Proteorhodopsins (PRs) found in marine microbes are the most abundant retinal-based photoreceptors on this planet. PR variants show high levels of environmental adaptation, as their colors are tuned to the optimal wavelength of available light. The two major green and blue subfamilies can be interconverted through a L/Q point mutation at position 105. Here we reveal the structural basis behind this intriguing color-tuning effect. High-field solid-state NMR spectroscopy was used to visualize structural changes within green PR directly within the lipid bilayer upon introduction of the green–blue L105Q mutation. The observed effects are localized within the binding pocket and close to retinal carbons C14 and C15. Subsequently, magic-angle spinning (MAS) NMR spectroscopy with sensitivity enhancement by dynamic nuclear polarization (DNP) was applied to determine precisely the retinal structure around C14–C15. Upon mutation, a significantly stretched C14–C15 bond, deshielding of C15, and a slight alteration of the retinal chain’s out-of-plane twist was observed. The L105Q blue switch therefore acts locally on the retinal itself and induces a conjugation defect between the isomerization region and the imine linkage. Consequently, the S0–S1 energy gap increases, resulting in the observed blue shift. The distortion of the chromophore structure also offers an explanation for the elongated primary reaction detected by pump–probe spectroscopy, while chemical shift perturbations within the protein can be linked to the elongation of late-photocycle intermediates studied by flash photolysis. Besides resolving a long-standing problem, this study also demonstrates that the combination of data obtained from high-field and DNP-enhanced MAS NMR spectroscopy together with time-resolved optical spectroscopy enables powerful synergies for in-depth functional studies of membrane proteins.

The proteorhodopsin family consists of retinal proteins of marine bacterial origin with optical properties adjusted to their local environments. For green proteorhodopsin, a highly specific mutation in the EF loop, A178R, has been found to cause a surprisingly large redshift of 20 nm despite its distance from the chromophore. Here, we analyze structural and functional consequences of this EF loop mutation by time-resolved optical spectroscopy and solid-state NMR. We found that the primary photoreaction and the formation of the K-like photo intermediate is almost pH-independent and slower compared to the wild-type, whereas the decay of the K-intermediate is accelerated, suggesting structural changes within the counterion complex upon mutation. The photocycle is significantly elongated mainly due to an enlarged lifetime of late photo intermediates. Multidimensional MAS-NMR reveals mutation-induced chemical shift changes propagating from the EF loop to the chromophore binding pocket, whereas dynamic nuclear polarization-enhanced (13)C-double quantum MAS-NMR has been used to probe directly the retinylidene conformation. Our data show a modified interaction network between chromophore, Schiff base, and counterion complex explaining the altered optical and kinetic properties. In particular, the mutation-induced distorted structure in the EF loop weakens interactions, which help reorienting helix F during the reprotonation step explaining the slower photocycle. These data lead to the conclusion that the EF loop plays an important role in proton uptake from the cytoplasm but our data also reveal a clear interaction pathway between the EF loop and retinal binding pocket, which might be an evolutionary conserved communication pathway in retinal proteins.

The simultaneous observation of interdependent reactions within different phases as catalyzed by membrane-bound enzymes is still a challenging task. One such enzyme, the Escherichia coli integral membrane protein diacylglycerol kinase (DGK), is a key player in lipid regulation. It catalyzes the generation of phosphatidic acid within the membrane through the transfer of the γ-phosphate from soluble MgATP to membrane-bound diacylglycerol. We demonstrate that time-resolved (31)P magic angle spinning NMR offers a unique opportunity to simultaneously and directly detect both ATP hydrolysis and diacylglycerol phosphorylation. This experiment demonstrates that solid-state NMR provides a general approach for the kinetic analysis of coupled reactions at the membrane interface regardless of their compartmentalization. The enzymatic activity of DGK was probed with different lipid substrates as well as ATP analogs. Our data yield conclusions about intersubunit cooperativity, reaction stoichiometries and phosphoryl transfer mechanism and are discussed in the context of known structural data.

A considerable limitation of NMR spectroscopy is its inherent low sensitivity. Approximately 90 % of the measuring time is used by the spin system to return to its Boltzmann equilibrium after excitation, which is determined by (1)H-T1 in cross-polarized solid-state NMR experiments. It has been shown that sample doping by paramagnetic relaxation agents such as Cu(2+)-EDTA accelerates this process considerably resulting in enhanced sensitivity. Here, we extend this concept to Gd(3+)-complexes. Their effect on (1)H-T1 has been assessed on the membrane protein proteorhodopsin, a 7TM light-driven proton pump. A comparison between Gd(3+)-DOTA, Gd(3+)-TTAHA, covalently attached Cu(2+)-EDTA-tags and Cu(2+)-EDTA reveals a 3.2-, 2.6-, 2.4- and 2-fold improved signal-to-noise ratio per unit time due to longitudinal paramagnetic relaxation enhancement. Furthermore, Gd(3+)-DOTA shows a remarkably high relaxivity, which is 77-times higher than that of Cu(2+)-EDTA. Therefore, an order of magnitude lower dopant concentration can be used. In addition, no line-broadening effects or peak shifts have been observed on proteorhodopsin in the presence of Gd(3+)-DOTA. These favourable properties make it very useful for solid-state NMR experiments on membrane proteins.

Membrane proteins catalyze reactions at the cell membrane and facilitate thetransport of molecules or signals across the membrane. Recently researchers have made great progress in understanding the structural biology of membrane proteins, mainly based on X-ray crystallography. In addition, the application of complementary spectroscopic techniques has allowed researchers to develop a functional understanding of these proteins. Solid-state NMR has become an indispensable tool for the structure-function analysis of insoluble proteins and protein complexes. It offers the possibility of investigating membrane proteins directly in their environment, which provides essential information about the intrinsic coupling of protein structure and functional dynamics within the lipid bilayer. However, to date, researchers have hardly explored the enzymology of mem-brane proteins. In this Account, we review the perspectives for investigating membrane-bound enzymes by solid-state NMR. Understanding enzyme mechanisms requires access to kinetic parameters, structural analysis of the catalytic center, knowledge of the 3D structure and methods to follow the structural dynamics of the enzyme during the catalytic cycle. In principle, solid-state NMR can address all of these issues. Researchers can characterize the enzyme kinetics by observing substrate turnover within the membrane or at the membrane interphase in a time-resolved fashion as shown for diacylglycerol kinase. Solid-state NMR has also provided a mechanistic understanding of soluble enzymes including triosephosphate isomerase (TIM) and different metal-binding proteins, which demonstrates a promising perspective also for membrane proteins. The increasing availability of high magnetic fields and the development of new experimental schemes and computational protocols have made it easier to determine 3D structure using solid-state NMR. Dynamic nuclear polarization, a key technique to boost sensitivity of solid-state NMR at low temperatures, can help with the analysis of thermally trapped catalytic intermediates, while methods to improve signal-to-noise per time unit enable the real-time measurement of kinetics of conformational changes during the catalytic cycle.