Biomedical subjects

Johan Lugtenburg

Publications and source records attributed to Johan Lugtenburg.

At least 19 recordsLinked to original sources

PubMed2006

Methyl substituents at the 11 or 12 position of retinal profoundly and differentially affect photochemistry and signalling activity of rhodopsin.

The C-11=C-12 double bond of the retinylidene chromophore of rhodopsin holds a central position in its light-induced photoisomerization and hence the photosensory function of this visual pigment. To probe the local environment of the HC-11=C-12H element we have prepared the 11-methyl and 12-methyl derivatives of 11-Z retinal and incorporated these into opsin to generate the rhodopsin analogs 11-methyl and 12-methyl rhodopsin. These analog pigments form with much slower kinetics and lower efficiency than the native pigment. The initial photochemistry and the signaling activity of the analog pigments were investigated by UV-vis and FTIR spectroscopy, and by a G protein activation assay. Our data indicate that the ultrafast formation of the first photointermediate is strongly perturbed by the presence of an 11-methyl substituent, but much less by a 12-methyl substituent. These results support the current concept of the mechanism of the primary photoisomerization event in rhodopsin. An important stronghold of this concept is an out-of-plane movement of the C-12H element, which is facilitated by torsion as well as extended positive charge delocalization into the C-10-C-13 segment of the chromophore. We argue that this mechanism is maintained principally with a methyl substituent at C-12. In addition, we show that both an 11-methyl and a 12-methyl substitutent perturb the photointermediate cascade and finally yield a low-activity state of the receptor. The 11-methyl pigment retains about 30% of the G protein activation rate of native rhodopsin, while the 12-methyl chromophore behaves like an inverse agonist up to at least 20 degrees C, trapping the protein in a perturbed Meta-I-like conformation. We conclude that the isomerization region of the chromophore and the spatial structure of the binding site are finely tuned, in order to achieve a high photosensory potential with an efficient pathway to a high-activity state.

Animals↗

PubMed2006

Accurate measurements of 13C-13C J-couplings in the rhodopsin chromophore by double-quantum solid-state NMR spectroscopy.

A new double-quantum solid-state NMR pulse sequence is presented and used to measure one-bond 13C-13C J-couplings in a set of 13C2-labeled rhodopsin isotopomers. The measured J-couplings reveal a perturbation of the electronic structure at the terminus of the conjugated chain but show no evidence for protein-induced electronic perturbation near the C11-C12 isomerization site. This work establishes NMR methodology for measuring accurate 1JCC values in noncrystalline macromolecules and shows that the measured J-couplings may reveal local electronic perturbations of mechanistic significance.

Carbon Isotopes↗

PubMed2006

Triplet state spectra and dynamics of geometric isomers of carotenoids.

The observation of preferential binding of cis-carotenoids in purple bacterial photosynthetic reaction centers versus trans-isomers in antenna pigment protein complexes has led to the hypothesis that the natural selection of stereoisomers has physiological significance. In order to test this hypothesis, we have undertaken a systematic series of investigations comparing the optical spectroscopic properties and excited state dynamics of cis and trans isomers of carotenoids. The present work compares the triplet state spectra, lifetimes, and energy transfer rates of all-trans-spheroidene and 13,14-locked-cis-spheroidene, the latter of which is incapable of isomerizing to the all-trans configuration, and therefore provides a unique opportunity to examine the triplet state properties of a structurally stable cis molecule. The data reveal only small differences in spectra, decay dynamics, and transfer times and suggest there is little intrinsic advantage in either triplet energy transfer or triplet state decay arising from the inherently different isomeric forms of cis compared to trans carotenoids.

Carotenoids↗

PubMed2005

Effect of isomer geometry on the steady-state absorption spectra and femtosecond time-resolved dynamics of carotenoids.

Steady-state absorption and femtosecond time-resolved optical spectroscopic studies have been carried out on all-trans-beta-carotene, 15,15'-cis-beta-carotene, all-trans-spheroidene, and 13,14-locked-cis-spheroidene. We examine in detail the effect of isomer geometry on the spectroscopic properties and photophysics of the low-lying S(1) (2(1)A(g)(-)) and S(2) (1(1)B(u)(+)) excited states of these molecules. The experiments on 13,14-locked-cis-spheroidene, a molecule incapable of undergoing cis-to-trans isomerization, provide a unique opportunity to examine the role of isomer geometry in controlling excited-state deactivation of carotenoids. The kinetic results have been obtained using both single wavelength transient absorption measurements and global fitting procedures. The overall scheme for the deactivation of these molecules after S(0) --> S(2) photon absorption is decay of S(2) to a vibrationally hot S(1) state, followed by vibrational relaxation within S(1), and finally, S(1) --> S(0) internal conversion back to the ground state. Changes in isomer geometry are shown to lead to small but noticeable alterations in the spectroscopic and kinetic behavior of the molecules. The effects are interpreted in terms of minor alterations in excited-state energy and vibrational coupling upon isomerization that bring about changes in the spectroscopic and kinetic behavior of this biologically important class of pigments.

Carotenoids↗

PubMed2005

Preparation of 13C4-6-methyl anthranilic ester via a Diels-Alder-type process. an experimental and theoretical study to characterize an unexpected isotope exchange.

Buta-2,3-dienoate reacts with vinyl ketenimine to give the corresponding substituted aniline through a Diels-Alder cycloaddition. Besides the expected Diels-Alder adduct 3a, the aniline 3b was also obtained in a ratio of 91:9. The observed (13)C exchange is explained on the basis of a reversible [2 + 2] cycloaddition competing with the [4 + 2] process. This is supported by B3LYP DFT computations, as a stepwise pathway lies very close in energy to the [4 + 2] concerted one. [reaction: see text]

Journal Article↗

PubMed2005

Selective interface detection: mapping binding site contacts in membrane proteins by NMR spectroscopy.

Intermolecular contact surfaces are important regions where specific interactions mediate biological function. We introduce a new magic angle spinning solid state NMR technique, dubbed "selective interface detection spectroscopy" (SIDY). In this technique, 13C-attached protons (1Hlig) are dephased by 1H-13C REDOR. A spin diffusion period is then used to enhance long distance 1H-1H correlations, and the results are detected by a short period of cross polarization to the 13C isotope labels. This SIDY approach allows selective observation of the interface between 13C-labeled and unlabeled moieties. We have used SIDY to probe the ligand-protein binding surface between a uniformly isotopically labeled ligand cofactor, U-13C20-11-cis-retinal, and its binding site in rhodopsin (Rho), an unlabeled, membrane-embedded G-protein coupled receptor (GPCR). The observed 1HGPCR-13Clig correlations indicate multiple close contacts between the protein and the ionone ring of the ligand, in agreement with binding studies. The polyene tail of the ligand displays fewer strong correlations in the SIDY spectrum. Some correlations can be assigned to the protein side chains lining the ligand binding site, in agreement with the crystal structure.

Binding Sites↗

PubMed2005

Spectroscopy and quantum chemical modeling reveal a predominant contribution of excitonic interactions to the bathochromic shift in alpha-crustacyanin, the blue carotenoprotein in the carapace of the lobster Homarus gammarus.

To resolve the molecular basis of the coloration mechanism of alpha-crustacyanin, we used (13)C-labeled astaxanthins as chromophores for solid-state (13)C NMR and resonance Raman spectroscopy of [6,6',7,7']-(13)C(4) alpha-crustacyanin and [8,8',9,9',10,10',11,11',20,20']-(13)C(10) alpha-crustacyanin. We complement the experimental data with time-dependent density functional theory calculations on several models based on the structural information available for beta-crustacyanin. The data rule out major changes and strong polarization effects in the ground-state electron density of astaxanthin upon binding to the protein. Conformational changes in the chromophore and hydrogen-bond interactions between the astaxanthin and the protein can account only for about one-third of the total bathochromic shift in alpha-crustacyanin. The exciton coupling due to the proximity of two astaxanthin chromophores is found to be large, suggesting that aggregation effects in the protein represent the primary source of the color change.

Animals↗

PubMed2005

Stereoisomers of carotenoids: spectroscopic properties of locked and unlocked cis-isomers of spheroidene.

A systematic optical spectroscopic and computational investigation of a series of locked-cis-isomers of spheroidene has been carried out with the goal being to better understand the relationships between stereochemistry, photochemistry, photophysics and biological function of geometric isomers of carotenoids. The spectroscopic properties of 15,15'-locked-cis-spheroidene, 13,14-locked-cis-spheroidene, 11, 12-locked-cis-spheroidene in solution are compared with those observed for unlocked spheroidene. The locked-cis bonds are incapable of undergoing cis-to-trans isomerization and therefore provide an effective means of exploring the relationship between specific stereoisomers and molecular spectroscopy. Samples of the molecules were purified using a high performance liquid chromatography (HPLC) apparatus equipped with a diode array detector, which records the absorption spectra immediately as the molecules emerge from the column and prior to any isomerization that might occur. For several stable isomers, resonance Raman (rR) spectroscopy was carried out to assign their configurations. Quantum computations of absorption spectra were performed using ZINDO/S and also MNDO-PSDCI methods employing nearly full single and double configuration interaction within the pi-electron manifold. Also, for a few test cases, ground state minimizations were done using density functional methods (B3LYP/6-31G(d)). The MNDO-PSDCI methods coupled with the density functional ground state minimization provide an accurate assignment of the positions of the 2(1)Ag - , 1(1)Bu +, and 1(1)Ag + excited states and also address the nature of the forbidden 1(1)Bu - state, whose location is uncertain for polyenes and carotenoids. We demonstrate that the configurational description of the 1(1)Bu - state is sufficiently unique to preclude assignment of its energy based on the characterization of surrounding excited singlet states. The experimental and computational data also offer important insights into the photochemical and photophysical properties of stereoisomers of carotenoids.

Carbon↗

PubMed2005

Accurate CSA measurements from uniformly isotopically labeled biomolecules at high magnetic field.

Obtaining chemical shift anisotropy (CSA) principal values from large biomolecular systems is often a laborious process of preparing many singly isotopically labeled samples and performing multiple independent CSA measurements. We present CSA tensor principal values measured in the biomolecular building blocks tyrosine.HCl, histidine.HCl, and all-E-retinal in both isotopically labeled and unlabeled forms at 17.6 T. The measured tensor values are identical for most carbon sites despite significant dipolar couplings between the spins. Quantum mechanical simulations of an arbitrary three spin system were used to evaluate the accuracy of direct CSA measurement as a function of applied magnetic field strength and molecular parameters. It was found that for a CSA asymmetry of 0.2 or more, an accurate measure of the CSA parameters is obtained when the CSA anisotropy is more than six times the largest dipolar coupling in frequency units. If the CSA asymmetry is more than 0.5, this requirement is relaxed, and accurate results are obtained if the anisotropy is more than three times the dipolar coupling. While these limits are insufficient for measurement of CSA's for alpha-carbons and aliphatic sidechain sites in proteins at current field strengths, they open the way for routine systematic CSA measurements of sites with relatively large CSA tensor values in extensively isotopically labeled biomolecules in widely available magnetic fields.

Anisotropy↗

PubMed2004

Solid-state NMR analysis of ligand--receptor interactions reveals an induced misfit in the binding site of isorhodopsin.

Rhodopsin is the photosensitive protein of the rod photoreceptor in the vertebrate retina and is a paradigm for the superfamily of G-protein-coupled receptors (GPCRs). Natural rhodopsin contains an 11-cis-retinylidene chromophore. We have prepared the 9-cis analogue isorhodopsin in a natural membrane environment using uniformly (13)C-enriched 9-cis retinal. Subsequently, we have determined the complete (1)H and (13)C assignments with ultra-high field solid-state magic angle spinning NMR. The 9-cis substrate conforms to the opsin binding pocket in isorhodopsin in a manner very similar to that of the 11-cis form in rhodopsin, but the NMR data reveal an improper fit of the 9-cis chromophore in this binding site. We introduce the term "induced misfit" to describe this event. Downfield proton NMR ligation shifts (Deltasigma(lig)(H) > 1 ppm) are observed for the 16,17,19-H and nearby protons of the ionone ring and for the 9-methyl protons. They provide converging evidence for global, nonspecific steric interactions between the chromophore and protein, and contrast with the specific interactions over the entire ionone ring and its substituents detected for rhodopsin. The Deltasigma(lig)(C) pattern of the polyene chain confirms the positive charge delocalization in the polyene associated with the protonation of the Schiff base nitrogen. In line with the misalignment of the ionone ring, an additional and anomalous perturbation of the (13)C response is detected in the region of the 9-cis bond. This provides evidence for strain in the isomerization region of the polyene and supports the hypothesis that perturbation of the conjugation around the cis bond induced by the protein environment assists the selective photoisomerization.

Binding Sites↗

PubMed2004

Constraints of the 9-methyl group binding pocket of the rhodopsin chromophore probed by 9-halogeno substitution.

Sterical constraints of the 9-methyl-binding pocket of the rhodopsin chromophore are probed using retinal analogues carrying substituents of increasing size at the 9 position (H, F, Cl, Br, CH(3), and I). The corresponding 11-Z retinals were employed to investigate formation of photosensitive pigment, and the primary photoproduct was identified by Fourier transform infrared difference spectroscopy. In addition, any effects of cumulative strain were studied by introduction of the 9-Z configuration and/or the alpha-retinal ring structure. Our results show that the 9-F analogue still can escape from the 9-methyl-binding pocket and that its photochemistry behaves very similar to the 9-demethyl analogue. The 9-Cl and 9-Br analogues behave very similar to the native 9-methyl pigments, but the 9-I retinal does not fit very well and shows poor pigment formation. This puts an upper limit on the radial dimension of the 9-methyl pocket at 0.45-0.50 nm. Introduction of the alpha-retinal ring constraint in the 11-Z series results in cumulative strain, because the 9-I and 9-Br derivatives cannot bind to generate a photopigment. The 9-Z configuration can partially compensate for the additional alpha-retinal strain. The corresponding 9-Br analogue does form a photopigment, and the other derivatives give increased photopigment yields compared to the corresponding 11-Z derivatives. In fact, 9-Z-alpha-retinal would be an interesting candidate for retinal supplementation studies. Our data provide direct support for the concept that the 9-methyl group is an important determinant in ligand anchoring and activation of the protein and in general agree with a three-point interaction model involving the ring, 9-methyl group, and aldehyde function.

Animals↗

PubMed2004

The ring of the rhodopsin chromophore in a hydrophobic activation switch within the binding pocket.

The current view that the beta-ionone ring of the rhodopsin chromophore vacates its binding pocket within the protein early in the photocascade has been adopted in efforts to provide structural models of photoreceptor activation. This event casts doubt on the ability of this covalently bonded ligand to participate directly in later stages involving activation of the photoreceptor and it is difficult to translate into predictions for the activation of related G protein-coupled receptors by diffusable ligands (e.g. neurotransmitters). The binding pocket fixes the formally equivalent pair of ring methyl groups (C16/C17) in different orientations that can be distinguished easily by (13)C NMR. Solid-state NMR observations on C16 and C17 are reported here that show instead that the ring is retained with strong selective interactions within the binding site into the activated state. We further show how increased steric interactions for this segment in the activated receptor can be explained by adjustment in the protein structure around the ring whilst it remains in its original location. This describes a plausible role for the ring in operating a hydrophobic switch from within the aromatic cluster of helix 6 of rhodopsin, which is coupled to electronic changes within the receptor through water-mediated, hydrogen-bonded networks between the conserved residues in G protein-coupled receptors.

Animals↗

PubMed2004

Protein-induced bonding perturbation of the rhodopsin chromophore detected by double-quantum solid-state NMR.

We have obtained carbon-carbon bond length data for the functional retinylidene chromophore of rhodopsin, with a spatial resolution of 3 pm. The very high resolution was obtained by performing double-quantum solid-state NMR on a set of noncrystalline isotopically labelled bovine rhodopsin samples. We detected localized perturbations of the carbon-carbon bond lengths of the retinylidene chromophore. The observations are consistent with a model in which the positive charge of the protonated Schiff base penetrates into the polyene chain and partially concentrates around the C13 position. This coincides with the proximity of a water molecule located between the glutamate-181 and serine-186 residues of the second extracellular loop, which is folded back into the transmembrane region. These measurements support the hypothesis that the polar residues of the second extracellular loop and the associated water molecule assist the rapid selective photoisomerization of the retinylidene chromophore by stabilizing a partial positive charge in the center of the polyene chain.

Carbon Isotopes↗

PubMed2003

Conformational similarities in the beta-ionone ring region of the rhodopsin chromophore in its ground state and after photoactivation to the metarhodopsin-I intermediate.

High-resolution solid-state NMR methods have been used to analyze the conformation of the chromophore in the late photointermediate metarhodopsin-I, from observation of (13)C nuclei introduced into the beta-ionone ring (at the C16, C17, and C18 methyl groups) and into the adjoining segment of the polyene chain (at C8). Bovine rhodopsin in its native membrane was also regenerated with retinal that was (13)C-labeled close to the 11-Z bond (C20 methyl group) to provide a reporter for optimizing and quantifying the photoconversion to metarhodopsin-I. Indirect photoconversion via the primary intermediate, bathorhodopin, was adopted as the preferred method since approximately 44% conversion to the metarhodopsin-I component could be achieved, with only low levels (approximately 18%) of ground-state rhodopsin remaining. The additional photoproduct, isorhodopsin, was resolved in (13)C spectra from C8 in the chain, at levels of approximately 38%, and was shown using rotational resonance NMR to adopt the 6-s-cis conformation between the ring and the polyene chain. The C8 resonance was not shifted in the metarhodopsin-I spectral component but was strongly broadened, revealing that the local conformation had become less well defined in this segment of the chain. This line broadening slowed rotational resonance exchange with the C17 and C18 ring methyl groups but was accounted for to show that, despite the chain being more relaxed in metarhodopsin-I, its average conformation with respect to the ring was similar to that in the ground state protein. Conformational restraints are also retained for the C16 and C17 methyl groups on photoactivation, which, together with the largely preserved conformation in the chain, argues convincingly that the ring remains with strong contacts in its binding pocket prior to activation of the receptor. Previous conclusions based on photocrosslinking studies are considered in view of the current findings.

Animals↗

PubMed2003

15N NMR spectroscopy of labeled alkoxyamines. 15N-labeled model compounds for nitroxide-trapping studies in free-radical (Co)polymerization.

Eight (15)N-labeled derivatives of 1-ethoxy-2,2,6,6-tetramethylpiperidine were synthesized in order to investigate the effects of their structural units on (15)N NMR spectra. A single peak is found for each alkoxyamine. The chemical shift depends extensively on the nature of the alpha carbon atom of the alkoxy group. The remote functional group attached to position 4 of the piperidine ring has a smaller but still significant effect. The results of the (15)N NMR measurements are supported by the detection of the N-H and N-C spin-spin coupling from the (1)H and (13)C NMR. The investigated alkoxyamines are model compounds for the radical-trapping products of styryl, methyl methacryloyl, alpha-methylstyryl, and methyl acryloyl radicals by (15)N-labeled nitroxides. The potential of (15)N NMR spectroscopy to analyze such products is discussed. In addition, it is shown that the (13)C chemical shifts of the alpha carbon atom of the alkoxy group fall in an empty part of the (13)C NMR spectrum, which allows the identification of trapped (macro)radicals via natural abundance (13)C NMR.

Journal Article↗

PubMed2003

Extraction of carotenoids from feces, enabling the bioavailability of beta-carotene to be studied in Indonesian children.

Previously, we have presented a method for quantifying beta-carotene bioavailability based on analysis in serum, following administration of (13)C-labeled beta-carotene. Because stool samples can be collected noninvasively, we have now extended the method to measure the bioavailability based on measurements in feces. An extraction method was developed to enable measurement of concentrations and degree of isotopic enrichment of retinol, retinyl palmitate and carotenoids in feces. Relative bioavailability of beta-carotene from pumpkin (n = 6) was found to be 1.8 times (interval, 0.6, 5.5) greater than that from spinach (n = 8), based on data from feces compared with 1.7 times (interval, 0.9, 3.1) based on data from serum.

Biological Availability↗

PubMed2003

Does different orientation of the methoxy groups of ubiquinone-10 in the reaction centre of Rhodobacter sphaeroides cause different binding at QA and QB?

The different roles of ubiquinone-10 (UQ10) at the primary and secondary quinone (QA and QB) binding sites of Rhodobacter sphaeroides R26 reaction centres are governed by the protein microenvironment. The 4C=O carbonyl group of QA is unusually strongly hydrogen-bonded, in contrast to QB. This asymmetric binding seems to determine their different functions. The asymmetric hydrogen-bonding at QA can be caused intrinsically by distortion of the methoxy groups or extrinsically by binding to specific amino-acid side groups. Different X-ray-based structural models show contradictory orientations of the methoxy groups and do not provide a clear picture. To elucidate if distortion of the methoxy groups induces this hydrogen-bonding, their (ring-)C-O vibrations were assigned by use of site-specifically labelled [5-13C]UQ10 and [6-13C]UQ10 reconstituted at either the QA or the QB binding site. Two infrared bands at 1288 cm(-1) and 1264 cm(-1) were assigned to the methoxy vibrations. They did not shift in frequency at either the QA or QB binding sites, as compared with unbound UQ10. As the frequencies of these vibrations and their coupling are sensitive to the conformations of the methoxy groups, different conformations of the C(5) and C(6) methoxy groups at the QA and QB binding sites can now be excluded. Both methoxy groups are oriented out of plane at QA and QB. Therefore, hydrogen-bonding to His M219 combined with electrostatic interactions with the Fe2+ ion seems to determine the strong asymmetric binding of QA.

Binding Sites↗

PubMed2002

(13)C MAS NMR and photo-CIDNP reveal a pronounced asymmetry in the electronic ground state of the special pair of Rhodobacter sphaeroides reaction centers.

Reaction centers of wild-type Rhodobacter sphaeroides were selectively (13)C-isotope labeled in bacteriochlorophyll and bacteriopheophytin. (13)C solid-state CP/MAS NMR and photo-CIDNP were used to provide insight into the electronic structure of the primary electron donor and acceptor on the atomic scale. The first 2-dimensional photochemically induced dynamic nuclear polarization (photo-CIDNP) (13)C-(13)C solid-state MAS NMR spectra reveal that negative charging of the two BChl rings of the primary donor is involved in ground-state tuning of the oxidation potential of these cofactors in the protein via local electrostatic interactions. In particular, the (13)C shifts show moderate differences in the electronic structure between the two BChl molecules of the special pair in the electronic ground state, which can be attributed to hydrogen bonding of one of the BChl molecules. The major fraction of the electron spin density is strongly delocalized over the two BChl molecules of the special pair and the photochemically active BPhe. A small fraction of the pi-spin density is distributed over a fourth component, which is assigned to the accessory BChl. Comparison of the photo-CIDNP data with "dark" NMR spectra obtained in ultra high field indicates a rigid special pair environment upon photoreaction and suggests that structural changes of the aromatic macrocycles of the two BChl molecules of the special pair do not significantly contribute to the reorganization energy associated with the charge-transfer process.

Bacteriochlorophylls↗