1
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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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2
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Johnson C, Harwood JS, Lipton M, Chmielewski J. A refined photo‐switchable cyclic peptide scaffold for use in β‐turn activation. Pept Sci (Hoboken) 2022. [DOI: 10.1002/pep2.24265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Corey Johnson
- Department of Chemistry Purdue University West Lafayette Indiana USA
| | - John S. Harwood
- Department of Chemistry Purdue University West Lafayette Indiana USA
| | - Mark Lipton
- Department of Chemistry Purdue University West Lafayette Indiana USA
| | - Jean Chmielewski
- Department of Chemistry Purdue University West Lafayette Indiana USA
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3
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Jeong M, Park J, Seo Y, Lee KJ, Pramanik S, Ahn S, Kwon S. Hydrazone Photoswitches for Structural Modulation of Short Peptides. Chemistry 2021; 28:e202103972. [PMID: 34962683 DOI: 10.1002/chem.202103972] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Indexed: 11/11/2022]
Abstract
Molecules that undergo light-driven structural transformations constitute the core components in photoswitchable molecular systems and materials. Among various families of photoswitches, photochromic hydrazones have recently emerged as a novel class of photoswitches with superb properties, such as high photochemical conversion, spectral tunability, thermal stability, and fatigue resistance. Hydrazone photoswitches have been adopted in various adaptive materials at different length scales, however, their utilization for modulating biomolecules still has not been explored. Herein we present new hydrazone switches that can photomodulate the structures of short peptides. Systematic investigation on a set of hydrazone derivatives revealed that installation of the amide group does not significantly alter the photoswitching behaviors. Importantly, a hydrazone switch comprising an upper phenyl ring and a lower quinolinyl ring was effective for structural control of peptides. We anticipate that this work, as a new milestone in the research of hydrazone switches, will open a new avenue for structural and functional control of biomolecules.
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Affiliation(s)
- Myeongsu Jeong
- Chung-Ang University - Seoul Campus: Chung-Ang University, Department of Chemistry, KOREA, REPUBLIC OF
| | - Jiyoon Park
- Chung-Ang University - Seoul Campus: Chung-Ang University, Department of Chemistry, KOREA, REPUBLIC OF
| | - Yejin Seo
- Chung-Ang University - Seoul Campus: Chung-Ang University, Department of Chemistry, KOREA, REPUBLIC OF
| | - Kwon Jung Lee
- Chung-Ang University - Seoul Campus: Chung-Ang University, Department of Chemistry, KOREA, REPUBLIC OF
| | - Susnata Pramanik
- SRM Institute of Science and Technology, Department of Chemistry, INDIA
| | - Sangdoo Ahn
- Chung-Ang University - Seoul Campus: Chung-Ang University, Department of Chemistry, KOREA, REPUBLIC OF
| | - Sunbum Kwon
- Chung-Ang University, Chemistry, 84 Heukseok-ro, Bldg106 Rm401-2, 06974, Seoul, KOREA, REPUBLIC OF
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4
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Garifullin R, Guler MO. Electroactive peptide-based supramolecular polymers. Mater Today Bio 2021; 10:100099. [PMID: 33778465 PMCID: PMC7985408 DOI: 10.1016/j.mtbio.2021.100099] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 01/31/2021] [Accepted: 02/02/2021] [Indexed: 12/20/2022] Open
Abstract
The electroactivity as a supramolecular feature of intelligently designed self-assembled systems stimulates a wide interest in development of new stimuli-responsive biomaterials. A diverse set of nanostructures are fabricated through programmed self-assembly of molecules for functional materials. Electroactive groups are conjugated as a functional moiety for organic semiconductor applications. In this review, we present recent examples of self-assembling peptide molecules and electroactive units for supramolecular functional electronic and optical materials with potential biomedical and bioelectronics applications.
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Affiliation(s)
- Ruslan Garifullin
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420021 Kazan, Russian Federation
| | - Mustafa O. Guler
- The Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, 60637, USA
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5
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Zhao X, Zheng W, Zhang Y, Huang W. cis alkenes stabilized by intramolecular sulphurπ interactions. Chem Commun (Camb) 2020; 56:814-817. [PMID: 31848539 DOI: 10.1039/c9cc08558k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A series of alkenes with bistable isomers were obtained containing a thiophene/azoheteroaryl backbone. Visible light and heat-induced reversible cis ⇌ trans isomerizations were evidenced by UV-Vis and 1H NMR spectra. The stabilization of cis alkenes was attributed to intramolecular sulphurπ (Sπ) interactions, which were further supported by theoretical calculations.
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Affiliation(s)
- Xiaolei Zhao
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, P. R. China.
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6
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Peddie V, Abell AD. Photocontrol of peptide secondary structure through non-azobenzene photoswitches. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2019. [DOI: 10.1016/j.jphotochemrev.2019.05.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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7
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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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8
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Fang Z, Wu F, Tao Q, Qin Q, Au C, Li Y, Zhang H, Wang N, Yi B. Substituent effects on the ultraviolet absorption properties of stilbene compounds-Models for molecular cores of absorbents. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 215:9-14. [PMID: 30825869 DOI: 10.1016/j.saa.2019.02.072] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 02/02/2019] [Accepted: 02/17/2019] [Indexed: 06/09/2023]
Abstract
The effects of substituent X and Y on ultraviolet (UV) absorption properties of stilbene compounds XPhCHCHPhY (XSBY) were studied both experimentally and computationally from the viewpoint of UV maximum absorption wavelength (λmax) and the corresponding energy (υmax). In the studies, the contribution of substituents on υmax shift was explored. The results show that with increase of electron withdrawing or electron donating ability of X or Y, there is an enhanced electron delocalization of XSBY that leads to bathochromic shift. Computational analyses based on density functional theory were conducted to elucidate the phenomena. It is disclosed that the υmax values are significantly affected by the excited state, though the electronic effect of ground state cannot be ignored. Finally, on the basis of the respective influences of X and Y, a quantitative model, which was proved reliable by the leave-one-out method, was developed to scale the effects of terminal substituents on υmax. According to the model, the effects of substituents X or Y exhibit almost the same action on υmax owing to the symmetric skeleton of the XSBY compounds. The findings provide deep insight into the effects of terminal substituents on UV absorption properties of stilbene compounds, and the derived model enables practical expression of the relationship between substituents and UV absorption.
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Affiliation(s)
- Zhengjun Fang
- Hunan Provincial Key Laboratory of Environmental Catalysis & Waste Recycling, School of Chemistry and Chemical Engineering, Hunan Institute of Engineering, Xiangtan 411104, China.
| | - Feng Wu
- Hunan Provincial Key Laboratory of Environmental Catalysis & Waste Recycling, School of Chemistry and Chemical Engineering, Hunan Institute of Engineering, Xiangtan 411104, China
| | - Qiang Tao
- Hunan Provincial Key Laboratory of Environmental Catalysis & Waste Recycling, School of Chemistry and Chemical Engineering, Hunan Institute of Engineering, Xiangtan 411104, China; Department of Chemistry and Bioscience, Aalborg University, Aalborg 9220, Denmark
| | - Qiwen Qin
- Hunan Provincial Key Laboratory of Environmental Catalysis & Waste Recycling, School of Chemistry and Chemical Engineering, Hunan Institute of Engineering, Xiangtan 411104, China
| | - Chaktong Au
- Hunan Provincial Key Laboratory of Environmental Catalysis & Waste Recycling, School of Chemistry and Chemical Engineering, Hunan Institute of Engineering, Xiangtan 411104, China
| | - Yajun Li
- Hunan Provincial Key Laboratory of Environmental Catalysis & Waste Recycling, School of Chemistry and Chemical Engineering, Hunan Institute of Engineering, Xiangtan 411104, China
| | - Houpeng Zhang
- Hunan Provincial Key Laboratory of Environmental Catalysis & Waste Recycling, School of Chemistry and Chemical Engineering, Hunan Institute of Engineering, Xiangtan 411104, China
| | - Nanfang Wang
- Hunan Provincial Key Laboratory of Environmental Catalysis & Waste Recycling, School of Chemistry and Chemical Engineering, Hunan Institute of Engineering, Xiangtan 411104, China.
| | - Bing Yi
- Hunan Provincial Key Laboratory of Environmental Catalysis & Waste Recycling, School of Chemistry and Chemical Engineering, Hunan Institute of Engineering, Xiangtan 411104, China.
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9
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Komarov IV, Afonin S, Babii O, Schober T, Ulrich AS. Efficiently Photocontrollable or Not? Biological Activity of Photoisomerizable Diarylethenes. Chemistry 2018; 24:11245-11254. [PMID: 29633378 DOI: 10.1002/chem.201801205] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Indexed: 12/14/2022]
Abstract
Diarylethene derivatives, the biological activity of which can be reversibly changed by irradiation with light of different wavelengths, have shown promise as scientific tools and as candidates for photocontrollable drugs. However, examples demonstrating efficient photocontrol of their biological activity are still relatively rare. This concept article discusses the possible reasons for this situation and presents a critical analysis of existing data and hypotheses in this field, in order to extract the design principles enabling the construction of efficient photocontrollable diarylethene-based molecules. Papers addressing biologically relevant interactions between diarylethenes and biomolecules are analyzed; however, in most published cases, the efficiency of photocontrol in living systems remains to be demonstrated. We hope that this article will encourage further discussion of design principles, primarily among pharmacologists, synthetic and medicinal chemists.
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Affiliation(s)
- Igor V Komarov
- Taras Shevchenko National University of Kyiv, vul. Volodymyrska 60, 01601, Kyiv, Ukraine.,Lumobiotics GmbH, Auer Str. 2, 76227, Karlsruhe, Germany
| | - Sergii Afonin
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, POB 3640, 76021, Karlsruhe, Germany
| | - Oleg Babii
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, POB 3640, 76021, Karlsruhe, Germany
| | - Tim Schober
- Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Anne S Ulrich
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, POB 3640, 76021, Karlsruhe, Germany.,Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
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10
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Danelius E, Pettersson M, Bred M, Min J, Waddell MB, Guy RK, Grøtli M, Erdelyi M. Flexibility is important for inhibition of the MDM2/p53 protein-protein interaction by cyclic β-hairpins. Org Biomol Chem 2018; 14:10386-10393. [PMID: 27731454 DOI: 10.1039/c6ob01510g] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Protein-protein interactions that have large, flat and featureless binding sites are difficult drug targets. In the development of their modulators conventional drug discovery strategies are often unsuccessful. Gaining a detailed understanding of the binding mode of protein-protein interaction inhibitors is therefore of vast importance for their future pharmaceutical use. The MDM2/p53 protein pair is a highly promising target for cancer treatment. Disruption of the protein complex using p53 α-helix mimetics has been shown to be a successful strategy to control p53 activity. To gain further insight into the binding of inhibitors to MDM2, the flexibility of four cyclic β-hairpins that act as α-helical mimetics and potential MDM2/p53 interaction inhibitors was investigated in relation to their inhibitory activity. MDM2-binding of the mimetics was determined using fluorescence polarization and surface plasmon resonance assays, whereas their conformation and dynamics in solution was described by the combined experimental and computational NAMFIS analysis. Molecular flexibility was shown to be important for the activity of the cyclic β-hairpin based MDM2 inhibitors.
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Affiliation(s)
- Emma Danelius
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-41296 Gothenburg, Sweden.
| | - Mariell Pettersson
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-41296 Gothenburg, Sweden.
| | - Matilda Bred
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-41296 Gothenburg, Sweden.
| | - Jaeki Min
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - M Brett Waddell
- Molecular Interaction Analysis Shared Resource, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - R Kiplin Guy
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Morten Grøtli
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-41296 Gothenburg, Sweden.
| | - Mate Erdelyi
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-41296 Gothenburg, Sweden. and Swedish NMR Centre, Medicinaregatan 5, SE-41390 Gothenburg, Sweden
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11
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Danelius E, Andersson H, Jarvoll P, Lood K, Gräfenstein J, Erdélyi M. Halogen Bonding: A Powerful Tool for Modulation of Peptide Conformation. Biochemistry 2017; 56:3265-3272. [PMID: 28581720 PMCID: PMC5510091 DOI: 10.1021/acs.biochem.7b00429] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
![]()
Halogen
bonding is a weak chemical force that has so far mostly
found applications in crystal engineering. Despite its potential for
use in drug discovery, as a new molecular tool in the direction of
molecular recognition events, it has rarely been assessed in biopolymers.
Motivated by this fact, we have developed a peptide model system that
permits the quantitative evaluation of weak forces in a biologically
relevant proteinlike environment and have applied it for the assessment
of a halogen bond formed between two amino acid side chains. The influence
of a single weak force is measured by detection of the extent to which
it modulates the conformation of a cooperatively folding system. We
have optimized the amino acid sequence of the model peptide on analogues
with a hydrogen bond-forming site as a model for the intramolecular
halogen bond to be studied, demonstrating the ability of the technique
to provide information about any type of weak secondary interaction.
A combined solution nuclear magnetic resonance spectroscopic and computational
investigation demonstrates that an interstrand halogen bond is capable
of conformational stabilization of a β-hairpin foldamer comparable
to an analogous hydrogen bond. This is the first report of incorporation
of a conformation-stabilizing halogen bond into a peptide/protein
system, and the first quantification of a chlorine-centered halogen
bond in a biologically relevant system in solution.
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Affiliation(s)
- Emma Danelius
- Department of Chemistry and Molecular Biology, University of Gothenburg , SE-41296 Gothenburg, Sweden
| | - Hanna Andersson
- Department of Chemistry and Molecular Biology, University of Gothenburg , SE-41296 Gothenburg, Sweden
| | - Patrik Jarvoll
- Department of Chemistry and Molecular Biology, University of Gothenburg , SE-41296 Gothenburg, Sweden
| | - Kajsa Lood
- Department of Chemistry and Molecular Biology, University of Gothenburg , SE-41296 Gothenburg, Sweden
| | - Jürgen Gräfenstein
- Department of Chemistry and Molecular Biology, University of Gothenburg , SE-41296 Gothenburg, Sweden
| | - Máté Erdélyi
- Department of Chemistry and Molecular Biology, University of Gothenburg , SE-41296 Gothenburg, Sweden.,Swedish NMR Centre , Medicinaregatan 5, SE-41390 Gothenburg, Sweden
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12
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Kitzig S, Thilemann M, Cordes T, Rück-Braun K. Light-Switchable Peptides with a Hemithioindigo Unit: Peptide Design, Photochromism, and Optical Spectroscopy. Chemphyschem 2016; 17:1252-63. [DOI: 10.1002/cphc.201501050] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Indexed: 12/21/2022]
Affiliation(s)
- S. Kitzig
- Institut für Chemie; Technische Universität Berlin; Str. des 17. Juni 135 10623 Berlin Germany
| | - M. Thilemann
- Institut für Chemie; Technische Universität Berlin; Str. des 17. Juni 135 10623 Berlin Germany
| | - T. Cordes
- Molecular Microscopy Research Group; Zernike Institute for Advanced Materials; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Karola Rück-Braun
- Institut für Chemie; Technische Universität Berlin; Str. des 17. Juni 135 10623 Berlin Germany
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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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Poloni C, Stuart MCA, van der Meulen P, Szymanski W, Feringa BL. Light and heat control over secondary structure and amyloid-like fiber formation in an overcrowded-alkene-modified Trp zipper. Chem Sci 2015; 6:7311-7318. [PMID: 28757990 PMCID: PMC5512536 DOI: 10.1039/c5sc02735g] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 09/18/2015] [Indexed: 12/14/2022] Open
Abstract
The external photocontrol over peptide folding, by the incorporation of molecular photoswitches into their structure, provides a powerful tool to study biological processes. However, it is limited so far to switches that exhibit only a rather limited geometrical change upon photoisomerization and that show thermal instability of the photoisomer. Here we describe the use of an overcrowded alkene photoswitch to control a model β-hairpin peptide. This photoresponsive unit undergoes a large conformational change and has two thermally stable isomers which has major influence on the secondary structure and the aggregation of the peptide, permitting the phototriggered formation of amyloid-like fibrils.
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Affiliation(s)
- Claudia Poloni
- Centre for Systems Chemistry , Stratingh Institute for Chemistry , Faculty of Mathematics and Natural Sciences , University of Groningen , Nijenborgh 4 , 9747AG Groningen , The Netherlands . ;
| | - Marc C A Stuart
- Centre for Systems Chemistry , Stratingh Institute for Chemistry , Faculty of Mathematics and Natural Sciences , University of Groningen , Nijenborgh 4 , 9747AG Groningen , The Netherlands . ;
| | - Pieter van der Meulen
- Centre for Systems Chemistry , Stratingh Institute for Chemistry , Faculty of Mathematics and Natural Sciences , University of Groningen , Nijenborgh 4 , 9747AG Groningen , The Netherlands . ;
| | - Wiktor Szymanski
- Centre for Systems Chemistry , Stratingh Institute for Chemistry , Faculty of Mathematics and Natural Sciences , University of Groningen , Nijenborgh 4 , 9747AG Groningen , The Netherlands . ;
- Department of Radiology , University of Groningen , University Medical Center Groningen , Hanzeplein 1 , 9713 GZ , Groningen , The Netherlands
| | - Ben L Feringa
- Centre for Systems Chemistry , Stratingh Institute for Chemistry , Faculty of Mathematics and Natural Sciences , University of Groningen , Nijenborgh 4 , 9747AG Groningen , The Netherlands . ;
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15
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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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16
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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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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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Structure-based inhibition of protein-protein interactions. Eur J Med Chem 2014; 94:480-8. [PMID: 25253637 DOI: 10.1016/j.ejmech.2014.09.047] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Revised: 09/03/2014] [Accepted: 09/12/2014] [Indexed: 12/24/2022]
Abstract
Protein-protein interactions (PPIs) are emerging as attractive targets for drug design because of their central role in directing normal and aberrant cellular functions. These interactions were once considered "undruggable" because their large and dynamic interfaces make small molecule inhibitor design challenging. However, landmark advances in computational analysis, fragment screening and molecular design have enabled development of a host of promising strategies to address the fundamental molecular recognition challenge. An attractive approach for targeting PPIs involves mimicry of protein domains that are critical for complex formation. This approach recognizes that protein subdomains or protein secondary structures are often present at interfaces and serve as organized scaffolds for the presentation of side chain groups that engage the partner protein(s). Design of protein domain mimetics is in principle rather straightforward but is enabled by a host of computational strategies that provide predictions of important residues that should be mimicked. Herein we describe a workflow proceeding from interaction network analysis, to modeling a complex structure, to identifying a high-affinity sub-structure, to developing interaction inhibitors. We apply the design procedure to peptidomimetic inhibitors of Ras-mediated signaling.
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Zatsepin TS, Abrosimova LA, Monakhova MV, Le Thi Hien, Pingoud A, Kubareva EA, Oretskaya TS. Design of photocontrolled biomolecules based on azobenzene derivatives. RUSSIAN CHEMICAL REVIEWS 2013. [DOI: 10.1070/rc2013v082n10abeh004355] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Szymański W, Beierle JM, Kistemaker HAV, Velema WA, Feringa BL. Reversible Photocontrol of Biological Systems by the Incorporation of Molecular Photoswitches. Chem Rev 2013; 113:6114-78. [DOI: 10.1021/cr300179f] [Citation(s) in RCA: 847] [Impact Index Per Article: 77.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Wiktor Szymański
- Stratingh Institute
for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The
Netherlands
| | - John M. Beierle
- Stratingh Institute
for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The
Netherlands
| | - Hans A. V. Kistemaker
- Stratingh Institute
for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The
Netherlands
| | - Willem A. Velema
- Stratingh Institute
for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The
Netherlands
| | - Ben L. Feringa
- Stratingh Institute
for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The
Netherlands
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Umezawa N, Noro Y, Ukai K, Kato N, Higuchi T. Photocontrol of Peptide Function: Backbone Cyclization Strategy with Photocleavable Amino Acid. Chembiochem 2011; 12:1694-8. [DOI: 10.1002/cbic.201100212] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Indexed: 11/07/2022]
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Denschlag R, Schreier WJ, Rieff B, Schrader TE, Koller FO, Moroder L, Zinth W, Tavan P. Relaxation time prediction for a light switchable peptide by molecular dynamics. Phys Chem Chem Phys 2010; 12:6204-18. [DOI: 10.1039/b921803c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Varedian M, Erdélyi M, Persson Å, Gogoll A. Interplaying factors for the formation of photoswitchable β-hairpins: the advantage of a flexible switch. J Pept Sci 2008; 15:107-13. [DOI: 10.1002/psc.1103] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Abstract
Chemical modification with photoisomerizable tethered ligands endows proteins with sensitivity to light. These optically actuated proteins are revolutionizing research in biology by making it possible to manipulate biological processes noninvasively and with unprecedented spatiotemporal resolution.
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Affiliation(s)
- Pau Gorostiza
- Institut de Bioenginyeria de Catalunya (IBEC), Institució Catalana de Recerca i Estudis Avançats (ICREA), and CIBER-BBN, Parc Científic de Barcelona, Barcelona, Spain
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Lindgren N, Varedian M, Gogoll A. Photochemical Regulation of an Artificial Hydrolase by a Backbone Incorporated Tertiary Structure Switch. Chemistry 2008; 15:501-5. [DOI: 10.1002/chem.200801808] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Varedian M, Langer V, Bergquist J, Gogoll A. An unexpected triethylsilane-triggered rearrangement of thioaurones to thioflavonols under SPPS conditions. Tetrahedron Lett 2008. [DOI: 10.1016/j.tetlet.2008.07.054] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Khakshoor O, Nowick JS. Artificial beta-sheets: chemical models of beta-sheets. Curr Opin Chem Biol 2008; 12:722-9. [PMID: 18775794 DOI: 10.1016/j.cbpa.2008.08.009] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2008] [Accepted: 08/04/2008] [Indexed: 12/01/2022]
Abstract
Chemical models provide tools with which to simplify and study complicated biological systems. Forces and chemical processes that govern the structure, function, and interactions of a biomacromolecule can be explored with a simple, easy-to-study synthetic molecule. Chemical models of beta-sheet structures have helped to elucidate the factors influencing protein structures and functions. Chemical models that mimic beta-sheet quaternary structure and interactions are emerging as valuable tools with which to better understand and control protein recognition and protein aggregation.
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Affiliation(s)
- Omid Khakshoor
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, USA
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Erdélyi M, Varedian M, Sköld C, Niklasson IB, Nurbo J, Persson Å, Bergquist J, Gogoll A. Chemistry and folding of photomodulable peptides – stilbene and thioaurone-type candidates for conformational switches. Org Biomol Chem 2008; 6:4356-73. [DOI: 10.1039/b812001c] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Schrader TE, Schreier WJ, Cordes T, Koller FO, Babitzki G, Denschlag R, Renner C, Löweneck M, Dong SL, Moroder L, Tavan P, Zinth W. Light-triggered beta-hairpin folding and unfolding. Proc Natl Acad Sci U S A 2007; 104:15729-34. [PMID: 17893334 PMCID: PMC1993841 DOI: 10.1073/pnas.0707322104] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A light-switchable peptide is transformed with ultrashort pulses from a beta-hairpin to an unfolded hydrophobic cluster and vice versa. The structural changes are monitored by mid-IR probing. Instantaneous normal mode analysis with a Hamiltonian combining density functional theory with molecular mechanics is used to interpret the absorption transients. Illumination of the beta-hairpin state triggers an unfolding reaction that visits several intermediates and reaches the unfolded state within a few nanoseconds. In this unfolding reaction to the equilibrium hydrophobic cluster conformation, the system does not meet significant barriers on the free-energy surface. The reverse folding process takes much longer because it occurs on the time scale of 30 micros. The folded state has a defined structure, and its formation requires an extended search for the correct hydrogen-bond pattern of the beta-strand.
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Affiliation(s)
- Tobias E. Schrader
- *Lehrstuhl für BioMolekulare Optik and Munich Center for Integrated Protein Science, Ludwig-Maximilians-Universität München, Oettingenstrasse 67, 80538 Munich, Germany; and
| | - Wolfgang J. Schreier
- *Lehrstuhl für BioMolekulare Optik and Munich Center for Integrated Protein Science, Ludwig-Maximilians-Universität München, Oettingenstrasse 67, 80538 Munich, Germany; and
| | - Thorben Cordes
- *Lehrstuhl für BioMolekulare Optik and Munich Center for Integrated Protein Science, Ludwig-Maximilians-Universität München, Oettingenstrasse 67, 80538 Munich, Germany; and
| | - Florian O. Koller
- *Lehrstuhl für BioMolekulare Optik and Munich Center for Integrated Protein Science, Ludwig-Maximilians-Universität München, Oettingenstrasse 67, 80538 Munich, Germany; and
| | - Galina Babitzki
- *Lehrstuhl für BioMolekulare Optik and Munich Center for Integrated Protein Science, Ludwig-Maximilians-Universität München, Oettingenstrasse 67, 80538 Munich, Germany; and
| | - Robert Denschlag
- *Lehrstuhl für BioMolekulare Optik and Munich Center for Integrated Protein Science, Ludwig-Maximilians-Universität München, Oettingenstrasse 67, 80538 Munich, Germany; and
| | - Christian Renner
- Max-Planck-Institut für Biochemie, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Markus Löweneck
- Max-Planck-Institut für Biochemie, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Shou-Liang Dong
- Max-Planck-Institut für Biochemie, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Luis Moroder
- Max-Planck-Institut für Biochemie, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Paul Tavan
- *Lehrstuhl für BioMolekulare Optik and Munich Center for Integrated Protein Science, Ludwig-Maximilians-Universität München, Oettingenstrasse 67, 80538 Munich, Germany; and
| | - Wolfgang Zinth
- *Lehrstuhl für BioMolekulare Optik and Munich Center for Integrated Protein Science, Ludwig-Maximilians-Universität München, Oettingenstrasse 67, 80538 Munich, Germany; and
- To whom correspondence should be addressed. E-mail:
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Kolano C, Helbing J, Bucher G, Sander W, Hamm P. Intramolecular Disulfide Bridges as a Phototrigger To Monitor the Dynamics of Small Cyclic Peptides. J Phys Chem B 2007; 111:11297-302. [PMID: 17764169 DOI: 10.1021/jp074184g] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Two cyclic disulfide-bridged tetrapeptides [cyclo(Boc-Cys-Pro-Aib-Cys-OMe) (1) and cyclo(Boc-Cys-Pro-Phe-Cys-OMe) (2)] have been monitored by time-resolved mid-IR spectroscopy in the C=O vibrational range. A conformational change is induced by cleavage of the intramolecular disulfide bridge upon UV excitation (lambda(exc) = 260 nm), giving rise to a pair of cysteinyl radicals (thiyl radicals), which diffuse apart allowing the peptide to change conformation before they undergo quenching. The amide I band reports on the dynamics of the peptide backbone, which evolves on a 100 ps time scale and then stays constant up to 10 micros at low enough concentrations ( approximately 100 mM). To probe specifically the lifetime of the free cysteinyl radicals, time-resolved UV laser flash photolysis has been applied. The concentration of the cysteinyl radical decays nonexponentially, but about 50% are still present after 1 ms. The photocleavable disulfide bridge hence may serve as an intrinsic, naturally occurring phototrigger to study peptide dynamics that opens a wide time-window from a few picoseconds to many hundreds of microseconds.
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Affiliation(s)
- Christoph Kolano
- Physikalisch-Chemisches Institut, Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland.
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Abstract
Biologically active compounds which are light-responsive offer experimental possibilities which are otherwise very difficult to achieve. Since light can be manipulated very precisely, for example, with lasers and microscopes rapid jumps in concentration of the active form of molecules are possible with exact control of the area, time, and dosage. The development of such strategies started in the 1970s. This review summarizes new developments of the last five years and deals with "small molecules", proteins, and nucleic acids which can either be irreversibly activated with light (these compounds are referred to as "caged compounds") or reversibly switched between an active and an inactive state.
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Affiliation(s)
- Günter Mayer
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany.
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Abstract
The photoinduced isomerization of azobenzene between the extended (trans) and compact (cis) conformations is reversibly triggered by light of two differing wavelengths. The resulting changes in molecular geometry have been extensively utilized to photoswitch transformations in chemical species reversibly for applications in optoelectronic devises as well as to photocontrol conformational states in (bio)polymers. The high isomerization yield, remarkable photostability and ultrafast kinetics (few ps) of azobenzene are well suited for the design of small, defined model systems that allow detailed folding studies to be carried out both experimentally and theoretically on the same molecules. In our and other laboratories such systems were recently obtained with cyclic peptides of defined conformational preferences as well as with alpha-helical and beta-hairpin peptides. These should, by comparison of simulation and experiment, permit an assessment and improvement of the theoretical description on the one hand and a detailed interpretation of the ultrafast conformational dynamics on the other. The phototriggered changes in conformational states lead to concurrent changes in biophysical properties that can be exploited in the photocontrol of biochemical and biological events, as exemplarily discussed with redox-active cyclic bis-cysteinyl peptides and receptor ligands.
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Affiliation(s)
- Christian Renner
- School of Biomedical and Natural Sciences, Nottingham Trent University, Nottingham, NG11 8NS, UK.
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