Structure of the biliverdin cofactor in the Pfr state of bathy and prototypical phytochromes.

Phytochromes act as photoswitches between the red- and far-red absorbing parent states of phytochromes (Pr and Pfr). Plant phytochromes display an additional thermal conversion route from the physiologically active Pfr to Pr. The same reaction pattern is found in prototypical biliverdin-binding bacteriophytochromes in contrast to the reverse thermal transformation in bathy bacteriophytochromes.

Improved electronic properties from third-order SCC-DFTB with cost efficient post-SCF extensions.

The present work outlines the implementation and performance of two cost efficient post-SCF extensions into the third-order SCC-DFTB code. The first one, the charge model 3 (CM3), corrects for errors in bond dipoles for an improved description of molecular charge distribution as compared to the standard Mulliken partitioning scheme. The second one focuses on the response of the charge density, that is, the electronic molecular polarizability, described inaccurately from SCC-DFTB due to the usage of a minimal atomic orbital basis.

Extended polarization in third-order SCC-DFTB from chemical-potential equalization.

In this work, we augment the approximate density functional method SCC-DFTB (DFTB3) with the chemical-potential equalization (CPE) approach in order to improve the performance for molecular electronic polarizabilities. The CPE method, originally implemented for the NDDO type of methods by Giese and York, has been shown to significantly emend minimal basis methods with respect to the response properties and has been applied to SCC-DFTB recently. CPE allows this inherent limitation of minimal basis methods to be overcome by supplying an additional response density.

Structure of the chromophore binding pocket in the Pr state of plant phytochrome phyA.

A homology structural model was generated for plant phytochrome phyA utilizing the crystal structure of the sensory module of cyanobacterial phytochrome Cph1 (Cph1Δ2). As chromophores, either the native phytochromobilin cofactor (PΦB) 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 Cph1Δ2.

Molecular dynamics of phycocyanobilin binding bacteriophytochromes: a detailed study of structural and dynamic properties.

The structural stability and conformational flexibility of two phycocyanobilin (PCB) binding bacteriaphytochromes, namely, Cph1 from Synechocystis and the GAF domain of SyB from Synechococcus, were studied using all-atoms molecular dynamics simulations techniques. In order to involve the tetrapyrrole cofactor in the simulation, new empirical force field parameters were developed for PCB which are compatible with the CHARMM22 force field for proteins. Special emphasis was made in understanding the conflicting NMR-based structures recently obtained for the two parent states, Pr and Pfr, of SyB(GAF) regarding the highly distorted cofactor conformation which is in contrast to all crystallographic measurements on other phytochrome species.

Raman spectra of the phycoviolobilin cofactor in phycoerythrocyanin calculated by QM/MM methods.

The Raman spectrum of the phycoviolobilin cofactor of the alpha-subunit of phycoerythrocyanin was computed using a hybrid quantum mechanical/molecular mechanics (QM/MM) method in order to evaluate the performance of the QM/MM approach for calculating the vibrational spectra of protein-bound tetrapyrroles as found in phytochrome photoreceptors. A good overall agreement between the experimental and the calculated spectra was achieved. In addition, calculation of the vibrational properties of several snapshots extracted from a molecular dynamics simulation allowed us to investigate in detail the effect of the protein environment on the vibrational spectra.

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

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.

Characterization of two thermostable cyanobacterial phytochromes reveals global movements in the chromophore-binding domain during photoconversion.

Photointerconversion between the red light-absorbing (Pr) form and the far-red light-absorbing (Pfr) form is the central feature that allows members of the phytochrome (Phy) superfamily to act as reversible switches in light perception. Whereas the chromophore structure and surrounding binding pocket of Pr have been described, those for Pfr have remained enigmatic for various technical reasons. Here we describe a novel pair of Phys from two thermophilic cyanobacteria, Synechococcus sp.