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Figueroa JD, Barroso-Torres N, Morales M, Herrera B, Aranda M, Dorta E, López-Alarcón C. Antioxidant Capacity of Free and Peptide Tryptophan Residues Determined by the ORAC (Oxygen Radical Absorbance Capacity) Assay Is Modulated by Radical-Radical Reactions and Oxidation Products. Foods 2023; 12:4360. [PMID: 38231845 DOI: 10.3390/foods12234360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 11/27/2023] [Accepted: 11/29/2023] [Indexed: 01/19/2024] Open
Abstract
The ORAC (Oxygen Radical Absorbance Capacity) assay is commonly employed for determining the antioxidant capacity of bioactive peptides. To gain insights into the meaning of this index for peptides containing a single Trp, we studied the consumption of this residue and fluorescein (FLH, the probe of ORAC method), induced by radicals generated by AAPH (2,2'-Azo-bis(2-amidinopropane) dihydrochloride) thermolysis. ORAC values were rationalized from kinetics and computational calculations of bond dissociation energies (BDE) of the N-H bond (indole ring of Trp). Free Trp, di- and tri- peptides, and three larger peptides were studied. Solutions containing 70 nM FLH, 1-5 μM free Trp or peptides, and 10 mM AAPH were incubated at 37 °C in phosphate buffer. Kinetic studies showed that FLH minimally affected Trp consumption. However, a clear protection of FLH, characterized by pseudo-lag times, was evidenced, reflecting radical-radical reactions and FLH repairing. Peptides showed similar ORAC values (~1.9-2.8 Trolox equivalents), while BDE varied between 91.9 and 103.5 kcal. These results, added to the protection of FLH observed after total consumption of Trp, indicate a lack of discrimination of the assay for the chemical structure of peptides and the contribution of oxidation products to the index.
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Affiliation(s)
- Juan David Figueroa
- Departamento de Química Física, Escuela de Química, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
| | - Noreima Barroso-Torres
- Departamento de Producción Vegetal, Instituto Canario de Investigaciones Agrarias (ICIA), 38270 San Cristóbal de la Laguna, Spain
| | - Marcela Morales
- Departamento de Química Física, Escuela de Química, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
| | - Bárbara Herrera
- Departamento de Química Física, Escuela de Química, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
| | - Mario Aranda
- Escuela de Farmacia, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
| | - Eva Dorta
- Departamento de Producción Vegetal, Instituto Canario de Investigaciones Agrarias (ICIA), 38270 San Cristóbal de la Laguna, Spain
| | - Camilo López-Alarcón
- Departamento de Química Física, Escuela de Química, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
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2
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Abstract
Endogenous photosensitizers play a critical role in both beneficial and harmful light-induced transformations in biological systems. Understanding their mode of action is essential for advancing fields such as photomedicine, photoredox catalysis, environmental science, and the development of sun care products. This review offers a comprehensive analysis of endogenous photosensitizers in human skin, investigating the connections between their electronic excitation and the subsequent activation or damage of organic biomolecules. We gather the physicochemical and photochemical properties of key endogenous photosensitizers and examine the relationships between their chemical reactivity, location within the skin, and the primary biochemical events following solar radiation exposure, along with their influence on skin physiology and pathology. An important take-home message of this review is that photosensitization allows visible light and UV-A radiation to have large effects on skin. The analysis presented here unveils potential causes for the continuous increase in global skin cancer cases and emphasizes the limitations of current sun protection approaches.
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Affiliation(s)
- Erick L Bastos
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, 05508-000 São Paulo, São Paulo, Brazil
| | - Frank H Quina
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, 05508-000 São Paulo, São Paulo, Brazil
- Department of Chemical Engineering, Polytechnic School, University of São Paulo, 05508-000 São Paulo, São Paulo, Brazil
| | - Maurício S Baptista
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, 05508-000 São Paulo, São Paulo, Brazil
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3
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Aires A, Fernández-Afonso Y, Guedes G, Guisasola E, Gutiérrez L, Cortajarena AL. Engineered Protein-Driven Synthesis of Tunable Iron Oxide Nanoparticles as T1 and T2 Magnetic Resonance Imaging Contrast Agents. CHEMISTRY OF MATERIALS : A PUBLICATION OF THE AMERICAN CHEMICAL SOCIETY 2022; 34:10832-10841. [PMID: 36590706 PMCID: PMC9798829 DOI: 10.1021/acs.chemmater.2c01746] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 11/15/2022] [Indexed: 05/14/2023]
Abstract
Iron oxide nanoparticles (IONPs) have become one of the most promising nanomaterials for biomedical applications because of their biocompatibility and physicochemical properties. This study demonstrates the use of protein engineering as a novel approach to design scaffolds for the tunable synthesis of ultrasmall IONPs. Rationally designed proteins, containing different number of metal-coordination sites, were evaluated to control the size and the physicochemical and magnetic properties of a set of protein-stabilized IONPs (Prot-IONPs). Prot-IONPs, synthesized through an optimized coprecipitation approach, presented good T1 and T2 relaxivity values, stability, and biocompatibility, showing potential for magnetic resonance imaging (MRI) applications.
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Affiliation(s)
- Antonio Aires
- Center
for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, Donostia-San Sebastián 20014, Spain
| | - Yilian Fernández-Afonso
- Instituto
de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, 50018 Zaragoza, Spain
| | - Gabriela Guedes
- Center
for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, Donostia-San Sebastián 20014, Spain
- University
of the Basque Country (UPV/EHU), 48940 Leioa, Spain
| | - Eduardo Guisasola
- Center
for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, Donostia-San Sebastián 20014, Spain
| | - Lucía Gutiérrez
- Instituto
de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, 50018 Zaragoza, Spain
- Centro
de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), 50018 Zaragoza, Spain
| | - Aitziber L. Cortajarena
- Center
for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, Donostia-San Sebastián 20014, Spain
- Ikerbasque, Basque Foundation for Science, 48009 Bilbao, Spain
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4
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Yao X, Höppener C, Schneidewind H, Hoeppener S, Tang Z, Buchholz A, König A, Mogavero S, Diegel M, Dellith J, Turchanin A, Plass W, Hube B, Deckert V. Targeted Suppression of Peptide Degradation in Ag-Based Surface-Enhanced Raman Spectra by Depletion of Hot Carriers. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2205080. [PMID: 36344458 DOI: 10.1002/smll.202205080] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 10/10/2022] [Indexed: 06/16/2023]
Abstract
Sample degradation, in particular of biomolecules, frequently occurs in surface-enhanced Raman spectroscopy (SERS) utilizing supported silver SERS substrates. Currently, thermal and/or photocatalytic effects are considered to cause sample degradation. This paper establishes the efficient inhibition of sample degradation using iodide which is demonstrated by a systematic SERS study of a small peptide in aqueous solution. Remarkably, a distinct charge separation-induced surface potential difference is observed for SERS substrates under laser irradiation using Kelvin probe force microscopy. This directly unveils the photocatalytic effect of Ag-SERS substrates. Based on the presented results, it is proposed that plasmonic photocatalysis dominates sample degradation in SERS experiments and the suppression of typical SERS sample degradation by iodide is discussed by means of the energy levels of the substrate under mild irradiation conditions. This approach paves the way toward more reliable and reproducible SERS studies of biomolecules under physiological conditions.
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Affiliation(s)
- Xiaobin Yao
- Leibniz Institute of Photonic Technology (IPHT), Albert-Einstein-Str. 9, 07745, Jena, Germany
- Institute of Physical Chemistry (IPC) and Abbe Center of Photonics, Friedrich Schiller University Jena, Lessingstr. 10, 07743, Jena, Germany
| | - Christiane Höppener
- Leibniz Institute of Photonic Technology (IPHT), Albert-Einstein-Str. 9, 07745, Jena, Germany
- Institute of Physical Chemistry (IPC) and Abbe Center of Photonics, Friedrich Schiller University Jena, Lessingstr. 10, 07743, Jena, Germany
| | - Henrik Schneidewind
- Leibniz Institute of Photonic Technology (IPHT), Albert-Einstein-Str. 9, 07745, Jena, Germany
| | - Stephanie Hoeppener
- Jena Center for Soft Matter (JCSM), Friedrich Schiller University Jena, Philosophenweg 7, 07743, Jena, Germany
- Laboratory of Organic and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstr. 10, 07743, Jena, Germany
| | - Zian Tang
- Institute of Physical Chemistry (IPC) and Abbe Center of Photonics, Friedrich Schiller University Jena, Lessingstr. 10, 07743, Jena, Germany
| | - Axel Buchholz
- Institute of Inorganic and Analytical Chemistry (IAAC), Friedrich Schiller University Jena, Humboldtstr. 8, 07743, Jena, Germany
| | - Annika König
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Selene Mogavero
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Marco Diegel
- Leibniz Institute of Photonic Technology (IPHT), Albert-Einstein-Str. 9, 07745, Jena, Germany
| | - Jan Dellith
- Leibniz Institute of Photonic Technology (IPHT), Albert-Einstein-Str. 9, 07745, Jena, Germany
| | - Andrey Turchanin
- Institute of Physical Chemistry (IPC) and Abbe Center of Photonics, Friedrich Schiller University Jena, Lessingstr. 10, 07743, Jena, Germany
| | - Winfried Plass
- Institute of Inorganic and Analytical Chemistry (IAAC), Friedrich Schiller University Jena, Humboldtstr. 8, 07743, Jena, Germany
| | - Bernhard Hube
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Beutenbergstrasse 11a, 07745, Jena, Germany
- Institute of Microbiology, Friedrich Schiller University Jena, Neugasse 25, 07743, Jena, Germany
| | - Volker Deckert
- Leibniz Institute of Photonic Technology (IPHT), Albert-Einstein-Str. 9, 07745, Jena, Germany
- Institute of Physical Chemistry (IPC) and Abbe Center of Photonics, Friedrich Schiller University Jena, Lessingstr. 10, 07743, Jena, Germany
- Institute For Quantum Science and Engineering (IQSE), Texas A&M University, College Station, TX, 77843, USA
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5
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Fuentes-Lemus E, Reyes JS, Gamon LF, López-Alarcón C, Davies MJ. Effect of macromolecular crowding on protein oxidation: Consequences on the rate, extent and oxidation pathways. Redox Biol 2021; 48:102202. [PMID: 34856437 PMCID: PMC8640551 DOI: 10.1016/j.redox.2021.102202] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 12/02/2022] Open
Abstract
Biological systems are heterogeneous and crowded environments. Such packed milieus are expected to modulate reactions both inside and outside the cell, including protein oxidation. In this work, we explored the effect of macromolecular crowding on the rate and extent of oxidation of Trp and Tyr, in free amino acids, peptides and proteins. These species were chosen as they are readily oxidized and contribute to damage propagation. Dextran was employed as an inert crowding agent, as this polymer decreases the fraction of volume available to other (macro)molecules. Kinetic analysis demonstrated that dextran enhanced the rate of oxidation of free Trp, and peptide Trp, elicited by AAPH-derived peroxyl radicals. For free Trp, the rates of oxidation were 15.0 ± 2.1 and 30.5 ± 3.4 μM min-1 without and with dextran (60 mg mL-1) respectively. Significant increases were also detected for peptide-incorporated Trp. Dextran increased the extent of Trp consumption (up to 2-fold) and induced short chain reactions. In contrast, Tyr oxidation was not affected by the presence of dextran. Studies on proteins, using SDS-PAGE and LC-MS, indicated that oxidation was also affected by crowding, with enhanced amino acid loss (45% for casein), chain reactions and altered extents of oligomer formation. The overall effects of dextran-mediated crowding were however dependent on the protein structure. Overall, these data indicate that molecular crowding, as commonly encountered in biological systems affect the rates, and extents of oxidation, and particularly of Trp residues, illustrating the importance of appropriate choice of in vitro systems to study biological oxidations.
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Affiliation(s)
- Eduardo Fuentes-Lemus
- Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, 2200, Denmark.
| | - Juan Sebastián Reyes
- Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Luke F Gamon
- Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, 2200, Denmark
| | - Camilo López-Alarcón
- Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Michael J Davies
- Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, 2200, Denmark.
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6
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A novel nonapeptide SSDAFFPFR from Antarctic krill exerts a protective effect on PC12 cells through the BCL-XL/Bax/Caspase-3/p53 signaling pathway. FOOD BIOSCI 2021. [DOI: 10.1016/j.fbio.2021.101345] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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7
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Ding Y, Zhao Z, Matysik J, Gärtner W, Losi A. Mapping the role of aromatic amino acids within a blue-light sensing LOV domain. Phys Chem Chem Phys 2021; 23:16767-16775. [PMID: 34319324 DOI: 10.1039/d1cp02217b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Photosensing LOV (Light, Oxygen, Voltage) domains detect and respond to UVA/Blue (BL) light by forming a covalent adduct between the flavin chromophore and a nearby cysteine, via the decay of the flavin triplet excited state. LOV domains where the reactive cysteine has been mutated are valuable fluorescent tools for microscopy and as genetically encoded photosensitisers for reactive oxygen species. Besides being convenient tools for applications, LOV domains without the reactive cysteine (naturally occurring or engineered) can still be functionally photoactivated via formation of a neutral flavin radical. Tryptophans and tyrosines are held as the main partners as potential electron donors to the flavin excited states. In this work, we explore the relevance of aromatic amino acids in determining the photophysical features of the LOV protein Mr4511 from Methylobacterium radiotolerans by introducing point mutations into the C71S variant that does not form the covalent adduct. By using an array of spectroscopic techniques we measured the fluorescence quantum yields and lifetimes, the triplet yields and lifetimes, and the efficiency of singlet oxygen (SO) formation for eleven Mr4511 variants. Insertion of Trp residues at distances between 0.6 and 1.5 nm from the flavin chromophore results in strong quenching of the flavin excited triplet state and, at the shorter distances even of the singlet excited state. The mutation F130W (ca. 0.6 nm) completely quenches the singlet excited state, preventing triplet formation: in this case, even if the cysteine is present, the photo-adduct is not formed. Tyrosines are also quenchers for the flavin excited states, although not as efficient as Trp residues, as demonstrated with their substitution with the inert phenylalanine. For one of these variants, C71S/Y116F, we found that the quantum yield of formation for singlet oxygen is 0.44 in aqueous aerobic solution, vs 0.17 for C71S. Based on our study with Mr4511 and on literature data for other LOV domains we suggest that Trp and Tyr residues too close to the flavin chromophore (at distances less than 0.9 nm) reduce the yield of photoproduct formation and that introduction of inert Phe residues in key positions can help in developing efficient, LOV-based photosensitisers.
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Affiliation(s)
- Yonghong Ding
- Institute for Analytical Chemistry, University of Leipzig, Linnéstrasse 3, 04103 Leipzig, Germany
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8
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Estevez M, Valesyan S, Jora M, Limbach PA, Addepalli B. Oxidative Damage to RNA is Altered by the Presence of Interacting Proteins or Modified Nucleosides. Front Mol Biosci 2021; 8:697149. [PMID: 34277707 PMCID: PMC8281250 DOI: 10.3389/fmolb.2021.697149] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 06/21/2021] [Indexed: 12/15/2022] Open
Abstract
Oxidative stress triggered by the Fenton reaction (chemical) or UVR exposure (photo) can damage cellular biomolecules including RNA through oxidation of nucleotides. Besides such xenobiotic chemical modifications, RNA also contains several post-transcriptional nucleoside modifications that are installed by enzymes to modulate structure, RNA-protein interactions, and biochemical functions. We examined the extent of oxidative damage to naturally modified RNA which is required for cellular protein synthesis under two different contexts. The extent of oxidative damage is higher when RNA is not associated with proteins, but the degree of damage is lower when the RNA is presented in the form of a ribonucleoprotein complex, such as an intact ribosome. Our studies also indicate that absence of methylations in ribosomal RNA at specific positions could make it more susceptible to photooxidative stress. However, the extent of guanosine oxidation varied with the position at which the modification is deficient, indicating position-dependent structural effects. Further, an E. coli strain deficient in 5-methylaminomethyl-2-thiouridine (mnm5s2U) (found in lysine and glutamate tRNA anticodon) is more vulnerable to oxidative RNA damage compared to its wildtype strain suggesting an auxiliary function for the mnm5s2U modification. These studies indicate that oxidative damage to RNA is altered by the presence of enzymatic modified nucleosides or protein association inside the cell.
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Affiliation(s)
- Mariana Estevez
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, United States
| | - Satenik Valesyan
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, United States
| | - Manasses Jora
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, United States
| | - Patrick A Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, United States
| | - Balasubrahmanyam Addepalli
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, United States
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9
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Abstract
Click chemistry has been established rapidly as one of the most valuable methods for the chemical transformation of complex molecules. Due to the rapid rates, clean conversions to the products, and compatibility of the reagents and reaction conditions even in complex settings, it has found applications in many molecule-oriented disciplines. From the vast landscape of click reactions, approaches have emerged in the past decade centered around oxidative processes to generate in situ highly reactive synthons from dormant functionalities. These approaches have led to some of the fastest click reactions know to date. Here, we review the various methods that can be used for such oxidation-induced "one-pot" click chemistry for the transformation of small molecules, materials, and biomolecules. A comprehensive overview is provided of oxidation conditions that induce a click reaction, and oxidation conditions are orthogonal to other click reactions so that sequential "click-oxidation-click" derivatization of molecules can be performed in one pot. Our review of the relevant literature shows that this strategy is emerging as a powerful approach for the preparation of high-performance materials and the generation of complex biomolecules. As such, we expect that oxidation-induced "one-pot" click chemistry will widen in scope substantially in the forthcoming years.
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Affiliation(s)
- Bauke Albada
- Laboratory of Organic Chemistry, Wageningen University & Research, Stippeneng 4, 6807 WE Wageningen, The Netherlands
| | - Jordi F Keijzer
- Laboratory of Organic Chemistry, Wageningen University & Research, Stippeneng 4, 6807 WE Wageningen, The Netherlands
| | - Han Zuilhof
- Laboratory of Organic Chemistry, Wageningen University & Research, Stippeneng 4, 6807 WE Wageningen, The Netherlands.,School of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin 300072, China.,Department of Chemical and Materials Engineering, Faculty of Engineering, King Abdulaziz University, 21589 Jeddah, Saudi Arabia
| | - Floris van Delft
- Laboratory of Organic Chemistry, Wageningen University & Research, Stippeneng 4, 6807 WE Wageningen, The Netherlands.,Synaffix BV, Industrielaan 63, 5349 AE, Oss, The Netherlands
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10
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Interrogating biological systems using visible-light-powered catalysis. Nat Rev Chem 2021; 5:322-337. [PMID: 37117838 DOI: 10.1038/s41570-021-00265-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/24/2021] [Indexed: 12/12/2022]
Abstract
Light-powered catalysis has found broad utility as a chemical transformation strategy, with widespread impact on energy, environment, drug discovery and human health. A noteworthy application impacting human health is light-induced sensitization of cofactors for photodynamic therapy in cancer treatment. The clinical adoption of this photosensitization approach has inspired the search for other photochemical methods, such as photoredox catalysis, to influence biological discovery. Over the past decade, light-mediated catalysis has enabled the discovery of valuable synthetic transformations, propelling it to become a highly utilized chemical synthesis strategy. The reaction components required to achieve a photoredox reaction are identical to photosensitization (catalyst, light source and substrate), making it ideally suited for probing biological environments. In this Review, we discuss the therapeutic application of photosensitization and advancements made in developing next-generation catalysts. We then highlight emerging uses of photoredox catalytic methods for protein bioconjugation and probing complex cellular environments in living cells.
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11
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Mechanisms and consequences of protein cysteine oxidation: the role of the initial short-lived intermediates. Essays Biochem 2020; 64:55-66. [PMID: 31919496 DOI: 10.1042/ebc20190053] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 12/10/2019] [Accepted: 12/12/2019] [Indexed: 12/27/2022]
Abstract
Thiol groups in protein cysteine (Cys) residues can undergo one- and two-electron oxidation reactions leading to the formation of thiyl radicals or sulfenic acids, respectively. In this mini-review we summarize the mechanisms and kinetics of the formation of these species by biologically relevant oxidants. Most of the latter react with the deprotonated form of the thiol. Since the pKa of the thiols in protein cysteines are usually close to physiological pH, the thermodynamics and the kinetics of their oxidation in vivo are affected by the acidity of the thiol. Moreover, the protein microenvironment has pronounced effects on cysteine residue reactivity, which in the case of the oxidation mediated by hydroperoxides, is known to confer specificity to particular protein cysteines. Despite their elusive nature, both thiyl radicals and sulfenic acids are involved in the catalytic mechanism of several enzymes and in the redox regulation of protein function and/or signaling pathways. They are usually short-lived species that undergo further reactions that converge in the formation of different stable products, resulting in several post-translational modifications of the protein. Some of these can be reversed through the action of specific cellular reduction systems. Others damage the proteins irreversibly, and can make them more prone to aggregation or degradation.
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12
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Abdelhameed SAM, Vandebroek L, de Azambuja F, Parac-Vogt TN. Redox Activity of Ce(IV)-Substituted Polyoxometalates toward Amino Acids and Peptides. Inorg Chem 2020; 59:10569-10577. [DOI: 10.1021/acs.inorgchem.0c00993] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
| | - Laurens Vandebroek
- KU Leuven, Department of Chemistry, Celestijnenlaan 200F, 3001 Leuven, Belgium
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13
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Ortiz-Rodríguez JC, Santana JA, Méndez-Hernández DD. Linear correlation models for the redox potential of organic molecules in aqueous solutions. J Mol Model 2020; 26:70. [PMID: 32146589 DOI: 10.1007/s00894-020-4331-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Accepted: 02/23/2020] [Indexed: 01/11/2023]
Abstract
In this study, we use the molecular orbital energy approximation (MOEA) and the energy difference approximation (EDA) to build linear correlation models for the redox potentials of 53 organic compounds in aqueous solutions. The molecules evaluated include nitroxides, phenols, and amines. Both the MOEA and EDA methods yield similar correlation models, however, the MOEA method is less computationally expensive. Correlation coefficients (R2) below 0.3 and mean absolute errors above 0.25 V were found for correlation models built without solvent effects. When explicit water molecules and a continuum solvent model are added to the calculations, correlation coefficients close to 0.8 are reached, and mean absolute errors below 0.18 V are obtained. The incorporation of solvent effects is necessary for good correlation models, particularly for redox processes of charged molecules in aqueous solutions. A comparison of the correlation models from different methodologies is provided. Graphical abstract.
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Affiliation(s)
| | - Juan A Santana
- Department of Chemistry, University of Puerto Rico at Cayey, Cayey, PR, 00736, USA
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14
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Xu L, Coote ML. Improving the Accuracy of PCM-UAHF and PCM-UAKS Calculations Using Optimized Electrostatic Scaling Factors. J Chem Theory Comput 2019; 15:6958-6967. [DOI: 10.1021/acs.jctc.9b00888] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Longkun Xu
- ARC Centre of Excellence for Electromaterials Science, Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Michelle L. Coote
- ARC Centre of Excellence for Electromaterials Science, Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia
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15
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Xu L, Coote ML. Methods To Improve the Calculations of Solvation Model Density Solvation Free Energies and Associated Aqueous pKa Values: Comparison between Choosing an Optimal Theoretical Level, Solute Cavity Scaling, and Using Explicit Solvent Molecules. J Phys Chem A 2019; 123:7430-7438. [DOI: 10.1021/acs.jpca.9b04920] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Longkun Xu
- ARC Centre of Excellence for Electromaterials Science, Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Michelle L. Coote
- ARC Centre of Excellence for Electromaterials Science, Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia
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Lin YS, Lin Y, Periasamy AP, Cang J, Chang HT. Parameters affecting the synthesis of carbon dots for quantitation of copper ions. NANOSCALE ADVANCES 2019; 1:2553-2561. [PMID: 36132712 PMCID: PMC9419006 DOI: 10.1039/c9na00137a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 05/10/2019] [Indexed: 05/20/2023]
Abstract
A simple, eco-friendly, and low-cost electrochemical approach has been applied to the synthesis of carbon dots (C dots) from histidine hydrochloride in the absence or presence of halides (Cl, Br, and I) at various potentials up to 10 V. The as-formed C dots refer to C dots, Cl-C, Br-C, and I-C dots. The time-evolution UV-vis absorption and photoluminescence (PL) spectra provide more detailed information about the formation of C dots. Upon increasing the reaction time from 1 to 120 min, more and more C dots are formed, leading to increased PL intensity. The halides play two important roles in determining the formation of C dots; controlling the reaction rate and surface states. When compared to chloride and bromide, iodide has a greater effect on varying surface states and inducing PL quenching through intersystem crossing. The PL intensities of the four types of C dots all decrease upon increasing Cu2+, Hg2+, and Ag+ concentrations. In the presence of 0.8 mM I-, I-C dots compared to C dots, Cl-C dots, and Br-C dots are slightly better for quantitation of Cu2+. Fourier transform infrared spectroscopy, cyclic voltammetry, electrochemical impedance spectroscopy, and X-ray photoelectron spectroscopy results of I-C dots reveal the interactions of Cu2+ with the surface ligands (imidazole and histidine). The I-C dot probe in the presence of 0.8 mM I- is selective toward Cu2+ over the tested metal ions such as Hg2+ and Ag+. The assay provides a limit of detection of 0.22 μM for Cu2+ at a signal-to-noise ratio of 3. Practicality of this probe has been validated by the analyses of tap, lake, and sea water samples, with negligible matrix effects.
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Affiliation(s)
- Yu-Syuan Lin
- Department of Chemistry, National Taiwan University Taipei 10617 Taiwan
| | - Yaling Lin
- Department of Chemistry, National Taiwan University Taipei 10617 Taiwan
| | | | - Jinshun Cang
- Department of Chemical Engineering, Yancheng Institute of Industry Technology Yancheng Jiangsu 224005 China
| | - Huan-Tsung Chang
- Department of Chemistry, National Taiwan University Taipei 10617 Taiwan
- Department of Chemistry, Chung Yuan Christian University Taoyuan City 32023 Taiwan
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Close DM, Bernhard WA. Comprehensive model for X-ray-induced damage in protein crystallography. JOURNAL OF SYNCHROTRON RADIATION 2019; 26:945-957. [PMID: 31274416 DOI: 10.1107/s1600577519005083] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 04/13/2019] [Indexed: 06/09/2023]
Abstract
Acquisition of X-ray crystallographic data is always accompanied by structural degradation owing to the absorption of energy. The application of high-fluency X-ray sources to large biomolecules has increased the importance of finding ways to curtail the onset of X-ray-induced damage. A significant effort has been under way with the aim of identifying strategies for protecting protein structure. A comprehensive model is presented that has the potential to explain, both qualitatively and quantitatively, the structural changes induced in crystalline protein at ∼100 K. The first step is to consider the qualitative question: what are the radiation-induced intermediates and expected end products? The aim of this paper is to assist in optimizing these strategies through a fundamental understanding of radiation physics and chemistry, with additional insight provided by theoretical calculations performed on the many schemes presented.
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Affiliation(s)
- David M Close
- Department of Physics, East Tennessee State University, Box 70652, Johnson City, TN 37614, USA
| | - William A Bernhard
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, NY 14642, USA
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Garreau M, Le Vaillant F, Waser J. C‐Terminal Bioconjugation of Peptides through Photoredox Catalyzed Decarboxylative Alkynylation. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201901922] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Marion Garreau
- Laboratory of Catalysis and Organic Synthesis Ecole Polytechnique Fédérale de Lausanne EPFL SB ISIC LCSO, BCH 4306 1015 Lausanne Switzerland
| | - Franck Le Vaillant
- Laboratory of Catalysis and Organic Synthesis Ecole Polytechnique Fédérale de Lausanne EPFL SB ISIC LCSO, BCH 4306 1015 Lausanne Switzerland
| | - Jerome Waser
- Laboratory of Catalysis and Organic Synthesis Ecole Polytechnique Fédérale de Lausanne EPFL SB ISIC LCSO, BCH 4306 1015 Lausanne Switzerland
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19
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Garreau M, Le Vaillant F, Waser J. C‐Terminal Bioconjugation of Peptides through Photoredox Catalyzed Decarboxylative Alkynylation. Angew Chem Int Ed Engl 2019; 58:8182-8186. [DOI: 10.1002/anie.201901922] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Indexed: 01/06/2023]
Affiliation(s)
- Marion Garreau
- Laboratory of Catalysis and Organic Synthesis Ecole Polytechnique Fédérale de Lausanne EPFL SB ISIC LCSO, BCH 4306 1015 Lausanne Switzerland
| | - Franck Le Vaillant
- Laboratory of Catalysis and Organic Synthesis Ecole Polytechnique Fédérale de Lausanne EPFL SB ISIC LCSO, BCH 4306 1015 Lausanne Switzerland
| | - Jerome Waser
- Laboratory of Catalysis and Organic Synthesis Ecole Polytechnique Fédérale de Lausanne EPFL SB ISIC LCSO, BCH 4306 1015 Lausanne Switzerland
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Li J, Koto T, Davis I, Liu A. Probing the Cys-Tyr Cofactor Biogenesis in Cysteine Dioxygenase by the Genetic Incorporation of Fluorotyrosine. Biochemistry 2019; 58:2218-2227. [PMID: 30946568 DOI: 10.1021/acs.biochem.9b00006] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Cysteine dioxygenase (CDO) is a nonheme iron enzyme that adds two oxygen atoms from dioxygen to the sulfur atom of l-cysteine. Adjacent to the iron site of mammalian CDO, there is a post-translationally generated Cys-Tyr cofactor, whose presence substantially enhances the oxygenase activity. The formation of the Cys-Tyr cofactor in CDO is an autocatalytic process, and it is challenging to study by traditional techniques because the cross-linking reaction is a side, uncoupled, single-turnover oxidation buried among multiple turnovers of l-cysteine oxygenation. Here, we take advantage of our recent success in obtaining a purely uncross-linked human CDO due to site-specific incorporation of 3,5-difluoro-l-tyrosine (F2-Tyr) at the cross-linking site through the genetic code expansion strategy. Using EPR spectroscopy, we show that nitric oxide (•NO), an oxygen surrogate, similarly binds to uncross-linked F2-Tyr157 CDO as in wild-type human CDO. We determined X-ray crystal structures of uncross-linked F2-Tyr157 CDO and mature wild-type CDO in complex with both l-cysteine and •NO. These structural data reveal that the active site cysteine (Cys93 in the human enzyme), rather than the generally expected tyrosine (i.e., Tyr157), is well-aligned to be oxidized should the normal oxidation reaction uncouple. This structure-based understanding is further supported by a computational study with models built on the uncross-linked ternary complex structure. Together, these results strongly suggest that the first target to oxidize during the iron-assisted Cys-Tyr cofactor biogenesis is Cys93. Based on these data, a plausible reaction mechanism implementing a cysteine radical involved in the cross-link formation is proposed.
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Affiliation(s)
- Jiasong Li
- Department of Chemistry , University of Texas at San Antonio , San Antonio , Texas 78249 , United States
| | - Teruaki Koto
- Department of Chemistry , University of Texas at San Antonio , San Antonio , Texas 78249 , United States
| | - Ian Davis
- Department of Chemistry , University of Texas at San Antonio , San Antonio , Texas 78249 , United States
| | - Aimin Liu
- Department of Chemistry , University of Texas at San Antonio , San Antonio , Texas 78249 , United States
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Microhydration and the Enhanced Acidity of Free Radicals. Molecules 2018; 23:molecules23020423. [PMID: 29443952 PMCID: PMC6017598 DOI: 10.3390/molecules23020423] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 02/09/2018] [Accepted: 02/14/2018] [Indexed: 12/02/2022] Open
Abstract
Recent theoretical research employing a continuum solvent model predicted that radical centers would enhance the acidity (RED-shift) of certain proton-donor molecules. Microhydration studies employing a DFT method are reported here with the aim of establishing the effect of the solvent micro-structure on the acidity of radicals with and without RED-shifts. Microhydration cluster structures were obtained for carboxyl, carboxy-ethynyl, carboxy-methyl, and hydroperoxyl radicals. The numbers of water molecules needed to induce spontaneous ionization were determined. The hydration clusters formed primarily round the CO2 units of the carboxylate-containing radicals. Only 4 or 5 water molecules were needed to induce ionization of carboxyl and carboxy-ethynyl radicals, thus corroborating their large RED-shifts.
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