19F nuclei are useful labels in solid-state NMR studies, since their chemical shift and tensor elements are very sensitive to the electrostatic and space-filling properties of their local... Show more19F nuclei are useful labels in solid-state NMR studies, since their chemical shift and tensor elements are very sensitive to the electrostatic and space-filling properties of their local environment. In this study we have exploited a fluorine substituent, strategically placed at the C-12-position of 11-cis retinal, the chromophore of visual rhodopsins. This label was used to explore the local environment of the chromophore in the ground state of bovine rhodopsin and its active photo-intermediate Meta II. In addition, the chemical shift and tensor elements of the chromophore in the free state in a membrane environment and the bound state in the protein were determined. Upon binding of the chromophore into rhodopsin and Meta II, the isotropic chemical shift changes in the opposite direction by +9.7 and -8.4 ppm, respectively. An unusually large isotropic shift difference of 35.9 ppm was observed between rhodopsin and Meta II. This partly originates in the light-triggered 11-cis to all-trans isomerization of the chromophore. The other part reflects the local conformational rearrangements in the chromophore and the binding pocket. These NMR data were correlated with the available X-ray structures of rhodopsin and Meta II using bond polarization theory. For this purpose hydrogen atoms have to be inserted and hereto a family of structures were derived that best correlated with the well-established 13C chemical shifts. Based upon these structures, a 12-F derivative was obtained that best corresponded with the experimentally determined 19F chemical shifts and tensor elements. The combined data indicate strong changes in the local environment of the C-12 position and a substantially different interaction pattern with the protein in Meta II as compared to rhodopsin. Show less
Loco, D.; Buda, F.; Lugtenburg, J.; Mennucci, B. 2018
Understanding the microscopic origin of the color tuning in pigment-protein complexes is a challenging yet fundamental issue in photoactive biological systems. Here, we propose a possible... Show moreUnderstanding the microscopic origin of the color tuning in pigment-protein complexes is a challenging yet fundamental issue in photoactive biological systems. Here, we propose a possible interpretation by using a state-of-the-art multiscale strategy based on the integration of quantum chemistry and polarizable atomistic embeddings into a dynamic description. By means of such a strategy we are able to resolve the long-standing dispute over the coloration mechanism in the crustacyanin protein. It is shown that the combination of the dynamical flexibility of the carotenoid pigments (astaxanthin) with the responsive protein environment is essential to obtain quantitative predictions of the spectral tuning. The strong linear correlation between the excitation energies and the bond length alternation in the long-chain carotenoids modulated by the dynamical protein environment is a novel finding explaining the high color tunability in crustacyanin. Show less
Vibronic coupling is key to efficient energy flow in molecular systems and a critical component of most mechanisms invoking quantum effects in biological processes. Despite increasing evidence for... Show moreVibronic coupling is key to efficient energy flow in molecular systems and a critical component of most mechanisms invoking quantum effects in biological processes. Despite increasing evidence for coherent coupling of electronic states being mediated by vibrational motion, it is not clear how and to what degree properties associated with vibrational coherence such as phase and coupling of atomic motion can impact the efficiency of light-induced processes under natural, incoherent illumination. Here, we show that deuteration of the H11–C11=C12–H12 double-bond of the 11-cis retinal chromophore in the visual pigment rhodopsin significantly and unexpectedly alters the photoisomerization yield while inducing smaller changes in the ultrafast isomerization dynamics assignable to known isotope effects. Combination of these results with non-adiabatic molecular dynamics simulations reveals a vibrational phase-dependent isotope effect that we suggest is an intrinsic attribute of vibronically coherent photochemical processes. Show less
A recently discovered natural family of light-gated anion channelrhodopsins (ACRs) from cryptophyte algae provides an effective means of optogenetically silencing neurons. The most extensively... Show moreA recently discovered natural family of light-gated anion channelrhodopsins (ACRs) from cryptophyte algae provides an effective means of optogenetically silencing neurons. The most extensively studied ACR is from Guillardia theta (GtACR1). Earlier studies of GtACR1 have established a correlation between formation of a blue-shifted L-like intermediate and the anion channel "open" state. To study structural changes of GtACR1 in the K and L intermediates of the photocycle, a combination of low-temperature Fourier transform infrared (FTIR) and ultraviolet–visible absorption difference spectroscopy was used along with stable-isotope retinal labeling and site-directed mutagenesis. In contrast to bacteriorhodopsin (BR) and other microbial rhodopsins, which form only a stable red-shifted K intermediate at 80 K, GtACR1 forms both stable K and L-like intermediates. Evidence includes the appearance of positive ethylenic and fingerprint vibrational bands characteristic of the L intermediate as well as a positive visible absorption band near 485 nm. FTIR difference bands in the carboxylic acid C=O stretching region indicate that several Asp/Glu residues undergo hydrogen bonding changes at 80 K. The Glu68 → Gln and Ser97 → Glu substitutions, residues located close to the retinylidene Schiff base, altered the K:L Show less
Bovee-Geurts, P.H.M.; Lugtenburg, J.; Grip, W.J. de 2017
Proteins and peptides play a preeminent role in the processes of living cells. The only way to study structure-function relationships of a protein at the atomic level without any perturbation is by... Show moreProteins and peptides play a preeminent role in the processes of living cells. The only way to study structure-function relationships of a protein at the atomic level without any perturbation is by using non-invasive isotope sensitive techniques with site-directed stable isotope incorporation at a predetermined amino acid residue in the protein chain. The method can be extended to study the protein chain tagged with stable isotope enriched amino acid residues at any position or combinations of positions in the system. In order to access these studies synthetic methods to prepare any possible isotopologue and isotopomer of the 22 genetically encoded amino acids have to be available. In this paper the synthetic schemes and the stable isotope enriched building blocks that are available via commercially available stable isotope enriched starting materials are described. Show less
Carotenoids and their metabolites are essential factors for the maintenance of important life processes such as photosynthesis. Animals cannot synthesize carotenoids de novo, they must obtain them... Show moreCarotenoids and their metabolites are essential factors for the maintenance of important life processes such as photosynthesis. Animals cannot synthesize carotenoids de novo, they must obtain them via their food. In order to make intensive animal husbandry possible and maintain human and animal health synthetic nature identical carotenoids are presently commercially available at the multi-tonnes scale per year. Synthetically accessible C-13 enriched carotenoids are essential to apply isotope sensitive techniques to obtain information at the atomic level without perturbation about the role of carotenoids in photosynthesis, nutrition, vision, animal development, etc. Simple highly C-13 enriched C-1, C-2 and C-3 building blocks are commercially available via 99% (CO)-C-13. The synthetic routes for the preparation of the C-13 enriched building blocks starting from the commercially available systems are discussed first. Then, how these building blocks are used for the synthesis of the various C-13 enriched carotenoids and apocarotenoids are reviewed next. The synthetic Schemes that resulted in C-13 enriched beta-carotene, spheroidene, beta-cryptoxanthin, canthaxanthin, astaxanthin, (3R,3'R)-zeaxanthin and (3R,3'R,6'R)-lutein are described. The Schemes that are reviewed can also be used to synthetically access any carotenoid and apocarotenoid in any C-13 isotopically enriched form up to the unitarily enriched form. Show less
The role of vitamin A and its metabolites in the life processes starting with the historical background and its up to date information is discussed in the introduction. Also the role of 11Z-retinal... Show moreThe role of vitamin A and its metabolites in the life processes starting with the historical background and its up to date information is discussed in the introduction. Also the role of 11Z-retinal in vision and retinoic acid in the biological processes is elucidated. The essential role of isotopically enriched systems in the progress of vision research, nutrition research etc. is discussed. In part B industrial commercial syntheses of vitamin A by the two leading companies Hoffmann-La Roche (now DSM) and BASF are discussed. The knowledge obtained via these pioneering syntheses has been essential for the further synthetic efforts in vitamin A field by other scientific groups. The rest of the paper is devoted to the synthetic efforts of the Leiden group that gives an access to the preparation of site directed high level isotope enrichment in retinals. First the synthesis of the retinals with deuterium incorporation in the conjugated side chain is reviewed. Then, C-13-labeled retinals are discussed. This is followed by the discussion of a convergent synthetic scheme that allows a rational access to prepare any isotopomer of retinals. The schemes that provide access to prepare any possible isotope enriched chemically modified systems are discussed. Finally, nor-retinals and bridged retinals that give access to a whole (as yet incomplete) library of possible isotopomers are reviewed. Show less
