Solution and biologically relevant conformations of enantiomeric 11-cis-locked cyclopropyl retinals (original) (raw)
Related papers
Constraints of Opsin Structure on the Ligand-binding Site: Studies with Ring-fused Retinals¶
Photochemistry and Photobiology, 2002
Ring-fused retinal analogs were designed to examine the hulatwist mode of the photoisomerization of the 9-cis retinylidene chromophore. Two 9-cis retinal analogs, the C11-C13 fivemembered ring-fused and the C12-C14 five-membered ringfused retinal derivatives, formed the pigments with opsin. The C11-C13 ring-fused analog was isomerized to a relaxed alltrans chromophore (l max > 400 nm) at even 22698C and the Schiff base was kept protonated at 08C. The C12-C14 ringfused analog was converted photochemically to a bathorhodopsin-like chromophore (l max 5 583 nm) at 21968C, which was further converted to the deprotonated Schiff base at 08C. The model-building study suggested that the analogs do not form pigments in the retinal-binding site of rhodopsin but form pigments with opsin structures, which have larger binding space generated by the movement of transmembrane helices. The molecular dynamics simulation of the isomerization of the analog chromophores provided a twisted C11-C12 double bond for the C12-C14 ring-fused analog and all relaxed double bonds with a highly twisted C10-C11 bond for the C11-C13 ring-fused analog. The structural model of the C11-C13 ring-fused analog chromophore showed a characteristic flip of the cyclohexenyl moiety toward transmembrane segments 3 and 4. The structural models suggested that hula twist is a primary process for the photoisomerization of the analog chromophores.
Journal of Natural Products, 2011
Retinal is the natural ligand (chromophore) of the vertebrate rod visual pigment. It occurs in either the 11-cis (rhodopsin) or the 9-cis (isorhodopsin) configuration. In its evolution to a G protein coupled photoreceptor, rhodopsin has acquired exceptional photochemical properties. Illumination isomerizes the chromophore to the alltrans isomer, which acts as a full agonist. This process is extremely efficient, and there is abundant evidence that the C-9 and C-13 methyl groups of retinal play a pivotal role in this process. To examine the steric limits of the C-9 and C-13 methyl binding pocket of the binding site, we have prepared C-9 and C-13 cyclopropyl and isopropyl derivatives of its native ligands and of R-retinal at C-9. Most isopropyl analogues show very poor binding, except for 9-cis-13-isopropylretinal. Most cyclopropyl derivatives exhibit intermediate binding activity, except for 9-cis-13-cyclopropylretinal, which presents good binding activity. In general, the binding site shows preference for the 9-cis analogues over the 11-cis analogues. In fact, 13-isopropyl-9-cisretinal acts as a superagonist after illumination. Another surprising finding was that 9-cyclopropylisorhodopsin is more like native rhodopsin with respect to spectral and photochemical properties, whereas 9-cyclopropylrhodopsin behaves more like native isorhodopsin in these aspects. II (λ max = 380 nm), which binds and activates its cognate G protein transducin (G t ). The photochemical performance of the 11-cis-retinal-opsin couple is exceptional, showing a photoisomerization quantum yield of 0.65 ( 0.02 and a fully selective reaction pathway (11-cis f all-trans) and generating within 200 fs a vibrationally hot intermediate (photorhodopsin) with a highly distorted, but already all-transoid chromophore. Within 1 ps photorhodopsin relaxes to Batho, which still contains a highly strained all-trans chromophore. Isorhodopsin exhibits similar features, except that its photochemistry is less efficient (slower kinetics and lower quantum yield of 0.26 ( 0.03). The crux of this top performance lies in an optimal nonbonding communication between ligand and protein. This aspect has been investigated in a large number of experimental studies, employing modified retinals that generate (iso)rhodopsin analogue pigments. [26][29][35][42] These studies have vastly expanded our insight in the binding site requirements. Relevant in the context
Biophysics, 2009
The molecular dynamics of the rhodopsin chromophore (11 cis retinal) has been followed over a 3 ns path, whereby 3 × 10 6 discrete conformational states of the molecule were recorded. It is shown that within a short time, 0.3-0.4 ns from the start of simulation, the retinal β ionone ring rotates about the C6-C7 bond through ~60° relative to the initial configuration, and the whole chromophore becomes twisted. The results of ab initio quantum chemical calculations indicate that for the final conformation of the chro mophore center (t = 3 ns) the rhodopsin absorption maximum is shifted by 10 nm toward longer wavelengths as compared with the initial state (t = 0). In other words, the energy of transition of such a system into the excited singlet state S1 upon photon capture will be lower than that for the molecule where the β ionone ring of the chromophore is coplanar to its polyene chain.
Biochemistry Usa, 1999
Rhodopsin is the G-protein coupled photoreceptor that initiates the rod phototransduction cascade in the vertebrate retina. Using specific isotope enrichment and magic angle spinning (MAS) NMR, we examine the spatial structure of the C10-C11dC12-C13-C20 motif in the native retinylidene chromophore, its 10-methyl analogue, and the predischarge photoproduct metarhodopsin-I. For the rhodopsin study 11-Z-[10,20-13 C 2 ]-and 11-Z-[11,20-13 C 2 ]-retinal were synthesized and incorporated into bovine opsin while maintaining a natural lipid environment. The ligand is covalently bound to Lys 296 in the photoreceptor. The C10-C20 and C11-C20 distances were measured using a novel 1-D CP/MAS NMR rotational resonance experimental procedure that was specifically developed for the purpose of these measurements [Verdegem, P. J. E., Helmle, M., Lugtenburg, J., and de Groot, H. J. M. (1997) J. Am. Chem. Soc. 119, 169]. We obtain r 10,20 ) 0.304 ( 0.015 nm and r 11,20 ) 0.293 ( 0.015 nm, which confirms that the retinylidene is 11-Z and shows that the C10-C13 unit is conformationally twisted. The corresponding torsional angle is about 44°as indicated by Car-Parrinello modeling studies. To increase the nonplanarity in the chromophore, 11-Z-[10,20-13 C 2 ]-10-methylretinal and 11-Z-[(10-CH 3 ),13-13 C 2 ]-10-methylretinal were prepared and incorporated in opsin. For the resulting analogue pigment r 10,20 ) 0.347 ( 0.015 nm and r (10-CH 3 ),13 ) 0.314 ( 0.015 nm were obtained, consistent with a more distorted chromophore. The analogue data are in agreement with the induced fit principle for the interaction of opsin with modified retinal chromophores. Finally, we determined the intraligand distances r 10,20 and r 11,20 also for the photoproduct metarhodopsin-I, which has a relaxed all-E structure. The results (r 10,20 g 0.435 nm and r 11,20 ) 0.283 ( 0.015 nm) fully agree with such a relaxed all-E structure, which further validates the 1-D rotational resonance technique for measuring intraligand distances and probing ligand structure. As far as we are aware, these results represent the first highly precise distance determinations in a ligand at the active site of a membrane protein. Overall, the MAS NMR data indicate a tight binding pocket, well defined to bind specifically only one enantiomer out of four possibilities and providing a steric complement to the chromophore in an ultrafast (∼200 fs) isomerization process. †
Chirality, 2004
An all-trans-retinal (ATR) dimer (1) isolated from photoreceptor outer segments was found to have a stereogenic center at C13′ flanked by tetraene (295 nm) and hexaenal (438 nm) chromophores. Analytical chiral HPLC (Chiralcel OD) revealed that the isolated retinoid had formed in 13% enantiomeric excess. Using a combination of 1H-1H NOESY constraints, molecular modeling, and CD exciton coupling analysis, it was determined that the favored enantiomer was 13′(R). Three low-energy conformers of the 13′(S) model were found with MMFF/DFT and were used to calculate the CD spectrum of the ATR dimer (DeVoe method). The Boltzmann weighted spectrum was found to exhibit a positive exciton couplet, in excellent agreement with the experimental spectrum for the first eluted enantiomer. This further suggested that despite the large energy difference between the two interacting chromophores, the dominant source of optical activity in the CD spectrum is the nondegenerate exciton mechanism. Chirality 16:637–641, 2004. © 2004 Wiley-Liss, Inc.
Photochemistry and Photobiology, 2009
It was previously shown that opsin can be regenerated with the newly synthesized 11-cis-7-methyl-retinal forming an artificial visual pigment. We now extend this study to include mutants at positions close to the retinal to further dissect the interactions of native and artificial chromophores with opsin. Several mutants at M207, W265 and Y268 have been obtained and regenerated with 11-cis-retinal and the 7-methyl analog. M207 is the site of the point mutation M207R associated with the retinal degenerative disease retinitis pigmentosa. All the studied mutants regenerated with 11-cis-retinal except for M207C which proved to be completely misfolded. The naturally occurring M207R mutant formed a pigment with an unprotonated Schiff base linkage, altered photobleaching and low MetarhodopsinII stability. Mutants regenerated with the 7-methyl analog showed altered photobleaching reflecting a structural perturbation in the vicinity of M207. The newly obtained mutants at M207 also showed reduced levels of transducin activation with M207R showing essentially no transducin activation. Our results highlight the tight coupling of the vicinity of C7 of retinal and M207 and support the involvement of this amino acid residue in the conformational changes associated with rhodopsin photoactivation.
Phase Transitions, 2002
The 11-cis-retinal protonated Schiff base is the chromophore of rhodopsin, the photoreceptor in the vertebrate eye. The photochemical isomerization from 11-cis to the all-trans form triggers a series of enzymatic reactions known as the visual cascade which eventually leads to a neural signal. Experiments such as resonance Raman, NMR etc., have shown that 11-cis-retinal is probably highly twisted in the protein pocket. Because detailed knowledge about the kind of interaction with the protein is missing, a theoretical description of the chromophore conformation is difficult. In the simulations the results of which will be presented here, we assume that the retinal chromophore, as a consequence of the steric fit into the protein binding pocket, undergoes a specific kind of conformational change. The structure we obtain is in good agreement with the experimentally observed highly twisted conformation of the chromophore backbone.
The molecular structure of a curl-shaped retinal isomer
Journal of Molecular Modeling, 2008
Computational studies of retinal protonated Schiff base (PSB) isomers show that a twisted curl-shaped conformation of the retinyl chain is a new low-lying minimum on the ground-state potential energy surface. The curl-shaped isomer has a twisted structure in the vicinity of the C 11 =C 12 double bond where the 11-cis retinal PSB isomerizes in the rhodopsin photoreaction. The twisted configuration is a trapped structure between the 11cis and all-trans isomers. Rotation around the C 10 -C 11 single bond towards the 11-cis structure is prevented by steric interactions of the two methyl groups on the retinyl chain and by the torsion barrier of the C 10 -C 11 bond in the other direction. Calculations of spectroscopic properties of the 11-cis, all-trans, and curl-shaped isomers provide useful data for future identification of the new retinal PSB isomer. Circular dichroism (CD) spectroscopy might be used to distinguish between the retinal PSB isomers. The potential energy surface for the orientation of the β-ionone ring of the 11-cis retinal PSB reveals three minima depending on the torsion angle of the β-ionone ring. Two of the minima correspond to 6-s-cis configurations and one has the βionone ring in 6-s-trans position. The calculated CD spectra for the two 6-s-cis configurations differ significantly indicating that the sign of the β-ionone ring torsion angle could be determined using CD spectroscopy. Calculations of the CD spectra suggest that a flip of the β-ionone ring might occur during the first 1 ps of the photoreaction. Rhodopsin has a negative torsion angle for the β-ionone ring, whereas the change in the sign of the first peak in the experimental CD spectrum for bathorhodopsin could suggest that it has a positive torsion angle for the β-ionone ring. Calculated nuclear magnetic resonance (NMR) shielding constants and infrared (IR) spectra are also reported for the retinal PSB isomers.
Journal of Molecular Biology, 2007
Rhodopsin is a prototype for G protein-coupled receptors (GPCRs) that are implicated in many biological responses in humans. A site-directed 2 H NMR approach was used for structural analysis of retinal within its binding cavity in the dark and pre-activated meta I states. Retinal was labeled with 2 H at the C5, C9, or C13 methyl groups by total synthesis, and was used to regenerate the opsin apoprotein. Solid-state 2 H NMR spectra were acquired for aligned membranes in the low-temperature lipid gel phase versus the tilt angle to the magnetic field. Data reduction assumed a static uniaxial distribution, and gave the retinylidene methyl bond orientations plus the alignment disorder (mosaic spread). The darkstate 2 H NMR structure of 11-cis-retinal shows torsional twisting of the polyene chain and the β-ionone ring. The ligand undergoes restricted motion, as evinced by order parameters of ≈ 0.9 for the spinning C-C 2 H 3 groups, with off-axial fluctuations of ≈ 15°. Retinal is accommodated within the rhodopsin binding pocket with a negative pre-twist about the C11 = C12 double bond that explains its rapid photochemistry and the trajectory of 11-cis to trans isomerization. In the cryo-trapped meta I state, the 2 H NMR structure shows a reduction of the polyene strain, while torsional twisting of the β-ionone ring is maintained. Distortion of the retinal conformation is interpreted through substituent control of receptor activation. Steric hindrance between trans retinal and Trp265 can trigger formation of the subsequent activated meta II state. Our results are pertinent to quantum and molecular mechanics simulations of ligands bound to GPCRs, and illustrate how 2 H NMR can be applied to study their biological mechanisms of action.