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Mroginski, M.A.; Von Stetten, D.; Escobar, F.V.; Strauss, H.M.; Kaminski, S.; Scheerer, P.; Günther, M.; Murgida, D.H.; Schmieder, P.; Bongards, C.; Gärtner, W.; Mailliet, J.; Hughes, J.; Essen, L.-O.; Hildebrandt, P. "Chromophore structure of cyanobacterial phytochrome Cph1 in the Pr state: Reconciling structural and spectroscopic data by QM/MM calculations" (2009) Biophysical Journal. 96(10):4153-4163
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Abstract:

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.

Registro:

Documento: Artículo
Título:Chromophore structure of cyanobacterial phytochrome Cph1 in the Pr state: Reconciling structural and spectroscopic data by QM/MM calculations
Autor:Mroginski, M.A.; Von Stetten, D.; Escobar, F.V.; Strauss, H.M.; Kaminski, S.; Scheerer, P.; Günther, M.; Murgida, D.H.; Schmieder, P.; Bongards, C.; Gärtner, W.; Mailliet, J.; Hughes, J.; Essen, L.-O.; Hildebrandt, P.
Filiación:Technische Universität Berlin, Institut für Chemie, Charité-Universitätsmedizin Berlin, Berlin, Germany
Leibniz-Institut für Molekulare Pharmakologie, Charité-Universitätsmedizin Berlin, Berlin, Germany
Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Berlin, Germany
INQUIMAE, Departamento de Química Inorgá Nica, Analítica Y Química Física, Universidad de Buenos Aires, Buenos Aires, Argentina
Max-Planck-Institut für Bioanorganische Chemie, Mülheim, Germany
Structural Biochemistry, Department of Chemistry, Philipps University Marburg, Marburg, Germany
Nanolytics GmbH, Potsdam, Germany
Palabras clave: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
Año:2009
Volumen:96
Número:10
Página de inicio:4153
Página de fin:4163
DOI: http://dx.doi.org/10.1016/j.bpj.2009.02.029
Título revista:Biophysical Journal
Título revista abreviado:Biophys. J.
ISSN:00063495
CODEN:BIOJA
CAS:histidine, 645-35-2, 7006-35-1, 71-00-1; hydrogen, 12385-13-6, 1333-74-0; nitrogen, 7727-37-9; phytochrome, 117102-58-6; praseodymium, 7440-10-0; protein, 67254-75-5; protein kinase, 9026-43-1; Bacterial Proteins; Cph1 phytochrome protein, bacteria, 2.7.3.-; Phycobilins; Phycocyanin, 11016-15-2; Phytochrome, 11121-56-5; Protein Kinases, 2.7.1.37; Solutions; phycocyanobilin, 20298-86-6
Registro:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_00063495_v96_n10_p4153_Mroginski

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Citas:

---------- APA ----------
Mroginski, M.A., Von Stetten, D., Escobar, F.V., Strauss, H.M., Kaminski, S., Scheerer, P., Günther, M.,..., Hildebrandt, P. (2009) . Chromophore structure of cyanobacterial phytochrome Cph1 in the Pr state: Reconciling structural and spectroscopic data by QM/MM calculations. Biophysical Journal, 96(10), 4153-4163.
http://dx.doi.org/10.1016/j.bpj.2009.02.029
---------- CHICAGO ----------
Mroginski, M.A., Von Stetten, D., Escobar, F.V., Strauss, H.M., Kaminski, S., Scheerer, P., et al. "Chromophore structure of cyanobacterial phytochrome Cph1 in the Pr state: Reconciling structural and spectroscopic data by QM/MM calculations" . Biophysical Journal 96, no. 10 (2009) : 4153-4163.
http://dx.doi.org/10.1016/j.bpj.2009.02.029
---------- MLA ----------
Mroginski, M.A., Von Stetten, D., Escobar, F.V., Strauss, H.M., Kaminski, S., Scheerer, P., et al. "Chromophore structure of cyanobacterial phytochrome Cph1 in the Pr state: Reconciling structural and spectroscopic data by QM/MM calculations" . Biophysical Journal, vol. 96, no. 10, 2009, pp. 4153-4163.
http://dx.doi.org/10.1016/j.bpj.2009.02.029
---------- VANCOUVER ----------
Mroginski, M.A., Von Stetten, D., Escobar, F.V., Strauss, H.M., Kaminski, S., Scheerer, P., et al. Chromophore structure of cyanobacterial phytochrome Cph1 in the Pr state: Reconciling structural and spectroscopic data by QM/MM calculations. Biophys. J. 2009;96(10):4153-4163.
http://dx.doi.org/10.1016/j.bpj.2009.02.029