Structural and Vibrational Characterization of the Chromophore Binding Site of Bacterial Phytochrome Agp1

Photochemistry and Photobiology
Aref TakidenMaria Andrea Mroginski

Abstract

Agp1 is a prototypical bacterial phytochrome from Agrobacterium fabrum harboring a biliverdin cofactor which reversibly photoconverts between a red-light-absorbing (Pr) and a far-red-light-absorbing (Pfr) states. The reaction mechanism involves the isomerization of the bilin-chromophore followed by large structural changes of the protein matrix that are coupled to protonation dynamics at the chromophore binding site. Histidines His250 and His280 participate in this process. Although the three-dimensional structure of Agp1 has been solved at high resolution, the precise position of hydrogen atoms and protonation pattern in the chromophore binding pocket has not been investigated yet. Here, we present protonated structure models of Agp1 in the Pr state involving appropriately placed hydrogen atoms that were generated by hybrid quantum mechanics/molecular mechanics- and electrostatic calculations and validated against experimental structural- and spectroscopic data. Although the effect of histidine protonation on the vibrational spectra is weak, our results favor charge neutral H250 and H280 both protonated at Nε. However, a neutral H250 with a proton at Nε and a cationic H280 may also be possible. Furthermore, the present QM/MM c...Continue Reading

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Citations

Mar 16, 2018·Chembiochem : a European Journal of Chemical Biology·Uzma ChoudryNigel S Scrutton
May 7, 2019·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Christian Wiebeler, Igor Schapiro
Dec 29, 2020·Photochemistry and Photobiology·Maria-Andrea MroginskiIgor Schapiro
Mar 4, 2021·Physical Chemistry Chemical Physics : PCCP·Moona KurttilaJanne A Ihalainen
Feb 26, 2021·Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy·Faez Iqbal KhanFeng Juan
Apr 25, 2020·The Journal of Physical Chemistry. B·Francisco Velazquez EscobarPeter Hildebrandt
Jul 28, 2019·Biochemistry·Maria Fernandez LopezPeter Hildebrandt
Nov 2, 2019·The Journal of Physical Chemistry. B·Ronald González, Maria A Mroginski
Nov 30, 2021·The Journal of Physical Chemistry. B·Anastasia KraskovPeter Hildebrandt

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