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Monakhova MV, Kubareva EA, Kolesnikov KK, Anashkin VA, Kosaretskiy EM, Zvereva MI, Romanova EA, Friedhoff P, Oretskaya TS, Zatsepin TS. Reactive Acrylamide-Modified DNA Traps for Accurate Cross-Linking with Cysteine Residues in DNA–Protein Complexes Using Mismatch Repair Protein MutS as a Model. Molecules 2022; 27:molecules27082438. [PMID: 35458636 PMCID: PMC9031232 DOI: 10.3390/molecules27082438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/06/2022] [Accepted: 04/08/2022] [Indexed: 02/01/2023] Open
Abstract
Covalent protein capture (cross-linking) by reactive DNA derivatives makes it possible to investigate structural features by fixing complexes at different stages of DNA–protein recognition. The most common cross-linking methods are based on reactive groups that interact with native or engineered cysteine residues. Nonetheless, high reactivity of most of such groups leads to preferential fixation of early-stage complexes or even non-selective cross-linking. We synthesised a set of DNA reagents carrying an acrylamide group attached to the C5 atom of a 2′-deoxyuridine moiety via various linkers and studied cross-linking with MutS as a model protein. MutS scans DNA for mismatches and damaged nucleobases and can form multiple non-specific complexes with DNA that may cause non-selective cross-linking. By varying the length of the linker between DNA and the acrylamide group and by changing the distance between the reactive nucleotide and a mismatch in the duplex, we showed that cross-linking occurs only if the distance between the acrylamide group and cysteine is optimal within the DNA–protein complex. Thus, acrylamide-modified DNA duplexes are excellent tools for studying DNA–protein interactions because of high selectivity of cysteine trapping.
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Affiliation(s)
- Mayya V. Monakhova
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskye Gory 1, 119991 Moscow, Russia; (E.A.K.); (V.A.A.); (E.A.R.); (T.S.O.)
- Correspondence: ; Tel.: +7-(903)-593-8905
| | - Elena A. Kubareva
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskye Gory 1, 119991 Moscow, Russia; (E.A.K.); (V.A.A.); (E.A.R.); (T.S.O.)
| | - Kirill K. Kolesnikov
- Department of Chemistry, Lomonosov Moscow State University, Leninskye Gory 1, 119991 Moscow, Russia; (K.K.K.); (M.I.Z.); (T.S.Z.)
| | - Viktor A. Anashkin
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskye Gory 1, 119991 Moscow, Russia; (E.A.K.); (V.A.A.); (E.A.R.); (T.S.O.)
| | - Egor M. Kosaretskiy
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskye Gory 1, 119991 Moscow, Russia;
| | - Maria I. Zvereva
- Department of Chemistry, Lomonosov Moscow State University, Leninskye Gory 1, 119991 Moscow, Russia; (K.K.K.); (M.I.Z.); (T.S.Z.)
| | - Elena A. Romanova
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskye Gory 1, 119991 Moscow, Russia; (E.A.K.); (V.A.A.); (E.A.R.); (T.S.O.)
| | - Peter Friedhoff
- Institute for Biochemistry, FB 08, Justus Liebig University, Heinrich-Buff-Ring 17, D-35392 Giessen, Germany;
| | - Tatiana S. Oretskaya
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskye Gory 1, 119991 Moscow, Russia; (E.A.K.); (V.A.A.); (E.A.R.); (T.S.O.)
| | - Timofei S. Zatsepin
- Department of Chemistry, Lomonosov Moscow State University, Leninskye Gory 1, 119991 Moscow, Russia; (K.K.K.); (M.I.Z.); (T.S.Z.)
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Lazareva NF, Gostevskii BA. Synthesis of 2,2′-Bis(silyl)azobenzenes by Oxidation of 2-(Silyl)anilines. RUSS J GEN CHEM+ 2020. [DOI: 10.1134/s1070363220010119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Pithan PM, Kuhlmann C, Engelhard C, Ihmels H. Synthesis of 5-Alkyl- and 5-Phenylamino-Substituted Azothiazole Dyes with Solvatochromic and DNA-Binding Properties. Chemistry 2019; 25:16088-16098. [PMID: 31523866 PMCID: PMC6973281 DOI: 10.1002/chem.201903657] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 09/09/2019] [Indexed: 01/24/2023]
Abstract
A series of new 5-mono- and 5,5'-bisamino-substituted azothiazole derivatives was synthesized from the readily available diethyl azothiazole-4,4'-dicarboxylate. This reaction most likely comprises an initial Michael-type addition by the respective primary alkyl and aromatic amines at the carbon atom C5 of the substrate. Subsequently, the resulting intermediates are readily oxidized by molecular oxygen to afford the amino-substituted azothiazole derivatives. The latter exhibit remarkably red-shifted absorption bands (λabs =507-661 nm) with high molar extinction coefficients and show a strong positive solvatochromism. As revealed by spectrometric titrations and circular and linear dichroism studies, the water-soluble, bis-(dimethylaminopropylamino)-substituted azo dye associates with duplex DNA by formation of aggregates along the phosphate backbone at high ligand-DNA ratios (LDR) and by intercalation at low LDR, which also leads to a significant increase of the otherwise low emission intensity at 671 nm.
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Affiliation(s)
- Phil M. Pithan
- Department of Chemistry and Biology, and Center of Micro- and Nanochemistry and EngineeringUniversity of SiegenAdolf-Reichwein-Str. 257068SiegenGermany
| | - Christopher Kuhlmann
- Department of Chemistry and Biology, and Center of Micro- and Nanochemistry and EngineeringUniversity of SiegenAdolf-Reichwein-Str. 257068SiegenGermany
| | - Carsten Engelhard
- Department of Chemistry and Biology, and Center of Micro- and Nanochemistry and EngineeringUniversity of SiegenAdolf-Reichwein-Str. 257068SiegenGermany
| | - Heiko Ihmels
- Department of Chemistry and Biology, and Center of Micro- and Nanochemistry and EngineeringUniversity of SiegenAdolf-Reichwein-Str. 257068SiegenGermany
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Jankovic B, Gulzar A, Zanobini C, Bozovic O, Wolf S, Stock G, Hamm P. Photocontrolling Protein–Peptide Interactions: From Minimal Perturbation to Complete Unbinding. J Am Chem Soc 2019; 141:10702-10710. [DOI: 10.1021/jacs.9b03222] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Brankica Jankovic
- Department of Chemistry, University of Zurich, Zurich CH-8057, Switzerland
| | - Adnan Gulzar
- Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University, Freiburg 79104, Germany
| | - Claudio Zanobini
- Department of Chemistry, University of Zurich, Zurich CH-8057, Switzerland
| | - Olga Bozovic
- Department of Chemistry, University of Zurich, Zurich CH-8057, Switzerland
| | - Steffen Wolf
- Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University, Freiburg 79104, Germany
| | - Gerhard Stock
- Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University, Freiburg 79104, Germany
| | - Peter Hamm
- Department of Chemistry, University of Zurich, Zurich CH-8057, Switzerland
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Aggarwal K, Banik M, Medellin B, Que EL. In Situ Photoregulation of Carbonic Anhydrase Activity Using Azobenzenesulfonamides. Biochemistry 2018; 58:48-53. [PMID: 30358990 DOI: 10.1021/acs.biochem.8b00947] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We report two small molecule azobenzenesulfonamide probes, CAP1 and CAP2, capable of photomodulating the activity of carbonic anhydrase (CA) on demand. In the trans form, CAP azobenzene probes adopt a linear shape, making them suitable for occupying the CA active site and interacting with Zn2+, thereby inhibiting enzyme activity. Following irradiation with either 365 or 410 nm light, the CAP probes isomerize to their cis form. Because of the change in steric profile, the probe exits the active site, and the activity of the enzyme is restored. The cis isomer can revert back to the trans isomer through thermal relaxation or via photoirradiation with 460 nm light and thereby inhibit protein activity again. This process can be repeated multiple times without any photodegradation and thus can be used to inhibit or activate the protein reversibly. Importantly, we demonstrate our ability to apply CAP azobenzene probes to regulate CA activity both in an isolated protein solution and in live cells, where the two isomers of CAP1 differentially regulate the intracellular cytosolic pH.
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Affiliation(s)
- Kanchan Aggarwal
- Department of Chemistry , The University of Texas at Austin , 105 East 24th Street, Stop A5300 , Austin , Texas 78712 , United States
| | - Mandira Banik
- Department of Chemistry , The University of Texas at Austin , 105 East 24th Street, Stop A5300 , Austin , Texas 78712 , United States
| | - Brenda Medellin
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology , The University of Texas at Austin , 100 East 24th Street, Stop A5000 , Austin , Texas 78712 , United States
| | - Emily L Que
- Department of Chemistry , The University of Texas at Austin , 105 East 24th Street, Stop A5300 , Austin , Texas 78712 , United States
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Liu Y, Gao X, Wei D, Ren Y. Reversible Photocontrol of Lipase Activity by Incorporating a Photoswitch into the Lid Domain. CHEMPHOTOCHEM 2017. [DOI: 10.1002/cptc.201700045] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Ying Liu
- State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology; Shanghai 200237 China
| | - Xin Gao
- State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology; Shanghai 200237 China
| | - Dongzhi Wei
- State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology; Shanghai 200237 China
| | - Yuhong Ren
- State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology; Shanghai 200237 China
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Bagchi D, Ghosh A, Singh P, Dutta S, Polley N, Althagafi II, Jassas RS, Ahmed SA, Pal SK. Allosteric Inhibitory Molecular Recognition of a Photochromic Dye by a Digestive Enzyme: Dihydroindolizine makes α-chymotrypsin Photo-responsive. Sci Rep 2016; 6:34399. [PMID: 27677331 PMCID: PMC5039621 DOI: 10.1038/srep34399] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 09/13/2016] [Indexed: 11/10/2022] Open
Abstract
The structural-functional regulation of enzymes by the administration of an external stimulus such as light could create photo-switches that exhibit unique biotechnological applications. However, molecular recognition of small ligands is a central phenomenon involved in all biological processes. We demonstrate herein that the molecular recognition of a photochromic ligand, dihydroindolizine (DHI), by serine protease α-chymotrypsin (CHT) leads to the photo-control of enzymatic activity. We synthesized and optically characterized the photochromic DHI. Light-induced reversible pyrroline ring opening and a consequent thermal back reaction via 1,5-electrocyclization are responsible for the photochromic behavior. Furthermore, DHI inhibits the enzymatic activity of CHT in a photo-controlled manner. Simultaneous binding of the well-known inhibitors 4-nitrophenyl anthranilate (NPA) or proflavin (PF) in the presence of DHI displays spectral overlap between the emission of CHT-NPA or CHT-PF with the respective absorption of cis or trans DHI. The results suggest an opportunity to explore the binding site of DHI using Förster resonance energy transfer (FRET). Moreover, to more specifically evaluate the DHI binding interactions, we employed molecular docking calculations, which suggested binding near the hydrophobic site of Cys-1-Cys-122 residues. Variations in the electrostatic interactions of the two conformers of DHI adopt unfavorable conformations, leading to the allosteric inhibition of enzymatic activity.
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Affiliation(s)
- Damayanti Bagchi
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 106, India
| | - Abhijit Ghosh
- Computer Service Cell, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 106, India
| | - Priya Singh
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 106, India
| | - Shreyasi Dutta
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 106, India
| | - Nabarun Polley
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 106, India
| | - Ismail I Althagafi
- Department of Chemistry, Faculty of Applied Sciences, Umm Al-Qura University, 21955 Makkah, Saudi Arabia
| | - Rabab S Jassas
- Department of Chemistry, Faculty of Applied Sciences, Umm Al-Qura University, 21955 Makkah, Saudi Arabia
| | - Saleh A Ahmed
- Department of Chemistry, Faculty of Applied Sciences, Umm Al-Qura University, 21955 Makkah, Saudi Arabia.,Chemistry Department, Faculty of Science, Assiut University, 71516 Assiut, Egypt
| | - Samir Kumar Pal
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 106, India
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Moreno M, Gelabert R, Lluch JM. The Quest for Photoswitches Activated by Near-Infrared Light: A Theoretical Study of the Photochemistry of BF2-Coordinated Azo Derivatives. Chemphyschem 2016; 17:2824-38. [DOI: 10.1002/cphc.201600543] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Miquel Moreno
- Departament de Química; Universitat Autònoma de Barcelona; 08193 Bellaterra Barcelona Spain
| | - Ricard Gelabert
- Departament de Química; Universitat Autònoma de Barcelona; 08193 Bellaterra Barcelona Spain
| | - José M. Lluch
- Departament de Químic and Institut de Biotecnologia i Biomedicina; Universitat Autònoma de Barcelona; 08193 Bellaterra Barcelona Spain
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Bridges CR, Guo C, Yan H, Miltenburg MB, Li P, Li Y, Seferos DS. Conjugated Polymers with Switchable Carrier Polarity. Macromolecules 2015. [DOI: 10.1021/acs.macromol.5b01225] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Colin R. Bridges
- Department
of Chemistry, Lash Miller Chemical Laboratories, University of Toronto, 80 Saint George Street, Toronto, Ontario M5S 3H6, Canada
| | - Chang Guo
- Department
of Chemical Engineering and Waterloo Institute for Nanotechnology
(WIN), University of Waterloo, 200 University Ave West ON, Waterloo, N2L 3G1, Canada
| | - Han Yan
- Department
of Chemistry, Lash Miller Chemical Laboratories, University of Toronto, 80 Saint George Street, Toronto, Ontario M5S 3H6, Canada
| | - Mark B. Miltenburg
- Department
of Chemistry, Lash Miller Chemical Laboratories, University of Toronto, 80 Saint George Street, Toronto, Ontario M5S 3H6, Canada
| | - Pengfei Li
- Department
of Chemistry, Lash Miller Chemical Laboratories, University of Toronto, 80 Saint George Street, Toronto, Ontario M5S 3H6, Canada
| | - Yuning Li
- Department
of Chemical Engineering and Waterloo Institute for Nanotechnology
(WIN), University of Waterloo, 200 University Ave West ON, Waterloo, N2L 3G1, Canada
| | - Dwight S. Seferos
- Department
of Chemistry, Lash Miller Chemical Laboratories, University of Toronto, 80 Saint George Street, Toronto, Ontario M5S 3H6, Canada
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Lohse M, Nowosinski K, Traulsen NL, Achazi AJ, von Krbek LKS, Paulus B, Schalley CA, Hecht S. Gating the photochromism of an azobenzene by strong host–guest interactions in a divalent pseudo[2]rotaxane. Chem Commun (Camb) 2015; 51:9777-80. [DOI: 10.1039/c5cc02811f] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Photoisomerisation of an E-configured azobenzene guest is controlled by a complementary host leading to formation of a divalent pseudo[2]rotaxane complex.
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Affiliation(s)
- Mirko Lohse
- Department of Chemistry
- Humboldt-Universität zu Berlin
- 12489 Berlin
- Germany
| | - Karol Nowosinski
- Institut für Chemie und Biochemie
- Freie Universität Berlin
- 14195 Berlin
- Germany
| | - Nora L. Traulsen
- Institut für Chemie und Biochemie
- Freie Universität Berlin
- 14195 Berlin
- Germany
| | - Andreas J. Achazi
- Institut für Chemie und Biochemie
- Freie Universität Berlin
- 14195 Berlin
- Germany
| | | | - Beate Paulus
- Institut für Chemie und Biochemie
- Freie Universität Berlin
- 14195 Berlin
- Germany
| | | | - Stefan Hecht
- Department of Chemistry
- Humboldt-Universität zu Berlin
- 12489 Berlin
- Germany
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