Raman Spectroscopy of an Atypical C15‑E,syn Bilin Chromophore in Cyanobacteriochrome RcaE
Cyanobacteriochromes (CBCRs) belong to the phytochrome superfamily of photoreceptors, the members of which utilize a linear tetrapyrrole (bilin) as a chromophore. RcaE is a representative member of a green/red-type CBCR subfamily that photoconverts between a green-absorbing dark state and red-absorb...
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| Published in | The journal of physical chemistry. B Vol. 126; no. 4; pp. 813 - 821 |
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| Main Authors | , , , , , , , , |
| Format | Journal Article |
| Language | English |
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United States
American Chemical Society
03.02.2022
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| Abstract | Cyanobacteriochromes (CBCRs) belong to the phytochrome superfamily of photoreceptors, the members of which utilize a linear tetrapyrrole (bilin) as a chromophore. RcaE is a representative member of a green/red-type CBCR subfamily that photoconverts between a green-absorbing dark state and red-absorbing photoproduct (Pr). Our recent crystallographic study showed that the phycocyanobilin (PCB) chromophore of RcaE adopts a unique C15-E,syn configuration in the Pr state, unlike the typical C15-E,anti configuration for the phytochromes and other CBCRs. Here, we measured Raman spectra of the Pr state of RcaE with 1064 nm excitation and explored the structure of PCB and its interacting residues under physiologically relevant aqueous conditions. We also performed measurements of RcaE in D2O as well as the sample reconstituted with the PCB labeled with 15N or with both 13C and 15N. The observed Raman spectra were analyzed by quantum mechanics/molecular mechanics (QM/MM) calculations together with molecular dynamics simulations. The Raman spectra and their isotope effects were well-reproduced by the simulated spectra of fully protonated PCB with the C15-E,syn configuration and allowed us to assign most of the observed bands. The present vibrational analysis of the all syn bilin chromophore using the QM/MM method will advance future studies on CBCRs and the related proteins by vibrational spectroscopy. |
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| AbstractList | Cyanobacteriochromes (CBCRs) belong to the phytochrome superfamily of photoreceptors, the members of which utilize a linear tetrapyrrole (bilin) as a chromophore. RcaE is a representative member of a green/red-type CBCR subfamily that photoconverts between a green-absorbing dark state and red-absorbing photoproduct (Pr). Our recent crystallographic study showed that the phycocyanobilin (PCB) chromophore of RcaE adopts a unique C15-E,syn configuration in the Pr state, unlike the typical C15-E,anti configuration for the phytochromes and other CBCRs. Here, we measured Raman spectra of the Pr state of RcaE with 1064 nm excitation and explored the structure of PCB and its interacting residues under physiologically relevant aqueous conditions. We also performed measurements of RcaE in D2O as well as the sample reconstituted with the PCB labeled with 15N or with both 13C and 15N. The observed Raman spectra were analyzed by quantum mechanics/molecular mechanics (QM/MM) calculations together with molecular dynamics simulations. The Raman spectra and their isotope effects were well-reproduced by the simulated spectra of fully protonated PCB with the C15-E,syn configuration and allowed us to assign most of the observed bands. The present vibrational analysis of the all syn bilin chromophore using the QM/MM method will advance future studies on CBCRs and the related proteins by vibrational spectroscopy.Cyanobacteriochromes (CBCRs) belong to the phytochrome superfamily of photoreceptors, the members of which utilize a linear tetrapyrrole (bilin) as a chromophore. RcaE is a representative member of a green/red-type CBCR subfamily that photoconverts between a green-absorbing dark state and red-absorbing photoproduct (Pr). Our recent crystallographic study showed that the phycocyanobilin (PCB) chromophore of RcaE adopts a unique C15-E,syn configuration in the Pr state, unlike the typical C15-E,anti configuration for the phytochromes and other CBCRs. Here, we measured Raman spectra of the Pr state of RcaE with 1064 nm excitation and explored the structure of PCB and its interacting residues under physiologically relevant aqueous conditions. We also performed measurements of RcaE in D2O as well as the sample reconstituted with the PCB labeled with 15N or with both 13C and 15N. The observed Raman spectra were analyzed by quantum mechanics/molecular mechanics (QM/MM) calculations together with molecular dynamics simulations. The Raman spectra and their isotope effects were well-reproduced by the simulated spectra of fully protonated PCB with the C15-E,syn configuration and allowed us to assign most of the observed bands. The present vibrational analysis of the all syn bilin chromophore using the QM/MM method will advance future studies on CBCRs and the related proteins by vibrational spectroscopy. Cyanobacteriochromes (CBCRs) belong to the phytochrome superfamily of photoreceptors, the members of which utilize a linear tetrapyrrole (bilin) as a chromophore. RcaE is a representative member of a green/red-type CBCR subfamily that photoconverts between a green-absorbing dark state and red-absorbing photoproduct (Pr). Our recent crystallographic study showed that the phycocyanobilin (PCB) chromophore of RcaE adopts a unique C15-E,syn configuration in the Pr state, unlike the typical C15-E,anti configuration for the phytochromes and other CBCRs. Here, we measured Raman spectra of the Pr state of RcaE with 1064 nm excitation and explored the structure of PCB and its interacting residues under physiologically relevant aqueous conditions. We also performed measurements of RcaE in D2O as well as the sample reconstituted with the PCB labeled with 15N or with both 13C and 15N. The observed Raman spectra were analyzed by quantum mechanics/molecular mechanics (QM/MM) calculations together with molecular dynamics simulations. The Raman spectra and their isotope effects were well-reproduced by the simulated spectra of fully protonated PCB with the C15-E,syn configuration and allowed us to assign most of the observed bands. The present vibrational analysis of the all syn bilin chromophore using the QM/MM method will advance future studies on CBCRs and the related proteins by vibrational spectroscopy. Cyanobacteriochromes (CBCRs) belong to the phytochrome superfamily of photoreceptors, the members of which utilize a linear tetrapyrrole (bilin) as a chromophore. RcaE is a representative member of a green/red-type CBCR subfamily that photoconverts between a green-absorbing dark state and red-absorbing photoproduct (Pr). Our recent crystallographic study showed that the phycocyanobilin (PCB) chromophore of RcaE adopts a unique C15- , configuration in the Pr state, unlike the typical C15- , configuration for the phytochromes and other CBCRs. Here, we measured Raman spectra of the Pr state of RcaE with 1064 nm excitation and explored the structure of PCB and its interacting residues under physiologically relevant aqueous conditions. We also performed measurements of RcaE in D O as well as the sample reconstituted with the PCB labeled with N or with both C and N. The observed Raman spectra were analyzed by quantum mechanics/molecular mechanics (QM/MM) calculations together with molecular dynamics simulations. The Raman spectra and their isotope effects were well-reproduced by the simulated spectra of fully protonated PCB with the C15- , configuration and allowed us to assign most of the observed bands. The present vibrational analysis of the all bilin chromophore using the QM/MM method will advance future studies on CBCRs and the related proteins by vibrational spectroscopy. Cyanobacteriochromes (CBCRs) belong to the phytochrome superfamily of photoreceptors, the members of which utilize a linear tetrapyrrole (bilin) as a chromophore. RcaE is a representative member of a green/red-type CBCR subfamily that photoconverts between a green-absorbing dark state and red-absorbing photoproduct (Pr). Our recent crystallographic study showed that the phycocyanobilin (PCB) chromophore of RcaE adopts a unique C15-E,syn configuration in the Pr state, unlike the typical C15-E,anti configuration for the phytochromes and other CBCRs. Here, we measured Raman spectra of the Pr state of RcaE with 1064 nm excitation and explored the structure of PCB and its interacting residues under physiologically relevant aqueous conditions. We also performed measurements of RcaE in D₂O as well as the sample reconstituted with the PCB labeled with ¹⁵N or with both ¹³C and ¹⁵N. The observed Raman spectra were analyzed by quantum mechanics/molecular mechanics (QM/MM) calculations together with molecular dynamics simulations. The Raman spectra and their isotope effects were well-reproduced by the simulated spectra of fully protonated PCB with the C15-E,syn configuration and allowed us to assign most of the observed bands. The present vibrational analysis of the all syn bilin chromophore using the QM/MM method will advance future studies on CBCRs and the related proteins by vibrational spectroscopy. |
| Author | Kamo, Takanari Unno, Masashi Nagae, Takayuki Okuda, Yuji Fujisawa, Tomotsumi Miyoshi, Risako Hirose, Yuu Mishima, Masaki Eki, Toshihiko |
| AuthorAffiliation | Department of Applied Chemistry and Life Science Tokyo University of Pharmacy and Life Sciences Synchrotron Radiation Research Center Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering Department of Molecular Biophysics, School of Pharmacy |
| AuthorAffiliation_xml | – name: Synchrotron Radiation Research Center – name: Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering – name: Department of Applied Chemistry and Life Science – name: Department of Molecular Biophysics, School of Pharmacy – name: Tokyo University of Pharmacy and Life Sciences |
| Author_xml | – sequence: 1 givenname: Yuji surname: Okuda fullname: Okuda, Yuji organization: Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering – sequence: 2 givenname: Risako surname: Miyoshi fullname: Miyoshi, Risako organization: Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering – sequence: 3 givenname: Takanari surname: Kamo fullname: Kamo, Takanari organization: Department of Applied Chemistry and Life Science – sequence: 4 givenname: Tomotsumi orcidid: 0000-0002-3282-6814 surname: Fujisawa fullname: Fujisawa, Tomotsumi organization: Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering – sequence: 5 givenname: Takayuki surname: Nagae fullname: Nagae, Takayuki organization: Synchrotron Radiation Research Center – sequence: 6 givenname: Masaki surname: Mishima fullname: Mishima, Masaki organization: Tokyo University of Pharmacy and Life Sciences – sequence: 7 givenname: Toshihiko surname: Eki fullname: Eki, Toshihiko organization: Department of Applied Chemistry and Life Science – sequence: 8 givenname: Yuu surname: Hirose fullname: Hirose, Yuu email: hirose@chem.tut.ac.jp organization: Department of Applied Chemistry and Life Science – sequence: 9 givenname: Masashi orcidid: 0000-0002-5016-6274 surname: Unno fullname: Unno, Masashi email: unno@cc.saga-u.ac.jp organization: Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering |
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| CitedBy_id | crossref_primary_10_1016_j_tetlet_2023_154570 crossref_primary_10_1126_sciadv_adn8386 crossref_primary_10_1021_acs_jpcb_5c00744 crossref_primary_10_3390_biom13061007 crossref_primary_10_1021_acs_jpcb_3c04983 crossref_primary_10_1016_j_bpj_2024_08_001 crossref_primary_10_1093_pcp_pcae085 |
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| Snippet | Cyanobacteriochromes (CBCRs) belong to the phytochrome superfamily of photoreceptors, the members of which utilize a linear tetrapyrrole (bilin) as a... |
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| SubjectTerms | B: Biophysical and Biochemical Systems and Processes Bacterial Proteins - chemistry Bile Pigments - chemistry molecular dynamics Molecular Dynamics Simulation Photoreceptors, Microbial - chemistry phytochrome Phytochrome - chemistry quantum mechanics Raman spectroscopy Spectrum Analysis, Raman |
| Title | Raman Spectroscopy of an Atypical C15‑E,syn Bilin Chromophore in Cyanobacteriochrome RcaE |
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