Structure of the Chromophore Binding Pocket in the Pr State of Plant Phytochrome phyA

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• 作者：Maria Andrea Mroginski ; Steve Kaminski ; David von Stetten ; Simone Ringsdorf ; Wolfgang G盲rtner ; Lars-Oliver Essen ; Peter Hildebrandt
• 刊名：Journal of Physical Chemistry B
• 出版年：2011
• 出版时间：February 10, 2011
• 年：2011
• 卷：115
• 期：5
• 页码：1220-1231
• 全文大小：1209K
• 年卷期：v.115,no.5(February 10, 2011)
• ISSN：1520-5207

文摘

A homology structural model was generated for plant phytochrome phyA utilizing the crystal structure of the sensory module of cyanobacterial phytochrome Cph1 (Cph1螖2). As chromophores, either the native phytochromobilin cofactor (P桅B) or phycocyanobilin (PCB), the natural cofactor in Cph1, was incorporated. These homology models were further optimized by molecular dynamics (MD) simulations revealing a satisfying overall agreement with the crystal structure of Cph1螖2. Notable differences in the P桅B adduct of phyA result from a restructuring of the small helical segment 伪₇ that leads to displacements of a few amino acids away from the cofactor. This repositioning of residues also include aspartate 218 such that, instead of its carbonyl function as in Cph1螖2, an additional water molecule forms hydrogen bonds with the ring B and C NH groups. To validate the phyA structural model in the chromophore binding pocket, Raman spectra of the cofactor were calculated by means of the quantum mechanics/molecular mechanics (QM/MM) hybrid methodology and compared with the experimental resonance Raman (RR) spectra. The satisfactory overall agreement between calculated and experimental spectra is taken as an indication for the good quality of the structural model. Moreover, the methine bridge stretching modes and the effects of isotopic labeling at selected positions of the chromophore are very well reproduced to allow confirming even details of the methine bridge geometry as predicted by the homology model. Specifically, it is demonstrated that the experimental RR spectra are consistent with a torsional angle of ring D with respect to ring C that is distinctly higher for phyA鈭扨CB (45掳) and phyA鈭扨桅B (42掳) than for Cph1螖2 (30掳). Raman spectra calculated from different points of the MD trajectory display variations of the mode frequencies and intensities reflecting the structural fluctuations from snapshot to snapshot. The snapshot spectrum of the lowest energy structure and the sum of all snapshot spectra afford an equally good description of the experimental data. Particularly large variations between the snapshots are noted for the N鈭扝 in-plane bending mode of the pyrrole rings B and C, which reflect alterations of the hydrogen bond interactions brought about by fluctuations of water molecules in the cofactor cavity. This overestimation of the water molecule mobility is a consequence of the deficiency of the current QM/MM methodology that, due to the lack of appropriate protein force fields, cannot adequately account for the electrostatics in the cofactor pocket.