Importance of the sphingosine base double-bond geometry for the structural and thermodynamic properties of sphingomyelin bilayers

The precise role of the sphingosine base trans double bond for the unique properties of sphingomyelins (SMs), one of the main lipid components in raftlike structures of biological membranes, has not been fully explored. Several reports comparing the hydration, lipid packing, and hydrogen-bonding behaviors of SM and glycerophospholipid bilayers found remarkable differences overall. However, the atomic interactions linking the double-bond geometry with these thermodynamic and structural changes remained elusive. A recent report on ceramides, which differ from SMs only by their hydroxyl headgroup, has shown that replacing the trans double bond of the sphingosine base by cis weakens the hydrogen-bonding potential of these lipids and thereby alters their biological activity. Based on data from extensive (a total 0.75 μs) atomistic molecular dynamics simulations of bilayers composed of all-trans, all-cis, and a trans/cis (4:1 ratio) racemic mixture of sphingomyelin lipids, here we show that the trans configuration allows for the formation of significantly more hydrogen bonds than the cis. The extra hydrogen bonds enabled tighter packing of lipids in the all-trans and trans/cis bilayers, thus reducing the average area per lipid while increasing the chain order and the bilayer thickness. Moreover, fewer water molecules access the lipid-water interface of the all-trans bilayer than of the all-cis bilayer. These results provide the atomic basis for the importance of the natural sphingomyelin trans double-bond conformation for the formation of ordered membrane domains.     

Coupling of retinal, protein, and water dynamics in squid rhodopsin

The light-induced isomerization of the retinal from 11-cis to all-trans triggers changes in the conformation of visual rhodopsins that lead to the formation of the activated state, which is ready to interact with the G protein. To begin to understand how changes in the structure and dynamics of the retinal are transmitted to the protein, we performed molecular dynamics simulations of squid rhodopsin with 11-cis and all-trans retinal, and with two different force fields for describing the retinal molecule. The results indicate that structural rearrangements in the binding pocket, albeit small, propagate toward the cytoplasmic side of the protein, and affect the dynamics of internal water molecules. The sensitivity of the active-site interactions on the retinal force-field parameters highlights the coupling between the retinal molecule and its immediate protein environment.     

Conformational order of the hydrocarbon chains in lipid bilayers. A raman spectroscopic study

Raman spectra of dihexadecylphosphatidic acid (DHPA) and of dimyristoylphosphatidylcholine (DMPC) and its longer chain homologues have been obtained as a function of temperature in order to study the conformational order of the hydrocarbon chains in lipid bilayers. The frequency of the longitudinal acoustical (LA) vibration band is evaluated in terms of the length of all-trans chain segments. In the ordered phase, the chains are found to be overwhelmingly in the all-trans conformation. In the fluid phase, definite all-trans segments occur predominantly, the length of which coincides with the extension of the order parameter plateau known from deuterium magnetic resonance (DMR). The frequency of the skeletal optical (SO) trans vibration band leads to the same result, if evaluated under the assumption of vibrational decoupling by gauche bands in the fluid phase, thus lending support to this assumption. The intensity of this band determined from the band area increases linearly with chain length in the ordered phase and is independent of chain length in the fluid phase. Evaluating the intensity for the length of all-trans segments, the same result for the chain conformation is obtained as derived from the frequencies, with the additional information that the length of the all-trans segments in the fluid phase does not vary with chain length.     

A stereochemical model for phospholipids. II: Conformational analysis and molecular packing of phosphatidylethanolamine (PE)

A partition energy method procedure was applied to select the energetically favoured conformations of phosphatidylethanolamine (PE) as polar constituents of phospholipid molecules. The result indicated a large degree of freedom for the two torsion angles of the ester bond of the phosphate and a gauche, gauche star conformation for the ethane bond.A packing process of the molecule was carried out through a potential energy calculation by considering the conformers selected above, using previously published procedure and conventions. All the arrangements which possess the best packing energy values were characterised by an orientation of the PN dipolar segment parallel to the lattice plain. Rotation of the internal torsion angles and rotation in the eulerian space of the molecule produced differences in the charged groups that interact. An additional minimum was present in the energy packing process of those conformers which have the first torsion angle of the phosphate in a trans conformation. This minimum, which corresponds to an orientation of the molecule orthogonal to the lattice plane, requires a complete neutralisation of the point charges on the system.The results of the calculation underline the importance of changes in the behaviour of the polar group of the phospholipids in the packing process.     

A Ligand Channel through the G Protein Coupled Receptor Opsin

The G protein coupled receptor rhodopsin contains a pocket within its seven-transmembrane helix (TM) structure, which bears the inactivating 11-cis-retinal bound by a protonated Schiff-base to Lys296 in TM7. Light-induced 11-cis-/all-trans-isomerization leads to the Schiff-base deprotonated active Meta II intermediate. With Meta II decay, the Schiff-base bond is hydrolyzed, all-trans-retinal is released from the pocket, and the apoprotein opsin reloaded with new 11-cis-retinal. The crystal structure of opsin in its active Ops* conformation provides the basis for computational modeling of retinal release and uptake. The ligand-free 7TM bundle of opsin opens into the hydrophobic membrane layer through openings A (between TM1 and 7), and B (between TM5 and 6), respectively. Using skeleton search and molecular docking, we find a continuous channel through the protein that connects these two openings and comprises in its central part the retinal binding pocket. The channel traverses the receptor over a distance of ca. 70 Å and is between 11.6 and 3.2 Å wide. Both openings are lined with aromatic residues, while the central part is highly polar. Four constrictions within the channel are so narrow that they must stretch to allow passage of the retinal β-ionone-ring. Constrictions are at openings A and B, respectively, and at Trp265 and Lys296 within the retinal pocket. The lysine enforces a 90° elbow-like kink in the channel which limits retinal passage. With a favorable Lys side chain conformation, 11-cis-retinal can take the turn, whereas passage of the all-trans isomer would require more global conformational changes. We discuss possible scenarios for the uptake of 11-cis- and release of all-trans-retinal. If the uptake gate of 11-cis-retinal is assigned to opening B, all-trans is likely to leave through the same gate. The unidirectional passage proposed previously requires uptake of 11-cis-retinal through A and release of photolyzed all-trans-retinal through B.     

Electrogenic transport properties of bacteriorhodopsin containing chemically modified retinal analogues

The electrical activity of bacteriorhodopsin (BR) containing the 13-substituted retinal analogues 13-demethyl and 13-methoxy as well as the naturally occurring retinal carrying a methyl group at C13 is compared. White membrane patches reconstituted with the different retinals are attached to a black lipid membrane, and the dependency of the photocurrent on light intensity is measured. This allows a comparison of the overall photocycle time and the number of protons transported per cycle for the various preparations. From previous work (Gärtner, W., Towner, P., Hopf, H. and Oesterhelt, D. (1983) Biochem. 22, 2637–2644, see also Gärtner, W. and Oesterhelt, D., unpublished data) the equilibrium isomeric distribution (all-trans and 13-cis) of the different retinals in the binding site is known. Taking into account that only all-trans retinal BR contributes to the pumping activity (Fahr, A. and Bamberg, E. (1982) FEBS Lett. 140, 251–253), it is shown, that the cycle time for the modified BRs is moderately changed, whereas the number of protons transported per cycle and transporting all-trans BR molecule is not affected by the substituent. It is concluded, that substituting the methyl group at position 13 of the retinal molecule by a hydrogen atom or a methoxy group only slightly affects the pumping activity of the trans-photocycle, but rather controls the biological function of BR via the equilibrium isomeric distribution of the retinal molecule in the binding site.     

Spectral characteristics of fluorophores formed via interaction between all-trans-retinal with rhodopsin and lipids in photoreceptor membrane of retina rod outer segments

It is shown that all-trans-retinal under model conditions of its excessive accumulation in photoreceptor membranes interacts with amino groups of rhodopsin and lipids, forming at least three distinct fluorophores with fluorescence quantum yield 20–40 times higher than that of free all-trans-retinal. These retinal derivatives are likely precursors of photo- and cytotoxic fluorophores of lipofuscin and in particular of A2E. Spectral characteristics of fluorophores have been described. Picosecond time-resolved laser fluorescence spectroscopy was used to study kinetics of fluorescence decay of both free and bound all-trans-retinal; fluorophores were determined and their lifetimes have been measured. Based on calculations it is shown that the decay kinetics of all-trans-retinal derivatives consists of three components with lifetimes equal to 48, 208, and 900 ps; kinetics of free all-trans-retinal is monoexponential with lifetime of 31 ps. The chemical nature of fluorophores with the lifetimes obtained is discussed.     

Conformational and biochemical characterization of a rat epididymis-specific lipocalin 12 expressed in Escherichia coli

Lipocalin 12 (Lcn12) is a recently identified epididymis-specific protein that might play a significant physiological role in male reproduction. However, the detailed structure and function of Lcn12 remain to be determined. In the present work, we cloned, expressed, and purified the rat Lcn12 (rLcn12) protein in Escherichia coli, introduced the Cys176Ala substitution to eliminate the aggregation problem associated with the wild-type protein. Homology modeling results demonstrated that rLcn12 adopted an eight-stranded, antiparallel β-barrel conformation containing a conserved disulfide bond between Cys98 and Cys203, which was in accordance with the physicochemical properties elucidated by a combination of mass, circular dichroism, and nuclear magnetic resonance spectrometry. The purified rLcn12 protein exhibited a high binding affinity for all-trans retinoic acid in fluorescence titration experiments, implying that rLcn12 could be involved in retinoic acid transport in the epididymis.     

Carotenoid differences in isogenic lines of tomato fruit colour mutants

The main pigment present in fruits of tomato lines isogenic with the cultivar ‘Ailsa-Craig’, but with different fruit colours, is all-trans-β-carotene. Most of the tomato lines also contain cis-phytoene, all-trans-phytofluene, all-trans-ζ-carotene, all-trans-neurosporene, all-trans-lycopene and all-trans-α-carotene. Delta-del fruits accumulate all-trans-δ-carotene as the major pigment, and Tangerine coloured fruits contain massive amounts of the intriguing di-cis-ζ-carotene, tri-cis-neurosporene and tetra-cis-lycopene (also known as ‘prolycopene’); smaller amounts of cis-phytoene and di-cis-phytofluene are also found in Tangerine tomato fruits.     

Structure refinement of a cyclic peptide from two-dimensional NMR data and molecular modeling

The conformational and dynamic properties of a cyclic peptide designed to inhibit human renin have been examined by using NMR and molecular modeling. From a quantitative analysis of a series of two-dimensional NOE data sets, proton-proton distances were calculated. Several different methods were explored and compared to incorporate these distance constraints as well as those derived from vicinal spin-spin coupling constants into computer-generated three-dimensional structures. These methods included interactive manual manipulation of the structures to fit the NMR-determined distance constraints, distance geometry, constrained energy minimizations, and constrained molecular dynamics. The advantages and disadvantages of the methods are discussed. In addition, to gain insight into the conformations accessible to the cyclic peptide and the relative flexibility of the different parts of the molecule, molecular dynamics calculations were performed at three different temperatures. Average interproton distances and dihedral angles were obtained from the structures generated in the dynamics trajectories and compared to those obtained from the NMR experiments. Despite the four methylene groups and ether linkage contained in the cyclic portion of the peptide, our NMR results indicated a preferred conformation for the macrocyclic ring of the peptide and supported the presence of a cis Phe-Ala peptide bond. In contrast, both the molecular dynamics and NMR data indicated a considerable amount of flexibility for the remaining noncyclic portion of the molecule. These results are used to propose an explanation for the cyclic peptide's inability to inhibit human renin.     

Conformational transitions and geometry differences between low-energy conformers of N-acetyl-N′-methyl alanineamide: An ab initio study at the 4-21G level with gradient relaxed geometries

Energy pathways between the α_R, β′, C, and β-regions of the conformational energy surface of N-acetyl-N′-methylalanyl amide were obtained by SCF ab initio calculations on the 4-21G level, with gradient geometry optimization at each point. The calculations indicate that no barrier exists at this computational level between α_R and β′. The variation of geometry (bond distances and bond angles) with conformation is analyzed in detail, and the most important geometrical parameters that should be treated as variables in both empirical energy calculations and in the fitting of polypeptide chains in proteins by x-ray methods are identified. In addition to the ?,ψ correlation discussed previously for the helical state, a correlation of these dihedral angles in the β-region is described.     

Application of a genetic algorithm in the conformational analysis of methylene-acetal-linked thymine dimers in DNA: Comparison with distance geometry calculations

The three-dimensional spatial structure of a methylene-acetal-linked thymine dimer presentin a 10 base-pair (bp) sense–antisense DNA duplex was studied with a geneticalgorithm designed to interpret NOE distance restraints. Trial solutions were represented bytorsion angles. This means that bond angles for the dimer trial structures are kept fixed duringthe genetic algorithm optimization. Bond angle values were extracted from a 10 bpsense–antisense duplex model that was subjected to energy minimization by means ofa modified AMBER force field. A set of 63 proton–proton distance restraints definingthe methylene-acetal-linked thymine dimer was available. The genetic algorithm minimizesthe difference between distances in the trial structures and distance restraints. A largeconformational search space could be covered in the genetic algorithm optimization byallowing a wide range of torsion angles. The genetic algorithm optimization in all cases ledto one family of structures. This family of the methylene-acetal-linked thymine dimer in theduplex differs from the family that was suggested from distance geometry calculations. It isdemonstrated that the bond angle geometry around the methylene-acetal linkage plays animportant role in the optimization.     

Redox potentials of the oriented film of the wild-type, the E194Q-, E204Q- and D96N-mutated bacteriorhodopsins

The redox potentials of the oriented films of the wild-type, the E194Q-, E204Q- and D96N-mutated bacteriorhodopsins (bR), prepared by adsorbing purple membrane (PM) sheets or its mutant on a Pt electrode, have been examined. The redox potentials (V) of the wild-type bR were −470 mV for the 13-cis configuration of the retinal Shiff base in bR and −757 mV for the all-trans configuration in H₂O, and −433 mV for the 13-cis configuration and −742 mV for the all-trans configuration in D₂O. The solvent isotope effect (ΔV=V(D₂O)−V(H₂O)), which shifts the redox potential to a higher value, originates from the cooperative rearrangements of the extensively hydrogen-bonded water molecules around the protonated CN part in the retinal Schiff base. The redox potential of bR was much higher for the 13-cis configuration than that for the all-trans configuration. The redox potentials for the E194Q mutant in the extracellular region were −507 mV for the 13-cis configuration and −788 mV for the all-trans configuration; and for the E204Q mutant they were −491 mV for the 13-cis configuration and −769 mV for the all-trans configuration. Replacement of the Glu¹⁹⁴ or Glu²⁰⁴ residues by Gln weakened the electron withdrawing interaction to the protonated CN bond in the retinal Schiff base. The E204 residue is less linked with the hydrogen-bonded network of the proton release pathway compared with E194. The redox potentials of the D96N mutant in the cytoplasmic region were −471 mV for the 13-cis configuration and −760 mV for the all-trans configuration which were virtually the same as those of the wild-type bR, indicating that the D to N point mutation of the 96 residue had no influence on the interaction between the D96 residue and the CN part in the Schiff base under the light-adapted condition. The results suggest that the redox potential of bR is closely correlated to the hydrogen-bonded network spanning from the retinal Schiff base to the extracellular surface of bR in the proton transfer pathway.     

Evidence for a 13,14-Cis Cycle in Bacteriorhodopsin

We discuss to what extent the vibrational spectra of bacteriorhodopsin that have been observed and assigned by Smith et al. (1, 2) by means of resonance Raman and by Gerwert and Siebert (EMBO (Eur. Mol. Biol. Organ.) J. In press) by means of infrared absorption experiments are in agreement with a photo-cycle of bacteriorhodopsin that involves the sequence BR, IO(all-trans) → K(13,14-cis) → L(13,14-cis) → M(13-cis) → N(13-cis) → O(all-trans). Our discussion is based on a quantumchemical modified neglect of diatomic overlap [MNDO] calculation of the vibrational spectra of the relevant isomers of the protonated retinal Schiff base. In particular, we investigated in these calculations the effects of different charge environments on the frequencies of the relevant C-C single bond stretching vibrations of these isomers.     

Conformation of dipeptides

The amide bond in L ,L - and L ,D -α-chloropropionylalanine methyl ester is shown to be trans by molar polarization and infrared spectroscopy. In these dipeptide diastereoisomer analogues, therefore, differences in physical properties, i.e., melting points, crystalline forms, gas chromatographic mobilities, etc., depend on preferred molecular conformations and not peptide bond configuration. Nuclear magnetic resonance spectra of both compounds were identical, indicating that no major chemical environment differences exist, which might have resulted from dissimilar side group interactions. Based on the data reported here and those of others, most dipeptide conformations can be eliminated because of contradiction with limits set by experimental or theoretical considerations. Of the remaining conformational possibilities, a single pair accounts for observed physical differences in dipeptide diastereoisomers, free or blocked. The preferred form contains α-hydrogens trans to each other and in the plane of the peptide bond. In this conformation, R¹–R² and amino–carboxyl distances are minimal in L ,D diastereomers and maximal in L ,L forms.     

Biosynthesis of 9-cis-Retinoic Acid from 9-cis-β-Carotene in Human Intestinal Mucosa in Vitro

The role of 9-cis-β-carotene (9-cis-β-C) as a potential precursor of 9-cis-retinoic acid (9-cis-RA) has been examined in human intestinal microcosa in vitro. By using HPLC, uv spectra, and chemical derivatization analysis, both 9-cis-RA and all-trans-retinoic acid (all-trans-RA) have been identified in the postnuclear fraction of human intestinal microcosa after incubation with 9-cis-β-C at 37°C. The biosynthesis of both 9-cis-RA and all-trans-RA from 9-cis-β-C was linear with increasing concentrations of 9-cis-β-C (2-30 μM) and was linear with respect to tissue protein concentration up to 0.75 mg/ml. Retinoic acid was not detected when a boiled incubation mixture was incubated in the presence of 9-cis-β-C. The rate of synthesis of 9-cis- and all-trans-RA from 4 μM 9-cis-β-C were 16 ± 1 and 18 ± 2 pmol/hr/mg of protein, respectively. However, when 2 μM all-trans-β-C was added to the 4 μM 9-cis-β-C, the rate of all-trans-RA synthesis was increased to 38 ± 6 pmol/hr/mg of protein, whereas the rate of 9-cis-RA synthesis remained the same. These results suggest that 9-cis-RA is produced directly from 9-cis-β-C. Furthermore, incubations of either 0.1 μM 9-cis- or all-trans-retinal under the same incubation conditions showed that 9-cis-RA could also arise through oxidative conversion of 9-cis-retinal. Although only 9-cis-RA was detected when 9-cis-RA was used as the substrate, the isomerization of the all-trans-RA to 9-cis-RA cannot be ruled out, since both all-trans-RA and trace amounts of 9-cis-RA were detected when all-trans-retinal was incubated as the substrate. These data indicate that 9-cis-β-C can be a source of 9-cis-RA in the human. This conversion may have a significance in the anticarcinogenic action of β-C.     

Simultaneous analysis of retinol,all-trans- and 13-cis-retinoic acid and 13-cis-4-oxoretinoic acid in plasma by liquid chromatography using on-column concentration after single-phase fluid extraction

A reversed-phase high-performance liquid chromatographic method for the simultaneous analysis of retinol, all-trans-retinoic acid, 13-cis-retinoic acid and 13-cis-4-oxoretinoic acid in human plasma and cell culture medium is described. Sample preparation involves precipitation of proteins and extraction of retinoids with 60% acetonitrile. After centrifugation, the acetonitrile content of the supernatant is reduced to 45%, allowing on-column concentration of analytes. Injection volumes up to 2.0 ml (equivalent to 0.525 ml of sample) can be used without compromising chromatographic resolution of all-trans-retinoic acid and 13-cis-retinoic acid. Retinoids were stable in this extract and showed no isomerization when stored in the dark in a cooled autosampler, allowing automated analysis of large series of samples. Recoveries from spiked plasma samples were between 95 and 103%. Although no internal standard was used, the inter-assay precision for all retinoids was better than 6% and 4% at concentrations of 30 nM and 100 nM, respectively. The method is a valuable tool for the study of cellular metabolism of all-trans-retinoic acid, as polar metabolites of this compound can be detected with high sensitivity in cell culture media.     

The molecular structure of a complex of a 2,6-diimino-pyridine as a bidentate ligand with molybdenum carbonyl

Reaction of the pyridyl-diimine ligand, 2,6-[1- (2,2-dimethylpropanimino)ethyl]pyridine (1) with Mo(CO)₆ has unexpectedly yielded [Mo(CO)₄1], in which the normally tridentate ligand, even under forcing conditions, is bidentate. A single crystal X-ray structure determination reveals the distorted octahedral molecule with the MoC distances trans to the nitrogen donor atoms 0.1 Å shorter than the other two MoC distances. Other bond lengths suggest delocalization of charge in the chelate ring and this is reinforced by proton NMR data which suggests electron flow from the metal into the pyridine ring.     

Resonance Raman studies of the conformations of all-Trans carotenoids in light-harvesting systems of photosynthetic bacteria

Comparison of the resonance Raman spectra of carotenoids in vivo and in vitro has revealed that in some species of photosynthetic bacteria the major fraction of carotenoids associated with the light-harvesting systems has forms distorted (twisted) from the planar all-trans conformation. These distorted forms are kept in isolated and purified light-harvesting bacteriochlorophyll-protein complexes.