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Plaper T, Merljak E, Fink T, Satler T, Ljubetič A, Lainšček D, Jazbec V, Benčina M, Stevanoska S, Džeroski S, Jerala R. Designed allosteric protein logic. Cell Discov 2024; 10:8. [PMID: 38228615 DOI: 10.1038/s41421-023-00635-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 12/03/2023] [Indexed: 01/18/2024] Open
Abstract
The regulation of protein function by external or internal signals is one of the key features of living organisms. The ability to directly control the function of a selected protein would represent a valuable tool for regulating biological processes. Here, we present a generally applicable regulation of proteins called INSRTR, based on inserting a peptide into a loop of a target protein that retains its function. We demonstrate the versatility and robustness of coiled-coil-mediated regulation, which enables designs for either inactivation or activation of selected protein functions, and implementation of two-input logic functions with rapid response in mammalian cells. The selection of insertion positions in tested proteins was facilitated by using a predictive machine learning model. We showcase the robustness of the INSRTR strategy on proteins with diverse folds and biological functions, including enzymes, signaling mediators, DNA binders, transcriptional regulators, reporters, and antibody domains implemented as chimeric antigen receptors in T cells. Our findings highlight the potential of INSRTR as a powerful tool for precise control of protein function, advancing our understanding of biological processes and developing biotechnological and therapeutic interventions.
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Affiliation(s)
- Tjaša Plaper
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
| | - Estera Merljak
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
| | - Tina Fink
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
| | - Tadej Satler
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
- Interdisciplinary doctoral study of biomedicine, Medical Faculty, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Ajasja Ljubetič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
| | - Duško Lainšček
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
| | - Vid Jazbec
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
- Interdisciplinary doctoral study of biomedicine, Medical Faculty, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Mojca Benčina
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
- Centre for Technologies of Gene and Cell Therapy, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
| | - Sintija Stevanoska
- Department of knowledge technologies, Jožef Stefan Institute, Jamova cesta 39, 1000, Ljubljana, Slovenia
| | - Sašo Džeroski
- Department of knowledge technologies, Jožef Stefan Institute, Jamova cesta 39, 1000, Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia.
- Centre for Technologies of Gene and Cell Therapy, Hajdrihova 19, SI-1000, Ljubljana, Slovenia.
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Jazbec V, Jerala R, Benčina M. Proteolytically Activated CRAC Effectors through Designed Intramolecular Inhibition. ACS Synth Biol 2022; 11:2756-2765. [PMID: 35802180 PMCID: PMC9396659 DOI: 10.1021/acssynbio.2c00151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Highly regulated intracellular calcium entry affects
numerous cellular
physiological events. External regulation of intracellular calcium
signaling presents a great opportunity for the artificial regulation
of cellular activity. Calcium entry can be mediated by STIM proteins
interacting with Orai calcium channels; therefore, the STIM1–Orai1
pair has become a tool for artificially modulating calcium entry.
We report on an innovative genetically engineered protease-activated
Orai activator called PACE. CAD self-dimerization and activation were
inhibited with a coiled-coil forming peptide pair linked to CAD via
a protease cleavage site. PACE generated sustained calcium entry after
its activation with a reconstituted split protease. We also generated
PACE, whose transcriptional activation of NFAT was triggered by PPV
or TEV protease. Using PACE, we successfully activated the native
NFAT signaling pathway and the production of cytokines in a T-cell
line. PACE represents a useful tool for generating sustained calcium
entry to initiate calcium-dependent protein translation. PACE provides
a promising template for the construction of links between various
protease activation pathways and calcium signaling.
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Affiliation(s)
- Vid Jazbec
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia.,Interfaculty Doctoral Study of Biomedicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia.,EN-FIST Centre of Excellence, Trg Osvobodilne fronte 13, SI-1000 Ljubljana, Slovenia
| | - Mojca Benčina
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia.,EN-FIST Centre of Excellence, Trg Osvobodilne fronte 13, SI-1000 Ljubljana, Slovenia
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Manček-Keber M, Hafner-Bratkovič I, Lainšček D, Benčina M, Govednik T, Orehek S, Plaper T, Jazbec V, Bergant V, Grass V, Pichlmair A, Jerala R. Disruption of disulfides within RBD of SARS-CoV-2 spike protein prevents fusion and represents a target for viral entry inhibition by registered drugs. FASEB J 2021; 35:e21651. [PMID: 34004056 PMCID: PMC8206760 DOI: 10.1096/fj.202100560r] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 12/11/2022]
Abstract
The SARS‐CoV‐2 pandemic imposed a large burden on health and society. Therapeutics targeting different components and processes of the viral infection replication cycle are being investigated, particularly to repurpose already approved drugs. Spike protein is an important target for both vaccines and therapeutics. Insights into the mechanisms of spike‐ACE2 binding and cell fusion could support the identification of compounds with inhibitory effects. Here, we demonstrate that the integrity of disulfide bonds within the receptor‐binding domain (RBD) plays an important role in the membrane fusion process although their disruption does not prevent binding of spike protein to ACE2. Several reducing agents and thiol‐reactive compounds are able to inhibit viral entry. N‐acetyl cysteine amide, L‐ascorbic acid, JTT‐705, and auranofin prevented syncytia formation, viral entry into cells, and infection in a mouse model, supporting disulfides of the RBD as a therapeutically relevant target.
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Affiliation(s)
- Mateja Manček-Keber
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia.,Centre of Excellence EN-FIST, Ljubljana, Slovenia
| | - Iva Hafner-Bratkovič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia.,Centre of Excellence EN-FIST, Ljubljana, Slovenia
| | - Duško Lainšček
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia.,Centre of Excellence EN-FIST, Ljubljana, Slovenia
| | - Mojca Benčina
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia.,Centre of Excellence EN-FIST, Ljubljana, Slovenia
| | - Tea Govednik
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia.,Graduate School of Biomedicine, University of Ljubljana, Ljubljana, Slovenia
| | - Sara Orehek
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia.,Graduate School of Biomedicine, University of Ljubljana, Ljubljana, Slovenia
| | - Tjaša Plaper
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia.,Graduate School of Biomedicine, University of Ljubljana, Ljubljana, Slovenia
| | - Vid Jazbec
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia.,Graduate School of Biomedicine, University of Ljubljana, Ljubljana, Slovenia
| | - Valter Bergant
- Immunopathology of Virus Infections Laboratory, Institute of Virology, Technical University of Munich, Munich, Germany
| | - Vincent Grass
- Immunopathology of Virus Infections Laboratory, Institute of Virology, Technical University of Munich, Munich, Germany
| | - Andreas Pichlmair
- Immunopathology of Virus Infections Laboratory, Institute of Virology, Technical University of Munich, Munich, Germany
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia.,Centre of Excellence EN-FIST, Ljubljana, Slovenia
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Ivica J, Lape R, Jazbec V, Yu J, Zhu H, Gouaux E, Gold MG, Sivilotti LG. The intracellular domain of homomeric glycine receptors modulates agonist efficacy. J Biol Chem 2021; 296:100387. [PMID: 33617876 PMCID: PMC7995613 DOI: 10.1074/jbc.ra119.012358] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/19/2020] [Indexed: 11/20/2022] Open
Abstract
Like other pentameric ligand-gated channels, glycine receptors (GlyRs) contain long intracellular domains (ICDs) between transmembrane helices 3 and 4. Structurally characterized GlyRs are generally engineered to have a very short ICD. We show here that for one such construct, zebrafish GlyREM, the agonists glycine, β-alanine, taurine, and GABA have high efficacy and produce maximum single-channel open probabilities greater than 0.9. In contrast, for full-length human α1 GlyR, taurine and GABA were clearly partial agonists, with maximum open probabilities of 0.46 and 0.09, respectively. We found that the elevated open probabilities in GlyREM are not due to the limited sequence differences between the human and zebrafish orthologs, but rather to replacement of the native ICD with a short tripeptide ICD. Consistent with this interpretation, shortening the ICD in the human GlyR increased the maximum open probability produced by taurine and GABA to 0.90 and 0.70, respectively, but further engineering it to resemble GlyREM (by introducing the zebrafish transmembrane helix 4 and C terminus) had no effect. Furthermore, reinstating the native ICD to GlyREM converted taurine and GABA to partial agonists, with maximum open probabilities of 0.66 and 0.40, respectively. Structural comparison of transmembrane helices 3 and 4 in short- and long-ICD GlyR subunits revealed that ICD shortening does not distort the orientation of these helices within each subunit. This suggests that the effects of shortening the ICD stem from removing a modulatory effect of the native ICD on GlyR gating, revealing a new role for the ICD in pentameric ligand-gated channels.
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Key Words
- 5-ht3, 5-hydroxytryptamine type 3
- dmem, dulbecco’s modified eagle’s medium
- ecd, extracellular domain
- glyr, glycine receptor
- icd, intracellular domain
- popen, open probability
- pdb, protein data bank
- plgic, pentameric ligand-gated ion channels
- tm, transmembrane
- zf, zebrafish
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Affiliation(s)
- Josip Ivica
- Department of Neuroscience, Physiology and Pharmacology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom
| | - Remigijus Lape
- Department of Neuroscience, Physiology and Pharmacology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom
| | - Vid Jazbec
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Jie Yu
- Vollum Institute, Oregon Health & Science University, Portland, Oregon 97239
| | - Hongtao Zhu
- Vollum Institute, Oregon Health & Science University, Portland, Oregon 97239
| | - Eric Gouaux
- Howard Hughes Medical Institute, Oregon Health & Science University, Portland, Oregon 97239
| | - Matthew G Gold
- Department of Neuroscience, Physiology and Pharmacology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom
| | - Lucia G Sivilotti
- Department of Neuroscience, Physiology and Pharmacology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom.
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