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 protonation site of His(260) in the chromophore-binding pocket such that either the delta-nitrogen (M-HSD) or the epsilon-nitrogen (M-HSE) carried a hydrogen. The optimized structures of the two models display small differences specifically in the orientation of His(260) 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.
Mroginski
Maria Andrea
MA
Technische Universität Berlin, Institut für Chemie, Berlin, Germany. andrea.mroginski@tu-berlin.de
von Stetten
David
D
Escobar
Francisco Velazquez
FV
Strauss
Holger M
HM
Kaminski
Steve
S
Scheerer
Patrick
P
Günther
Mina
M
Murgida
Daniel H
DH
Schmieder
Peter
P
Bongards
Christian
C
Gärtner
Wolfgang
W
Mailliet
Jo
J
Hughes
Jon
J
Essen
Lars-Oliver
LO
Hildebrandt
Peter
P
D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D018360:Crystallography, X-Ray; D008958:Models, Molecular; D020283:Photoreceptors, Microbial; D052980:Phycobilins / Q000737:chemistry / Q000378:metabolism; D010798:Phycocyanin / Q000737:chemistry / Q000378:metabolism; D010834:Phytochrome / Q000737:chemistry* / Q000378:metabolism; D011487:Protein Conformation; D011494:Protein Kinases / Q000737:chemistry* / Q000378:metabolism; D055550:Protein Stability; D011789:Quantum Theory; D012996:Solutions; D013059:Spectrum Analysis, Raman; D046939:Synechocystis
D001426:Bacterial Proteins; D020283:Photoreceptors, Microbial; D052980:Phycobilins; D012996:Solutions; D010798:Phycocyanin; D010834:Phytochrome; C011069:phycocyanobilin; D011494:Protein Kinases; C413623:Cph1 phytochrome protein, bacteria