Enantioselective binding of an 11-cis-locked cyclopropyl retinal. The conformation of retinal in bovine rhodopsin

[formula: see text] The conformation of the retinal chromophore in rhodopsin is central for understanding the visual transduction process. The absolute twist around the 12-s bond of the chromophore in rhodopsin has been determined by studies with 11-cis-locked 11,12-cyclopropylretinal analogues (11S,12R)-2 and (11R,12S)-3, enantioselectively synthesized with the aid of an enzyme. The finding that enantiomer 2 binds to opsin while the other 3 does not defines the absolute sense of twist around the 12-s bond.     

Towards a correlation of absolute configuration and chiroptical properties of alkyl aryl sulfoxides: a coupled-oscillator foundation of the empirical Mislow rule?

The absorption and circular dichroism (CD) data for a series of alkyl aryl sulfoxides 1-16 of known S configuration have been analyzed. The strong bathochromic effect exerted by the nitro group in the para position of the phenyl sulfoxides indicates that the sulfur atom acts as an electron donor moiety towards the phenyl ring. Such behavior requires a significant 2p(C)-3sp3(S) overlap, and therefore the phenyl (and p-substituted phenyl) sulfoxides 1-12, as well as the 2-naphthyl sulfoxides 15 and 16, must assume a conformation which permits such orbital overlap. The steric effect of the peri hydrogen in 1-naphthyl-substituted compounds 13 and 14 does not allow a conformation of this type, and in these compounds the above-mentioned 2p(C) and 3sp3(S) orbitals are positioned in almost orthogonal planes. This conformational difference is clearly shown by the absorption spectra: compounds 1-12, 15, and 16 show the lowest energy sigma --> sigma* transition of the sulfoxide chromophore at approximately 250 nm, indicating the existence of a conjugated S=O chromophore. In contrast, the corresponding absorption in 13 and 14 occurs at about 200 nm, indicating the presence of an isolated S=O chromophore. The CD spectra of 13 and 14 show a negative, couplet-like feature between 250 and 200 nm. This spectral feature can be interpreted in terms of exciton coupling between the allowed sigma --> sigma* transition of the isolated S=O chromophore at 200 nm and the 1B transition of the naphthalene chromophore. In fact, the Harada-Nakanishi rule predicts a negative CD couplet for an S-configured sulfoxide in the conformation found by UV analysis, as found experimentally. The CD spectrum of 13 is quantitatively reproduced by DeVoe coupled-oscillator calculations, strongly implying that a coupled-oscillator mechanism is operative in determining the optical activity of 13 and 14. This approach has also tentatively been extended to the conjugated sulfoxides 1-12, taking into account the coupling of the benzene chromophore 1La transition with the sigma --> sigma* transition of the S=O chromophore. In this case the Harada-Nakanishi rule also predicts a negative CD couplet for the S-configured sulfoxides, as found experimentally.     

Constraints of opsin structure on the ligand-binding site: studies with ring-fused retinals

Ring-fused retinal analogs were designed to examine the hula-twist mode of the photoisomerization of the 9-cis retinylidene chromophore. Two 9-cis retinal analogs, the C11-C13 five-membered ring-fused and the C12-C14 five-membered ring-fused retinal derivatives, formed the pigments with opsin. The C11-C13 ring-fused analog was isomerized to a relaxed all-trans chromophore (lambda(max) > 400 nm) at even -269 degrees C and the Schiff base was kept protonated at 0 degrees C. The C12-C14 ring-fused analog was converted photochemically to a bathorhodopsin-like chromophore (lambda(max) = 583 nm) at -196 degrees C, which was further converted to the deprotonated Schiff base at 0 degrees C. 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.     

INCORPORATION OF 11,12-DIHYDRORETINAL INTO THE RETINAE OF VITAMIN A DEPRIVED RATS

Abstract— The incorporation of 11,12-[15–³H]-dihydroretinal, a retinal in which the crucial 11-ene is saturated, into the retinae of vitamin A deficient rats as a result of intraperitoneal injection of the corresponding alcohol was shown by the presence of the tritium label in the rod outer segments and by identification of the extracted retinals using high pressure liquid chromatography. The amplitude of the electroretinogram (ERG) b-wave, diminished as the result of vitamin A deprivation, was not affected by administration of the analogue, although similar treatment of deprived litter mates with trans retinal restored the ERG b-wave amplitude to a normal level.
The evidence that the analogue is bound to opsin forming 11,12-dihydrorhodopsin is as follows: (1) when incubated with 11- cis retinal, extracts from vitamin A deficient rats regenerate 1.4 nmol rhodopsin while extracts from rats deficient in vitamin A and supplemented with 11,12-dihydroretinal regenerate 0.6 nmol rhodopsin indicating binding of the dihydroretinal blocks rhodopsin regeneration. (2) 11,12-dihydroretinal is shown to remain unchanged in hexane-washed retinae after extraction with methylene chloride and (3) injection of retinal into animals previously injected with 11,12-dihydroretinal also fails to restore visual sensitivity as measured by the ERG b-wave. Our results indicate that the dihydro-chromophore occupies the same binding site as the natural 11- cis retinal and that occupation of the chromophore binding site of opsin is not sufficient to restore the visual sensitivity in a vitamin-A-deprived animal.     

THE CONFORMATIONAL ANALYSIS AND PHOTOISOMERIZATION OF RETINOCHROME ANALOGS WITH POLYENALS

Abstract— 3, 7-Dimethyl-2, 4, 6, 8, 10-dodecapentaenal was synthesized for reconstitution of the retinochrome analog. Its opsin shift was 1000 cm ¹ smaller than that of native retinochrome, whose chromophore contains the same number of double bonds. The conformational change from 6-s-trans to 6-s-cis , as figured in a retinal molecule, plays an important role in the formation of the retinochrome analog, based on the estimation of opsin shifts for retinal analogs locked in the 6-s conformation. Thus the conformation of the 6–7 single bond in the native retinochrome was suggested to be 6 -cis . Analysis of the circular dichroic spectra of retinochrome analogs revealed that the 6-s conformation is independent of the appearance of the β-band. The stereoselectivity in the photoisomerization of the retinal analogs by a retinochrome template depends on the hydrophobic binding in the region of the β-ionone ring.     

Recent bioorganic studies on rhodopsin and visual transduction

Rhodopsin, the pigment responsible for vision in animals, insect and fish is a typical G protein (guanyl-nucleotide binding protein) consisting of seven transmembrane alpha helices and their interconnecting extramembrane loops. In the case of bovine rhodopsin, the best studied of the visual pigments, the chromophore is 11-cis retinal attached to the terminal amino group of Lys296 through a protonated Schiff base linkage. Photoaffinity labeling with a 3-diazo-4-oxo-retinoid shows that C-3 of the ionone ring moiety is close to Trp265 in helix F (VI) in dark inactivated rhodopsin. Irradiation causes a cis to trans isomerization of the 11-cis double bond giving rise to the highly strained intermediate bathorhodopsin. This undergoes a series of thermal relaxation through lumi-, meta-I and meta-II intermediates after which the retinal chromophore is expelled from the opsin binding pocket. Photoaffinity labeling performed with 3-diazo-4-oxoretinal at -196 degrees C for batho-, -80 degrees C for lumi-, -40 degrees C for meta-I, and 0 degrees C for meta-II rhodopsin showed that in bathorhodopsin the ring is still close to Trp265. However, in lumi-, meta-I and meta-II intermediates crosslinking occurs unexpectedly at A169 in helix D (IV). This shows that large movements in the helical arrangements and a flip over of the ring moiety accompanies the transduction (or bleaching) process. These changes in retinal/opsin interactions are necessarily accompanied by movements of the extramembrane loops, which in turn lead to activation of the G protein residing in the cytoplasmic side. Of the numerous G protein coupled receptors, this is the first time that the outline of transduction pathway has been clarified.     

Rhodopsin regeneration is accelerated via noncovalent 11-cis retinal-opsin complex--a role of retinal binding pocket of opsin

The regeneration of bovine rhodopsin from its apoprotein opsin and the prosthetic group 11-cis retinal involves the formation of a retinylidene Schiff base with the epsilon-amino group of the active lysine residue of opsin. The pH dependence of a Schiff base formation in solution follows a typical bell-shaped profile because of the pH dependence of the formation and the following dehydration of a 1-aminoethanol intermediate. Unexpectedly, however, we find that the formation of rhodopsin from 11-cis retinal and opsin does not depend on pH over a wide pH range. These results are interpreted by the Matsumoto and Yoshizawa (Nature 258 [1975] 523) model of rhodopsin regeneration in which the 11-cis retinal chromophore binds first to opsin through the beta-ionone ring, followed by the slow formation of the retinylidene Schiff base in a restricted space. We find the second-order rate constant of the rhodopsin formation is 6100+/-300 mol(-1) s(-1) at 25 degrees C over the pH range 5-10. The second-order rate constant is much greater than that of a model Schiff base in solution by a factor of more than 10(7). A previous report by Pajares and Rando (J Biol Chem 264 [1989] 6804) suggests that the lysyl epsilon-NH(2) group of opsin is protonated when the beta-ionone ring binding site is unoccupied. The acceleration of the Schiff base formation in rhodopsin is explained by stabilization of the deprotonated form of the lysyl epsilon-NH(2) group which might be induced when the beta-ionone ring binding site is occupied through the noncovalent binding of 11-cis retinal to opsin at the initial stage of rhodopsin regeneration, followed by the proximity and orientation effect rendered by the formation of noncovalent 11-cis retinal-opsin complex.     

Stairway to the conical intersection: a computational study of the retinal isomerization

The potential-energy surface of the first excited state of the 11-cis-retinal protonated Schiff base (PSB11) chromophore has been studied at the density functional theory (DFT) level using the time-dependent perturbation theory approach (TDDFT) in combination with Becke's three-parameter hybrid functional (B3LYP). The potential-energy curves for torsion motions around single and double bonds of the first excited state have also been studied at the coupled-cluster approximate singles and doubles (CC2) level. The corresponding potential-energy curves for the ground state have been calculated at the B3LYP DFT and second-order M?ller-Plesset (MP2) levels. The TDDFT study suggests that the electronic excitation initiates a turn of the beta-ionone ring around the C6-C7 bond. The torsion is propagating along the retinyl chain toward the cis to trans isomerization center at the C11=C12 double bond. The torsion twist of the C10-C11 single bond leads to a significant reduction in the deexcitation energy indicating that a conical intersection is being reached by an almost barrierless rotation around the C10-C11 single bond. The energy released when passing the conical intersection can assist the subsequent cis to trans isomerization of the C11=C12 double bond. The CC2 calculations also show that the torsion barrier for the twist of the retinyl C10-C11 single bond adjacent to the isomerization center almost vanishes for the excited state. Because of the reduced torsion barriers of the single bonds, the retinyl chain can easily deform in the excited state. Thus, the CC2 and TDDFT calculations suggest similar reaction pathways on the potential-energy surface of the excited state leading toward the conical intersection and resulting in a cis to trans isomerization of the retinal chromophore. According to the CC2 calculations the cis to trans isomerization mechanism does not involve any significant torsion motion of the beta-ionone ring.     

Diterpenoide Chinomethane,vinyloge Chinone und ein Phyllocladan-Derivat aus Plectranthus purpuratus HARV. (Labiatae)

Diterpenoids from Leaf Glands of Plectranthus purpuratus: p-Quinomethanes, Extended Quinones, p-Acylcatechols and a Novel Phyllocladanon Derivative From the complex mixture of terpenoids from the title plant, the following novel diterpenoids have been isolated: 11-hydroxy-19-(3-methyl-2-butenoyloxy)- and 11-hydroxy-19-(3-methylbutanoyloxy)-5,7,9 (11), 13-abietatetraen-12-one ( 1a / 1b ), 11-hydroxy-19-(3-methyl-2-butenoyloxy)- and 11-hydroxy-19-(3-methylbutanoyl-oxy)-7,9(11), 13-abietatrien-6,12-dione ( 2a / 2b ), 6α, 11-dihydroxy-19-(3-methyl-2-butenoyloxy)- and 6α, 11 -dihydroxy-19-(3-methylbutanoyloxy)-7,9 (11), 13-abieta-trien-12-one ( 3a / 3b ), 11,12-dihydroxy-19-(3-methyl-2-butenoyloxy)- and 11,12-di-hydroxy-19-(3-methylbutanoyloxy)-8,11,13-abietatrien-7-one ( 4a / 4b ), and (16R)-17,19-diacetoxy-16-hydroxy-13β-kauran-3-one (=(16R)-17,19-diacetoxy-16-hydro-xyphyllocladan-3-one; 10 ). Compounds 2 and 3 are derivates of taxodione and taxodone, respectively, 4 is a derivative of cryptojaponol. The structure of 10 is Wised on a single-crystal- X -ray analysis and CD . data.     

Primary events in dim light vision: a chemical and spectroscopic approach toward understanding protein/chromophore interactions in rhodopsin

The visual pigment rhodopsin (bovine) is a 40 kDa protein consisting of 348 amino acids, and is a prototypical member of the subfamily A of G protein-coupled receptors (GPCRs). This remarkably efficient light-activated protein (quantum yield = 0.67) binds the chromophore 11-cis-retinal covalently by attachment to Lys296 through a protonated Schiff base. The 11-cis geometry of the retinylidene chromophore keeps the partially active opsin protein locked in its inactive state (inverse agonist). Several retinal analogs with defined configurations and stereochemistry have been incorporated into the apoprotein to give rhodopsin analogs. These incorporation results along with the spectroscopic properties of the rhodopsin analogs clarify the mode of entry of the chromophore into the apoprotein and the biologically relevant conformation of the chromophore in the rhodopsin binding site. In addition, difference UV, CD, and photoaffinity labeling studies with a 3-diazo-4-oxo analog of 11-cis-retinal have been used to chart the movement of the retinylidene chromophore through the various intermediate stages of visual transduction.     

Assignment of absolute configuration of a chiral phenyl-substituted dihydrofuroangelicin

A phenyl-substituted chiral dihydrofuroangelicin, 4-methyl-8-(2-E-phenylethenyl)-8,9-dihydro-2H-furo[2,3-h]- 1-benzopyran-2-one, synthesized in racemic form, has been resolved by HPLC chiral separation, and its absolute configuration determined by the non-empirical exciton chirality method. The solution conformation has been investigated through NMR and molecular modeling methods: two minima found by molecular mechanics and DFT methods are in keeping with observed 1H-1H 3J coupling constants and NOE effects. The experimental CD spectrum for the second eluted enantiomer shows a positive couplet between 230 and 350 nm (amplitude A = + 15.7); by application of the exciton chirality method, the absolute configuration of this enantiomer at C8 is determined as (S). The experimental spectrum is in very good agreement with the one evaluated by means of DeVoe coupled-oscillator calculations, using the DFT calculated geometries.     

EFFECT OF THE PHYSICAL STATE OF PHOSPHOLIPID ON RHODOPSIN REGENERATION FROM RETINYLIDENE PHOSPHOLIPID

Abstract— Rhodopsin regeneration in rod membranes involves reactions of all -trans retinal (released from bleached pigment) with phosphatidylethanolamine, photic isomerization of retinal, and binding of 11-cis retinal to opsin. This investigation demonstrated that formation of retinylidene phospholipid and retinal binding to opsin were both affected by the physical state of phospholipid. A fluid membraneous environment provided by the acyl chains of phospholipid was essential for these reactions to proceed efficiently. The retinal moiety of retinylidene phospholipid appeared to be directly transferred to opsin by transimination.     

A new case of induced helical chirality in a bichromophoric system: absolute configuration of transparent and flexible diols from the analysis of the electronic circular dichroism spectra of the corresponding di(1-naphthyl)ketals

Di(1-naphthyl)ketals of 1, n-diols show couplet effects allied to the (1)B naphthalene transition in their CD spectra. This means that they assume a conformation with a prevailing sense of twist of the naphthalene rings, imposed by the absolute configuration (AC) of the starting diols and by the nature of the R 1 groups. A positive couplet for aliphatic diols is a probe of ( R, R), AC while the opposite sign is found for ( R, R) aromatic diols.     

Synthesis and properties of oligonucleotides having a phosphorus chiral center by incorporation of conformationally rigid 5'-cyclouridylic acid derivatives

This paper describes the design and synthesis of a conformationally rigid dimer building block Umpc3Um as a chiral center at the phosphate group with the S/N junction where c3 refers to a propylene bridge linked between the uracil 5-position and 5'-phosphate group of pUm. The extensive H1 NMR analysis of Umpc3Um suggests that the 5'-upstream Um has predominantly a C2'-endo conformation and the pc3Um moiety exists almost exclusively in a C3'-endo conformation. The absolute configuration of the diastereomers Umpc3Um(fast) (8a) and Umpc3Um(slow) (8b) was determined by CD spectroscopy as well as computer simulations. The oligonucleotides U4[Umpc3Um(fast)]U4 (13a) and U4[Umpc3Um(slow)]U4 (13b) incorporating 8a and 8b were synthesized by use of the phosphoramidite building blocks 11a and 11b, respectively. The Tm experiments of the duplexes formed between these modified oligomers and the complementary oligomers imply that the modified oligomer 13a having Umpc3Um(fast) has the Sp configuration at the chiral phosphoryl group.     

Porphyrins conjugated to DNA as CD reporters of the salt-induced B to Z-DNA transition

The porphyrin chromophore incorporated at the 5'-position of an oligonucleotide allows the simultaneous detection of the B- to Z-DNA transition via the porphyrin Soret band circular dichroism exciton couplet signal around 420 nm and the oligonucleotide CD region below 300 nm, at micromolar concentrations.     

On the chiroptical properties of ketimine structures derived from 5-chloro-2-hydroxybenzophenone

The CD curves of several ketimines derived from condensation of 5-chloro-2-hydroxybenzophenone with optically active amino compounds have been measured. The geometric relationship between the chromophoric groups in the amino moiety and the 5-chloro-2-hydroxybenzophenone chromophore, which depends on the absolute configuration and conformation of the molecule, is more important than chirality at the asymmetric C atom in determining the chiroptical properties of these compounds.     

Rhodopsin deactivation is affected by mutations of Tyrl91

The 9-methyl group of 11-cis retinal is important in the efficient formation of the active conformation of rhodopsin, Meta II. Here, Tyrl91 rhodopsin mutants were generated because of its proximity to that methyl group in the dark structure. If photoactivation results in movement of the 9-methyl group toward Tyrl91, the steric interactions involved with activation and/or deactivation might not be as tightly coupled in mutant proteins with smaller amino acids at that position. Tyrl91 mutations have no effect on the dark pigment. However, after photobleaching, the lifetime of Meta II is shorter; Meta II decays quickly into two inactive species: (1) a Meta III or Meta III-like species and (2) opsin and free retinal. The Meta III-like fraction maintains the covalent Schiff base linkage of the chromophore much longer than the wild type. On the other hand, the fast chromophore release is similar to cone pigments. Taken together, the data suggest that the role of the 9-methyl group after photo-isomerization is not only to form Meta II efficiently, but also to maintain its active conformation and allow for the timely hydrolysis of the Schiff base. Perturbation of this interaction effects changes in the hydrolysis of the Schiff base and for the case of the Y191A mutation the folded structure of the protein after photobleaching.     

THEORETICAL STUDY OF COLOR CONTROL MECHANISM IN RETINAL PROTEINS. I. ROLE OF THE TRYPTOPHAN RESIDUE, TYROSINE RESIDUE and WATER MOLECULE

Abstract –We calculated the opsin shift due to the electrostatic interaction between tryptophan or tyrosine residues and the chromophore by the perturbation method for various mutual configurations. The obtained opsin shift maps for these configurations demonstrated that when the above residues reside around the ionone ring side, the positive opsin shift (bathochromic shift) is obtained, and when they reside around the Schiff-base side, the negative opsin shift (hypsochromic shift) is obtained. These properties hold true, irrespective of the orientation of those residues, indicating that higher order multipoles of the group play a central role. The maximum value of the opsin shift by these groups amounts to several hundred wavenumbers. These results indicate that the location of some of those amino acid residues at proper positions around the chromophore can cause a considerable opsin shift. We also calculated opsin shift maps for the various mutual configurations between a water molecule and the chromophore for comparison.     

THE ORIGIN OF THE RED-SHIFTED ABSORPTION MAXIMUM OF THE M412 INTERMEDIATE IN THE BACTERIORHODOPSIN PHOTOCYCLE

The factors that red shift the absorption maximum of the retinal Schiff base chromophore in the M₄₁₂ intermediate of bacteriorhodopsin photocycle relative to absorption in solution were investigated using a series of artificial pigments and studies of model compounds in solution. The artificial pigments derived from retinal analogs that perturb chromophore-protein interactions in the vicinity of the ring moiety indicate that a considerable part of the red shift may originate from interactions in the vicinity of the Schiff base linkage. Studies with model compounds revealed that hydrogen bonding to the Schiff base moiety can significantly red shift the absorption maximum. Furthermore, it was demonstrated that although s-trans ring-chain planarity prevails in the M₄₁₂ intermediate it does not contribute significantly (only ca 750 cm⁻¹) to the opsin shift observed in M₄₁₂. It is suggested that in M₄₁₂, the Schiff base linkage is hydrogen bonded to bound water and/or protein residues inducing a considerable red shift in the absorption maximum of the retinal chromophore.     

Sub-5-fs real-time spectroscopy of transition states in bacteriorhodopsin during retinal isomerization

By using a sub-5-fs visible laser pulse, we have made the first observation of the vibrational spectra of the transition state during trans-cis isomerization in the retinal chromophore of bacteriorhodopsin (bR(S68). No instant isomerization of the retinal occurs in spite of electron promotion from the bonding pi-orbital to the anti-bonding pi*-orbital. The difference between the in-plane and out-of-plane vibrational frequencies (about 1150-1250 and 900-1000 cm(-1), respectively) is reduced during the first time period. The vibrational spectra after this period became very broad and weak and are ascribed to a "silent state." The silent state lasts for 700-900 fs until the chromophore isomerizes to the cis-C13 = C14 conformation. The frequency of the C = C stretching mode was modulated by the torsion mode of the C13 = C14 double bond with a period of 200 fs. The modulation was clearly observed for four to five periods. Using the empirical equation for the relation between bond length and stretching frequency, we determined the transitional C = C bond length with about 0.01 angstroms accuracy during the torsion motion around the double bond with 1-fs time resolution.