Structure of a retinal chromophore of dark-adapted middle rhodopsin as studied by solid-state nuclear magnetic resonance spectroscopy

Abstract

electrostatic interaction with the counter ion. Therefore, the resulting structural information exhibited the property of stable retinal conformations of dark-adapted MR.

Solid-state NMR for the characterization of retinal chromophore and Schiff base in TAT rhodopsin embedded in membranes under weakly acidic conditions

“… 1) From references of [ 17 ], [ 18 ]. 2) From reference of [ 19 ]. * The 13 C and 15 N chemical shifts in this table were calibrated to the reference chemical shifts of DSS and 15 NH 4 Cl.…”

“…Solid-state nuclear magnetic resonance (SSNMR) studies of microbial rhodopsins have provided structural information regarding the local electronic environment of the RPSB and retinal configurations, as well as the conformation and dynamics of protein [17][18][19]. Since the electronic environment of RPSB is related to its hydrogen bond strength with the counterion relating to the regulation of the pKa of RPSB and the color tuning, the 15 N chemical shift values are particularly important for that detection and evaluation.…”

“…All rhodopsins, except for the TAT rhodopsin plotted in Figure 3 (B), have at least one Asp residue in helix C as a counterion. Interestingly, the plot of TAT significantly deviated from the linear relationship, resulting in the highest magnetic field resonance compared with those of other microbial rhodopsins, such as BR, MR, sensory rhodopsin II from Natronomonas pharaonis (NpSRII), Thermophilic rhodopsin (TR), Anabaena sensory rhodopsin (ASR), and Krokinobacter rhodopsin 2 (KR2) [19,[23][24][25][26][27][28]. In particular, the unique 15 N isotropic chemical shift value of TAT suggests that the electronic environment of the RPSB nitrogen in TAT is considerably different from that of other microbial rhodopsins and that the hydrogen bonding strength of the RPSB with counterions is largely weakened.…”

Ion-transporting mechanism in microbial rhodopsins: Mini-review relating to the session 5 at the 19th International Conference on Retinal Proteins

“…It is widely recognized that three dimensional atomic structures obtained by X-ray crystallography and cryogenic electron microscope (Cryo-EM) successfully established the solid bases for exploring molecular mechanisms of microbial rhodopsins. Nuclear magnetic resonance (NMR) techniques also provide valuable structural information of the chromophores and the protein moieties [27][28][29].…”

Recent advances in signaling and activation mechanism in microbial rhodopsins: Report for the session 6 at the 19^th International Conference on Retinal Proteins

“…Solid-state NMR data of sodium ion pumping rhodopsin Krokinobacter rhodopsin 2 (KR2) and HeR embedded in the membrane were presented by Dr. Izuru Kawamura (Yokohama National University). To begin, he emphasized that the 15 N chemical shifts of retinal protonated Schiff base (RPSB), which relate to the electronic environment of nitrogen, are highly correlated with the maximum absorption of some microbial rhodopsins (e.g., BR, sensory rhodopsin II, and middle rhodopsin) based on the strength of hydrogen bonding with counterion [ 6 ]. Using the 15 N RPSB signal of KR2 and H30A, he and his colleagues discovered that changes in RPSB with Asp116 in helix C (counterion) were induced by Na + binding at the extracellular protein interface [ 7 ].…”