Dynamics of Bacteriorhodopsin in the Dark‐Adapted State from Solution Nuclear Magnetic Resonance Spectroscopy

Abstract

To achieve efficient proton pumping in the light‐driven proton pump bacteriorhodopsin (bR), the protein must be tightly coupled to the retinal to rapidly convert retinal isomerization into protein structural rearrangements. Methyl group dynamics of bR embedded in lipid nanodiscs were determined in the dark‐adapted state, and were found to be mostly well ordered at the cytosolic side. Methyl groups in the M145A mutant of bR, which displays only 10 % residual proton pumping activity, are less well ordered, suggesting a link between side‐chain dynamics on the cytosolic side of the bR cavity and proton pumping activity. In addition, slow conformational exchange, attributed to low frequency motions of aromatic rings, was indirectly observed for residues on the extracellular side of the bR cavity. This may be related to reorganization of the water network. These observations provide a detailed picture of previously undescribed equilibrium dynamics on different time scales for ground‐state bR.

Structures of the archaerhodopsin-3 transporter reveal that disordering of internal water networks underpins receptor sensitization

“…Long-standing questions in the field have concerned the energetics of the transformation from the LA ground state to the DA state and, in particular, how the thermodynamic equilibrium between all-trans and 13-cis retinal in the DA state is established in the absence of light and with no apparent input of energy. (There is limited structural data for the DA states of other microbial rhodopsins and the only DA crystal structure currently deposited in the PDB is for bR 27,57 .) It is perhaps surprising that, in AR3, there are minimal changes in the positions of the side chains that line the retinal binding pocket between the two states and it would therefore appear that the favoring of the cis isomer in the DA state, does not arise from changes in the binding energy of the chromophore.…”

Function-Related Dynamics in Multi-Spanning Helical Membrane Proteins Revealed by Solution NMR

“…The strategy was also applied to obtain mechanistic insights into allosteric regulation of the A 2A R by physiological cations [ 56 ] and ligand-dependent conformational equilibria in the transmembrane regions in β 1 AR [ 57 ]. It should also be noted that fast methyl dynamics were quantified in the presence of different ligands in A 2A R by using triple-quantum relaxation data [ 58 ], as well as in sensory rhodopsin II [ 59 ] and bacteriorhodopsin [ 60 ].…”