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Ramachandran RP, Nandi I, Haritan N, Zlotkin-Rivkin E, Keren Y, Danieli T, Lebendiker M, Melamed-Book N, Breuer W, Reichmann D, Aroeti B. EspH interacts with the host active Bcr related (ABR) protein to suppress RhoGTPases. Gut Microbes 2022; 14:2130657. [PMID: 36219160 PMCID: PMC9559323 DOI: 10.1080/19490976.2022.2130657] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Enteropathogenic Escherichia coli are bacterial pathogens that colonize the gut and cause severe diarrhea in humans. Upon intimate attachment to the intestinal epithelium, these pathogens translocate via a type III secretion system virulent proteins, termed effectors, into the host cells. These effectors manipulate diverse host cell organelles and functions for the pathogen's benefit. However, the precise mechanisms underlying their activities are not fully understood despite intensive research. EspH, a critical effector protein, has been previously reported to disrupt the host cell actin cytoskeleton by suppressing RhoGTPase guanine exchange factors. However, native host proteins targeted by EspH to mediate these activities remained unknown. Here, we identified the active Bcr related (ABR), a protein previously characterized to possess dual Rho guanine nucleotide exchange factor and GTPase activating protein (GAP) domains, as a native EspH interacting partner. These interactions are mediated by the effector protein's C-terminal 38 amino acid segment. The effector primarily targets the GAP domain of ABR to suppress Rac1 and Cdc42, host cell cytotoxicity, bacterial invasion, and filopodium formation at infection sites. Knockdown of ABR expression abolished the ability of EspH to suppress Rac1, Cdc42. Our studies unravel a novel mechanism by which host RhoGTPases are hijacked by bacterial effectors.
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Affiliation(s)
- Rachana Pattani Ramachandran
- Department of Cell and Developmental Biology, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ipsita Nandi
- Department of Cell and Developmental Biology, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Nir Haritan
- Department of Cell and Developmental Biology, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Efrat Zlotkin-Rivkin
- Department of Cell and Developmental Biology, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yael Keren
- The Protein Production Facility, Wolfson Centre for Applied Structural Biology, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Tsafi Danieli
- The Protein Production Facility, Wolfson Centre for Applied Structural Biology, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Mario Lebendiker
- The Protein Production Facility, Wolfson Centre for Applied Structural Biology, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Naomi Melamed-Book
- Bioimaging Unit, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - William Breuer
- Proteomics and Mass Spectrometry Unit, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Dana Reichmann
- Proteomics and Mass Spectrometry Unit, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel,Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Benjamin Aroeti
- Department of Cell and Developmental Biology, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel,CONTACT Benjamin Aroeti Department of Cell and Developmental Biology, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem91904, Israel
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Zahradník J, Schreiber G. Protein Engineering in the Design of Protein-Protein Interactions: SARS-CoV-2 Inhibitors as a Test Case. Biochemistry 2021; 60:3429-3435. [PMID: 34196543 PMCID: PMC8613841 DOI: 10.1021/acs.biochem.1c00356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/01/2021] [Indexed: 11/28/2022]
Abstract
The formation of specific protein-protein interactions (PPIs) drive most biological processes. Malfunction of such interactions is the molecular driver of many diseases. Our ability to engineer existing PPIs or create new ones has become a vital research tool. In addition, engineered proteins with new or altered interactions are among the most critical drugs that have been developed in recent years. These include antibodies, cytokines, inhibitors, and others. Here, we provide a perspective on the current status of the methods used to engineer new or altered PPIs. The emergence of the COVID-19 pandemic, which resulted in a worldwide quest to develop specific PPI inhibitors as drugs, provided an up-to-date and state-of-the-art status report on the methodologies for engineering PPIs targeting the interaction of the viral spike protein with its cellular target, ACE2. Multiple, very high affinity binders were generated within a few months using in vitro evolution by itself, or in combination with computational design. The different experimental and computational methods used to block this interaction provide a road map for the future of PPI engineering.
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Affiliation(s)
- Jiří Zahradník
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Gideon Schreiber
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
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Jiang L, Kirshenbaum K. A modular approach for organizing dimeric coiled coils on peptoid oligomer scaffolds. Org Biomol Chem 2020; 18:2312-2320. [PMID: 32159574 DOI: 10.1039/d0ob00453g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a general approach to promote the folding of synthetic oligopeptides capable of forming homodimeric coiled coil assemblies. By pre-organizing the peptides on macrocyclic oligomer scaffolds, the stability of the coiled coils is enhanced with an observed increase in the melting temperature of 30 °C to 40 °C. Molecular dynamics simulations substantiate the hypothesis that the enhanced stability is established by constraining motion at the peptide termini and by pre-organizing intramolecular helix-helix contacts. We demonstrate the modularity of this approach by using a family of peptoid scaffolds to promote the folding of a dimeric coiled coil. Importantly, this strategy for templating coiled coils allows preservation of native amino acid sequences. Comparing a macrocyclic peptoid scaffold to its linear counterparts indicates that both types of assemblies are effective for organizing stable coiled coils. These results will guide future designs of coiled coil peptides for biomedical applications and as building blocks for more complex supramolecular assemblies.
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Affiliation(s)
- Linhai Jiang
- Chemistry Department, New York University, New York, NY 10003, USA.
| | - Kent Kirshenbaum
- Chemistry Department, New York University, New York, NY 10003, USA.
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Liu P, Ryczko M, Xie X, Baardsnes J, Lord-Dufour S, Duroche Y, Hicks EA, Taiyab A, Sheardown H, Quaggin SE, Jin J. New soluble angiopoietin analog of Hepta-ANG1 prevents pathological vascular leakage. Biotechnol Bioeng 2020; 118:423-432. [PMID: 32970320 DOI: 10.1002/bit.27580] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/16/2020] [Accepted: 09/20/2020] [Indexed: 11/09/2022]
Abstract
Vascular leak is a key driver of organ injury in diseases, and strategies that reduce enhanced permeability and vascular inflammation are promising therapeutic targets. Activation of the angiopoietin-1 (ANG1)-Tie2 tyrosine kinase signaling pathway is an important regulator of vascular quiescence. Here we describe the design and construction of a new soluble ANG1 mimetic that is a potent activator of endothelial Tie2 in vitro and in vivo. Using a chimeric fusion strategy, we replaced the extracellular matrix (ECM) binding and oligomerization domain of ANG1 with a heptameric scaffold derived from the C-terminus of serum complement protein C4-binding protein α. We refer to this new fusion protein biologic as Hepta-ANG1, which forms a stable heptamer and induces Tie2 phosphorylation in cultured cells, and in the lung following intravenous injection of mice. Injection of Hepta-ANG1 ameliorates vascular endothelial growth factor- and lipopolysaccharide-induced vascular leakage, in keeping with the known functions of Angpt1-Tie2 in maintaining quiescent vascular stability. The new Hepta-ANG1 fusion is easy to produce and displays remarkable stability with high multimericity that can potently activate Tie2. It could be a new candidate ANG1 mimetic therapy for treatments of inflammatory vascular leak, such as acute respiratory distress syndrome and sepsis.
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Affiliation(s)
- Pan Liu
- Department of Medicine/Nephrology, Feinberg School of Medicine, Feinberg Cardiovascular and Renal Research Institute, Northwestern University, Chicago, Illinois, USA
| | | | - Xinfang Xie
- Department of Medicine/Nephrology, Feinberg School of Medicine, Feinberg Cardiovascular and Renal Research Institute, Northwestern University, Chicago, Illinois, USA.,Department of Nephrology, The First Affiliated Hospital of Medical College, Xi'an Jiaotong University, Xi'an, China
| | - Jason Baardsnes
- Human Health Therapeutics Research Centre, National Research Council of Canada, Montreal, Qubec, Canada
| | - Simon Lord-Dufour
- Human Health Therapeutics Research Centre, National Research Council of Canada, Montreal, Qubec, Canada
| | - Yves Duroche
- Human Health Therapeutics Research Centre, National Research Council of Canada, Montreal, Qubec, Canada
| | - Emily Anne Hicks
- Department of Chemical Engineering, McMaster University, Hamilton, Ontario, Canada
| | - Aftab Taiyab
- Department of Chemical Engineering, McMaster University, Hamilton, Ontario, Canada
| | - Heather Sheardown
- Department of Chemical Engineering, McMaster University, Hamilton, Ontario, Canada
| | - Susan E Quaggin
- Department of Medicine/Nephrology, Feinberg School of Medicine, Feinberg Cardiovascular and Renal Research Institute, Northwestern University, Chicago, Illinois, USA
| | - Jing Jin
- Department of Medicine/Nephrology, Feinberg School of Medicine, Feinberg Cardiovascular and Renal Research Institute, Northwestern University, Chicago, Illinois, USA
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Kobayashi N, Inano K, Sasahara K, Sato T, Miyazawa K, Fukuma T, Hecht MH, Song C, Murata K, Arai R. Self-Assembling Supramolecular Nanostructures Constructed from de Novo Extender Protein Nanobuilding Blocks. ACS Synth Biol 2018; 7:1381-1394. [PMID: 29690759 DOI: 10.1021/acssynbio.8b00007] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The design of novel proteins that self-assemble into supramolecular complexes is important for development in nanobiotechnology and synthetic biology. Recently, we designed and created a protein nanobuilding block (PN-Block), WA20-foldon, by fusing an intermolecularly folded dimeric de novo WA20 protein and a trimeric foldon domain of T4 phage fibritin (Kobayashi et al., J. Am. Chem. Soc. 2015, 137, 11285). WA20-foldon formed several types of self-assembling nanoarchitectures in multiples of 6-mers, including a barrel-like hexamer and a tetrahedron-like dodecamer. In this study, to construct chain-like polymeric nanostructures, we designed de novo extender protein nanobuilding blocks (ePN-Blocks) by tandemly fusing two de novo binary-patterned WA20 proteins with various linkers. The ePN-Blocks with long helical linkers or flexible linkers were expressed in soluble fractions of Escherichia coli, and the purified ePN-Blocks were analyzed by native PAGE, size exclusion chromatography-multiangle light scattering (SEC-MALS), small-angle X-ray scattering (SAXS), and transmission electron microscopy. These results suggest formation of various structural homo-oligomers. Subsequently, we reconstructed hetero-oligomeric complexes from extender and stopper PN-Blocks by denaturation and refolding. The present SEC-MALS and SAXS analyses show that extender and stopper PN-Block (esPN-Block) heterocomplexes formed different types of extended chain-like conformations depending on their linker types. Moreover, atomic force microscopy imaging in liquid suggests that the esPN-Block heterocomplexes with metal ions further self-assembled into supramolecular nanostructures on mica surfaces. Taken together, the present data demonstrate that the design and construction of self-assembling PN-Blocks using de novo proteins is a useful strategy for building polymeric nanoarchitectures of supramolecular protein complexes.
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Affiliation(s)
- Naoya Kobayashi
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
| | | | | | - Takaaki Sato
- Center for Energy and Environmental Science, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Nagano, Nagano 380-8553, Japan
| | - Keisuke Miyazawa
- Division of Electrical Engineering and Computer Science, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Takeshi Fukuma
- Division of Electrical Engineering and Computer Science, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Michael H Hecht
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Chihong Song
- National Institute for Physiological Sciences, Okazaki, Aichi 444-8585, Japan
| | - Kazuyoshi Murata
- National Institute for Physiological Sciences, Okazaki, Aichi 444-8585, Japan
| | - Ryoichi Arai
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, Tsurumi, Yokohama 230-0045, Japan
- Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Matsumoto, Nagano 390-8621, Japan
- Department of Supramolecular Complexes, Research Center for Fungal and Microbial Dynamism, Shinshu University, Minamiminowa, Nagano 399-4598, Japan
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Hall D, Takagi J, Nakamura H. Foreword to 'Multiscale structural biology: biophysical principles and mechanisms underlying the action of bio-nanomachines', a special issue in Honour of Fumio Arisaka's 70th birthday. Biophys Rev 2018; 10:105-129. [PMID: 29500796 PMCID: PMC5899743 DOI: 10.1007/s12551-018-0401-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 01/29/2018] [Indexed: 02/08/2023] Open
Abstract
This issue of Biophysical Reviews, titled 'Multiscale structural biology: biophysical principles and mechanisms underlying the action of bio-nanomachines', is a collection of articles dedicated in honour of Professor Fumio Arisaka's 70th birthday. Initially, working in the fields of haemocyanin and actin filament assembly, Fumio went on to publish important work on the elucidation of structural and functional aspects of T4 phage biology. As his career has transitioned levels of complexity from proteins (hemocyanin) to large protein complexes (actin) to even more massive bio-nanomachinery (phage), it is fitting that the subject of this special issue is similarly reflective of his multiscale approach to structural biology. This festschrift contains articles spanning biophysical structure and function from the bio-molecular through to the bio-nanomachine level.
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Affiliation(s)
- Damien Hall
- Institute for Protein Research, Osaka University, 3-1- Yamada-oka, Suita, Osaka, 565-0871 Japan
- Research School of Chemistry, Australian National University, Acton, ACT 2601 Australia
| | - Junichi Takagi
- Institute for Protein Research, Osaka University, 3-1- Yamada-oka, Suita, Osaka, 565-0871 Japan
| | - Haruki Nakamura
- Institute for Protein Research, Osaka University, 3-1- Yamada-oka, Suita, Osaka, 565-0871 Japan
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Arai R. Hierarchical design of artificial proteins and complexes toward synthetic structural biology. Biophys Rev 2017; 10:391-410. [PMID: 29243094 DOI: 10.1007/s12551-017-0376-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 11/23/2017] [Indexed: 12/14/2022] Open
Abstract
In multiscale structural biology, synthetic approaches are important to demonstrate biophysical principles and mechanisms underlying the structure, function, and action of bio-nanomachines. A central goal of "synthetic structural biology" is the design and construction of artificial proteins and protein complexes as desired. In this paper, I review recent remarkable progress of an array of approaches for hierarchical design of artificial proteins and complexes that signpost the path forward toward synthetic structural biology as an emerging interdisciplinary field. Topics covered include combinatorial and protein-engineering approaches for directed evolution of artificial binding proteins and membrane proteins, binary code strategy for structural and functional de novo proteins, protein nanobuilding block strategy for constructing nano-architectures, protein-metal-organic frameworks for 3D protein complex crystals, and rational and computational approaches for design/creation of artificial proteins and complexes, novel protein folds, ideal/optimized protein structures, novel binding proteins for targeted therapeutics, and self-assembling nanomaterials. Protein designers and engineers look toward a bright future in synthetic structural biology for the next generation of biophysics and biotechnology.
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Affiliation(s)
- Ryoichi Arai
- Department of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, Ueda, Nagano 386-8567, Japan. .,Department of Supramolecular Complexes, Research Center for Fungal and Microbial Dynamism, Shinshu University, Minamiminowa, Nagano 399-4598, Japan. .,Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Matsumoto, Nagano 390-8621, Japan. .,Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.
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