Enhancing the Inhomogeneonus Photodynamics of Canonical Bacteriophytochrome

The ability of phytochromes to act as photoswitches in plants and microorganisms depends on interactions between a bilin-like chromophore and a protein. The interconversion occurs between the spectrally distinct red (Pr) and far-red (Pfr) conformers. This conformational change is triggered by the photoisomerization of the chromophore D-ring pyrrole. In this study, as a representative example of a phytochrome-bilin system, we take biliverdin IXα (BV) bound to bacteriophytochrome (BphP) from Deinococcus radiodurans. In the absence of light, we use an enhanced sampling molecular dynamics (MD) method to overcome the photoisomerization energy barrier. We find that the calculated free energy (FE) barriers between essential metastable states agree with spectroscopic results. We show that the enhanced dynamics of the BV chromophore in BphP triggers nanometer-scale conformational movements that propagate by two experimentally determined signal transduction pathways. Most importantly, we describe how the metastable states enable a thermal transition known as the dark reversion between Pfr and Pr, through a previously unknown intermediate state of Pfr. Here, for the first time, the heterogeneity of temperature-dependent Pfr states is presented at the atomistic level. This work paves a way toward understanding the complete mechanism of the photoisomerization of a bilin-like chromophore in phytochromes.

Enhancing the Inhomogeneonus Photodynamics of Canonical Bacteriophytochrome

The ability of phytochromes to act as photoswitches in plants and microorganisms depends on interactions between a bilin-like chromophore and a protein. The interconversion occurs between the spectrally distinct red (Pr) and far-red (Pfr) conformers. This conformational change is triggered by the photoisomerization of the chromophore D-ring pyrrole. In this study, as a representative example of a phytochrome-bilin system, we take biliverdin IXα (BV) bound to bacteriophytochrome (BphP) from Deinococcus radiodurans. In the absence of light, we use an enhanced sampling molecular dynamics (MD) method to overcome the photoisomerization energy barrier. We find that the calculated free energy (FE) barriers between essential metastable states agree with spectroscopic results. We show that the enhanced dynamics of the BV chromophore in BphP triggers nanometer-scale conformational movements that propagate by two experimentally determined signal transduction pathways. Most importantly, we describe how the metastable states enable a thermal transition known as the dark reversion between Pfr and Pr, through a previously unknown intermediate state of Pfr. Here, for the first time, the heterogeneity of temperature-dependent Pfr states is presented at the atomistic level. This work paves a way toward understanding the complete mechanism of the photoisomerization of a bilin-like chromophore in phytochromes.

Anionic surfactant sulfate dodecyl sodium (SDS)-induced thermodynamics and conformational changes of collagen by ultrasensitive microcalorimetry

In this communication, sulfate dodecyl sodium (SDS)-induced thermodynamics and conformational changes of collagen were studied. We used ultrasensitive differential scanning calorimetry (US-DSC) to directly monitor the thermal transition of collagen in the presence of SDS. The results show that SDS affects the conformation and thermal stability of collagen very differently depending on its concentrations. At CSDS ≤ 0.05 mM, the enhanced thermal stability of collagen indicates the stabilizing effect by SDS. However, a further increase of SDS leads to the denaturation of collagen, verifying the well-known ability of SDS to unfold proteins. This striking difference in thermodynamics and conformational changes of collagen caused by SDS concentrations can be explained in terms of their interactions. With increasing SDS, the binding of SDS to collagen can be dominated by electrostatic interaction shifting to hydrophobic interaction, and the latter plays a key role in loosening and unfolding the triple-helix structure of collagen. The important finding in the present study is the stabilizing effect of SDS on collagen molecules at extreme low concentration. Graphical abstract

Diacyl peroxides, practical reagents as aryl and alkyl radical sources

Diacyl peroxides, which can be easily synthesized from corresponding carboxylic acids, are commonly utilized as radical initiators and one electron oxidants. Under thermal, transition-metal catalysis or irradiation conditions the cleavage...