1
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Taniguchi T, Agbo DO, Yang Q, Kapitán J, Wu T, Oyama S, Akai S, Sawama Y, Bouř P. Raman optical activity study of deuterated sugars: deuterium labelling as a tool for structural analysis. Phys Chem Chem Phys 2024; 26:21568-21574. [PMID: 39082369 DOI: 10.1039/d4cp02406k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
Abstract
Structural analyses using Raman optical activity (ROA) spectroscopy conventionally rely on vibrational signals in the fingerprint region ranging from 100 to 1800 cm-1. Use of deuterium labelling to observe ROA signals in the C-D stretching region provides additional information about a local structure of large molecular systems. So far, the potential of C-D stretching ROA signals for structural analysis has rarely been explored. In the present work, we synthesized model deuterated glucose monosaccharides and studied their ROA properties by employing molecular dynamics and density functional theory to interpret the spectra. A good agreement between the simulated and experimental spectra is achieved when the proper conformer ratios are considered. This shows the usefulness of ROA spectroscopy assisted by deuterium labelling for stereochemical and conformational analysis.
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Affiliation(s)
- Tohru Taniguchi
- Frontier Research Center for Advanced Material and Life Science, Faculty of Advanced Life Science, Hokkaido University, North 21 West 11, Sapporo 001-0021, Japan.
| | - Davidson Obinna Agbo
- Frontier Research Center for Advanced Material and Life Science, Faculty of Advanced Life Science, Hokkaido University, North 21 West 11, Sapporo 001-0021, Japan.
| | - Qin Yang
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic
| | - Josef Kapitán
- Department of Optics, Palacký University Olomouc, 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Tao Wu
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic
| | - Shuki Oyama
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Shuji Akai
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yoshinari Sawama
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic
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2
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Ni R, Ge K, Luo Y, Zhu T, Hu Z, Li M, Tao P, Chi J, Li G, Yuan H, Pang Q, Gao W, Zhang P, Zhu Y. Highly sensitive microfluidic sensor using integrated optical fiber and real-time single-cell Raman spectroscopy for diagnosis of pancreatic cancer. Biosens Bioelectron 2024; 264:116616. [PMID: 39137518 DOI: 10.1016/j.bios.2024.116616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 07/26/2024] [Accepted: 07/29/2024] [Indexed: 08/15/2024]
Abstract
Pancreatic cancer is notoriously lethal due to its late diagnosis and poor patient response to treatments, posing a significant clinical challenge. This study introduced a novel approach that combines a single-cell capturing platform, tumor-targeted silver (Ag) nanoprobes, and precisely docking tapered fiber integrated with Raman spectroscopy. This approach focuses on early detection and progression monitoring of pancreatic cancer. Utilizing tumor-targeted Ag nanoparticles and tapered multimode fibers enhances Raman signals, minimizes light loss, and reduces background noise. This advanced Raman system allows for detailed molecular spectroscopic examination of individual cells, offering more practical information and enabling earlier detection and accurate staging of pancreatic cancer compared to conventional multicellular Raman spectroscopy. Transcriptomic analysis using high-throughput gene screening and transcriptomic databases confirmed the ability and accuracy of this method to identify molecular changes in normal, early, and metastatic pancreatic cancer cells. Key findings revealed that cell adhesion, migration, and the extracellular matrix are closely related to single-cell Raman spectroscopy (SCRS) results, highlighting components such as collagen, phospholipids, and carotene. Therefore, the SCRS approach provides a comprehensive view of the molecular composition, biological function, and material changes in cells, offering a novel, accurate, reliable, rapid, and efficient method for diagnosing and monitoring pancreatic cancer.
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Affiliation(s)
- Renhao Ni
- Health Science Center, Ningbo University, Ningbo, 315211, China
| | - Kaixin Ge
- Key Laboratory of Photoelectric Materials and Devices of Zhejiang Province, Ningbo University, Ningbo, 315211, China; Engineering Research Center for Advanced Infrared Photoelectric Materials and Devices of Zhejiang Province, Ningbo University, Ningbo, 315211, China
| | - Yang Luo
- Health Science Center, Ningbo University, Ningbo, 315211, China
| | - Tong Zhu
- Health Science Center, Ningbo University, Ningbo, 315211, China
| | - Zeming Hu
- Health Science Center, Ningbo University, Ningbo, 315211, China
| | - Min Li
- College of Information Science and Engineering, Ningbo University, Ningbo, 315211, China
| | - Pan Tao
- Key Laboratory of Photoelectric Materials and Devices of Zhejiang Province, Ningbo University, Ningbo, 315211, China; Engineering Research Center for Advanced Infrared Photoelectric Materials and Devices of Zhejiang Province, Ningbo University, Ningbo, 315211, China
| | - Jinyi Chi
- Health Science Center, Ningbo University, Ningbo, 315211, China
| | - Guanron Li
- Health Science Center, Ningbo University, Ningbo, 315211, China; The First Affiliated Hospital of Ningbo University, Ningbo, 315020, China
| | - Haojun Yuan
- College of Information Science and Engineering, Ningbo University, Ningbo, 315211, China
| | - Qian Pang
- Health Science Center, Ningbo University, Ningbo, 315211, China
| | - Wanlei Gao
- College of Information Science and Engineering, Ningbo University, Ningbo, 315211, China.
| | - Peiqing Zhang
- Key Laboratory of Photoelectric Materials and Devices of Zhejiang Province, Ningbo University, Ningbo, 315211, China; Engineering Research Center for Advanced Infrared Photoelectric Materials and Devices of Zhejiang Province, Ningbo University, Ningbo, 315211, China.
| | - Yabin Zhu
- Health Science Center, Ningbo University, Ningbo, 315211, China.
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3
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Hachlica N, Stefańska M, Mach M, Kowalska M, Wydro P, Domagała A, Kessler J, Zając G, Kaczor A. Organization of Carotenoid Aggregates in Membranes Studied Selectively using Resonance Raman Optical Activity. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2306707. [PMID: 38247201 DOI: 10.1002/smll.202306707] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 11/28/2023] [Indexed: 01/23/2024]
Abstract
In living organisms, carotenoids are incorporated in biomembranes, remarkably modulating their mechanical characteristics, fluidity, and permeability. Significant resonance enhancement of Raman optical activity (ROA) signals of carotenoid chiral aggregates makes resonance ROA (RROA), a highly selective tool to study exclusively carotenoid assemblies in model membranes. Hence, RROA is combined with electronic circular dichroism (ECD), dynamic light scattering (DLS), molecular dynamics, and quantum-chemical calculations to shed new light on the carotenoid aggregation in dipalmitoylphosphatidylcholine (DPPC) liposomes. Using representative members of the carotenoid family: apolar α-carotene and more polar fucoxanthin and zeaxanthin, the authors demonstrate that the stability of carotenoid aggregates is directly linked with their orientation in membranes and the monomer structures inside the assemblies. In particular, polyene chain distortion of α-carotene molecules is an important feature of J-aggregates that show increased orientational freedom and stability inside liposomes compared to H-assemblies of more polar xanthophylls. In light of these results, RROA emerges as a new tool to study active compounds and drugs embedded in membranes.
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Affiliation(s)
- Natalia Hachlica
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, Krakow, 30-387, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, S. Łojasiewicza 11, Krakow, 30-348, Poland
| | - Marta Stefańska
- Biozentrum, University of Basel, Spitalstrasse 41, Basel, 4056, Switzerland
| | - Marzena Mach
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, Krakow, 30-387, Poland
| | - Magdalena Kowalska
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, Krakow, 30-387, Poland
| | - Pawel Wydro
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, Krakow, 30-387, Poland
| | - Agnieszka Domagała
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, S. Łojasiewicza 11, Krakow, 30-348, Poland
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzyńskiego 14, Krakow, 30-348, Poland
| | - Jiři Kessler
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo namestı 2, Prague, 16610, Czech Republic
| | - Grzegorz Zając
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzyńskiego 14, Krakow, 30-348, Poland
| | - Agnieszka Kaczor
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, Krakow, 30-387, Poland
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4
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Machalska E, Halat M, Tani T, Fujisawa T, Unno M, Kudelski A, Baranska M, Zając G. Why Does One Measure Resonance Raman Optical Activity? A Unique Case of Measurements under Strong Resonance versus Far-from-Resonance Conditions. J Phys Chem Lett 2024; 15:4913-4919. [PMID: 38684076 PMCID: PMC11089565 DOI: 10.1021/acs.jpclett.4c00270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 04/19/2024] [Accepted: 04/24/2024] [Indexed: 05/02/2024]
Abstract
Raman optical activity (ROA) spectroscopy exhibits significant potential in the study of (bio)molecules as it encodes information on their molecular structure, chirality, and conformations. Furthermore, the method reveals details on excited electronic states when applied under resonance conditions. Here, we present a combined study of the far from resonance (FFR)-ROA and resonance ROA (RROA) of a single relatively small molecular system. Notably, this study is the first to employ the density functional theory (DFT) analysis of both FFR-ROA and RROA spectra. This is illustrated for cobalamin derivatives using near-infrared and visible light excitation. Although the commonly observed monosignate RROA spectra lose additional information visible in bisignate nonresonance ROA spectra, the RROA technique acts as a complement to nonresonance ROA spectroscopy. In particular, the combination of these methods integrated with DFT calculations can reveal a complete spectral picture of the structural and conformational differences between tested compounds.
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Affiliation(s)
- Ewa Machalska
- Jagiellonian
Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, 30-348 Krakow, Poland
- Laboratory
for Spectroscopy, Molecular Modeling and Structure Determination, Institute of Nuclear Chemistry and Technology, Dorodna 16, 03-195 Warsaw, Poland
| | - Monika Halat
- Department
of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture, Al. Mickiewicza 21, 31-120 Krakow, Poland
| | - Takumi Tani
- Department
of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Tomotsumi Fujisawa
- Department
of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Masashi Unno
- Department
of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Andrzej Kudelski
- Faculty of
Chemistry, University of Warsaw, Ludwika Pasteura 1, 02-093 Warsaw, Poland
| | - Malgorzata Baranska
- Jagiellonian
Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, 30-348 Krakow, Poland
- Faculty of
Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Grzegorz Zając
- Jagiellonian
Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, 30-348 Krakow, Poland
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5
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Fujisawa T, Unno M. Near-Infrared Excited Raman Optical Activity as a Tool to Uncover Active Sites of Photoreceptor Proteins. J Phys Chem B 2024; 128:2228-2235. [PMID: 38441478 DOI: 10.1021/acs.jpcb.4c00094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2024]
Abstract
Raman optical activity (ROA) is a chiral sensitive technique to measure the difference in Raman scattering intensity between right and left circularly polarized light. The method has been applied to the study of biological molecules such as proteins, and it is now recognized as a powerful tool for investigating biomolecular structures. We have expanded the capability of this chiroptical technique to colored molecules, such as photoreceptor proteins, by using a near-infrared excitation. A photoreceptor protein contains a light-absorbing chromophore as an active site, and the precise determination of its structure is vital for comprehending the protein's function at the atomic level. In a photoreceptor protein, the protein environment can distort an achiral chromophore into a chiral conformation. ROA spectroscopy offers detailed structural information about the chromophore under physiological conditions. Here we explore recent progress in near-infrared ROA spectroscopy and its application to biological systems.
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Affiliation(s)
- Tomotsumi Fujisawa
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Masashi Unno
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
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6
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Yang Q, Bloino J, Šestáková H, Šebestík J, Kessler J, Hudecová J, Kapitán J, Bouř P. Combination of Resonance and Non-Resonance Chiral Raman Scattering in a Cobalt(III) Complex. Angew Chem Int Ed Engl 2023; 62:e202312521. [PMID: 37728178 DOI: 10.1002/anie.202312521] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 09/18/2023] [Accepted: 09/20/2023] [Indexed: 09/21/2023]
Abstract
Resonance Raman optical activity (RROA) spectra with high sensitivity reveal details on molecular structure, chirality, and excited electronic properties. Despite the difficulty of the measurements, the recorded data for the Co(III) complex with S,S-N,N-ethylenediaminedisuccinic acid are of exceptional quality and, coupled with the theory, spectacularly document the molecular behavior in resonance. This includes a huge enhancement of the chiral scattering, contribution of the antisymmetric polarizabilities to the signal, and the Herzberg-Teller effect significantly shaping the spectra. The chiral component is by about one order of magnitude bigger than for an analogous aluminum complex. The band assignment and intensity profile were confirmed by simulations based on density functional and vibronic theories. The resonance was attributed to the S0 →S3 transition, with the strongest signal enhancement of Raman and ROA spectral bands below about 800 cm-1 . For higher wavenumbers, other excited electronic states contribute to the scattering in a less resonant way. RROA spectroscopy thus appears as a unique tool to study the structure and electronic states of absorbing molecules in analytical chemistry, biology, and material science.
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Affiliation(s)
- Qin Yang
- Institute of Organic Chemistry and Biochemistry Academy of Sciences, Flemingovo náměstí 2, 16610, Prague, Czech Republic
| | - Julien Bloino
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - Hana Šestáková
- Institute of Organic Chemistry and Biochemistry Academy of Sciences, Flemingovo náměstí 2, 16610, Prague, Czech Republic
- University of Chemistry and Technology, Technická 5, 16628, Prague 6, Czech Republic
| | - Jaroslav Šebestík
- Institute of Organic Chemistry and Biochemistry Academy of Sciences, Flemingovo náměstí 2, 16610, Prague, Czech Republic
| | - Jiří Kessler
- Institute of Organic Chemistry and Biochemistry Academy of Sciences, Flemingovo náměstí 2, 16610, Prague, Czech Republic
| | - Jana Hudecová
- Department of Optics, Palacký University Olomouc, 17. listopadu 12, 77146, Olomouc, Czech Republic
| | - Josef Kapitán
- Department of Optics, Palacký University Olomouc, 17. listopadu 12, 77146, Olomouc, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry Academy of Sciences, Flemingovo náměstí 2, 16610, Prague, Czech Republic
- University of Chemistry and Technology, Technická 5, 16628, Prague 6, Czech Republic
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7
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Fujisawa T, Shingae T, Ren J, Haraguchi S, Hanamoto T, Hoff WD, Unno M. Spectroscopic Validation of Crystallographic Structures of a Protein Active Site by Chiroptical Spectroscopy. J Phys Chem Lett 2023; 14:9304-9309. [PMID: 37816034 DOI: 10.1021/acs.jpclett.3c01954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/12/2023]
Abstract
Out-of-plane distortions of a cofactor molecule in a protein active site are functionally important, and in photoreceptors, it has been proposed that they are crucial for spectral tuning and energy storage in photocycle intermediates. However, these subtle structural features are often beyond the grasp of structural biology. This issue is strikingly exemplified by photoactive yellow protein: its 14 independently determined crystal structures exhibit considerable differences in the dihedral angles defining the chromophore geometry, even though most of these are at excellent resolution. Here we developed a strategy to verify cofactor distortions in crystal structures by using quantum chemical calculations and chiroptical spectroscopy, particularly Raman optical activity and electronic circular dichroism spectroscopies. Based on this approach, we identify seven crystal structures with the chromophore geometries inconsistent with the experimentally observed data. The strategy implemented here promises to be widely applicable to uncovering cofactor distortions at active sites and to studies of reaction intermediates.
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Affiliation(s)
- Tomotsumi Fujisawa
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Takahito Shingae
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Jie Ren
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Shojiro Haraguchi
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Takeshi Hanamoto
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Wouter D Hoff
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Masashi Unno
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
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8
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Nishikawa K, Kuroiwa R, Tamogami J, Unno M, Fujisawa T. Raman Optical Activity of Retinal Chromophore in Sensory Rhodopsin II. J Phys Chem B 2023; 127:7244-7250. [PMID: 37556781 DOI: 10.1021/acs.jpcb.3c02391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
Raman optical activity (ROA) spectroscopy was used to study the conformation of the retinal chromophore in sensory rhodopsin II (SRII), which is a blue-green light sensor of microbes. The ROA spectrum consisted of the negative vibrational bands of the chromophore, whose relative intensities are similar to those of the parent Raman spectrum. This spectral feature was explained by the left-handed helical twist of the retinal chromophore on the basis of quantum chemical calculations. On the other hand, we found that the chromophore conformation based on the crystal structures of SRII has a right-handed helical twist, which does not agree with the observation. This specific result suggests that the consistency with chiro-optical properties can be a key criterion for the accurate prediction and/or evaluation of chromophore conformation in retinal-binding proteins.
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Affiliation(s)
- Kouhei Nishikawa
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Ryosuke Kuroiwa
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Jun Tamogami
- College of Pharmaceutical Sciences, Matsuyama University, Matsuyama, Ehime 790-8578, Japan
| | - Masashi Unno
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Tomotsumi Fujisawa
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
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9
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Ohya M, Kikukawa T, Matsuo J, Tsukamoto T, Nagaura R, Fujisawa T, Unno M. Structure and Heterogeneity of Retinal Chromophore in Chloride Pump Rhodopsins Revealed by Raman Optical Activity. J Phys Chem B 2023. [PMID: 37201188 DOI: 10.1021/acs.jpcb.3c01801] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Chloride transport by microbial rhodopsins is actively being researched to understand how light energy is converted to drive ion pumping across cell membranes. Chloride pumps have been identified in archaea and eubacteria, and there are similarities and differences in the active site structures between these groups. Thus, it has not been clarified whether a common mechanism underlies the ion pump processes for all chloride-pumping rhodopsins. Here, we applied Raman optical activity (ROA) spectroscopy to two chloride pumps, Nonlabens marinus rhodopsin-3 (NM-R3) and halorhodopsin from the cyanobacterium Mastigocladopsis repens (MrHR). ROA is a vibrational spectroscopy that provides chiral sensitivity, and the sign of ROA signals can reveal twisting of cofactor molecules within proteins. Our ROA analysis revealed that the retinal Schiff base NH group orients toward the C helix and forms a direct hydrogen bond with a nearby chloride ion in NM-R3. In contrast, MrHR is suggested to contain two retinal conformations twisted in opposite directions; one conformation has a hydrogen bond with a chloride ion like NM-R3, while the other forms a hydrogen bond with a water molecule anchored by a G helix residue. These results suggest a general pump mechanism in which the chloride ion is "dragged" by the flipping Schiff base NH group upon photoisomerization.
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Affiliation(s)
- Masaiku Ohya
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Takashi Kikukawa
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Junpei Matsuo
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Takashi Tsukamoto
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Ryota Nagaura
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Tomotsumi Fujisawa
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Masashi Unno
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
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10
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Orlef A, Stanek E, Czamara K, Wajda A, Kaczor A. Formation of carotenoid supramolecular aggregates in nanocarriers monitored via aggregation-sensitive chiroptical output of enantiopure (3 S,3' S)-astaxanthin. Chem Commun (Camb) 2022; 58:9022-9025. [PMID: 35875940 DOI: 10.1039/d2cc02649j] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The aggregation-sensitive chiroptical (ECD and RROA) output, provided by enantiopure (3S,3'S)-astaxanthin, was used to investigate and control the assembling processes of the carotenoid in Pluronic F-127 nanoparticles. The process of carotenoid J-aggregation inside nanocarriers is interfered with by the formation of kinetically stabilized H1 self-assemblies outside the micelles. Nanocarriers with encapsulated stable J-aggregates provide controlled release of carotenoid molecules to primary murine adipocytes.
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Affiliation(s)
- Aleksandra Orlef
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Krakow, Poland.
| | - Ewa Stanek
- Jagiellonian Centre for Experimental Therapeutics, Jagiellonian University, Bobrzynskiego 14, 30-348, Krakow, Poland
| | - Krzysztof Czamara
- Jagiellonian Centre for Experimental Therapeutics, Jagiellonian University, Bobrzynskiego 14, 30-348, Krakow, Poland
| | - Aleksandra Wajda
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Krakow, Poland.
| | - Agnieszka Kaczor
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Krakow, Poland. .,Jagiellonian Centre for Experimental Therapeutics, Jagiellonian University, Bobrzynskiego 14, 30-348, Krakow, Poland
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11
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Wu T, Kapitán J, Bouř P. Resolving Resonant Electronic States in Chiral Metal Complexes by Raman Optical Activity Spectroscopy. J Phys Chem Lett 2022; 13:3873-3877. [PMID: 35467874 DOI: 10.1021/acs.jpclett.2c00653] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Chiral metal complexes exhibit rich photophysical properties and are important for applications ranging from biosensing to photocatalysis. We present a combined experimental and computational approach leading to information about energies and transition moments of excited electronic states, documented on two chiral metal complexes. The experimental protocol for measurement of the resonance Raman optical activity comprises multiple techniques, i.e., absorption, circular dichroism, and polarized and differential Raman scattering. An accurate formula for subtraction of the interfering circular dichroism/polarized Raman scattering effect is given. An analysis of the spectra based on density functional theory calculations unveils the geometric and electronic structures of the molecules. Such insight into molecular electronic states of chromophores may be useful for understanding and tuning photochemical properties of metal-containing complexes, biomolecules, and supramolecules.
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Affiliation(s)
- Tao Wu
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic
| | - Josef Kapitán
- Department of Optics, Palacký University Olomouc, 17 Listopadu 12, 77146 Olomouc, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic
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12
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Zając G, Bouř P. Measurement and Theory of Resonance Raman Optical Activity for Gases, Liquids, and Aggregates. What It Tells about Molecules. J Phys Chem B 2021; 126:355-367. [PMID: 34792364 DOI: 10.1021/acs.jpcb.1c08370] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Resonance Raman Optical Activity (RROA) appeared as a natural extension of the nonresonance branch. It combines the structural sensitivity of chiroptical spectroscopy with the signal enhancement coming from the resonance of molecular electronic transitions with the excitation laser light. However, the idea has been hampered by many technical and theoretical problems that are being clarified only in recent years. We provide the theoretical basis and several examples documenting the problems, achievements, and potential of RROA, in particular in biomolecular studies.
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Affiliation(s)
- Grzegorz Zając
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, Krakow 30-348, Poland
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, Prague, 16610, Czech Republic
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13
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Machalska E, Hachlica N, Zajac G, Carraro D, Baranska M, Licini G, Bouř P, Zonta C, Kaczor A. Chiral recognition via a stereodynamic vanadium probe using the electronic circular dichroism effect in differential Raman scattering. Phys Chem Chem Phys 2021; 23:23336-23340. [PMID: 34633399 DOI: 10.1039/d1cp03020e] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Intermolecular interactions sensitive to chirality occur in many biological events. We report a complex formation between a versatile vanadium-based probe and a chiral co-ligand monitored via the combination of electronic circular dichroism (ECD) and Raman scattering. This "ECD-Raman" effect was discovered relatively recently and can be measured using a Raman optical activity (ROA) spectrometer. Simulated spectra based on experimental ECD and degree of circularity (DOC) values agree with the observed ones. Sensitive recognition of the chiral enantiopure co-ligand is thus enabled by a combination of resonance of the excitation light with the diastereoisomeric complex, co-ligand complexation, circular dichroism, and polarized Raman scattering from the achiral solvent. Relatively dilute solutions could be detected (10-4 mol dm-3), about 1000× less than is necessary for conventional ROA detection of the pure co-ligand and comparable to concentrations needed for conventional ECD spectroscopy. The results thus show that differential ECD-Raman measurements can be conveniently used to monitor molecular interactions and molecular spectroscopic properties.
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Affiliation(s)
- Ewa Machalska
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, Krakow 30-387, Poland. .,Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, Krakow 30-348, Poland
| | - Natalia Hachlica
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, Krakow 30-387, Poland. .,Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, Krakow 30-348, Poland
| | - Grzegorz Zajac
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, Krakow 30-348, Poland.,Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610, Prague, Czech Republic.
| | - Davide Carraro
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova and CIRCC, Padova Unit, 35131 Padova, Italy.
| | - Malgorzata Baranska
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, Krakow 30-387, Poland. .,Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, Krakow 30-348, Poland
| | - Giulia Licini
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova and CIRCC, Padova Unit, 35131 Padova, Italy.
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610, Prague, Czech Republic.
| | - Cristiano Zonta
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova and CIRCC, Padova Unit, 35131 Padova, Italy.
| | - Agnieszka Kaczor
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, Krakow 30-387, Poland. .,Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, Krakow 30-348, Poland
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14
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Fujisawa T, Nishikawa K, Tamogami J, Unno M. Conformational Analysis of a Retinal Schiff Base Chromophore in Proteorhodopsin by Raman Optical Activity. J Phys Chem Lett 2021; 12:9564-9568. [PMID: 34581580 DOI: 10.1021/acs.jpclett.1c02552] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Raman optical activity (ROA) spectroscopy was used to study the conformation of the retinal Schiff base chromophore in green-light-absorbing proteorhodopsin, which is a globally distributed light-driven proton pump of aquatic bacteria. The ROA spectrum consisted mostly of the negative vibrational bands of the chromophore, while the hydrogen out-of-plane mode (at 960 cm-1) appeared as the sole positive band. This distinct spectral feature was not explained by the twisted structure of the retinal Schiff base but was reproduced by the structural model in which the polyene chain on the β-ionone ring side was bent out-of-plane. The bent chromophore structure potentially couples with proton pumping through the motion of the sixth helix in contact with the β-ionone ring.
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Affiliation(s)
- Tomotsumi Fujisawa
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Kouhei Nishikawa
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Jun Tamogami
- College of Pharmaceutical Sciences, Matsuyama University, Matsuyama, Ehime 790-8578, Japan
| | - Masashi Unno
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
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15
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All-dielectric chiral-field-enhanced Raman optical activity. Nat Commun 2021; 12:3062. [PMID: 34031409 PMCID: PMC8144208 DOI: 10.1038/s41467-021-23364-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 04/20/2021] [Indexed: 11/10/2022] Open
Abstract
Raman optical activity (ROA) is effective for studying the conformational structure and behavior of chiral molecules in aqueous solutions and is advantageous over X-ray crystallography and nuclear magnetic resonance spectroscopy in sample preparation and cost performance. However, ROA signals are inherently minuscule; 3–5 orders of magnitude weaker than spontaneous Raman scattering due to the weak chiral light–matter interaction. Localized surface plasmon resonance on metallic nanoparticles has been employed to enhance ROA signals, but suffers from detrimental spectral artifacts due to its photothermal heat generation and inability to efficiently transfer and enhance optical chirality from the far field to the near field. Here we demonstrate all-dielectric chiral-field-enhanced ROA by devising a silicon nanodisk array and exploiting its dark mode to overcome these limitations. Specifically, we use it with pairs of chemical and biological enantiomers to show >100x enhanced chiral light–molecule interaction with negligible artifacts for ROA measurements. Raman optical activity (ROA) is useful for studying conformational structure and behavior of chiral molecules, but is limited by the weak signals. Here, the authors demonstrate 100x signal enhancement via an all-dielectric approach, using a silicon nanodisk array and exploiting its dark mode.
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16
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Unno M, Hirose Y, Mishima M, Kikukawa T, Fujisawa T, Iwata T, Tamogami J. Spectroscopic approach for exploring structure and function of photoreceptor proteins. Biophys Physicobiol 2021; 18:127-130. [PMID: 34178563 PMCID: PMC8214923 DOI: 10.2142/biophysico.bppb-v18.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 05/11/2021] [Indexed: 12/01/2022] Open
Affiliation(s)
- Masashi Unno
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Yuu Hirose
- Department of Environmental and Life Sciences, Toyohashi University of Technology, Toyohashi, Aichi 441-8580, Japan
| | - Masaki Mishima
- Department of Molecular Biophysics, Tokyo University of Pharmacy and Life Sciences, School of Pharmacy, Hachioji, Tokyo 192-0392, Japan
| | - Takashi Kikukawa
- Faculty of Advanced Life Science and Global Station for Soft Matter, Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Tomotsumi Fujisawa
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Tatsuya Iwata
- Department of Pharmaceutical Sciences, Toho University, Funabashi, Chiba 274-8510, Japan
| | - Jun Tamogami
- College of Pharmaceutical Sciences, Matsuyama University, Matsuyama, Ehime 790-8578, Japan
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17
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Bondanza M, Cupellini L, Faccioli P, Mennucci B. Molecular Mechanisms of Activation in the Orange Carotenoid Protein Revealed by Molecular Dynamics. J Am Chem Soc 2020; 142:21829-21841. [PMID: 33332967 PMCID: PMC7775743 DOI: 10.1021/jacs.0c10461] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Light-harvesting
in photosynthesis is accompanied by photoprotective
processes. In cyanobacteria, the photoprotective role is played by
a specialized complex, the orange carotenoid protein, which is activated
by strong blue-green light. This photoactivation involves a unique
series of structural changes which terminate with an opening of the
complex into two separate domains, one of which acts as a quencher
for the light-harvesting complexes. Many experimental studies have
tried to reveal the molecular mechanisms through which the energy
absorbed by the carotenoid finally leads to the large conformational
change of the complex. Here, for the first time, these mechanisms
are revealed by simulating at the atomistic level the whole dynamics
of the complex through an effective combination of enhanced sampling
techniques. On the basis of our findings, we can conclude that the
carotenoid does not act as a spring that, releasing its internal strain,
induces the dissociation, as was previously proposed, but as a “latch”
locking together the two domains. The photochemically triggered displacement
of the carotenoid breaks this balance, allowing the complex to dissociate.
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Affiliation(s)
- Mattia Bondanza
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Pietro Faccioli
- Physics Department, Trento University, Via Sommarive 14, 38128 Povo, Trento, Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
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18
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Giovannini T, Egidi F, Cappelli C. Theory and algorithms for chiroptical properties and spectroscopies of aqueous systems. Phys Chem Chem Phys 2020; 22:22864-22879. [PMID: 33043930 DOI: 10.1039/d0cp04027d] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Chiroptical properties and spectroscopies are valuable tools to study chiral molecules and assign absolute configurations. The spectra that result from chiroptical measurements may be very rich and complex, and hide much of their information content. For this reason, the interplay between experiments and calculations is especially useful, provided that all relevant physico-chemical interactions that are present in the experimental sample are accurately modelled. The inherent difficulty associated to the calculation of chiral signals of systems in aqueous solutions requires the development of specific tools, able to account for the peculiarities of water-solute interactions, and especially its ability to form hydrogen bonds. In this perspective we discuss a multiscale approach, which we have developed and challenged to model the most used chiroptical techniques.
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Affiliation(s)
- Tommaso Giovannini
- Department of Chemistry, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
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19
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Matsuo J, Kikukawa T, Fujisawa T, Hoff WD, Unno M. "Watching" a Molecular Twist in a Protein by Raman Optical Activity. J Phys Chem Lett 2020; 11:8579-8584. [PMID: 32945678 DOI: 10.1021/acs.jpclett.0c02448] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Light-absorbing chromophores in photoreceptors contain a π-electron system and are intrinsically planar molecules. However, within a protein environment these cofactors often become nonplanar and chiral in a manner that is widely believed to be functionally important. When the same chromophore is out-of-plane distorted in opposite directions in different members of a protein family, such conformers become a set of enantiomers. In techniques using chiral optical spectroscopy such as Raman optical activity (ROA), such proteins are expected to show opposite signs in their spectra. Here we use two microbial rhodopsins, Gloeobacter rhodopsin and sodium ion pump rhodopsin (NaR), to provide the first experimental and theoretical evidence that the twist direction of the retinal chromophore indeed determines the sign of the ROA spectrum. We disrupt the hydrogen bond responsible for the distortion of the retinal in NaR and show that the sign of the ROA signals of this nonfunctional mutant is flipped. The reported ROA spectra are monosignate, a property that has been seen for a variety of photoreceptors, which we attribute to an energetically favorable gradual curvature of the chromophore.
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Affiliation(s)
- Junpei Matsuo
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Takashi Kikukawa
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
- Global Station for Soft Matter, Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo 060-0810, Japan
| | - Tomotsumi Fujisawa
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Wouter D Hoff
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Masashi Unno
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
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20
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Bondanza M, Cupellini L, Lipparini F, Mennucci B. The Multiple Roles of the Protein in the Photoactivation of Orange Carotenoid Protein. Chem 2020. [DOI: 10.1016/j.chempr.2019.10.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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21
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Bogaerts J, Desmet F, Aerts R, Bultinck P, Herrebout W, Johannessen C. A combined Raman optical activity and vibrational circular dichroism study on artemisinin-type products. Phys Chem Chem Phys 2020; 22:18014-18024. [DOI: 10.1039/d0cp03257c] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Artemisinin and two of its derivatives, dihydroartemisinin and artesunate, front line drugs against malaria, were studied using Raman optical activity (ROA), vibrational circular dichroism (VCD) experiments and density functional theory (DFT) calculations.
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Affiliation(s)
| | - Filip Desmet
- Department of Chemistry
- University of Antwerp
- B-2020 Antwerp
- Belgium
| | - Roy Aerts
- Department of Chemistry
- University of Antwerp
- B-2020 Antwerp
- Belgium
| | | | - Wouter Herrebout
- Department of Chemistry
- University of Antwerp
- B-2020 Antwerp
- Belgium
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22
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Dudek M, Machalska E, Oleszkiewicz T, Grzebelus E, Baranski R, Szcześniak P, Mlynarski J, Zajac G, Kaczor A, Baranska M. Chiral Amplification in Nature: Studying Cell‐Extracted Chiral Carotenoid Microcrystals via the Resonance Raman Optical Activity of Model Systems. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201901441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Monika Dudek
- Faculty of ChemistryJagiellonian University Gronostajowa 2 30-387 Cracow Poland
| | - Ewa Machalska
- Faculty of ChemistryJagiellonian University Gronostajowa 2 30-387 Cracow Poland
| | - Tomasz Oleszkiewicz
- Institute of Plant Biology and BiotechnologyFaculty of Biotechnology and HorticultureUniversity of Agriculture in Krakow AL. 29 Listopada 54 31-425 Cracow Poland
| | - Ewa Grzebelus
- Institute of Plant Biology and BiotechnologyFaculty of Biotechnology and HorticultureUniversity of Agriculture in Krakow AL. 29 Listopada 54 31-425 Cracow Poland
| | - Rafal Baranski
- Institute of Plant Biology and BiotechnologyFaculty of Biotechnology and HorticultureUniversity of Agriculture in Krakow AL. 29 Listopada 54 31-425 Cracow Poland
| | - Piotr Szcześniak
- Institute of Organic ChemistryPolish Academy of Sciences Kasprzaka 44/52 01-224 Warsaw Poland
| | - Jacek Mlynarski
- Institute of Organic ChemistryPolish Academy of Sciences Kasprzaka 44/52 01-224 Warsaw Poland
| | - Grzegorz Zajac
- Faculty of ChemistryJagiellonian University Gronostajowa 2 30-387 Cracow Poland
- Jagiellonian Centre for Experimental Therapeutics (JCET)Jagiellonian University Bobrzynskiego 14 30-348 Cracow Poland
| | - Agnieszka Kaczor
- Faculty of ChemistryJagiellonian University Gronostajowa 2 30-387 Cracow Poland
- Jagiellonian Centre for Experimental Therapeutics (JCET)Jagiellonian University Bobrzynskiego 14 30-348 Cracow Poland
| | - Malgorzata Baranska
- Faculty of ChemistryJagiellonian University Gronostajowa 2 30-387 Cracow Poland
- Jagiellonian Centre for Experimental Therapeutics (JCET)Jagiellonian University Bobrzynskiego 14 30-348 Cracow Poland
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23
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Dudek M, Machalska E, Oleszkiewicz T, Grzebelus E, Baranski R, Szcześniak P, Mlynarski J, Zajac G, Kaczor A, Baranska M. Chiral Amplification in Nature: Studying Cell-Extracted Chiral Carotenoid Microcrystals via the Resonance Raman Optical Activity of Model Systems. Angew Chem Int Ed Engl 2019; 58:8383-8388. [PMID: 30974037 DOI: 10.1002/anie.201901441] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 03/21/2019] [Indexed: 12/11/2022]
Abstract
Carotenoid microcrystals, extracted from cells of carrot roots and consisting of 95 % of achiral β-carotene, exhibit a very intense chiroptical (ECD and ROA) signal. The preferential chirality of crystalline aggregates that consist mostly of achiral building blocks is a newly observed phenomenon in nature, and may be related to asymmetric information transfer from the chiral seeds (small amount of α-carotene or lutein) present in carrot cells. To confirm this hypothesis, we synthesized several model aggregates from various achiral and chiral carotenoids. Because of the sergeant-and-soldier behavior, a small number of chiral sergeants (α-carotene or astaxanthin) force the achiral soldier molecules (β- or 11,11'-[D2 ]-β-carotene) to jointly form supramolecular assemblies of induced chirality. The chiral amplification observed in these model systems confirmed that chiral microcrystals appearing in nature might consist predominantly of achiral building blocks and their supramolecular chirality might result from the co-crystallization of chiral and achiral analogues.
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Affiliation(s)
- Monika Dudek
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Cracow, Poland
| | - Ewa Machalska
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Cracow, Poland
| | - Tomasz Oleszkiewicz
- Institute of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, AL. 29 Listopada 54, 31-425, Cracow, Poland
| | - Ewa Grzebelus
- Institute of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, AL. 29 Listopada 54, 31-425, Cracow, Poland
| | - Rafal Baranski
- Institute of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, AL. 29 Listopada 54, 31-425, Cracow, Poland
| | - Piotr Szcześniak
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Jacek Mlynarski
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Grzegorz Zajac
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Cracow, Poland.,Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, 30-348, Cracow, Poland
| | - Agnieszka Kaczor
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Cracow, Poland.,Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, 30-348, Cracow, Poland
| | - Malgorzata Baranska
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Cracow, Poland.,Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, 30-348, Cracow, Poland
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24
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Mezzetti A, Alexandre M, Thurotte A, Wilson A, Gwizdala M, Kirilovsky D. Two-Step Structural Changes in Orange Carotenoid Protein Photoactivation Revealed by Time-Resolved Fourier Transform Infrared Spectroscopy. J Phys Chem B 2019; 123:3259-3266. [DOI: 10.1021/acs.jpcb.9b01242] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Alberto Mezzetti
- Sorbonne Université, CNRS, Laboratoire Réactivité de Surface, UMR CNRS 7197, F-75252 Paris, France
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette, France
| | - Maxime Alexandre
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette, France
- Department of Physics and Astronomy, Faculty of Sciences, VU University, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Adrien Thurotte
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette, France
- Metabolism, Engineering of Microalgal Molecules and Applications (MIMMA) Team, Mer, Molécules, Santé/Sea, Molecules & Health (EA2160), Département de Biologie et Géosciences, Le Mans Université, Avenue Olivier Messiaen, 72085 Le Mans cedex 9, France
| | - Adjelé Wilson
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette, France
| | - Michal Gwizdala
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette, France
- Department of Physics, Faculty of Natural and Agricultural Sciences, University of Pretoria, Private bag X20, 0028 Hatfield, South Africa
- Department of Physics and Astronomy, Faculty of Sciences, VU University, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Diana Kirilovsky
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette, France
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25
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Squires AH, Dahlberg PD, Liu H, Magdaong NCM, Blankenship RE, Moerner WE. Single-molecule trapping and spectroscopy reveals photophysical heterogeneity of phycobilisomes quenched by Orange Carotenoid Protein. Nat Commun 2019; 10:1172. [PMID: 30862823 PMCID: PMC6414729 DOI: 10.1038/s41467-019-09084-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 02/15/2019] [Indexed: 11/09/2022] Open
Abstract
The Orange Carotenoid Protein (OCP) is a cytosolic photosensor that is responsible for non-photochemical quenching (NPQ) of the light-harvesting process in most cyanobacteria. Upon photoactivation by blue-green light, OCP binds to the phycobilisome antenna complex, providing an excitonic trap to thermally dissipate excess energy. At present, both the binding site and NPQ mechanism of OCP are unknown. Using an Anti-Brownian ELectrokinetic (ABEL) trap, we isolate single phycobilisomes in free solution, both in the presence and absence of activated OCP, to directly determine the photophysics and heterogeneity of OCP-quenched phycobilisomes. Surprisingly, we observe two distinct OCP-quenched states, with lifetimes 0.09 ns (6% of unquenched brightness) and 0.21 ns (11% brightness). Photon-by-photon Monte Carlo simulations of exciton transfer through the phycobilisome suggest that the observed quenched states are kinetically consistent with either two or one bound OCPs, respectively, underscoring an additional mechanism for excitation control in this key photosynthetic unit. Upon photoactivation the Orange Carotenoid Protein (OCP) binds to the phycobilisome and prevents damage by thermally dissipating excess energy. Here authors use an Anti-Brownian ELectrokinetic trap to determine the photophysics of single OCP-quenched phycobilisomes and observe two distinct OCP-quenched states with either one or two OCPs bound.
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Affiliation(s)
- Allison H Squires
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Peter D Dahlberg
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Haijun Liu
- Departments of Biology and Chemistry, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Nikki Cecil M Magdaong
- Departments of Biology and Chemistry, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Robert E Blankenship
- Departments of Biology and Chemistry, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - W E Moerner
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA.
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26
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Konold PE, van Stokkum IHM, Muzzopappa F, Wilson A, Groot ML, Kirilovsky D, Kennis JTM. Photoactivation Mechanism, Timing of Protein Secondary Structure Dynamics and Carotenoid Translocation in the Orange Carotenoid Protein. J Am Chem Soc 2019; 141:520-530. [PMID: 30511841 PMCID: PMC6331140 DOI: 10.1021/jacs.8b11373] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Indexed: 01/10/2023]
Abstract
The orange carotenoid protein (OCP) is a two-domain photoactive protein that noncovalently binds an echinenone (ECN) carotenoid and mediates photoprotection in cyanobacteria. In the dark, OCP assumes an orange, inactive state known as OCPO; blue light illumination results in the red active state, known as OCPR. The OCPR state is characterized by large-scale structural changes that involve dissociation and separation of C-terminal and N-terminal domains accompanied by carotenoid translocation into the N-terminal domain. The mechanistic and dynamic-structural relations between photon absorption and formation of the OCPR state have remained largely unknown. Here, we employ a combination of time-resolved UV-visible and (polarized) mid-infrared spectroscopy to assess the electronic and structural dynamics of the carotenoid and the protein secondary structure, from femtoseconds to 0.5 ms. We identify a hereto unidentified carotenoid excited state in OCP, the so-called S* state, which we propose to play a key role in breaking conserved hydrogen-bond interactions between carotenoid and aromatic amino acids in the binding pocket. We arrive at a comprehensive reaction model where the hydrogen-bond rupture with conserved aromatic side chains at the carotenoid β1-ring in picoseconds occurs at a low yield of <1%, whereby the β1-ring retains a trans configuration with respect to the conjugated π-electron chain. This event initiates structural changes at the N-terminal domain in 1 μs, which allow the carotenoid to translocate into the N-terminal domain in 10 μs. We identified infrared signatures of helical elements that dock on the C-terminal domain β-sheet in the dark and unfold in the light to allow domain separation. These helical elements do not move within the experimental range of 0.5 ms, indicating that domain separation occurs on longer time scales, lagging carotenoid translocation by at least 2 decades of time.
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Affiliation(s)
- Patrick E. Konold
- Department of Physics
and Astronomy, Faculty of Sciences, Vrije
Universiteit, De Boelelaan
1081, 1081HV Amsterdam, The Netherlands
| | - Ivo H. M. van Stokkum
- Department of Physics
and Astronomy, Faculty of Sciences, Vrije
Universiteit, De Boelelaan
1081, 1081HV Amsterdam, The Netherlands
| | - Fernando Muzzopappa
- Institute for Integrative Biology of the
Cell (I2BC), CEA, CNRS, Universite Paris-Sud,
Universite Paris-Saclay, 91198 Gif-sur-Yvette, France
- Institut Joliot, Commissariat a l’Energie
Atomique (CEA), 91191 Gif-sur-Yvette, France
| | - Adjélé Wilson
- Institute for Integrative Biology of the
Cell (I2BC), CEA, CNRS, Universite Paris-Sud,
Universite Paris-Saclay, 91198 Gif-sur-Yvette, France
- Institut Joliot, Commissariat a l’Energie
Atomique (CEA), 91191 Gif-sur-Yvette, France
| | - Marie-Louise Groot
- Department of Physics
and Astronomy, Faculty of Sciences, Vrije
Universiteit, De Boelelaan
1081, 1081HV Amsterdam, The Netherlands
| | - Diana Kirilovsky
- Institute for Integrative Biology of the
Cell (I2BC), CEA, CNRS, Universite Paris-Sud,
Universite Paris-Saclay, 91198 Gif-sur-Yvette, France
- Institut Joliot, Commissariat a l’Energie
Atomique (CEA), 91191 Gif-sur-Yvette, France
| | - John T. M. Kennis
- Department of Physics
and Astronomy, Faculty of Sciences, Vrije
Universiteit, De Boelelaan
1081, 1081HV Amsterdam, The Netherlands
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Spectroscopic ruler for measuring active-site distortions based on Raman optical activity of a hydrogen out-of-plane vibration. Proc Natl Acad Sci U S A 2018; 115:8671-8675. [PMID: 30104345 DOI: 10.1073/pnas.1806491115] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Photoactive yellow protein (PYP), from the phototrophic bacterium Halorhodospira halophila, is a small water-soluble photoreceptor protein and contains p-coumaric acid (pCA) as a chromophore. PYP has been an attractive model for studying the physical chemistry of protein active sites. Here, we explore how Raman optical activity (ROA) can be used to extract quantitative information on distortions of the pCA chromophore at the active site in PYP. We use 13C8-pCA to assign an intense signal at 826 cm-1 in the ROA spectrum of PYP to a hydrogen out-of-plane vibration of the ethylenic moiety of the chromophore. Quantum-chemical calculations based on density functional theory demonstrate that the sign of this ROA band reports the direction of the distortion in the dihedral angle about the ethylenic C=C bond, while its amplitude is proportional to the dihedral angle. These results document the ability of ROA to quantify structural deformations of a cofactor molecule embedded in a protein moiety.
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28
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Gurchiek JK, Bao H, Domínguez-Martín MA, McGovern SE, Marquardt CE, Roscioli JD, Ghosh S, Kerfeld CA, Beck WF. Fluorescence and Excited-State Conformational Dynamics of the Orange Carotenoid Protein. J Phys Chem B 2018; 122:1792-1800. [DOI: 10.1021/acs.jpcb.7b09435] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | | | | | | | | | | | - Cheryl A. Kerfeld
- Molecular
Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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29
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The photocycle of orange carotenoid protein conceals distinct intermediates and asynchronous changes in the carotenoid and protein components. Sci Rep 2017; 7:15548. [PMID: 29138423 PMCID: PMC5686206 DOI: 10.1038/s41598-017-15520-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 10/27/2017] [Indexed: 11/30/2022] Open
Abstract
The 35-kDa Orange Carotenoid Protein (OCP) is responsible for photoprotection in cyanobacteria. It acts as a light intensity sensor and efficient quencher of phycobilisome excitation. Photoactivation triggers large-scale conformational rearrangements to convert OCP from the orange OCPO state to the red active signaling state, OCPR, as demonstrated by various structural methods. Such rearrangements imply a complete, yet reversible separation of structural domains and translocation of the carotenoid. Recently, dynamic crystallography of OCPO suggested the existence of photocycle intermediates with small-scale rearrangements that may trigger further transitions. In this study, we took advantage of single 7 ns laser pulses to study carotenoid absorption transients in OCP on the time-scale from 100 ns to 10 s, which allowed us to detect a red intermediate state preceding the red signaling state, OCPR. In addition, time-resolved fluorescence spectroscopy and the assignment of carotenoid-induced quenching of different tryptophan residues derived thereof revealed a novel orange intermediate state, which appears during the relaxation of photoactivated OCPR to OCPO. Our results show asynchronous changes between the carotenoid- and protein-associated kinetic components in a refined mechanistic model of the OCP photocycle, but also introduce new kinetic signatures for future studies of OCP photoactivity and photoprotection.
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