Distinct chromophore?protein environments enable asymmetric activation of a bacteriophytochrome-activated diguanylate cyclase
JOURNAL OF BIOLOGICAL CHEMISTRY
Authors: Buhrke, David; Gourinchas, Geoffrey; Mueller, Melanie; Michael, Norbert; Hildebrandt, Peter; Winkler, Andreas
Abstract
Sensing of red and far-red light by bacteriophytochromes involves intricate interactions between their bilin chromophore and the protein environment. The light-triggered rearrangements of the cofactor configuration and eventually the protein conformation enable bacteriophytochromes to interact with various protein effector domains for biological modulation of diverse physiological functions. Excitation of the holoproteins by red or far-red light promotes the photoconversion to their far-red light?absorbing Pfr state or the red light-absorbing Pr state, respectively. Because prototypical bacteriophytochromes have a parallel dimer architecture, it is generally assumed that symmetric activation with two Pfr state protomers constitutes the signaling-active species. However, the bacteriophytochrome from Idiomarina species A28L (IsPadC) has recently been reported to enable long-range signal transduction also in asymmetric dimers containing only one Pfr protomer. By combining crystallography, hydrogen?deuterium exchange coupled to MS, and vibrational spectroscopy, we show here that Pfr of IsPadC is in equilibrium with an intermediate ?Pfr-like? state that combines features of Pfr and Meta-R states observed in other bacteriophytochromes. We also show that structural rearrangements in the N-terminal segment (NTS) can stabilize this Pfr-like state and that the PHY-tongue conformation of IsPadC is partially uncoupled from the initial changes in the NTS. This uncoupling enables structural asymmetry of the overall homodimeric assembly and allows signal transduction to the covalently linked physiological diguanylate cyclase output module in which asymmetry might play a role in the enzyme-catalyzed reaction. The functional differences to other phytochrome systems identified here highlight opportunities for using additional red-light sensors in artificial sensor?effector systems.
The adsorption characteristics and thermo-mechanical properties of BxCyNz heteronanotubes under physical adsorption of Ni(II)tetramethyldibenzotetraaza [14] annulene (NiTMTAA): Insight from molecular dynamics approach
COMPUTATIONAL MATERIALS SCIENCE
Authors: Pashmforoush, F.; Ajori, S.
Abstract
In this study, the adsorption characteristics together with the modified thermomechanical properties of stable BxCyNz heteronanotubes, i.e. BC2N, BC3, and NC3, in ambient conditions have been explored under the adsorption of NiTMTAA molecules (NiTMTAA/heteronanotube). Employing molecular dynamics study, it is observed that pi-pi stacking interaction plays a major role in the adsorption of NiTMTAA. The radius of gyration and circumferential distribution along the axis of NTs demonstrate the higher agglomeration of molecules near the wall of CNT and BC3 than that of other NTs. Moreover, it is observed that CNT and BNNT possess the highest Young's modulus and thermal conductivity than those of heteronanotubes. According to the results, the adsorption of NiTMTAA molecules reduces thermal conductivity. Unlikely, Young's modulus of NiTMTAA/heteronanotubes for small weight percentage of NiTMTAA molecules (< similar to 20%) is slightly higher than pure heteronanotubes. Furthermore, it is shown that for more than 20%, the thermomechanical properties are approximately converged to the slightly lower value than that of pure heteronanotubes. Finally, it is demonstrated that the presence of both boron (B) and nitrogen (N) atoms in heteronanotubes, i.e. BC2N, results in higher thermomechanical properties than the individual presence of B and N.