins as versatile selective glycosidase inhibitors and, potentially, as enzymatic inhibitors in general.
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Affiliation(s)
- Agustín Correa
- Institut Pasteur de Montevideo, Recombinant Protein Unit, Montevideo, Uruguay
- Institut Pasteur, Unité de Microbiologie Structurale, CNRS UMR 3528, Paris, France
| | - Sabino Pacheco
- Institut Pasteur, Unité de Microbiologie Structurale, CNRS UMR 3528, Paris, France
- INSERM UMR 892 - CRCNA, Nantes, France
- CNRS UMR 6299, Nantes, France
- University of Nantes, Nantes, France
| | - Ariel E. Mechaly
- Institut Pasteur, Unité de Microbiologie Structurale, CNRS UMR 3528, Paris, France
| | - Gonzalo Obal
- Institut Pasteur de Montevideo, Protein Biophysics Unit, Montevideo, Uruguay
| | - Ghislaine Béhar
- INSERM UMR 892 - CRCNA, Nantes, France
- CNRS UMR 6299, Nantes, France
- University of Nantes, Nantes, France
| | - Barbara Mouratou
- INSERM UMR 892 - CRCNA, Nantes, France
- CNRS UMR 6299, Nantes, France
- University of Nantes, Nantes, France
| | - Pablo Oppezzo
- Institut Pasteur de Montevideo, Recombinant Protein Unit, Montevideo, Uruguay
| | - Pedro M. Alzari
- Institut Pasteur, Unité de Microbiologie Structurale, CNRS UMR 3528, Paris, France
| | - Frédéric Pecorari
- INSERM UMR 892 - CRCNA, Nantes, France
- CNRS UMR 6299, Nantes, France
- University of Nantes, Nantes, France
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91
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Diem MD, Hyun L, Yi F, Hippensteel R, Kuhar E, Lowenstein C, Swift EJ, O'Neil KT, Jacobs SA. Selection of high-affinity Centyrin FN3 domains from a simple library diversified at a combination of strand and loop positions. Protein Eng Des Sel 2014; 27:419-29. [PMID: 24786107 DOI: 10.1093/protein/gzu016] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Alternative scaffold molecules represent a class of proteins important to the study of protein design and mechanisms of protein-protein interactions, as well as for the development of therapeutic proteins. Here, we describe the generation of a library built upon the framework of a consensus FN3 domain sequence resulting in binding proteins we call Centyrins. This new library employs diversified positions within the C-strand, CD-loop, F-strand and FG-loop of the FN3 domain. CIS display was used to select high-affinity Centyrin variants against three targets; c-MET, murine IL-17A and rat TNFα and scanning mutagenesis studies were used to define the positions of the library most important for target binding. Contributions from both the strand and loop positions were noted, although the pattern was different for each molecule. In addition, an affinity maturation scheme is described that resulted in a significant improvement in the affinity of one selected Centyrin variant. Together, this work provides important data contributing to our understanding of potential FN3 binding interfaces and a new tool for generating high-affinity scaffold molecules.
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Affiliation(s)
- Michael D Diem
- Janssen Research & Development, L.L.C., 1400 McKean Road, PO Box 776, Spring House, PA 19477, USA
| | - Linus Hyun
- Janssen Research & Development, L.L.C., 1400 McKean Road, PO Box 776, Spring House, PA 19477, USA
| | - Fang Yi
- Janssen Research & Development, L.L.C., 1400 McKean Road, PO Box 776, Spring House, PA 19477, USA
| | - Randi Hippensteel
- Janssen Research & Development, L.L.C., 1400 McKean Road, PO Box 776, Spring House, PA 19477, USA
| | - Elise Kuhar
- Janssen Research & Development, L.L.C., 1400 McKean Road, PO Box 776, Spring House, PA 19477, USA
| | - Cassandra Lowenstein
- Janssen Research & Development, L.L.C., 1400 McKean Road, PO Box 776, Spring House, PA 19477, USA
| | - Edward J Swift
- Janssen Research & Development, L.L.C., 1400 McKean Road, PO Box 776, Spring House, PA 19477, USA
| | - Karyn T O'Neil
- Janssen Research & Development, L.L.C., 1400 McKean Road, PO Box 776, Spring House, PA 19477, USA
| | - Steven A Jacobs
- Janssen Research & Development, L.L.C., 1400 McKean Road, PO Box 776, Spring House, PA 19477, USA
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92
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Zayner JP, Antoniou C, French AR, Hause RJ, Sosnick TR. Investigating models of protein function and allostery with a widespread mutational analysis of a light-activated protein. Biophys J 2014; 105:1027-36. [PMID: 23972854 DOI: 10.1016/j.bpj.2013.07.010] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 06/17/2013] [Accepted: 07/01/2013] [Indexed: 10/26/2022] Open
Abstract
To investigate the relationship between a protein's sequence and its biophysical properties, we studied the effects of more than 100 mutations in Avena sativa light-oxygen-voltage domain 2, a model protein of the Per-Arnt-Sim family. The A. sativa light-oxygen-voltage domain 2 undergoes a photocycle with a conformational change involving the unfolding of the terminal helices. Whereas selection studies typically search for winners in a large population and fail to characterize many sites, we characterized the biophysical consequences of mutations throughout the protein using NMR, circular dichroism, and ultraviolet/visible spectroscopy. Despite our intention to introduce highly disruptive substitutions, most had modest or no effect on function, and many could even be considered to be more photoactive. Substitutions at evolutionarily conserved sites can have minimal effect, whereas those at nonconserved positions can have large effects, contrary to the view that the effects of mutations, especially at conserved positions, are predictable. Using predictive models, we found that the effects of mutations on biophysical function and allostery reflect a complex mixture of multiple characteristics including location, character, electrostatics, and chemistry.
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Affiliation(s)
- Josiah P Zayner
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
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93
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Tiede C, Tang AAS, Deacon SE, Mandal U, Nettleship JE, Owen RL, George SE, Harrison DJ, Owens RJ, Tomlinson DC, McPherson MJ. Adhiron: a stable and versatile peptide display scaffold for molecular recognition applications. Protein Eng Des Sel 2014; 27:145-55. [PMID: 24668773 PMCID: PMC4000234 DOI: 10.1093/protein/gzu007] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
We have designed a novel non-antibody scaffold protein, termed Adhiron, based on a phytocystatin consensus sequence. The Adhiron scaffold shows high thermal stability (Tm ca. 101°C), and is expressed well in Escherichia coli. We have determined the X-ray crystal structure of the Adhiron scaffold to 1.75 Å resolution revealing a compact cystatin-like fold. We have constructed a phage-display library in this scaffold by insertion of two variable peptide regions. The library is of high quality and complexity comprising 1.3 × 1010 clones. To demonstrate library efficacy, we screened against the yeast Small Ubiquitin-like Modifier (SUMO). In selected clones, variable region 1 often contained sequences homologous to the known SUMO interactive motif (V/I-X-V/I-V/I). Four Adhirons were further characterised and displayed low nanomolar affinities and high specificity for yeast SUMO with essentially no cross-reactivity to human SUMO protein isoforms. We have identified binders against >100 target molecules to date including as examples, a fibroblast growth factor (FGF1), platelet endothelial cell adhesion molecule (PECAM-1; CD31), the SH2 domain Grb2 and a 12-aa peptide. Adhirons are highly stable and well expressed allowing highly specific binding reagents to be selected for use in molecular recognition applications.
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Affiliation(s)
- Christian Tiede
- Biomedical Health Research Centre, BioScreening Technology Group, University of Leeds, Leeds LS2 9JT, UK
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94
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Luo J, Teplyakov A, Obmolova G, Malia TJ, Chan W, Jacobs SA, O'Neil KT, Gilliland GL. N-terminal β-strand swapping in a consensus-derived alternative scaffold driven by stabilizing hydrophobic interactions. Proteins 2014; 82:1527-33. [PMID: 24464739 DOI: 10.1002/prot.24517] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 01/09/2014] [Accepted: 01/16/2014] [Indexed: 11/08/2022]
Abstract
The crystal structure of an N-terminal β-strand-swapped consensus-derived tenascin FN3 alternative scaffold has been determined. A comparison with the unswapped structure reveals that the side chain of residue F88 orients differently and packs more tightly with the hydrophobic core of the domain. Dimer formation also results in the burial of a hydrophobic patch on the surface of the domain. Thus, it appears that tighter packing of F88 in the hydrophobic core and burial of surface hydrophobicity provide the driving forces for the N-terminal β-strand swapping, leading to the formation of a stable compact dimer.
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Affiliation(s)
- Jinquan Luo
- Biotechnology Center of Excellence, Janssen Research & Development LLC, Spring House, Pennsylvania, 19477
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95
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Teplyakov A, Obmolova G, Malia TJ, Luo J, Jacobs SA, Chan W, Domingo D, Baker A, O'Neil KT, Gilliland GL. C-terminal β-strand swapping in a consensus-derived fibronectin Type III scaffold. Proteins 2014; 82:1359-69. [PMID: 24375666 DOI: 10.1002/prot.24502] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 12/09/2013] [Accepted: 12/17/2013] [Indexed: 11/07/2022]
Abstract
The crystal structures of six different fibronectin Type III consensus-derived Tencon domains, whose solution properties exhibit no, to various degrees of, aggregation according to SEC, have been determined. The structures of the five variants showing aggregation reveal 3D domain swapped dimers. In all five cases, the swapping involves the C-terminal β-strand resulting in the formation of Tencon dimers in which the target-binding surface is blocked. All of the variants differ in sequence in the FG loop, which is the hinge loop in the β-strand-swapped dimers. The six tencon variants have between 0 and 5 residues inserted between positions 77 and 78 in the FG loop. Analysis of the structures suggests that a non-glycine residue at position 77 and insertions of <4 residues may destabilize the β-turn in the FG loop promoting β-strand swapping. Swapped dimers with an odd number of inserted residues may be less stable, particularly if they contain proline residues, because they cannot form perfect β-bridges in the FG regions that link the swapped dimers. The Tencon β-swapped variants with the longest FG sequences are observed to form higher order hexameric or helical oligomeric structures in the crystal correlating well with the aggregation properties of these domains observed in solution. Understanding the structural basis for domain-swapped dimerization and oligomerization will support engineering efforts of the Tencon domain to produce variants with desired biophysical properties.
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Affiliation(s)
- Alexey Teplyakov
- Janssen Research & Development, LLC, Biotechnology Center of Excellence, 1400 McKean Road, Spring House, Pennsylvania, 19477
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96
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Dissection of the BCR-ABL signaling network using highly specific monobody inhibitors to the SHP2 SH2 domains. Proc Natl Acad Sci U S A 2013; 110:14924-9. [PMID: 23980151 DOI: 10.1073/pnas.1303640110] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The dysregulated tyrosine kinase BCR-ABL causes chronic myelogenous leukemia in humans and forms a large multiprotein complex that includes the Src-homology 2 (SH2) domain-containing phosphatase 2 (SHP2). The expression of SHP2 is necessary for BCR-ABL-dependent oncogenic transformation, but the precise signaling mechanisms of SHP2 are not well understood. We have developed binding proteins, termed monobodies, for the N- and C-terminal SH2 domains of SHP2. Intracellular expression followed by interactome analysis showed that the monobodies are essentially monospecific to SHP2. Two crystal structures revealed that the monobodies occupy the phosphopeptide-binding sites of the SH2 domains and thus can serve as competitors of SH2-phosphotyrosine interactions. Surprisingly, the segments of both monobodies that bind to the peptide-binding grooves run in the opposite direction to that of canonical phosphotyrosine peptides, which may contribute to their exquisite specificity. When expressed in cells, monobodies targeting the N-SH2 domain disrupted the interaction of SHP2 with its upstream activator, the Grb2-associated binder 2 adaptor protein, suggesting decoupling of SHP2 from the BCR-ABL protein complex. Inhibition of either N-SH2 or C-SH2 was sufficient to inhibit two tyrosine phosphorylation events that are critical for SHP2 catalytic activity and to block ERK activation. In contrast, targeting the N-SH2 or C-SH2 revealed distinct roles of the two SH2 domains in downstream signaling, such as the phosphorylation of paxillin and signal transducer and activator of transcription 5. Our results delineate a hierarchy of function for the SH2 domains of SHP2 and validate monobodies as potent and specific antagonists of protein-protein interactions in cancer cells.
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97
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Recombinant antibodies to histone post-translational modifications. Nat Methods 2013; 10:992-5. [PMID: 23955773 PMCID: PMC3828030 DOI: 10.1038/nmeth.2605] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 07/29/2013] [Indexed: 12/19/2022]
Abstract
Variability in the quality of antibodies to histone post-translational modifications (PTMs) presents widely recognized hindrance in epigenetics research. Here, by using antibody engineering technologies we produced recombinant antibodies directed to the trimethylated lysine residues of histone H3 with high specificity and affinity and no lot-to-lot variation. These recombinant antibodies performed well in common epigenetics applications, and their high specificity enabled us to identify positive and negative correlations among histone PTMs.
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98
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Zhao B, Tan PH, Li SSC, Pei D. Systematic characterization of the specificity of the SH2 domains of cytoplasmic tyrosine kinases. J Proteomics 2013; 81:56-69. [PMID: 23313216 DOI: 10.1016/j.jprot.2012.12.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2012] [Revised: 12/18/2012] [Accepted: 12/29/2012] [Indexed: 01/26/2023]
Abstract
Cytoplasmic tyrosine kinases (CTK) generally contain a Src-homology 2 (SH2) domain, whose role in the CTK family is not fully understood. Here we report the determination of the specificity of 25 CTK SH2 domains by screening one-bead-one-compound (OBOC) peptide libraries. Based on the peptide sequences selected by the SH2 domains, we built Support Vector Machine (SVM) models for the prediction of binding ligands for the SH2 domains. These models yielded support for the progressive phosphorylation model for CTKs in which the overlapping specificity of the CTK SH2 and kinase domains has been proposed to facilitate targeting of the CTK substrates with at least two potential phosphotyrosine (pTyr) sites. We curated 93 CTK substrates with at least two pTyr sites catalyzed by the same CTK, and showed that 71% of these substrates had at least two pTyr sites predicted to bind a common CTK SH2 domain. More importantly, we found 34 instances where there was at least one pTyr site predicted to be recognized by the SH2 domain of the same CTK, suggesting that the SH2 and kinase domains of the CTKs may cooperate to achieve progressive phosphorylation of a protein substrate. This article is part of a Special Issue entitled: From protein structures to clinical applications.
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Affiliation(s)
- Bing Zhao
- Department of Biochemistry and Siebens-Drake Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada N6A 5C1
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99
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New concepts and aids to facilitate crystallization. Curr Opin Struct Biol 2013; 23:409-16. [PMID: 23578532 DOI: 10.1016/j.sbi.2013.03.003] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Revised: 03/08/2013] [Accepted: 03/13/2013] [Indexed: 12/20/2022]
Abstract
Novel tools and technologies are required to obtain structural information of difficult to crystallize complex biological systems such as membrane proteins, multiprotein assemblies, transient conformational states and intrinsically disordered proteins. One promising approach is to select a high affinity and specificity-binding partner (crystallization chaperone), form a complex with the protein of interest and crystallize the complex. Often the chaperone reduces the conformational freedom of the target protein and additionally facilitates the formation of well-ordered crystals. This review provides an update on the recent successes in chaperone-assisted crystallography. We also stress the importance of synergistic approaches involving protein engineering, crystallization chaperones and crystallization additives. Recent examples demonstrate that investment in such approaches can be key to success.
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100
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Ma X, Barthelemy PA, Rouge L, Wiesmann C, Sidhu SS. Design of synthetic autonomous VH domain libraries and structural analysis of a VH domain bound to vascular endothelial growth factor. J Mol Biol 2013; 425:2247-59. [PMID: 23507309 DOI: 10.1016/j.jmb.2013.03.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Revised: 03/06/2013] [Accepted: 03/09/2013] [Indexed: 10/27/2022]
Abstract
We compared the capacity of an autonomous heavy chain variable (VH) domain (VH-B1a) to support diversity within its antigen-binding site relative to the conventional antigen-binding fragment (Fab) from which it was derived. We find that VH-B1a can tolerate significant diversity within all three complementarity-determining regions (CDRs) and also within framework 3, and thus, VH-B1a and the Fab are similar in terms of the regions of the antigen-binding site that can tolerate diversity without compromising stability. We constructed libraries of synthetic VH domains and isolated binders with moderate affinity for vascular endothelial growth factor (VEGF) from a library in which only CDR3 was randomized. One binder was subjected to affinity maturation to derive an autonomous VH domain (VH-V1a) that recognized both human and mouse VEGF with high affinity (KD=16nM or 10nM, respectively). Structural analysis revealed that VH-V1a binds to an epitope that is distinct from the epitopes of a natural VEGF receptor and six different anti-VEGF Fabs. Moreover, VH-V1a recognizes VEGF by using an unusual paratope consisting predominantly of CDR3 but with significant contributions from framework residues within the former light chain interface. These results suggest that VH-B1a and other autonomous VH domains may be useful scaffolds to support both conventional libraries with antigen-binding sites built from the three CDR loops and, also, nonconventional libraries with antigen-binding sites built from CDR3 and the former light chain interface.
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Affiliation(s)
- Xiaolei Ma
- Department of Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
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