Chromophore Structure of Cyanobacterial Phytochrome Cph1 in the Pr State: Reconciling Structural and Spectroscopic Data by QM/MM Calculations |
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Authors: | Maria Andrea Mroginski David von Stetten Holger M Strauss Patrick Scheerer Daniel H Murgida Christian Bongards Jo Mailliet Lars-Oliver Essen |
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Institution: | † Technische Universität Berlin, Institut für Chemie, Berlin, Germany ‡ Leibniz-Institut für Molekulare Pharmakologie, Berlin, Germany § Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Berlin, Germany ¶ INQUIMAE, Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina ‖ Max-Planck-Institut für Bioanorganische Chemie, Mülheim, Germany ∗∗ Plant Physiology, Justus-Liebig University Gießen, Giessen, Germany †† Structural Biochemistry, Department of Chemistry, Philipps University Marburg, Marburg, Germany |
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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 ?-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.Abbreviations: Agp1, phytochrome from Agrobacterium tumefaciens; α-CPC, α-subunit of C-phycocyanin; BV, biliverdin IXα; B3LYP, three-parameter exchange functional according to Becke, Lee, Yang, and Parr; DFT, density functional theory; DrBphP, phytochrome from Deinococcus radiodurans; GAF, domain found in cGMP-specific phosphodiesterases; MM, molecular mechanics; MD, molecular dynamics; N-H ip, N-H in-plane bending; PCB, phycocyanobilin; PED, potential energy distribution; phyA, plant phytochrome; Pr, Pfr, red- and far-red absorbing parent states of phytochrome; PΦB, phytochromobilin; QM, quantum mechanics; RMSD, root mean-square deviation; RR, resonance Raman |
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Keywords: | Agp1 phytochrome from Agrobacterium tumefaciens α-CPC α-subunit of C-phycocyanin BV biliverdin IXα B3LYP three-parameter exchange functional according to Becke Lee Yang and Parr DFT density functional theory DrBphP phytochrome from Deinococcus radiodurans GAF domain found in cGMP-specific phosphodiesterases MM molecular mechanics MD molecular dynamics N-H ip N-H in-plane bending PCB phycocyanobilin PED potential energy distribution phyA plant phytochrome Pr Pfr red- and far-red absorbing parent states of phytochrome PΦB phytochromobilin QM quantum mechanics RMSD root mean-square deviation RR resonance Raman |
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