Curated Optogenetic Publication Database

Search precisely and efficiently by using the advantage of the hand-assigned publication tags that allow you to search for papers involving a specific trait, e.g. a particular optogenetic switch or a host organism.

Showing 1 - 4 of 4 results

Selective Photoinduced Dimerization and Slow Recovery of a BLUF Domain of EB1.

blue BLUF domains Background
J Phys Chem B, 28 Jan 2022 DOI: 10.1021/acs.jpcb.1c10100 Link to full text
Abstract: The EAL-BLUF fragment from Magnetococcus marinus BldP1 (EB1) light-dependently hydrolyzes c-di-GMP. Herein, the photoreaction of the BLUF domain of EB1 (eBLUF) is studied. It is found for the first time that a monomeric BLUF domain forms a dimer upon illumination and its dark recovery is very slow. The dimer of light- and dark-state protomers (LD-dimer) is much more stable than that of two light-state protomers (LL-dimer), and the dark recovery of the LD-dimer is approximately 20 times slower than that of the LL-dimer, which is suitable for optogenetic tools. The secondary structure of the L-monomer is different from those of the D-monomer and the LD-dimer. The transient grating measurements reveal that this conformational change occurs simultaneously with dimerization. Although the W91A mutant exhibits a spectral red shift, it forms a heterodimer with the L-monomer of wild-type eBLUF with similar stability to the LD-dimer. This suggests that the conformation of the dimerization site of W91A is similar to that of the dark state (dark-mimic mutant); that is, the light-induced structural changes in the chromophore cavity are not transferred to the other part of the protein. The selective photoinduced dimerization of eBLUF is potentially useful to control interprotein interactions between two different effector domains bound to these proteins.

Slow conformational changes of blue light sensor BLUF proteins in milliseconds.

blue BLUF domains Background
bioRxiv, 16 Dec 2021 DOI: 10.1101/2021.12.13.472511 Link to full text
Abstract: BLUF (blue light sensor using flavin) proteins consist of flavin-binding BLUF domains and functional domains. Upon blue light excitation, the hydrogen bond network around the flavin chromophore changes, and the absorption spectrum in the visible region exhibits red-shift. Ultimately, the light information received in the BLUF domain is transmitted to the functional region. It has been believed that this red-shift is complete within nanoseconds. Contrary to this commonly accepted scheme, in this study, slow reaction kinetics were discovered in milliseconds (τ1- and τ2-phase) for all the BLUF proteins examined (AppA, OaPAC, BlrP1, YcgF, PapB, SyPixD, and TePixD). Despite extensive reports on BLUF, this is the first clear observation of the BLUF protein absorption change with the duration in the millisecond time region. From the measurements of some domain-deleted mutants of OaPAC and two chimeric mutants of PixD proteins, it was found that the slower dynamics (τ2-phase) are strongly affected by the size and nature of the C-terminal region adjacent to the BLUF domain. Hence, this millisecond reaction is a significant indicator of conformational changes in the C-terminal region, which is essential for the biological functions. On the other hand, the τ1-phase commonly exists in all BLUF proteins, including any mutants. The origin of the slow dynamics was studied using site-specific mutants. These results clearly show the importance of Trp in the BLUF domain. Based on this, a reaction scheme for the BLUF reaction is proposed.

A unique photochromic UV-A sensor protein, Rc-PYP, interacting with the PYP-binding protein.

blue Fluorescent proteins Background
Phys Chem Chem Phys, 16 Aug 2021 DOI: 10.1039/d1cp02731j Link to full text
Abstract: Photoactive yellow protein (PYP) is one of the typical light sensor proteins. Although its photoreaction has been extensively studied, no downstream partner protein has been identified to date. In this study, the intermolecular interaction dynamics observed between PYP from Rhodobacter capsulatus (Rc-PYP) and a possible downstream protein, PYP-binding protein (PBP), were investigated. It was found that UV light induced a long-lived product (pUV*), which interacts with PBP to form a stable hetero-hexamer (Complex-2). The reaction scheme for this interaction was revealed using transient absorption and transient grating methods. Time-resolved diffusion detection showed that a hetero-trimer (Complex-1) is formed transiently, which produced Complex-2 via a second-order reaction. Any other intermediates, including those from pBL, do not interact with PBP. The reaction scheme and kinetics are determined. Interestingly, long-lived Complex-2 dissociates upon excitation with blue light. These results demonstrate that Rc-PYP is a photochromic and new type of UV sensor to sense the relative intensities of UV-A and blue light.

Time-resolved tracking of interprotein signal transduction: Synechocystis PixD-PixE complex as a sensor of light intensity.

blue BLUF domains Background
J Am Chem Soc, 11 May 2012 DOI: 10.1021/ja301540r Link to full text
Abstract: PixD (Slr1694) is a blue light receptor that contains a BLUF (blue light sensors using a flavin chromophore) domain. A protein-protein interaction between PixD and a response regulator PixE (Slr1693) is essential to achieve light signal transduction for phototaxis of the species. Although the initial photochemical reaction of PixD, the red shift of the flavin absorption spectrum, has been investigated, the subsequent reaction dynamics remain largely unresolved. Only the disassembly of the PixD(10)-PixE(5) dark complex has been characterized by static size exclusion chromatography. In this report, interprotein reaction dynamics were examined using time-resolved transient grating spectroscopy. The dissociation process was clearly observed as the light-induced diffusion coefficient change in the time domain, and the kinetics was determined. More strikingly, disassembly was found to take place only after photoactivation of two PixD subunits in the complex. This result suggests that the biological response of PixD does not follow a linear correlation with the light intensity but appears to be light-intensity-dependent.
Submit a new publication to our database