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Wilkinson IVL, Bottlinger M, El Harraoui Y, Sieber SA. Profiling the Heme-Binding Proteomes of Bacteria Using Chemical Proteomics. Angew Chem Int Ed Engl 2023; 62:e202212111. [PMID: 36495310 DOI: 10.1002/anie.202212111] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 12/08/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022]
Abstract
Heme is a cofactor with myriad roles and essential to almost all living organisms. Beyond classical gas transport and catalytic functions, heme is increasingly appreciated as a tightly controlled signalling molecule regulating protein expression. However, heme acquisition, biosynthesis and regulation is poorly understood beyond a few model organisms, and the heme-binding proteome has not been fully characterised in bacteria. Yet as heme homeostasis is critical for bacterial survival, heme-binding proteins are promising drug targets. Herein we report a chemical proteomics method for global profiling of heme-binding proteins in live cells for the first time. Employing a panel of heme-based clickable and photoaffinity probes enabled the profiling of 32-54 % of the known heme-binding proteomes in Gram-positive and Gram-negative bacteria. This simple-to-implement profiling strategy could be interchangeably applied to different cell types and systems and fuel future research into heme biology.
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Affiliation(s)
- Isabel V L Wilkinson
- Centre for Functional Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Straße 8, 85748, Garching, Germany
| | - Max Bottlinger
- Centre for Functional Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Straße 8, 85748, Garching, Germany
| | - Yassmine El Harraoui
- Centre for Functional Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Straße 8, 85748, Garching, Germany
| | - Stephan A Sieber
- Centre for Functional Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Straße 8, 85748, Garching, Germany
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2
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Ashley BK, Sui J, Javanmard M, Hassan U. Functionalization of hybrid surface microparticles for in vitro cellular antigen classification. Anal Bioanal Chem 2021; 413:555-564. [PMID: 33156401 PMCID: PMC7855916 DOI: 10.1007/s00216-020-03026-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/07/2020] [Accepted: 10/23/2020] [Indexed: 01/06/2023]
Abstract
Hybrid material surfaces on microparticles are emerging as vehicles for many biomedical multiplexing applications. Functionalization of these hybrid surface microparticles to biomolecules presents unique challenges related to optimization of surface chemistries including uniformity, repeatability, and sample sparring. Hybrid interfaces between microlevel surfaces and individual biomolecules will provide different microenvironments impacting the surface functionalization optimization and efficiency. Here, we propose and validate the first demonstration of streptavidin adsorption-based antibody functionalization on unmodified, hybrid surface microparticles for in vitro analysis. We test this analytical technique and fabricate hybrid surface microparticles with a polystyrene core and aluminum oxide semi-coating. Additionally, we optimize the streptavidin-biotin functionalization chemistry in both assay implementation and sample sparring via analytical mass balances for these microparticles and subsequently conjugate anti-human CD11b antibodies. Result confirmation and characterization occurs from ultraviolet protein absorbance and ImageJ processing of fluorescence microscopy images. Additionally, we design and implement the multi-sectional imaging (MSI) approach to support functionalization uniformity on the hybrid surface microparticles. Finally, as a proof-of-concept performance, we validate anti-CD11b antibodies functionalization by visualizing hybrid surface microparticles conjugate to human neutrophils isolated from blood samples collected from potentially septic patients. Our study introduces and defines a category of functionalization for hybrid surface microparticles with the intent of minuscule sample volumes, low cost, and low environmental impact to be used for many cellular or proteomic in vitro multiplexing applications in the future. Graphical abstract.
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Affiliation(s)
- Brandon K Ashley
- Department of Biomedical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Jianye Sui
- Department of Electrical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Mehdi Javanmard
- Department of Biomedical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
- Department of Electrical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Umer Hassan
- Department of Biomedical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA.
- Department of Electrical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA.
- Global Health Institute, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA.
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3
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Affiliation(s)
- Aleksei Solomonov
- Department of Materials and Interfaces Weizmann Institute of Science 7610001 Rehovot Israel
| | - Ulyana Shimanovich
- Department of Materials and Interfaces Weizmann Institute of Science 7610001 Rehovot Israel
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4
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Churchfield LA, Alberstein RG, Williamson LM, Tezcan FA. Determining the Structural and Energetic Basis of Allostery in a De Novo Designed Metalloprotein Assembly. J Am Chem Soc 2018; 140:10043-10053. [PMID: 29996654 PMCID: PMC6085756 DOI: 10.1021/jacs.8b05812] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Despite significant progress in protein design, the construction of protein assemblies that display complex functions (e.g., catalysis or allostery) remains a significant challenge. We recently reported the de novo construction of an allosteric supramolecular protein assembly (Zn-C38/C81/C96R14) in which the dissociation and binding of ZnII ions were coupled over a distance of 15 Å to the selective hydrolytic breakage and formation of a single disulfide bond. Zn-C38/C81/C96R14 was constructed by ZnII-templated assembly of a monomeric protein (R1, a derivative of cytochrome cb562) into a tetramer, followed by progressive incorporation of noncovalent and disulfide bonding interactions into the protein-protein interfaces to create a strained quaternary architecture. The interfacial strain thus built allowed mechanical coupling between the binding/dissociation of ZnII and formation/hydrolysis of a single disulfide bond (C38-C38) out of a possible six. While the earlier study provided structural evidence for the two end-states of allosteric coupling, the energetic basis for allosteric coupling and the minimal structural requirements for building this allosteric system were not understood. Toward this end, we have characterized the structures and Zn-binding properties of two related protein constructs (C38/C96R1 and C38R1) which also possess C38-C38 disulfide bonds. In addition, we have carried out extensive molecular dynamics simulations of C38/C81/C96R14 to understand the energetic basis for the selective cleavage of the C38-C38 disulfide bond upon ZnII dissociation. Our analyses reveal that the local interfacial environment around the C38-C38 bond is key to its selective cleavage, but this cleavage is only possible within the context of a stable quaternary architecture which enables structural coupling between ZnII coordination and the protein-protein interfaces.
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Affiliation(s)
- Lewis A. Churchfield
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0356 United States
| | - Robert G. Alberstein
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0356 United States
| | - Laura M. Williamson
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0356 United States
| | - F. Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0356 United States
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5
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Onoda A, Taniguchi T, Inoue N, Kamii A, Hayashi T. Anchoring Cytochrome
b
562
on a Gold Nanoparticle by a Heme–Heme Pocket Interaction. Eur J Inorg Chem 2016. [DOI: 10.1002/ejic.201600301] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Akira Onoda
- Department of Applied ChemistryGraduate School of EngineeringOsaka University2‐1 Yamadaoka565‐0871SuitaJapan
| | - Tomoaki Taniguchi
- Department of Applied ChemistryGraduate School of EngineeringOsaka University2‐1 Yamadaoka565‐0871SuitaJapan
| | - Nozomu Inoue
- Department of Applied ChemistryGraduate School of EngineeringOsaka University2‐1 Yamadaoka565‐0871SuitaJapan
| | - Ayumi Kamii
- Department of Applied ChemistryGraduate School of EngineeringOsaka University2‐1 Yamadaoka565‐0871SuitaJapan
| | - Takashi Hayashi
- Department of Applied ChemistryGraduate School of EngineeringOsaka University2‐1 Yamadaoka565‐0871SuitaJapan
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Ono T, Hisaoka Y, Onoda A, Oohora K, Hayashi T. Oxygen-binding Protein Fiber and Microgel: Supramolecular Myoglobin-Poly(acrylate) Conjugates. Chem Asian J 2016; 11:1036-42. [DOI: 10.1002/asia.201501415] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Indexed: 12/30/2022]
Affiliation(s)
- Toshikazu Ono
- Department of Chemistry and Biochemistry, Center for Molecular Systems (CMS); Kyushu University; 744 Motooka, Nishi-ku Fukuoka 819-0395 Japan
- Japan Science and Technology Agency (JST)-PRESTO; 4-1-8 Honcho, Kawaguchi Saitama 332-0012 Japan
- Department of Applied Chemistry; Graduate School of Engineering; Osaka University; Suita 565-0871 Japan
| | - Yasushi Hisaoka
- Department of Applied Chemistry; Graduate School of Engineering; Osaka University; Suita 565-0871 Japan
| | - Akira Onoda
- Department of Applied Chemistry; Graduate School of Engineering; Osaka University; Suita 565-0871 Japan
| | - Koji Oohora
- Department of Applied Chemistry; Graduate School of Engineering; Osaka University; Suita 565-0871 Japan
- Frontier Research Base for Global Young Researchers; Graduate School of Engineering; Osaka University; 2-1 Yamadaoka Suita Osaka 565-0871 Japan
| | - Takashi Hayashi
- Department of Applied Chemistry; Graduate School of Engineering; Osaka University; Suita 565-0871 Japan
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Avinash MB, Samanta PK, Sandeepa KV, Pati SK, Govindaraju T. Molecular Architectonics of Stereochemically Constrained π-Complementary Functional Modules. European J Org Chem 2013. [DOI: 10.1002/ejoc.201300677] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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