Molecular dynamics simulations of the chromophore binding site of Deinococcus radiodurans bacteriophytochrome using new force field parameters for the phytochromobilin chromophore

The Journal of Physical Chemistry. B
Steve KaminskiMaria Andrea Mroginski

Abstract

The conformational flexibility of the tetrapyrrolic phytochromobilin (PPhiB) chromophore of the bacteriophytochrome Deinococcus radiodurans (DrCBD) in the Pr state has been investigated by molecular dynamics simulations. Because these simulations require accurate force field parameters for the prosthetic group, in the present work we developed new empirical force field parameters for the PPhiB molecule that are compatible with the CHARMM22 force field for proteins. For this reason, the new force field parameters for the nonbonded (partial atomic charges) and bonded (bonds, angles, dihedrals, improper) energy terms were derived by reproducing ab initio target data following the methodology used in the development of the CHARMM22 force field. This new set of parameters was employed to analyze structural and dynamical features of PPhiB inside DrCBD. The 45 ns all-atom molecular dynamics (MD) simulation reveals the existence of two stable conformational states of the chromophore characterized by distinct torsional angles around the C-C bond at the methine bridge connecting rings A and B of the tetrapyrrole. This result supports experimental observations derived from NMR and resonance Raman spectroscopy. Furthermore, statistical ana...Continue Reading

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Citations

Nov 5, 2010·The Journal of Physical Chemistry. B·Alex A SammaMarc Zimmer
Sep 30, 2016·Structural Dynamics·Heikki TakalaSebastian Westenhoff
May 14, 2017·Photochemistry and Photobiology·Aref TakidenMaria Andrea Mroginski
May 18, 2017·Physical Chemistry Chemical Physics : PCCP·Laura Katharina Scarbath-EversDaniel Sebastiani
May 19, 2017·Journal of the American Chemical Society·Mi Kyung LeeDavid F Coker
May 7, 2019·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Christian Wiebeler, Igor Schapiro
Jan 22, 2011·Critical Reviews in Biochemistry and Molecular Biology·Michele E Auldridge, Katrina T Forest
May 15, 2015·The Journal of Biological Chemistry·Heikki TakalaJanne A Ihalainen
Jan 6, 2021·Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy·Sean R TachibanaChong Fang
Jun 23, 2012·The Journal of Physical Chemistry. B·Lucy H FreerDelmar S Larsen
Feb 18, 2015·Journal of Chemical Theory and Computation·Alexander BjörlingSebastian Westenhoff
Dec 18, 2013·Biochemistry·Francisco Velazquez EscobarPeter Hildebrandt
Dec 4, 2010·The Journal of Physical Chemistry. B·Steve Kaminski, Maria Andrea Mroginski
Nov 2, 2019·The Journal of Physical Chemistry. B·Ronald González, Maria A Mroginski

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