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Abstract
Many kinases use reversible docking interactions to augment the specificity of their catalytic domains. Such docking interactions are often structurally independent of the catalytic domain, which allow for a flexible combination of modules in evolution and in bioengineering. The affinity of docking interactions spans several orders of magnitude. This led us to ask how the affinity of the docking interaction affects enzymatic activity and how to pick the optimal interaction module to complement a given substrate. Here, we develop equations that predict the optimal binding strength of a kinase docking interaction and validate it using numerical simulations and steady-state phosphorylation kinetics for tethered protein kinase A. We show that a kinase-substrate pair has an optimum docking strength that depends on their enzymatic constants, the tether architecture, the substrate concentration, and the kinetics of the docking interactions. We show that a reversible tether enhances phosphorylation rates most when 1) the docking strength is intermediate, 2) the substrate is nonoptimal, 3) the substrate concentration is low, 4) the docking interaction has rapid exchange kinetics, and 5) the tether optimizes the effective concentration of the intramolecular reaction. This work serves as a framework for interpreting mutations in kinase docking interactions and as a design guide for engineering enzyme scaffolds.
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Antipin IS, Alfimov MV, Arslanov VV, Burilov VA, Vatsadze SZ, Voloshin YZ, Volcho KP, Gorbatchuk VV, Gorbunova YG, Gromov SP, Dudkin SV, Zaitsev SY, Zakharova LY, Ziganshin MA, Zolotukhina AV, Kalinina MA, Karakhanov EA, Kashapov RR, Koifman OI, Konovalov AI, Korenev VS, Maksimov AL, Mamardashvili NZ, Mamardashvili GM, Martynov AG, Mustafina AR, Nugmanov RI, Ovsyannikov AS, Padnya PL, Potapov AS, Selektor SL, Sokolov MN, Solovieva SE, Stoikov II, Stuzhin PA, Suslov EV, Ushakov EN, Fedin VP, Fedorenko SV, Fedorova OA, Fedorov YV, Chvalun SN, Tsivadze AY, Shtykov SN, Shurpik DN, Shcherbina MA, Yakimova LS. Functional supramolecular systems: design and applications. RUSSIAN CHEMICAL REVIEWS 2021. [DOI: 10.1070/rcr5011] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Baranda Pellejero L, Mahdifar M, Ercolani G, Watson J, Brown T, Ricci F. Using antibodies to control DNA-templated chemical reactions. Nat Commun 2020; 11:6242. [PMID: 33288745 PMCID: PMC7721721 DOI: 10.1038/s41467-020-20024-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 11/11/2020] [Indexed: 11/09/2022] Open
Abstract
DNA-templated synthesis takes advantage of the programmability of DNA-DNA interactions to accelerate chemical reactions under diluted conditions upon sequence-specific hybridization. While this strategy has proven advantageous for a variety of applications, including sensing and drug discovery, it has been so far limited to the use of nucleic acids as templating elements. Here, we report the rational design of DNA templated synthesis controlled by specific IgG antibodies. Our approach is based on the co-localization of reactants induced by the bivalent binding of a specific IgG antibody to two antigen-conjugated DNA templating strands that triggers a chemical reaction that would be otherwise too slow under diluted conditions. This strategy is versatile, orthogonal and adaptable to different IgG antibodies and can be employed to achieve the targeted synthesis of clinically-relevant molecules in the presence of specific IgG biomarker antibodies.
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Affiliation(s)
- Lorena Baranda Pellejero
- Chemistry Department, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Malihe Mahdifar
- Chemistry Department, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Gianfranco Ercolani
- Chemistry Department, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Jonathan Watson
- ATDBio Ltd, Magdalen Centre, Oxford Science Park, Robert Robinson Avenue, Oxford, OX4 4GA, UK
| | - Tom Brown
- ATDBio Ltd, Magdalen Centre, Oxford Science Park, Robert Robinson Avenue, Oxford, OX4 4GA, UK
| | - Francesco Ricci
- Chemistry Department, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy.
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Wang L, Dietz C, Zhou F, Erfanzadeh M, Zhu Q, Smith MB, Yao X. Treasure hunt for peptides with undefined chemical modifications: Proteomics identification of differential albumin adducts of 2-nitroimidazole-indocyanine green in hypoxic tumor. JOURNAL OF MASS SPECTROMETRY : JMS 2020; 55:e4376. [PMID: 31128078 DOI: 10.1002/jms.4376] [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: 01/17/2019] [Revised: 05/07/2019] [Accepted: 05/13/2019] [Indexed: 06/09/2023]
Abstract
2-Nitroimidazole is a well-known chemical probe targeting hypoxic environments of solid tumors, and its derivatives are widely used as imaging agents to investigate tissue and tumor hypoxia. However, the underlying chemistry for the hypoxia-detection capability of 2-nitroimidazole is still unclear. In this study, we deployed a biotin conjugate of 2-nitroimidazole-indocyanine green (2-nitro-ICG) for the investigation of in vivo hypoxia-probing mechanism of 2-nitro-ICG compounds. By implementing mass spectrometry-based proteomics and exhaustive data mining, we report that 2-nitro-ICG and its fragments modify mouse serum albumin as the primary protein target but at two structurally distinct sites and possibly via two different mechanisms. The identification of probe-modified peptides not only contributes to the understanding of the in vivo metabolism of 2-nitroimidazole compounds but also demonstrates a competent analytical workflow that enables the search for peptides with undefined modifications in complex proteome digests.
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Affiliation(s)
- Lei Wang
- Department of Chemistry, University of Connecticut, Storrs, CT, 06269
| | - Christopher Dietz
- Department of Chemistry, University of Connecticut, Storrs, CT, 06269
| | - Feifei Zhou
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT, 06269
| | - Mohsen Erfanzadeh
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT, 06269
| | - Quing Zhu
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT, 06269
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, 63130
| | - Michael B Smith
- Department of Chemistry, University of Connecticut, Storrs, CT, 06269
| | - Xudong Yao
- Department of Chemistry, University of Connecticut, Storrs, CT, 06269
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Nakata E, Dinh H, Nguyen TM, Morii T. DNA binding adaptors to assemble proteins of interest on DNA scaffold. Methods Enzymol 2019; 617:287-322. [PMID: 30784406 DOI: 10.1016/bs.mie.2018.12.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
DNA nanostructures serve as the ideal scaffolds to assemble materials of interest. Among these, proteins are of particularly interesting class of molecules to assemble because of their huge functional variability. Sequence-specific DNA binding proteins have been applied as adaptors to stably locate the fused proteins at defined positions of DNA scaffold in high loading yields. The strategy allows to control the number of enzyme molecules and to maintain the catalytic activity. By fusing a chemoselective self-ligating protein tag to the DNA binding protein, the modular adaptors formed covalent bonds at respective sequences on DNA scaffold with fast reaction kinetics. Application of a set of orthogonal modular adaptors enables spatial organization of multiple types of enzymes.
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Affiliation(s)
- Eiji Nakata
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, Japan
| | - Huyen Dinh
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, Japan
| | | | - Takashi Morii
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, Japan.
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Alemán García MÁ, Magdalena Estirado E, Milroy LG, Brunsveld L. Dual-Input Regulation and Positional Control in Hybrid Oligonucleotide/Discotic Supramolecular Wires. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201800148] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Miguel Ángel Alemán García
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems; Department of Biomedical Engineering; Eindhoven University of Technology; PO Box 513 5600MB Eindhoven The Netherlands
| | - Eva Magdalena Estirado
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems; Department of Biomedical Engineering; Eindhoven University of Technology; PO Box 513 5600MB Eindhoven The Netherlands
| | - Lech-Gustav Milroy
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems; Department of Biomedical Engineering; Eindhoven University of Technology; PO Box 513 5600MB Eindhoven The Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems; Department of Biomedical Engineering; Eindhoven University of Technology; PO Box 513 5600MB Eindhoven The Netherlands
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Alemán García MÁ, Magdalena Estirado E, Milroy L, Brunsveld L. Dual-Input Regulation and Positional Control in Hybrid Oligonucleotide/Discotic Supramolecular Wires. Angew Chem Int Ed Engl 2018; 57:4976-4980. [PMID: 29457856 PMCID: PMC5969285 DOI: 10.1002/anie.201800148] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 02/14/2018] [Indexed: 12/27/2022]
Abstract
The combination of oligonucleotides and synthetic supramolecular systems allows for novel and long‐needed modes of regulation of the self‐assembly of both molecular elements. Discotic molecules were conjugated with short oligonucleotides and their assembly into responsive supramolecular wires studied. The self‐assembly of the discotic molecules provides additional stability for DNA‐duplex formation owing to a cooperative effect. The appended oligonucleotides allow for positional control of the discotic elements within the supramolecular wire. The programmed assembly of these hybrid architectures can be modulated through the DNA, for example, by changing the number of base pairs or salt concentration, and through the discotic platform by the addition of discotic elements without oligonucleotide handles. These hybrid supramolecular‐DNA structures allow for advanced levels of control over 1D dynamic platforms with responsive regulatory elements at the interface with biological systems.
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Affiliation(s)
- Miguel Ángel Alemán García
- Laboratory of Chemical Biology and Institute for Complex Molecular SystemsDepartment of Biomedical EngineeringEindhoven University of TechnologyPO Box 5135600MBEindhovenThe Netherlands
| | - Eva Magdalena Estirado
- Laboratory of Chemical Biology and Institute for Complex Molecular SystemsDepartment of Biomedical EngineeringEindhoven University of TechnologyPO Box 5135600MBEindhovenThe Netherlands
| | - Lech‐Gustav Milroy
- Laboratory of Chemical Biology and Institute for Complex Molecular SystemsDepartment of Biomedical EngineeringEindhoven University of TechnologyPO Box 5135600MBEindhovenThe Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology and Institute for Complex Molecular SystemsDepartment of Biomedical EngineeringEindhoven University of TechnologyPO Box 5135600MBEindhovenThe Netherlands
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Nguyen TM, Nakata E, Saimura M, Dinh H, Morii T. Design of Modular Protein Tags for Orthogonal Covalent Bond Formation at Specific DNA Sequences. J Am Chem Soc 2017; 139:8487-8496. [PMID: 28521084 DOI: 10.1021/jacs.7b01640] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Simultaneous formation of specific covalent linkages at nucleotides in given DNA sequences demand distinct orthogonal reactivity of DNA modification agents. Such highly specific reactions require well-balanced reactivity and affinity of the DNA modification agents. Conjugation of a sequence-specific DNA binding zinc finger protein and a self-ligating protein tag provides a modular adaptor that expedites formation of a covalent bond between the protein tag and a substrate-modified nucleotide at a specific DNA sequence. The modular adaptor stably locates a protein of interest fused to it at the target position on DNA scaffold in its functional form. Modular adaptors with orthogonal selectivity and fast reaction kinetics to specific DNA sequences enable site-specific location of different protein molecules simultaneously. Three different modular adaptors consisting of zinc finger proteins with distinct DNA sequence specificities and self-ligating protein tags with different substrate specificities achieved orthogonal covalent bond formation at respective sequences on the same DNA scaffold with an overall coassembly yield over 90%. Application of this unique set of orthogonal modular adaptors enabled construction of a cascade reaction of three enzymes from xylose metabolic pathway on DNA scaffold.
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Affiliation(s)
- Thang Minh Nguyen
- Institute of Advanced Energy, Kyoto University , Uji, Kyoto 611-0011, Japan
| | - Eiji Nakata
- Institute of Advanced Energy, Kyoto University , Uji, Kyoto 611-0011, Japan
| | - Masayuki Saimura
- Institute of Advanced Energy, Kyoto University , Uji, Kyoto 611-0011, Japan
| | - Huyen Dinh
- Institute of Advanced Energy, Kyoto University , Uji, Kyoto 611-0011, Japan
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University , Uji, Kyoto 611-0011, Japan
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Barbeyron R, Vasseur JJ, Baraguey C, Smietana M. Synthesis of 3′-deoxy-3′-iminodiacetic acid and 3′-deoxy-3′-aminodiethanol thymidine analogues and NMR study of their complexation with boronic acids. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.03.033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Catalano MJ, Price NE, Gates KS. Effective molarity in a nucleic acid-controlled reaction. Bioorg Med Chem Lett 2016; 26:2627-30. [PMID: 27117430 DOI: 10.1016/j.bmcl.2016.04.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 04/07/2016] [Accepted: 04/08/2016] [Indexed: 12/30/2022]
Abstract
Positioning of reactive functional groups within a DNA duplex can enable chemical reactions that otherwise would not occur to an appreciable extent. However, few studies have quantitatively defined the extent to which the enforced proximity of reaction partners in duplex DNA can favor chemical processes. Here, we measured substantial effective molarities (as high as 25M) afforded by duplex DNA to a reaction involving interstrand cross-link formation between 2'-deoxyadenosine and a 2-deoxyribose abasic (Ap) site.
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Affiliation(s)
- Michael J Catalano
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Nathan E Price
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Kent S Gates
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States; University of Missouri, Department of Biochemistry, 125 Chemistry Building, Columbia, MO 65211, United States.
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11
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Artificial signal transduction therapy: a futuristic approach to disease treatment. Future Med Chem 2015; 7:2091-3. [DOI: 10.4155/fmc.15.147] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Zaretsky S, Hickey JL, Tan J, Pichugin D, St Denis MA, Ler S, Chung BKW, Scully CCG, Yudin AK. Mechanistic investigation of aziridine aldehyde-driven peptide macrocyclization: the imidoanhydride pathway. Chem Sci 2015; 6:5446-5455. [PMID: 29861887 PMCID: PMC5949604 DOI: 10.1039/c5sc01958c] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 07/07/2015] [Indexed: 01/30/2023] Open
Abstract
Aziridine aldehydes participate in a multicomponent reaction with α-amino amides and isocyanides to generate reactive imidoanhydride intermediates.
Aziridine aldehyde dimers, peptides, and isocyanides participate in a multicomponent reaction to yield peptide macrocycles. We have investigated the selectivity and kinetics of this process and performed a detailed analysis of its chemoselectivity. While the reactants encompass all of the elements of the traditional Ugi four-component condensation, there is a significant deviation from the previously proposed mechanism. Our results provide evidence for an imidoanhydride pathway in peptide macrocyclization and lend justification for the diastereoselectivity and high effective molarity observed in the reaction.
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Affiliation(s)
- Serge Zaretsky
- Davenport Research Laboratories , Department of Chemistry , University of Toronto , 80 St. George Street , Toronto , Ontario M5S 3H6 , Canada .
| | - Jennifer L Hickey
- Davenport Research Laboratories , Department of Chemistry , University of Toronto , 80 St. George Street , Toronto , Ontario M5S 3H6 , Canada . .,Encycle Therapeutics Inc. , 101 College Street, Suite 314 , Toronto , Ontario M5G 1L7 , Canada
| | - Joanne Tan
- Davenport Research Laboratories , Department of Chemistry , University of Toronto , 80 St. George Street , Toronto , Ontario M5S 3H6 , Canada .
| | - Dmitry Pichugin
- Center for Structural Investigations of Complex Organic Molecules and Polymers , Department of Chemistry , University of Toronto , 80 St. George Street , Toronto , Ontario M5S 3H6 , Canada
| | - Megan A St Denis
- Davenport Research Laboratories , Department of Chemistry , University of Toronto , 80 St. George Street , Toronto , Ontario M5S 3H6 , Canada . .,Encycle Therapeutics Inc. , 101 College Street, Suite 314 , Toronto , Ontario M5G 1L7 , Canada
| | - Spencer Ler
- Davenport Research Laboratories , Department of Chemistry , University of Toronto , 80 St. George Street , Toronto , Ontario M5S 3H6 , Canada .
| | - Benjamin K W Chung
- Davenport Research Laboratories , Department of Chemistry , University of Toronto , 80 St. George Street , Toronto , Ontario M5S 3H6 , Canada .
| | - Conor C G Scully
- Davenport Research Laboratories , Department of Chemistry , University of Toronto , 80 St. George Street , Toronto , Ontario M5S 3H6 , Canada .
| | - Andrei K Yudin
- Davenport Research Laboratories , Department of Chemistry , University of Toronto , 80 St. George Street , Toronto , Ontario M5S 3H6 , Canada .
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Paffen TFE, Ercolani G, de Greef TFA, Meijer EW. Supramolecular Buffering by Ring–Chain Competition. J Am Chem Soc 2015; 137:1501-9. [DOI: 10.1021/ja5110377] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Gianfranco Ercolani
- Dipartimento
di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Via della Ricerca Scientifica, 00133 Roma, Italy
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