Chromophore structure of cyanobacterial phytochrome Cph1 in the Pr state: Reconciling structural and spectroscopic data by QM/MM calculations
A quantum mechanics (QM)/molecular mechanics (MM) hybrid method was applied to the Pr state of the cyanobacterial phytochrome Cph1 to calculate the Raman spectra of the bound PCB cofactor. Two QM/MM models were derived from the atomic coordinates of the crystal structure. The models differed in the...
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2009
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| Acceso en línea: | https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_00063495_v96_n10_p4153_Mroginski http://hdl.handle.net/20.500.12110/paper_00063495_v96_n10_p4153_Mroginski |
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paper:paper_00063495_v96_n10_p4153_Mroginski2023-06-08T14:31:18Z Chromophore structure of cyanobacterial phytochrome Cph1 in the Pr state: Reconciling structural and spectroscopic data by QM/MM calculations chemical compound histidine hydrogen nitrogen phycocyanobilin phytochrome phytochrome Cph1 praseodymium protein unclassified drug bacterial protein Cph1 phytochrome protein, bacteria phycobilin phycocyanin protein kinase article binding site calculation chromatophore comparative study controlled study crystal structure cyanobacterium experimental study geometry hydrogen bond model molecular mechanics nonhuman protein interaction proton transport quantum mechanics Raman spectrometry chemical structure chemistry metabolism protein conformation protein stability quantum theory Raman spectrometry solution and solubility Synechocystis X ray crystallography Cyanobacteria Bacterial Proteins Crystallography, X-Ray Models, Molecular Phycobilins Phycocyanin Phytochrome Protein Conformation Protein Kinases Protein Stability Quantum Theory Solutions Spectrum Analysis, Raman Synechocystis A quantum mechanics (QM)/molecular mechanics (MM) hybrid method was applied to the Pr state of the cyanobacterial phytochrome Cph1 to calculate the Raman spectra of the bound PCB cofactor. Two QM/MM models were derived from the atomic coordinates of the crystal structure. The models differed in the protonation site of His260 in the chromophore-binding pocket such that either the δ-nitrogen (M-HSD) or the ε-nitrogen (M-HSE) carried a hydrogen. The optimized structures of the two models display small differences specifically in the orientation of His260 with respect to the PCB cofactor and the hydrogen bond network at the cofactor-binding site. For both models, the calculated Raman spectra of the cofactor reveal a good overall agreement with the experimental resonance Raman (RR) spectra obtained from Cph1 in the crystalline state and in solution, including Cph1 adducts with isotopically labeled PCB. However, a distinctly better reproduction of important details in the experimental spectra is provided by the M-HSD model, which therefore may represent an improved structure of the cofactor site. Thus, QM/MM calculations of chromoproteins may allow for refining crystal structure models in the chromophore-binding pocket guided by the comparison with experimental RR spectra. Analysis of the calculated and experimental spectra also allowed us to identify and assign the modes that sensitively respond to chromophore-protein interactions. The most pronounced effect was noted for the stretching mode of the methine bridge A-B adjacent to the covalent attachment site of PCB. Due a distinct narrowing of the A-B methine bridge bond angle, this mode undergoes a large frequency upshift as compared with the spectrum obtained by QM calculations for the chromophore in vacuo. This protein-induced distortion of the PCB geometry is the main origin of a previous erroneous interpretation of the RR spectra based on QM calculations of the isolated cofactor. © 2009 by the Biophysical Society. 2009 https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_00063495_v96_n10_p4153_Mroginski http://hdl.handle.net/20.500.12110/paper_00063495_v96_n10_p4153_Mroginski |
| institution |
Universidad de Buenos Aires |
| institution_str |
I-28 |
| repository_str |
R-134 |
| collection |
Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) |
| topic |
chemical compound histidine hydrogen nitrogen phycocyanobilin phytochrome phytochrome Cph1 praseodymium protein unclassified drug bacterial protein Cph1 phytochrome protein, bacteria phycobilin phycocyanin protein kinase article binding site calculation chromatophore comparative study controlled study crystal structure cyanobacterium experimental study geometry hydrogen bond model molecular mechanics nonhuman protein interaction proton transport quantum mechanics Raman spectrometry chemical structure chemistry metabolism protein conformation protein stability quantum theory Raman spectrometry solution and solubility Synechocystis X ray crystallography Cyanobacteria Bacterial Proteins Crystallography, X-Ray Models, Molecular Phycobilins Phycocyanin Phytochrome Protein Conformation Protein Kinases Protein Stability Quantum Theory Solutions Spectrum Analysis, Raman Synechocystis |
| spellingShingle |
chemical compound histidine hydrogen nitrogen phycocyanobilin phytochrome phytochrome Cph1 praseodymium protein unclassified drug bacterial protein Cph1 phytochrome protein, bacteria phycobilin phycocyanin protein kinase article binding site calculation chromatophore comparative study controlled study crystal structure cyanobacterium experimental study geometry hydrogen bond model molecular mechanics nonhuman protein interaction proton transport quantum mechanics Raman spectrometry chemical structure chemistry metabolism protein conformation protein stability quantum theory Raman spectrometry solution and solubility Synechocystis X ray crystallography Cyanobacteria Bacterial Proteins Crystallography, X-Ray Models, Molecular Phycobilins Phycocyanin Phytochrome Protein Conformation Protein Kinases Protein Stability Quantum Theory Solutions Spectrum Analysis, Raman Synechocystis Chromophore structure of cyanobacterial phytochrome Cph1 in the Pr state: Reconciling structural and spectroscopic data by QM/MM calculations |
| topic_facet |
chemical compound histidine hydrogen nitrogen phycocyanobilin phytochrome phytochrome Cph1 praseodymium protein unclassified drug bacterial protein Cph1 phytochrome protein, bacteria phycobilin phycocyanin protein kinase article binding site calculation chromatophore comparative study controlled study crystal structure cyanobacterium experimental study geometry hydrogen bond model molecular mechanics nonhuman protein interaction proton transport quantum mechanics Raman spectrometry chemical structure chemistry metabolism protein conformation protein stability quantum theory Raman spectrometry solution and solubility Synechocystis X ray crystallography Cyanobacteria Bacterial Proteins Crystallography, X-Ray Models, Molecular Phycobilins Phycocyanin Phytochrome Protein Conformation Protein Kinases Protein Stability Quantum Theory Solutions Spectrum Analysis, Raman Synechocystis |
| description |
A quantum mechanics (QM)/molecular mechanics (MM) hybrid method was applied to the Pr state of the cyanobacterial phytochrome Cph1 to calculate the Raman spectra of the bound PCB cofactor. Two QM/MM models were derived from the atomic coordinates of the crystal structure. The models differed in the protonation site of His260 in the chromophore-binding pocket such that either the δ-nitrogen (M-HSD) or the ε-nitrogen (M-HSE) carried a hydrogen. The optimized structures of the two models display small differences specifically in the orientation of His260 with respect to the PCB cofactor and the hydrogen bond network at the cofactor-binding site. For both models, the calculated Raman spectra of the cofactor reveal a good overall agreement with the experimental resonance Raman (RR) spectra obtained from Cph1 in the crystalline state and in solution, including Cph1 adducts with isotopically labeled PCB. However, a distinctly better reproduction of important details in the experimental spectra is provided by the M-HSD model, which therefore may represent an improved structure of the cofactor site. Thus, QM/MM calculations of chromoproteins may allow for refining crystal structure models in the chromophore-binding pocket guided by the comparison with experimental RR spectra. Analysis of the calculated and experimental spectra also allowed us to identify and assign the modes that sensitively respond to chromophore-protein interactions. The most pronounced effect was noted for the stretching mode of the methine bridge A-B adjacent to the covalent attachment site of PCB. Due a distinct narrowing of the A-B methine bridge bond angle, this mode undergoes a large frequency upshift as compared with the spectrum obtained by QM calculations for the chromophore in vacuo. This protein-induced distortion of the PCB geometry is the main origin of a previous erroneous interpretation of the RR spectra based on QM calculations of the isolated cofactor. © 2009 by the Biophysical Society. |
| title |
Chromophore structure of cyanobacterial phytochrome Cph1 in the Pr state: Reconciling structural and spectroscopic data by QM/MM calculations |
| title_short |
Chromophore structure of cyanobacterial phytochrome Cph1 in the Pr state: Reconciling structural and spectroscopic data by QM/MM calculations |
| title_full |
Chromophore structure of cyanobacterial phytochrome Cph1 in the Pr state: Reconciling structural and spectroscopic data by QM/MM calculations |
| title_fullStr |
Chromophore structure of cyanobacterial phytochrome Cph1 in the Pr state: Reconciling structural and spectroscopic data by QM/MM calculations |
| title_full_unstemmed |
Chromophore structure of cyanobacterial phytochrome Cph1 in the Pr state: Reconciling structural and spectroscopic data by QM/MM calculations |
| title_sort |
chromophore structure of cyanobacterial phytochrome cph1 in the pr state: reconciling structural and spectroscopic data by qm/mm calculations |
| publishDate |
2009 |
| url |
https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_00063495_v96_n10_p4153_Mroginski http://hdl.handle.net/20.500.12110/paper_00063495_v96_n10_p4153_Mroginski |
| _version_ |
1768544253322985472 |