1
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Kapun M, Pérez-Areales FJ, Ashman N, Rowling PJE, Schober T, Fowler E, Itzhaki LS, Spring DR. Red-light modulated ortho-chloro azobenzene photoswitch for peptide stapling via aromatic substitution. RSC Chem Biol 2024; 5:49-54. [PMID: 38179193 PMCID: PMC10763561 DOI: 10.1039/d3cb00176h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 10/05/2023] [Indexed: 01/06/2024] Open
Abstract
The application of peptide stapling using photoswitchable linkers has gained notable interest for potential therapeutic applications. However, many existing methodologies of photoswitching still rely on the use of tissue-damaging and weakly skin-penetrating UV light. Herein, we describe the development of a tetra-ortho-chloro azobenzene linker that was successfully used for cysteine-selective peptide stapling via SNAr. This linker facilitates precise photocontrol of peptide structure via trans to cis isomerisation under red light irradiation. As a proof-of-concept, we applied the developed peptide stapling platform to a modified PMI peptide, targeting the inhibition of MDM2/p53 protein-protein interaction (PPI). Biophysical characterisation of the photoswitchable peptide by competitive fluorescence polarisation showed a significant difference in affinity between the trans and cis isomer for the p53-interacting domain of the human MDM2. Remarkably, the cis isomer displayed a >240-fold higher potency. To the best of our knowledge, this is the highest reported difference in binding affinity between isoforms of a photoswitchable therapeutic peptide. Overall, our findings demonstrate the potential of this novel photoswitchable peptide stapling system for tuneable, selective modulation of PPIs via visible-light isomerisation with deeply-tissue penetrating red light.
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Affiliation(s)
- Mia Kapun
- Yusuf Hamied Department of Chemistry, University of Cambridge Cambridge CB2 1EW UK
| | | | - Nicola Ashman
- Yusuf Hamied Department of Chemistry, University of Cambridge Cambridge CB2 1EW UK
| | - Pamela J E Rowling
- Department of Pharmacology, University of Cambridge Tennis Court Road CB2 1PD Cambridge UK
| | - Tim Schober
- Yusuf Hamied Department of Chemistry, University of Cambridge Cambridge CB2 1EW UK
| | - Elaine Fowler
- Yusuf Hamied Department of Chemistry, University of Cambridge Cambridge CB2 1EW UK
| | - Laura S Itzhaki
- Department of Pharmacology, University of Cambridge Tennis Court Road CB2 1PD Cambridge UK
| | - David R Spring
- Yusuf Hamied Department of Chemistry, University of Cambridge Cambridge CB2 1EW UK
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2
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Lāce I, Bazzi S, Uranga J, Schirmacher A, Diederichsen U, Mata RA, Simeth NA. Modulating Secondary Structure Motifs Through Photo-Labile Peptide Staples. Chembiochem 2023; 24:e202300270. [PMID: 37216330 DOI: 10.1002/cbic.202300270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/17/2023] [Accepted: 05/22/2023] [Indexed: 05/24/2023]
Abstract
Peptide-protein interactions (PPIs) are facilitated by the well-defined three-dimensional structure of bioactive peptides, interesting compounds for the development of new therapeutic agents. Their secondary structure and thus their propensity to engage in PPIs can be influenced by the introduction of peptide staples on the side chains. In particular, light-controlled staples based on azobenzene photoswitches and their structural influence on helical peptides have been studied extensively. In contrast, photolabile staples bearing photocages as a structural key motif, have mainly been used to block supramolecular interactions. Their influence on the secondary structure of the target peptide is under-investigated. Thus, in this study we use a combination of spectroscopic techniques and in silico simulations to systematically study a series of helical peptides with varying length of the photo-labile staple to obtain a detailed insight into the structure-property relationship in such photoresponsive biomolecules.
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Affiliation(s)
- Ilze Lāce
- Institute for Organic and Biomolecular Chemistry, Department of Chemistry, University of Göttingen, Tammannstr. 2, 37077, Göttingen, Germany
| | - Sophia Bazzi
- Institute for Physical Chemistry, Department of Chemistry, University of Göttingen, Tammannstr. 6, 37077, Göttingen, Germany
| | - Jon Uranga
- Institute for Physical Chemistry, Department of Chemistry, University of Göttingen, Tammannstr. 6, 37077, Göttingen, Germany
| | - Anastasiya Schirmacher
- Institute for Organic and Biomolecular Chemistry, Department of Chemistry, University of Göttingen, Tammannstr. 2, 37077, Göttingen, Germany
| | - Ulf Diederichsen
- Institute for Organic and Biomolecular Chemistry, Department of Chemistry, University of Göttingen, Tammannstr. 2, 37077, Göttingen, Germany
| | - Ricardo A Mata
- Institute for Physical Chemistry, Department of Chemistry, University of Göttingen, Tammannstr. 6, 37077, Göttingen, Germany
| | - Nadja A Simeth
- Institute for Organic and Biomolecular Chemistry, Department of Chemistry, University of Göttingen, Tammannstr. 2, 37077, Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), Universitätsmedizin Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany
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3
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Cataldi E, Raschig M, Gutmann M, Geppert PT, Ruopp M, Schock M, Gerwe H, Bertermann R, Meinel L, Finze M, Nowak-Król A, Decker M, Lühmann T. Amber Light Control of Peptide Secondary Structure by a Perfluoroaromatic Azobenzene Photoswitch. Chembiochem 2023; 24:e202200570. [PMID: 36567253 DOI: 10.1002/cbic.202200570] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/23/2022] [Accepted: 12/23/2022] [Indexed: 12/27/2022]
Abstract
The incorporation of photoswitches into the molecular structure of peptides and proteins enables their dynamic photocontrol in complex biological systems. Here, a perfluorinated azobenzene derivative triggered by amber light was site-specifically conjugated to cysteines in a helical peptide by perfluoroarylation chemistry. In response to the photoisomerization (trans→cis) of the conjugated azobenzene with amber light, the secondary structure of the peptide was modulated from a disorganized into an amphiphilic helical structure.
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Affiliation(s)
- Eleonora Cataldi
- Universität Würzburg, Institute for Pharmacy and Food Chemistry, Am Hubland, 97074, Würzburg, Germany
| | - Martina Raschig
- Universität Würzburg, Institute for Pharmacy and Food Chemistry, Am Hubland, 97074, Würzburg, Germany
| | - Marcus Gutmann
- Universität Würzburg, Institute for Pharmacy and Food Chemistry, Am Hubland, 97074, Würzburg, Germany
| | - Patrick T Geppert
- Universität Würzburg, Institute of Inorganic Chemistry and Institute for Sustainable Chemistry and Catalysis with Boron, Am Hubland, 97074, Würzburg, Germany
| | - Matthias Ruopp
- Universität Würzburg, Institute for Pharmacy and Food Chemistry, Am Hubland, 97074, Würzburg, Germany
| | - Marvin Schock
- Universität Würzburg, Institute for Pharmacy and Food Chemistry, Am Hubland, 97074, Würzburg, Germany
| | - Hubert Gerwe
- Universität Würzburg, Institute for Pharmacy and Food Chemistry, Am Hubland, 97074, Würzburg, Germany
| | - Rüdiger Bertermann
- Universität Würzburg, Institute of Inorganic Chemistry and Institute for Sustainable Chemistry and Catalysis with Boron, Am Hubland, 97074, Würzburg, Germany
| | - Lorenz Meinel
- Universität Würzburg, Institute for Pharmacy and Food Chemistry, Am Hubland, 97074, Würzburg, Germany.,Helmholtz Institute for RNA-Based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), 97080, Würzburg, Germany
| | - Maik Finze
- Universität Würzburg, Institute of Inorganic Chemistry and Institute for Sustainable Chemistry and Catalysis with Boron, Am Hubland, 97074, Würzburg, Germany
| | - Agnieszka Nowak-Król
- Universität Würzburg, Institute of Inorganic Chemistry and Institute for Sustainable Chemistry and Catalysis with Boron, Am Hubland, 97074, Würzburg, Germany
| | - Michael Decker
- Universität Würzburg, Institute for Pharmacy and Food Chemistry, Am Hubland, 97074, Würzburg, Germany
| | - Tessa Lühmann
- Universität Würzburg, Institute for Pharmacy and Food Chemistry, Am Hubland, 97074, Würzburg, Germany
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4
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Volarić J, Thallmair S, Feringa BL, Szymanski W. Photoswitchable, Water‐soluble Bis‐azobenzene Cross‐linkers with Enhanced Properties for Biological Applications. CHEMPHOTOCHEM 2022. [DOI: 10.1002/cptc.202200170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Jana Volarić
- University of Groningen: Rijksuniversiteit Groningen Stratingh Institute for Chemistry NETHERLANDS
| | - Sebastian Thallmair
- Frankfurt Institute for Advanced Studies Frankfurt Institute for Advanced Studies GERMANY
| | - Ben L. Feringa
- University of Groningen: Rijksuniversiteit Groningen Stratingh Institute for Chemistry NETHERLANDS
| | - Wiktor Szymanski
- University Medical Center Groningen Department of Radiology Hanzeplein 1 9747AG Groningen NETHERLANDS
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5
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Yasuike N, Kachi-Terajima C, Karin A, Mino T, Woolley GA. Modification of proteins with azobenzene crosslinkers using reversible covalent bonds. Org Biomol Chem 2022; 20:8649-8656. [DOI: 10.1039/d2ob01656g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Bis-cyanoacrylate azobenzene (BCNA) targets di-thiol peptides in the presence of mono-thiols and enables photoswitching of helical structure.
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Affiliation(s)
- Nobuo Yasuike
- Graduate School of Engineering, Chiba University, 1-33, Yayoi-cho, Inage-ku, Chiba 263-8522, Japan
- JSR Corporation, 1-9-2, Higashi-Shinbashi, Minato-ku, Tokyo, 105-8640, Japan
| | - Chihiro Kachi-Terajima
- Department of Chemistry, Faculty of Science, Toho University, Funabashi, Chiba, 274-8510, Japan
| | - Amir Karin
- Department of Chemistry, University of Toronto, Toronto, Canada
| | - Takashi Mino
- Graduate School of Engineering, Chiba University, 1-33, Yayoi-cho, Inage-ku, Chiba 263-8522, Japan
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6
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Volarić J, Szymanski W, Simeth NA, Feringa BL. Molecular photoswitches in aqueous environments. Chem Soc Rev 2021; 50:12377-12449. [PMID: 34590636 PMCID: PMC8591629 DOI: 10.1039/d0cs00547a] [Citation(s) in RCA: 132] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Indexed: 12/17/2022]
Abstract
Molecular photoswitches enable dynamic control of processes with high spatiotemporal precision, using light as external stimulus, and hence are ideal tools for different research areas spanning from chemical biology to smart materials. Photoswitches are typically organic molecules that feature extended aromatic systems to make them responsive to (visible) light. However, this renders them inherently lipophilic, while water-solubility is of crucial importance to apply photoswitchable organic molecules in biological systems, like in the rapidly emerging field of photopharmacology. Several strategies for solubilizing organic molecules in water are known, but there are not yet clear rules for applying them to photoswitchable molecules. Importantly, rendering photoswitches water-soluble has a serious impact on both their photophysical and biological properties, which must be taken into consideration when designing new systems. Altogether, these aspects pose considerable challenges for successfully applying molecular photoswitches in aqueous systems, and in particular in biologically relevant media. In this review, we focus on fully water-soluble photoswitches, such as those used in biological environments, in both in vitro and in vivo studies. We discuss the design principles and prospects for water-soluble photoswitches to inspire and enable their future applications.
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Affiliation(s)
- Jana Volarić
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, Faculty for Science and Engineering, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
| | - Wiktor Szymanski
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, Faculty for Science and Engineering, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
- Department of Radiology, Medical Imaging Center, University of Groningen, University Medical Centre Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Nadja A Simeth
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, Faculty for Science and Engineering, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
- Institute for Organic and Biomolecular Chemistry, University of Göttingen, Tammannstr. 2, 37077 Göttingen, Germany
| | - Ben L Feringa
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, Faculty for Science and Engineering, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
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7
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Cheng HB, Zhang S, Qi J, Liang XJ, Yoon J. Advances in Application of Azobenzene as a Trigger in Biomedicine: Molecular Design and Spontaneous Assembly. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2007290. [PMID: 34028901 DOI: 10.1002/adma.202007290] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 12/10/2020] [Indexed: 06/12/2023]
Abstract
Azobenzene is a well-known derivative of stimulus-responsive molecular switches and has shown superior performance as a functional material in biomedical applications. The results of multiple studies have led to the development of light/hypoxia-responsive azobenzene for biomedical use. In recent years, long-wavelength-responsive azobenzene has been developed. Matching the longer wavelength absorption and hypoxia-response characteristics of the azobenzene switch unit to the bio-optical window results in a large and effective stimulus response. In addition, azobenzene has been used as a hypoxia-sensitive connector via biological cleavage under appropriate stimulus conditions. This has resulted in on/off state switching of properties such as pharmacology and fluorescence activity. Herein, recent advances in the design and fabrication of azobenzene as a trigger in biomedicine are summarized.
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Affiliation(s)
- Hong-Bo Cheng
- State Key Laboratory of Organic-Inorganic Composites, Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, 15 North Third Ring Road, Beijing, 100029, P. R. China
| | - Shuchun Zhang
- State Key Laboratory of Organic-Inorganic Composites, Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, 15 North Third Ring Road, Beijing, 100029, P. R. China
| | - Ji Qi
- State Key Laboratory of Organic-Inorganic Composites, Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, 15 North Third Ring Road, Beijing, 100029, P. R. China
| | - Xing-Jie Liang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, No. 11, First North Road, Zhongguancun, Beijing, 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Juyoung Yoon
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, 03760, Korea
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8
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Albert L, Vázquez O. Photoswitchable peptides for spatiotemporal control of biological functions. Chem Commun (Camb) 2019; 55:10192-10213. [PMID: 31411602 DOI: 10.1039/c9cc03346g] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Light is unsurpassed in its ability to modulate biological interactions. Since their discovery, chemists have been fascinated by photosensitive molecules capable of switching between isomeric forms, known as photoswitches. Photoswitchable peptides have been recognized for many years; however, their functional implementation in biological systems has only recently been achieved. Peptides are now acknowledged as excellent protein-protein interaction modulators and have been important in the emergence of photopharmacology. In this review, we briefly explain the different classes of photoswitches and summarize structural studies when they are incorporated into peptides. Importantly, we provide a detailed overview of the rapidly increasing number of examples, where biological modulation is driven by the structural changes. Furthermore, we discuss some of the remaining challenges faced in this field. These exciting proof-of-principle studies highlight the tremendous potential of photocontrollable peptides as optochemical tools for chemical biology and biomedicine.
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Affiliation(s)
- Lea Albert
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35043, Marburg, Germany.
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9
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Murawska GM, Poloni C, Simeth NA, Szymanski W, Feringa BL. Comparative Study of Photoswitchable Zinc-Finger Domain and AT-Hook Motif for Light-Controlled Peptide-DNA Binding. Chemistry 2019; 25:4965-4973. [PMID: 30735272 DOI: 10.1002/chem.201900090] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Indexed: 12/20/2022]
Abstract
DNA-peptide interactions are involved in key life processes, including DNA recognition, replication, transcription, repair, organization, and modification. Development of tools that can influence DNA-peptide binding non-invasively with high spatiotemporal precision could aid in determining its role in cells and tissues. Here, the design, synthesis, and study of photocontrolled tools for sequence-specific small peptide-DNA major and minor groove interactions are reported, shedding light on DNA binding by transcriptionally active peptides. In particular, photoswitchable moieties were implemented in the peptide backbone or turn region. In each case, DNA binding was affected by photochemical isomerization, as determined in fluorescent displacement assays on model DNA strands, which provides promising tools for DNA modulation.
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Affiliation(s)
- Gosia M Murawska
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, The Netherlands
| | - Claudia Poloni
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, The Netherlands
| | - Nadja A Simeth
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, The Netherlands
| | - Wiktor Szymanski
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, The Netherlands.,Department of Radiology, University of Groningen, University Medical Centre Groningen, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
| | - Ben L Feringa
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, The Netherlands
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10
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Yasuike N, Lu H, Xia P, Woolley GA. Intramolecular cross-linking of proteins with azobenzene-based cross-linkers. Methods Enzymol 2019; 624:129-149. [DOI: 10.1016/bs.mie.2019.04.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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11
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Regulation of Protein Structural Changes by Incorporation of a Small-Molecule Linker. Int J Mol Sci 2018; 19:ijms19123714. [PMID: 30469528 PMCID: PMC6321067 DOI: 10.3390/ijms19123714] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 11/16/2018] [Accepted: 11/19/2018] [Indexed: 12/12/2022] Open
Abstract
Proteins have the potential to serve as nanomachines with well-controlled structural movements, and artificial control of their conformational changes is highly desirable for successful applications exploiting their dynamic structural characteristics. Here, we demonstrate an experimental approach for regulating the degree of conformational change in proteins by incorporating a small-molecule linker into a well-known photosensitive protein, photoactive yellow protein (PYP), which is sensitized by blue light and undergoes a photo-induced N-terminal protrusion coupled with chromophore-isomerization-triggered conformational changes. Specifically, we introduced thiol groups into specific sites of PYP through site-directed mutagenesis and then covalently conjugated a small-molecule linker into these sites, with the expectation that the linker is likely to constrain the structural changes associated with the attached positions. To investigate the structural dynamics of PYP incorporated with the small-molecule linker (SML-PYP), we employed the combination of small-angle X-ray scattering (SAXS), transient absorption (TA) spectroscopy and experiment-restrained rigid-body molecular dynamics (MD) simulation. Our results show that SML-PYP exhibits much reduced structural changes during photo-induced signaling as compared to wild-type PYP. This demonstrates that incorporating an external molecular linker can limit photo-induced structural dynamics of the protein and may be used as a strategy for fine control of protein structural dynamics in nanomachines.
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12
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Kim GC, Ahn JH, Oh JH, Nam S, Hyun S, Yu J, Lee Y. Photoswitching of Cell Penetration of Amphipathic Peptides by Control of α-Helical Conformation. Biomacromolecules 2018; 19:2863-2869. [DOI: 10.1021/acs.biomac.8b00428] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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13
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García-Iriepa C, Gueye M, Léonard J, Martínez-López D, Campos PJ, Frutos LM, Sampedro D, Marazzi M. A biomimetic molecular switch at work: coupling photoisomerization dynamics to peptide structural rearrangement. Phys Chem Chem Phys 2016; 18:6742-53. [DOI: 10.1039/c5cp07599h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A combined experimental and computational study of a peptide-linked retinal-like molecular switch shows the effects on photoreactivity and the α-helix structure.
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Affiliation(s)
- Cristina García-Iriepa
- Departamento de Química
- Centro de Investigación en Síntesis Química (CISQ)
- Universidad de La Rioja
- E-26006 Logroño
- Spain
| | - Moussa Gueye
- Institut de Physique et Chimie des Matériaux de Strasbourg & Labex NIE
- Université de Strasbourg
- Strasbourg 67034
- France
| | - Jérémie Léonard
- Institut de Physique et Chimie des Matériaux de Strasbourg & Labex NIE
- Université de Strasbourg
- Strasbourg 67034
- France
| | - David Martínez-López
- Departamento de Química
- Centro de Investigación en Síntesis Química (CISQ)
- Universidad de La Rioja
- E-26006 Logroño
- Spain
| | - Pedro J. Campos
- Departamento de Química
- Centro de Investigación en Síntesis Química (CISQ)
- Universidad de La Rioja
- E-26006 Logroño
- Spain
| | | | - Diego Sampedro
- Departamento de Química
- Centro de Investigación en Síntesis Química (CISQ)
- Universidad de La Rioja
- E-26006 Logroño
- Spain
| | - Marco Marazzi
- Department of Theoretical Chemical Biology
- Institute of Physical Chemistry
- KIT
- 76131 Karlsruhe
- Germany
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14
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Ritterson RS, Hoersch D, Barlow KA, Kortemme T. Design of Light-Controlled Protein Conformations and Functions. Methods Mol Biol 2016; 1414:197-211. [PMID: 27094293 DOI: 10.1007/978-1-4939-3569-7_12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
In recent years, interest in controlling protein function with light has increased. Light offers a number of unique advantages over other methods, including spatial and temporal control and high selectivity. Here, we describe a general protocol for engineering a protein to be controllable with light via reaction with an exogenously introduced photoisomerizable small molecule and illustrate our protocol with two examples from the literature: the engineering of the calcium affinity of the cell-cell adhesion protein cadherin, which is an example of a protein that switches from a native to a disrupted state (Ritterson et al. J Am Chem Soc (2013) 135:12516-12519), and the engineering of the opening and closing of the chaperonin Mm-cpn, an example of a switch between two functional states (Hoersch et al.: Nat Nanotechn (2013) 8:928-932). This protocol guides the user from considering which proteins may be most amenable to this type of engineering, to considerations of how and where to make the desired changes, to the assays required to test for functionality.
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Affiliation(s)
- Ryan S Ritterson
- California Institute for Quantitative Biomedical Research and Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, 1700 4th Street, Byers Hall 308 E, San Francisco, CA, 94158, USA
| | - Daniel Hoersch
- California Institute for Quantitative Biomedical Research and Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, 1700 4th Street, Byers Hall 308 E, San Francisco, CA, 94158, USA
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Kyle A Barlow
- Graduate Program in Bioinformatics, California Institute for Quantitative Biomedical Research, and Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, 1700 4th Street, Byers Hall 308 E, San Francisco, CA, 94158, USA
| | - Tanja Kortemme
- California Institute for Quantitative Biomedical Research and Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, 1700 4th Street, Byers Hall 308 E, San Francisco, CA, 94158, USA.
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15
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Müller A, Kobarg H, Chandrasekaran V, Gronow J, Sönnichsen FD, Lindhorst TK. Synthesis of Bifunctional Azobenzene Glycoconjugates for Cysteine-Based Photosensitive Cross-Linking with Bioactive Peptides. Chemistry 2015; 21:13723-31. [DOI: 10.1002/chem.201501571] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Indexed: 01/31/2023]
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16
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Ali AM, Forbes MW, Woolley GA. Optimizing the Photocontrol of bZIP Coiled Coils with Azobenzene Crosslinkers: Role of the Crosslinking Site. Chembiochem 2015; 16:1757-63. [DOI: 10.1002/cbic.201500191] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Indexed: 11/07/2022]
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17
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QIN CG, LU CX, OUYANG GW, QIN K, ZHANG F, SHI HT, WANG XH. Progress of Azobenzene-based Photoswitchable Molecular Probes and Sensory Chips for Chemical and Biological Analysis. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2015. [DOI: 10.1016/s1872-2040(15)60809-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Podewin T, Rampp MS, Turkanovic I, Karaghiosoff KL, Zinth W, Hoffmann-Röder A. Photocontrolled chignolin-derived β-hairpin peptidomimetics. Chem Commun (Camb) 2015; 51:4001-4. [DOI: 10.1039/c4cc10304a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The synthesis of novel, chignolin-derived peptides comprising the azobenzene photoswitch [3-(3-aminomethyl)phenylazo]phenylacetic acid (AMPP) is reported.
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Affiliation(s)
- T. Podewin
- Department of Organic Chemistry
- Faculty of Chemistry and Pharmacy
- Ludwig-Maximilians-University LMU
- 81377 Munich
- Germany
| | - M. S. Rampp
- Department for BioMolecular Optics
- Faculty of Physics
- Ludwig-Maximilians-University LMU
- 80538 Munich
- Germany
| | - I. Turkanovic
- Department for BioMolecular Optics
- Faculty of Physics
- Ludwig-Maximilians-University LMU
- 80538 Munich
- Germany
| | - K. L. Karaghiosoff
- Department of Organic Chemistry
- Faculty of Chemistry and Pharmacy
- Ludwig-Maximilians-University LMU
- 81377 Munich
- Germany
| | - W. Zinth
- Department for BioMolecular Optics
- Faculty of Physics
- Ludwig-Maximilians-University LMU
- 80538 Munich
- Germany
| | - A. Hoffmann-Röder
- Department of Organic Chemistry
- Faculty of Chemistry and Pharmacy
- Ludwig-Maximilians-University LMU
- 81377 Munich
- Germany
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19
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Karlsson C, Blom M, Johansson (neé Varedian) M, Jansson AM, Scifo E, Karlén A, Govender T, Gogoll A. Phototriggerable peptidomimetics for the inhibition of Mycobacterium tuberculosis ribonucleotide reductase by targeting protein–protein binding. Org Biomol Chem 2015; 13:2612-21. [DOI: 10.1039/c4ob01926a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Peptidomimetic inhibitors with photomodulable affinity for the R1–R2 subunit association site were designed based on the R2-subunit C-terminal.
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Affiliation(s)
| | - Magnus Blom
- Department of Chemistry – BMC
- Uppsala University
- S-751 23 Uppsala
- Sweden
| | | | - Anna M. Jansson
- Department of Cell and Molecular Biology
- Structural Biology
- Uppsala University
- S-751 24 Uppsala
- Sweden
| | - Enzo Scifo
- Department of Cell and Molecular Biology
- Structural Biology
- Uppsala University
- S-751 24 Uppsala
- Sweden
| | - Anders Karlén
- Department of Medicinal Chemistry
- Organic Pharmaceutical Chemistry
- Uppsala University
- S-751 23 Uppsala
- Sweden
| | - Thavendran Govender
- Catalysis and Peptide Research Unit
- University of KwaZulu Natal
- Durban 4000
- South Africa
| | - Adolf Gogoll
- Department of Chemistry – BMC
- Uppsala University
- S-751 23 Uppsala
- Sweden
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20
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Markiewicz BN, Culik RM, Gai F. Tightening up the structure, lighting up the pathway: Application of molecular constraints and light to manipulate protein folding, self-assembly and function. Sci China Chem 2014; 57:1615-1624. [PMID: 25722715 PMCID: PMC4337807 DOI: 10.1007/s11426-014-5225-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Chemical cross-linking provides an effective avenue to reduce the conformational entropy of polypeptide chains and hence has become a popular method to induce or force structural formation in peptides and proteins. Recently, other types of molecular constraints, especially photoresponsive linkers and functional groups, have also found increased use in a wide variety of applications. Herein, we provide a concise review of using various forms of molecular strategies to constrain proteins, thereby stabilizing their native states, gaining insight into their folding mechanisms, and/or providing a handle to trigger a conformational process of interest with light. The applications discussed here cover a wide range of topics, ranging from delineating the details of the protein folding energy landscape to controlling protein assembly and function.
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Affiliation(s)
| | - Robert M. Culik
- Department of Biochemistry and Biophysics, University of Pennsylvania, PA, 19104, USA
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, PA, 19104, USA
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21
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Hatai J, Bandyopadhyay S. Photoreversible assembly-disassembly of a polymeric structure by using an azobenzene photoswitch and Al3+ ions. Chemistry 2014; 20:10020-6. [PMID: 25044420 DOI: 10.1002/chem.201402321] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2014] [Indexed: 11/08/2022]
Abstract
A nonmacrocyclic azobenzene-based photochromic receptor in its E isomer forms an extended polymeric assembly with Al(3+) ions. Exposure of the E form to UV light at λ = 366 nm causes a disassembly of the polymeric structure due to the change in the molecular geometry of the ligand. The linear polymeric structure was regenerated on exposure to visible light.
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Affiliation(s)
- Joydev Hatai
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur Campus, Mohanpur WB 741246 (India)
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