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Dang DT. Molecular Approaches to Protein Dimerization: Opportunities for Supramolecular Chemistry. Front Chem 2022; 10:829312. [PMID: 35211456 PMCID: PMC8861298 DOI: 10.3389/fchem.2022.829312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 01/14/2022] [Indexed: 11/17/2022] Open
Abstract
Protein dimerization plays a key role in many biological processes. Most cellular events such as enzyme activation, transcriptional cofactor recruitment, signal transduction, and even pathogenic pathways are significantly regulated via protein-protein interactions. Understanding and controlling the molecular mechanisms that regulate protein dimerization is crucial for biomedical applications. The limitations of engineered protein dimerization provide an opportunity for molecular chemistry to induce dimerization of protein in biological events. In this review, molecular control over dimerization of protein and activation in this respect are discussed. The well known molecule glue-based approaches to induced protein dimerization provide powerful tools to modulate the functionality of dimerized proteins and are shortly highlighted. Subsequently metal ion, nucleic acid and host-guest chemistry are brought forward as novel approaches for orthogonal control over dimerization of protein. The specific focus of the review will be on host-guest systems as novel, robust and versatile supramolecular approaches to modulate the dimerization of proteins, using functional proteins as model systems.
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Affiliation(s)
- Dung Thanh Dang
- Faculty of Biotechnology, Ho Chi Minh City Open University, Ho Chi Minh City, Vietnam
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2
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Barbero H, Masson E. Design and recognition of cucurbituril-secured platinum-bound oligopeptides. Chem Sci 2021; 12:9962-9968. [PMID: 34349966 PMCID: PMC8317623 DOI: 10.1039/d1sc02637b] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 06/16/2021] [Indexed: 11/21/2022] Open
Abstract
Platinum terpyridyl complexes, stacked on top of one another and secured as dimers with cucurbit[8]uril (CB[8]) in aqueous medium, were functionalized quantitatively and in situ with a pair of pentapeptides Phe-(Gly)3-Cys by grafting their cysteine residues to the Pt centers. The resulting CB[8]·(Pt·peptide)2 assemblies were used to target secondary hosts CB[7] and CB[8] via their pair of phenylalanine residues, again in situ. A series of well-defined architectures, including a supramolecular “pendant necklace” with hybrid head-to-head and head-to-tail arrangements inside CB[8], were obtained during the self-sorting process after combining only 3 or 4 simple building units. A platinum terpyridyl complex, pentapeptide Phe-(Gly)3-Cys and cucurbit[8]uril assemble into a “pendant necklace” with hybrid head-to-head and head-to-tail arrangements in aqueous medium.![]()
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Affiliation(s)
- Héctor Barbero
- Department of Chemistry and Biochemistry, Ohio University Athens Ohio 45701 USA
| | - Eric Masson
- Department of Chemistry and Biochemistry, Ohio University Athens Ohio 45701 USA
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3
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Hirayama S, Oohora K, Uchihashi T, Hayashi T. Thermoresponsive Micellar Assembly Constructed from a Hexameric Hemoprotein Modified with Poly( N-isopropylacrylamide) toward an Artificial Light-Harvesting System. J Am Chem Soc 2020; 142:1822-1831. [PMID: 31904965 DOI: 10.1021/jacs.9b10080] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Artificial protein assemblies inspired by nature have significant potential in development of emergent functional materials. In order to construct an artificial protein assembly, we employed a mutant of a thermostable hemoprotein, hexameric tyrosine-coordinated heme protein (HTHP), as a building block. The HTHP mutant which has cysteine residues introduced on the bottom surface of its columnar structure was reacted with maleimide-tethering thermoresponsive poly(N-isopropylacrylamide), PNIPAAm, to generate the protein assembly upon heating. The site-specific modification of the cysteine residues with PNIPAAm on the protein surface was confirmed by SDS-PAGE and analytical size exclusion chromatography (SEC). The PNIPAAm-modified HTHP (PNIPAAm-HTHP) is found to provide a 43 nm spherical structure at 60 °C, and the structural changes observed between the assembled and the disassembled forms were duplicated at least five times. High-speed atomic force microscopic measurements of the micellar assembly supported by cross-linkage with glutaraldehyde indicate that the protein matrices are located on the surface of the sphere and cover the inner PNIPAAm core. Furthermore, substitution of heme with a photosensitizer, Zn protoporphyrin IX (ZnPP), in the micellar assembly provides an artificial light-harvesting system. Photochemical measurements of the ZnPP-substituted micellar assembly demonstrate that energy migration among the arrayed ZnPP molecules occurs within the range of several tens of picoseconds. Our present work represents the first example of an artificial light-harvesting system based on an assembled hemoprotein oligomer structure to replicate natural light-harvesting systems.
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Affiliation(s)
| | | | - Takayuki Uchihashi
- Department of Physics , Nagoya University , Nagoya 464-8602 , Japan.,Exploratory Research Center on Life and Living Systems (ExCELLS) , Okazaki 444-8787 , Japan
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4
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Kuan SL, Bergamini FRG, Weil T. Functional protein nanostructures: a chemical toolbox. Chem Soc Rev 2018; 47:9069-9105. [PMID: 30452046 PMCID: PMC6289173 DOI: 10.1039/c8cs00590g] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Indexed: 01/08/2023]
Abstract
Nature has evolved an optimal synthetic factory in the form of translational and posttranslational processes by which millions of proteins with defined primary sequences and 3D structures can be built. Nature's toolkit gives rise to protein building blocks, which dictates their spatial arrangement to form functional protein nanostructures that serve a myriad of functions in cells, ranging from biocatalysis, formation of structural networks, and regulation of biochemical processes, to sensing. With the advent of chemical tools for site-selective protein modifications and recombinant engineering, there is a rapid development to develop and apply synthetic methods for creating structurally defined, functional protein nanostructures for a broad range of applications in the fields of catalysis, materials and biomedical sciences. In this review, design principles and structural features for achieving and characterizing functional protein nanostructures by synthetic approaches are summarized. The synthetic customization of protein building blocks, the design and introduction of recognition units and linkers and subsequent assembly into structurally defined protein architectures are discussed herein. Key examples of these supramolecular protein nanostructures, their unique functions and resultant impact for biomedical applications are highlighted.
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Affiliation(s)
- Seah Ling Kuan
- Max-Planck Institute for Polymer Research
,
Ackermannweg 10
, 55128 Mainz
, Germany
.
;
- Institute of Inorganic Chemistry I – Ulm University
,
Albert-Einstein-Allee 11
, 89081 Ulm
, Germany
| | - Fernando R. G. Bergamini
- Institute of Chemistry
, Federal University of Uberlândia – UFU
,
38400-902 Uberlândia
, MG
, Brazil
| | - Tanja Weil
- Max-Planck Institute for Polymer Research
,
Ackermannweg 10
, 55128 Mainz
, Germany
.
;
- Institute of Inorganic Chemistry I – Ulm University
,
Albert-Einstein-Allee 11
, 89081 Ulm
, Germany
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5
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Hou C, Zeng X, Gao Y, Qiao S, Zhang X, Xu J, Liu J. Cucurbituril As A Versatile Tool to Tune the Functions of Proteins. Isr J Chem 2017. [DOI: 10.1002/ijch.201700105] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Chunxi Hou
- State Key laboratory of Supramolecular Structure and Materials; College of Chemistry, and
| | - Xiangzhi Zeng
- College of Life Science; Jilin University; 2699 Qianjin Road Changchun 130012 China
| | - Yuzhou Gao
- Suzhou Institute of Biomedical Engineering and Technology; Chinese Academy of Sciences; No.88, Keling Road Suzhou New District, Suzhou 215163 China
| | - Shanpeng Qiao
- State Key laboratory of Supramolecular Structure and Materials; College of Chemistry, and
| | - Xin Zhang
- State Key laboratory of Supramolecular Structure and Materials; College of Chemistry, and
| | - Jiayun Xu
- State Key laboratory of Supramolecular Structure and Materials; College of Chemistry, and
| | - Junqiu Liu
- State Key laboratory of Supramolecular Structure and Materials; College of Chemistry, and
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6
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Hou C, Huang Z, Fang Y, Liu J. Construction of protein assemblies by host–guest interactions with cucurbiturils. Org Biomol Chem 2017; 15:4272-4281. [DOI: 10.1039/c7ob00686a] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Protein assembly is important in nature and bionics. Herein, we have reviewed the recent progress in protein assemblies induced by cucurbituril-based supramolecular interactions and their applications.
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Affiliation(s)
- Chunxi Hou
- State Key laboratory of Supramolecular Structure and Materials
- College of Chemistry
- Jilin University
- Changchun 130012
- China
| | - Zupeng Huang
- State Key laboratory of Supramolecular Structure and Materials
- College of Chemistry
- Jilin University
- Changchun 130012
- China
| | - Yu Fang
- State Key laboratory of Supramolecular Structure and Materials
- College of Chemistry
- Jilin University
- Changchun 130012
- China
| | - Junqiu Liu
- State Key laboratory of Supramolecular Structure and Materials
- College of Chemistry
- Jilin University
- Changchun 130012
- China
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Mallon M, Dutt S, Schrader T, Crowley PB. Protein Camouflage: Supramolecular Anion Recognition by Ubiquitin. Chembiochem 2016; 17:774-83. [PMID: 26818656 DOI: 10.1002/cbic.201500477] [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: 09/17/2015] [Indexed: 11/11/2022]
Abstract
Progress in the field of bio-supramolecular chemistry, the bottom-up assembly of protein-ligand systems, relies on a detailed knowledge of molecular recognition. To address this issue, we have characterised complex formation between human ubiquitin (HUb) and four supramolecular anions. The ligands were: pyrenetetrasulfonic acid (4PSA), p-sulfonato-calix[4]arene (SCLX4), bisphosphate tweezers (CLR01) and meso-tetrakis (4-sulfonatophenyl)porphyrin (TPPS), which vary in net charge, size, shape and hydrophobicity. All four ligands induced significant changes in the HSQC spectrum of HUb. Chemical shift perturbations and line-broadening effects were used to identify binding sites and to quantify affinities. Supporting data were obtained from docking simulations. It was found that these weakly interacting ligands bind to extensive surface patches on HUb. A comparison of the data suggests some general indicators for the protein-binding specificity of supramolecular anions. Differences in binding were observed between the cavity-containing and planar ligands. The former had a preference for the arginine-rich, flexible C terminus of HUb.
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Affiliation(s)
- Madeleine Mallon
- School of Chemistry, National University of Ireland Galway, University Road, Galway, Ireland
| | - Som Dutt
- Institute for Organic Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45117, Essen, Germany
| | - Thomas Schrader
- Institute for Organic Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45117, Essen, Germany
| | - Peter B Crowley
- School of Chemistry, National University of Ireland Galway, University Road, Galway, Ireland.
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8
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Barrow SJ, Kasera S, Rowland MJ, del Barrio J, Scherman OA. Cucurbituril-Based Molecular Recognition. Chem Rev 2015; 115:12320-406. [DOI: 10.1021/acs.chemrev.5b00341] [Citation(s) in RCA: 1188] [Impact Index Per Article: 132.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Steven J. Barrow
- Melville
Laboratory for Polymer Synthesis, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Setu Kasera
- Melville
Laboratory for Polymer Synthesis, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Matthew J. Rowland
- Melville
Laboratory for Polymer Synthesis, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Jesús del Barrio
- Melville
Laboratory for Polymer Synthesis, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Oren A. Scherman
- Melville
Laboratory for Polymer Synthesis, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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