1
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Fulton DA, Dura G, Peters DT. The polymer and materials science of the bacterial fimbriae Caf1. Biomater Sci 2023; 11:7229-7246. [PMID: 37791425 PMCID: PMC10628683 DOI: 10.1039/d3bm01075a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 09/22/2023] [Indexed: 10/05/2023]
Abstract
Fimbriae are long filamentous polymeric protein structures located upon the surface of bacteria. Often implicated in pathogenicity, the biosynthesis and function of fimbriae has been a productive topic of study for many decades. Evolutionary pressures have ensured that fimbriae possess unique structural and mechanical properties which are advantageous to bacteria. These properties are also difficult to engineer with well-known synthetic and natural fibres, and this has raised an intriguing question: can we exploit the unique properties of bacterial fimbriae in useful ways? Initial work has set out to explore this question by using Capsular antigen fragment 1 (Caf1), a fimbriae expressed naturally by Yersina pestis. These fibres have evolved to 'shield' the bacterium from the immune system of an infected host, and thus are rather bioinert in nature. Caf1 is, however, very amenable to structural mutagenesis which allows the incorporation of useful bioactive functions and the modulation of the fibre's mechanical properties. Its high-yielding recombinant synthesis also ensures plentiful quantities of polymer are available to drive development. These advantageous features make Caf1 an archetype for the development of new polymers and materials based upon bacterial fimbriae. Here, we cover recent advances in this new field, and look to future possibilities of this promising biopolymer.
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Affiliation(s)
- David A Fulton
- Chemistry-School of Natural Science and Environmental Sciences, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK.
| | - Gema Dura
- Chemistry-School of Natural Science and Environmental Sciences, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK.
- Departamento de Química Inorgánica Orgánica y Bioquímica Universidad de Castilla-La Mancha Facultad de Ciencias y Tecnologías Químicas-IRICAAvda, C. J. Cela, 10, Ciudad Real 13071, Spain
| | - Daniel T Peters
- Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
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2
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Li C, Lv W, Yang F, Li C, Huang C, Zhen S. Logic Control of Directional Long-Range Resonance Energy Transfer On 2D DNA Nanosheet. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2301811. [PMID: 37093177 DOI: 10.1002/smll.202301811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/23/2023] [Indexed: 05/03/2023]
Abstract
By arranging fluorophores in a directional way on a 2D DNA nanosheet that transfers energy from the initial donor to the acceptor through homogeneous Förster resonance energy transfer (homo-FRET), it is found that the photonic wires (PWs) based on cascade long-range resonance energy transfer (LrRET) up to 15.6 nm can be effectively achieved through the rational selection of the fluorophores and the adjustment of their position with different distance. Then, logic control of directional energy transfer is achieved with the blocking of the energy transfer pathway, making two tumor-associated microRNA (miRNA) inputs produce an obvious output with the association of tumor diagnosis only when they present simultaneously. This research provides a new thought for development of PWs on 2D DNA nanosheets and a smart application of LrRET-based DNA AND logic control of intracellular miRNA imaging and tumor cells recognition.
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Affiliation(s)
- Chunhong Li
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, P. R. China
- Key Laboratory of Luminescent and Real-Time Analytical System (Southwest University), Chongqing Science and Technology Bureau, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, P. R. China
| | - Wenyi Lv
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, P. R. China
| | - Feifan Yang
- Key Laboratory of Luminescent and Real-Time Analytical System (Southwest University), Chongqing Science and Technology Bureau, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, P. R. China
| | - Chunmei Li
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, P. R. China
| | - Chengzhi Huang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, P. R. China
| | - Shujun Zhen
- Key Laboratory of Luminescent and Real-Time Analytical System (Southwest University), Chongqing Science and Technology Bureau, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, P. R. China
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3
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Zhou S, Wei Y. Kaleidoscope megamolecules synthesis and application using self-assembly technology. Biotechnol Adv 2023; 65:108147. [PMID: 37023967 DOI: 10.1016/j.biotechadv.2023.108147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 02/20/2023] [Accepted: 04/02/2023] [Indexed: 04/08/2023]
Abstract
The megamolecules with high ordered structures play an important role in chemical biology and biomedical engineering. Self-assembly, a long-discovered but very appealing technique, could induce many reactions between biomacromolecules and organic linking molecules, such as an enzyme domain and its covalent inhibitors. Enzyme and its small-molecule inhibitors have achieved many successes in medical application, which realize the catalysis process and theranostic function. By employing the protein engineering technology, the building blocks of enzyme fusion protein and small molecule linker can be assembled into a novel architecture with the specified organization and conformation. Molecular level recognition of enzyme domain could provide both covalent reaction sites and structural skeleton for the functional fusion protein. In this review, we will discuss the range of tools available to combine functional domains by using the recombinant protein technology, which can assemble them into precisely specified architectures/valences and develop the kaleidoscope megamolecules for catalytic and medical application.
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Affiliation(s)
- Shengwang Zhou
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, PR China.
| | - Yuan Wei
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, PR China
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4
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Hamerlynck LM, Bischoff AJ, Rogers JR, Roberts TD, Dai J, Geissler PL, Francis MB, Ginsberg NS. Static Disorder has Dynamic Impact on Energy Transport in Biomimetic Light-Harvesting Complexes. J Phys Chem B 2022; 126:7981-7991. [PMID: 36191182 PMCID: PMC9574921 DOI: 10.1021/acs.jpcb.2c06614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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Despite extensive studies, many questions remain about
what structural
and energetic factors give rise to the remarkable energy transport
efficiency of photosynthetic light-harvesting protein complexes, owing
largely to the inability to synthetically control such factors in
these natural systems. Herein, we demonstrate energy transfer within
a biomimetic light-harvesting complex consisting of identical chromophores
attached in a circular array to a protein scaffold derived from the
tobacco mosaic virus coat protein. We confirm the capability of energy
transport by observing ultrafast depolarization in transient absorption
anisotropy measurements and a redshift in time-resolved emission spectra
in these complexes. Modeling the system with kinetic Monte Carlo simulations
recapitulates the observed anisotropy decays, suggesting an inter-site
hopping rate as high as 1.6 ps–1. With these simulations,
we identify static disorder in orientation, site energy, and degree
of coupling as key remaining factors to control to achieve long-range
energy transfer in these systems. We thereby establish this system
as a highly promising, bottom-up model for studying long-range energy
transfer in light-harvesting protein complexes.
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Affiliation(s)
- Leo M Hamerlynck
- Department of Chemistry, University of California Berkeley, Berkeley, California94720, United States.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California94720, United States
| | - Amanda J Bischoff
- Department of Chemistry, University of California Berkeley, Berkeley, California94720, United States.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California94720, United States
| | - Julia R Rogers
- Department of Chemistry, University of California Berkeley, Berkeley, California94720, United States
| | - Trevor D Roberts
- Department of Chemistry, University of California Berkeley, Berkeley, California94720, United States
| | - Jing Dai
- Department of Chemistry, University of California Berkeley, Berkeley, California94720, United States
| | - Phillip L Geissler
- Department of Chemistry, University of California Berkeley, Berkeley, California94720, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California94720, United States
| | - Matthew B Francis
- Department of Chemistry, University of California Berkeley, Berkeley, California94720, United States.,Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California94720, United States.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California94720, United States
| | - Naomi S Ginsberg
- Department of Chemistry, University of California Berkeley, Berkeley, California94720, United States.,Department of Physics, University of California Berkeley, Berkeley, California94720, United States.,Kavli Energy NanoSciences Institute, Berkeley, California94720, United States.,Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California94720, United States.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California94720, United States
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5
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Kimmel BR, Mrksich M. Development of an Enzyme-Inhibitor Reaction Using Cellular Retinoic Acid Binding Protein II for One-Pot Megamolecule Assembly. Chemistry 2021; 27:17843-17848. [PMID: 34713526 DOI: 10.1002/chem.202103059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Indexed: 12/19/2022]
Abstract
This paper presents an enzyme building block for the assembly of megamolecules. The system is based on the inhibition of the human-derived cellular retinoic acid binding protein II (CRABP2) domain. We synthesized a synthetic retinoid bearing an arylfluorosulfate group, which uses sulfur fluoride exchange click chemistry to covalently inhibit CRABP2. We conjugated both the inhibitor and a fluorescein tag to an oligo(ethylene glycol) backbone and measured a second-order rate constant for the protein inhibition reaction of approximately 3,600 M-1 s-1 . We used this new enzyme-inhibitor pair to assemble multi-protein structures in one-pot reactions using three orthogonal assembly chemistries to demonstrate exact control over the placement of protein domains within a single, homogeneous molecule. This work enables a new dimension of control over specificity, orientation, and stoichiometry of protein domains within atomically precise nanostructures.
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Affiliation(s)
- Blaise R Kimmel
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Milan Mrksich
- Department of Biomedical Engineering, Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
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6
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Zhou S, He P, Dhindwal S, Grum-Tokars VL, Li Y, Parker K, Modica JA, Bleher R, Dos Reis R, Zuchniarz J, Dravid VP, Voth GA, Roux B, Mrksich M. Synthesis, Characterization, and Simulation of Four-Armed Megamolecules. Biomacromolecules 2021; 22:2363-2372. [PMID: 33979120 DOI: 10.1021/acs.biomac.1c00118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This paper describes the synthesis, characterization, and modeling of a series of molecules having four protein domains attached to a central core. The molecules were assembled with the "megamolecule" strategy, wherein enzymes react with their covalent inhibitors that are substituted on a linker. Three linkers were synthesized, where each had four oligo(ethylene glycol)-based arms terminated in a para-nitrophenyl phosphonate group that is a covalent inhibitor for cutinase. This enzyme is a serine hydrolase and reacts efficiently with the phosphonate to give a new ester linkage at the Ser-120 residue in the active site of the enzyme. Negative-stain transmission electron microscopy (TEM) images confirmed the architecture of the four-armed megamolecules. These cutinase tetramers were also characterized by X-ray crystallography, which confirmed the active-site serine-phosphonate linkage by electron-density maps. Molecular dynamics simulations of the tetracutinase megamolecules using three different force field setups were performed and compared with the TEM observations. Using the Amberff99SB-disp + pH7 force field, the two-dimensional projection distances of the megamolecules were found to agree with the measured dimensions from TEM. The study described here, which combines high-resolution characterization with molecular dynamics simulations, will lead to a comprehensive understanding of the molecular structures and dynamics for this new class of molecules.
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Affiliation(s)
- Shengwang Zhou
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, P. R. China
| | - Peng He
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Sonali Dhindwal
- Department of Materials Science, Northwestern University, Evanston, Illinois 60208, United States
| | - Valerie L Grum-Tokars
- Department of Molecular Pharmacology and Biological Chemistry, Northwestern University, Chicago, Illinois 60611, United States
| | - Ying Li
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, United States
| | - Kelly Parker
- Department of Materials Science, Northwestern University, Evanston, Illinois 60208, United States
| | - Justin A Modica
- Departments of Chemistry and Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Reiner Bleher
- Department of Materials Science, Northwestern University, Evanston, Illinois 60208, United States
| | - Roberto Dos Reis
- Department of Materials Science, Northwestern University, Evanston, Illinois 60208, United States
| | - Joshua Zuchniarz
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Vinayak P Dravid
- Department of Materials Science, Northwestern University, Evanston, Illinois 60208, United States
| | - Gregory A Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, United States
| | - Milan Mrksich
- Departments of Chemistry and Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
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7
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Metcalf KJ, Kimmel BR, Sykora DJ, Modica JA, Parker KA, Berens E, Dai R, Dravid VP, Werb Z, Mrksich M. Synthetic Tuning of Domain Stoichiometry in Nanobody-Enzyme Megamolecules. Bioconjug Chem 2020; 32:143-152. [PMID: 33301672 DOI: 10.1021/acs.bioconjchem.0c00578] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
This paper presents a method to synthetically tune atomically precise megamolecule nanobody-enzyme conjugates for prodrug cancer therapy. Previous efforts to create heterobifunctional protein conjugates suffered from heterogeneity in domain stoichiometry, which in part led to the failure of antibody-enzyme conjugates in clinical trials. We used the megamolecule approach to synthesize anti-HER2 nanobody-cytosine deaminase conjugates with tunable numbers of nanobody and enzyme domains in a single, covalent molecule. Linking two nanobody domains to one enzyme domain improved avidity to a human cancer cell line by 4-fold but did not increase cytotoxicity significantly due to lowered enzyme activity. In contrast, a megamolecule composed of one nanobody and two enzyme domains resulted in an 8-fold improvement in the catalytic efficiency and increased the cytotoxic effect by over 5-fold in spheroid culture, indicating that the multimeric structure allowed for an increase in local drug activation. Our work demonstrates that the megamolecule strategy can be used to study structure-function relationships of protein conjugate therapeutics with synthetic control of protein domain stoichiometry.
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Affiliation(s)
- Kevin J Metcalf
- Department of Anatomy, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, California 94143, United States.,Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Blaise R Kimmel
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Daniel J Sykora
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Justin A Modica
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Kelly A Parker
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Eric Berens
- Department of Anatomy, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, California 94143, United States
| | - Raymond Dai
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Vinayak P Dravid
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Zena Werb
- Department of Anatomy, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, California 94143, United States
| | - Milan Mrksich
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States.,Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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8
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Abeywickrama CS, Wijesinghe KJ, Plescia CB, Fisher LS, Goodson T, Stahelin RV, Pang Y. A pyrene-based two-photon excitable fluorescent probe to visualize nuclei in live cells. Photochem Photobiol Sci 2020; 19:1152-1159. [PMID: 32639494 DOI: 10.1039/d0pp00107d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The two-photon absorption properties of a pyrene-pyridinium dye (1) were studied for potential application in two-photon spectroscopy. When probe 1 was used in cellular two-photon fluorescence microscopy imaging, it allowed the visualization of nuclei in live cells with a relatively low probe concentration (such as 1 μM). Spectroscopic evidence further revealed that probe 1 interacted with DNA as an intercalator. The proposed DNA intercalation properties of probe 1 were consistent with the experimental findings that suggested that the observed nucleus staining ability is dependent on the substituents on the pyridinium fragment of the probe.
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Affiliation(s)
| | - Kaveesha J Wijesinghe
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Caroline B Plescia
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 47907, West Lafayette, Indiana, USA
| | - Lloyd S Fisher
- Department of Chemistry, University of Michigan, 48109, Ann Arbor, MI, USA
| | - Theodore Goodson
- Department of Chemistry, University of Michigan, 48109, Ann Arbor, MI, USA
| | - Robert V Stahelin
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 47907, West Lafayette, Indiana, USA
| | - Yi Pang
- Department of Chemistry, University of Akron, 44325, Akron, Ohio, USA. .,Maurice Morton Institute of Polymer Science, University of Akron, 44325, Akron, Ohio, USA.
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9
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Modica JA, Iderzorig T, Mrksich M. Design and Synthesis of Megamolecule Mimics of a Therapeutic Antibody. J Am Chem Soc 2020; 142:13657-13661. [PMID: 32706963 DOI: 10.1021/jacs.0c05093] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
This communication describes the design, synthesis, and biological activity of a megamolecule mimic of an anti-HER2 antibody. The antibody mimic was prepared by linking two Fabs from the therapeutic antibody trastuzumab, which are fused through the heavy chain variable domain to either cutinase or SnapTag, with a linker terminated in an irreversible inhibitor for each enzyme. This mimic binds HER2 with comparable avidity to trastuzumab, has similar activity in a cell-based assay, and can arrest tumor growth in a mouse xenograft BT474 tumor model. A panel of 16 bivalent anti-HER2 antibodies were prepared wherein each varied in the orientation of the fusion domain on the Fabs. The analogs displayed a range of cytotoxic activity, and surprisingly, the most active mimic binds to cells with a 10-fold lower avidity than the least active variant suggesting that structure plays a large role in their efficacy. This work suggests that the megamolecule approach can be used to prepare antibody mimics having a broad structural diversity.
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Affiliation(s)
- Justin A Modica
- Northwestern University, Departments of Chemistry and Biomedical Engineering, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Tsatsral Iderzorig
- Northwestern University, Departments of Chemistry and Biomedical Engineering, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Milan Mrksich
- Northwestern University, Departments of Chemistry and Biomedical Engineering, 2145 Sheridan Road, Evanston, Illinois 60208, United States
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10
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Kimmel BR, Modica JA, Parker K, Dravid V, Mrksich M. Solid-Phase Synthesis of Megamolecules. J Am Chem Soc 2020; 142:4534-4538. [PMID: 32105451 PMCID: PMC8672447 DOI: 10.1021/jacs.9b12003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
This paper presents a solid-phase strategy to efficiently assemble multiprotein scaffolds-known as megamolecules-without the need for protecting groups and with precisely defined nanoscale architectures. The megamolecules are assembled through sequential reactions of linkers that present irreversible inhibitors for enzymes and fusion proteins containing the enzyme domains. Here, a fusion protein containing an N-terminal cutinase and a C-terminal SnapTag domain react with an ethyl p-nitrophenyl phosphonate (pNPP) or a chloro-pyrimidine (CP) group, respectively, to give covalent products. By starting with resin beads that are functionalized with benzylguanine, a series of reactions lead to linear, branched, and dendritic structures that are released from the solid support by addition of TEV protease and that have sizes up to approximately 25 nm.
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