Molecular evolution of proteins involved in vertebrate phototransduction

Vision is one of the most important senses for vertebrates. As a result, vertebrates have evolved a highly organized system of retinal photoreceptors. Light triggers an enzymatic cascade, called the phototransduction cascade, that leads to the hyperpolarization of photoreceptors. It is expected that a systematic comparison of phototransduction cascades of various vertebrates can provide insights into the diversity of vertebrate photoreceptors and into the evolution of vertebrate vision. However, only a few attempts have been made to compare each phototransduction protein participating in this cascade. Here, we determine phylogenetic trees of the vertebrate phototransduction proteins and compare them. It is demonstrated that vertebrate opsin sequences fall into five fundamental subfamilies. It is speculated that this is crucial for the diversity of the spectral sensitivity observed in vertebrate photoreceptors and provides the vertebrates with the molecular tools to discriminate the color of incident light. Other phototransduction proteins can be classified into only a few subfamilies. Cones generally share isoforms of phototransduction proteins that are different from those found in rods. The difference in sensitivity to light between rods and cones is likely due to the difference in the molecular properties of these isoforms. The phototransduction proteins seem to have co-evolved as a system. Switching the expression of these isoforms may characterize individual vertebrate photoreceptors.     

Structural elucidation of some orange juice carotenoids

The structure of some carotenoids of Valencia orange juice were elucidated by chemical tests and MS of the free pigments and their derivatives. A new apocarotenal was shown to be 3-hydroxy-5,8-epoxy-5,8-dihydro-8′-apo-β-caroten-8′-al. Two UV-fluorescent apocarotenols found recently in avocado were also present. For the pigments previously designated trollixanthin and trollichrome, the new structures 5,6-dihydro-β,β-carotene-3-3′,5,6-tetrol and 5,8-epoxy-5,8,5′,6′-tetrahydro-β,β-carotene-3,3′,5′,6′-tetrol are assigned, both containing a trihydroxylated ring as in heteroxanthin.     

Structural elucidation of novel degradation product of brotizolam

When the drug product of brotizolam (1) is decomposed according to the interview form and patent, hydrolysate (2) is obtained, but its physicochemical data are still missing. To elucidate the structure based on a spectroscopic approach, the above-mentioned degradation product was isolated and applied to the structural analysis. As a result, the structure of decomposed product was found to be different from that of 2. In this report, its isolation and structure elucidation by NMR and MS spectra are described.     

Dynamic sensitivity and nonlinear interactions influence the system-level evolutionary patterns of phototransduction proteins

Determining the influence of complex, molecular-system dynamics on the evolution of proteins is hindered by the significant challenge of quantifying the control exerted by the proteins on system output. We have employed a combination of systems biology and molecular evolution analyses in a first attempt to unravel this relationship. We employed a comprehensive mathematical model of mammalian phototransduction to predict the degree of influence that each protein in the system exerts on the high-level dynamic behaviour. We found that the genes encoding the most dynamically sensitive proteins exhibit relatively relaxed evolutionary constraint. We also investigated the evolutionary and epistatic influences of the many nonlinear interactions between proteins in the system and found several pairs to have coevolved, including those whose interactions are purely dynamical with respect to system output. This evidence points to a key role played by nonlinear system dynamics in influencing patterns of molecular evolution.     

Structural elucidation of limonoids and steroids from Trichilia connaroides

Six limonoids, trijugins D-H (1-5) and methyl 8alpha-hydroxy-8,30-dihydroangolensate (6), two degraded limonoids, trichiconnarins A and B (7-8), and a pregnane steroid, 3beta,4alpha-dihydroxypregnan-21-one (9), along with the known trijugin C (10) and 3beta,4alpha-dihydroxypregnan-16-one (11) were isolated from twigs and leaves of Trichilia connaroides. Their structures were established on the basis of extensive spectroscopic analysis.     

Reweighting methods for elucidation of conformation ensembles of proteins

Proteins are inherently dynamic macromolecules that exist in equilibrium among multiple conformational states, and motions of protein backbone and side chains are fundamental to biological function. The ability to characterize the conformational landscape is particularly important for intrinsically disordered proteins, multidomain proteins, and weakly bound complexes, where single-structure representations are inadequate. As the focus of structural biology shifts from relatively rigid macromolecules toward larger and more complex systems and molecular assemblies, there is a need for structural approaches that can paint a more realistic picture of such conformationally heterogeneous systems. Here, we review reweighting methods for elucidation of structural ensembles based on experimental data, with the focus on applications to multidomain proteins.     

Structure elucidation of dimeric transmembrane domains of bitopic proteins

The interaction between transmembrane helices is of great interest because it directly determines biological activity of a membrane protein. Either destroying or enhancing such interactions can result in many diseases related to dysfunction of different tissues in human body. One much studied form of membrane proteins known as bitopic protein is a dimer containing two membrane-spanning helices associating laterally. Establishing structure-function relationship as well as rational design of new types of drugs targeting membrane proteins requires precise structural information about this class of objects. At present time, to investigate spatial structure and internal dynamics of such transmembrane helical dimers, several strategies were developed based mainly on a combination of NMR spectroscopy, optical spectroscopy, protein engineering and molecular modeling. These approaches were successfully applied to homo- and heterodimeric transmembrane fragments of several bitopic proteins, which play important roles in normal and in pathological conditions of human organism.Key words: bitopic proteins, transmembrane domain dimer, spatial structure, dynamics, protein-protein interactions, protein-membrane interactions, molecular modeling, NMR     

Structure elucidation of dimeric transmembrane domains of bitopic proteins

The interaction between transmembrane helices is of a great interest because it directly determines biological activity of a membrane protein. Either destroying or enhancing such interactions can result in many diseases related to dysfunction of different tissues in human body. One much studied form of membrane proteins known as bitopic protein is a dimer containing two membrane-spanning helices associating laterally. Establishing structure-function relationship as well as rational design of new types of drugs targeting membrane proteins requires precise structural information about this class of objects. At present time, to investigate spatial structure and internal dynamics of such transmembrane helical dimers, several strategies were developed based mainly on a combination of NMR spectroscopy, optical spectroscopy, protein engineering and molecular modeling. These approaches were successfully applied to homo- and heterodimeric transmembrane fragments of several bitopic proteins, which play important roles in normal and in pathological conditions of human organism.     

Structural elucidation of the disulfated oligosaccharide from bovine lutropin

The Asn-linked oligosaccharides of the pituitary hormone lutropin (LH) contain both sulfate and GalNAc. Bovine pituitary explants incorporate [3H]glucosamine, [3H]mannose, [3H]fucose, and [35S]sulfate into the Asn-linked oligosaccharides of LH. Endoglycosidase F or N-glycanase releases the [3H]glucosamine- and [3H]mannose-labeled oligosaccharides from the protein, which resolve on anion-exchange high pressure liquid chromatography as neutral (S-0), mono- (S-1), and disulfated (S-2) species. Based on sequential enzyme digestion, methylation, periodate oxidation, and nuclear magnetic resonance studies, the proposed structure for S-2 is as follows: formula see text. Sulfate is confined to position 3 or 4 of GalNAc based on periodate and methylation data and can be removed by methanolysis. The presence of beta-linked GalNAc at a position typically occupied by Gal has not previously been observed.     

Structural elucidation of new phenolic glycolipids from Mycobaclerium tuberculosis

From one clinical isolate of Mycobacterium tuberculosis, two new phenolic glycolipids(PGLs) were obtained as its major PGLs. These were dimycocerosyl esters of 2,4-di-O-methyl-fucopyranosyl-(α1 → 3)-rhamnopyranosyl-(α1 → 3)-2-0-methyl-rhamno-pyranosyl-(α1 →)-phenolph A and -phenolphthiotriol A, which were produced by this strain at a ratio of about 5:1. Another clinical isolate of this species was found to produce PGL-tb1 and its analogue, 2,3,4-tri-O-methyl-fucopyranosyl-(α1 → 3)-rhamnopyranosyl-(α1 → 3)-2-O-methyl-rhamnopyranosyl-(α1 →)-phenolphthiotriol A at a ratio of about 1:3. The fact that different strains of M. tuberculosis produce chemically different PGLs as their major PGLs may be related to the diversity of virulence of the clinical isolates of M. tuberculosis.     

Structural elucidation of chalcone reductase and implications for deoxychalcone biosynthesis

4,2',4',6'-Tetrahydroxychalcone (chalcone) and 4,2',4'-trihydroxychalcone (deoxychalcone) serve as precursors of ecologically important flavonoids and isoflavonoids. Deoxychalcone formation depends on chalcone synthase and chalcone reductase; however, the identity of the chalcone reductase substrate out of the possible substrates formed during the multistep reaction catalyzed by chalcone synthase remains experimentally elusive. We report here the three-dimensional structure of alfalfa chalcone reductase bound to the NADP+ cofactor and propose the identity and binding mode of its substrate, namely the non-aromatized coumaryl-trione intermediate of the chalcone synthase-catalyzed cyclization of the fully extended coumaryl-tetraketide thioester intermediate. In the absence of a ternary complex, the quality of the refined NADP+-bound chalcone reductase structure serves as a template for computer-assisted docking to evaluate the likelihood of possible substrates. Interestingly, chalcone reductase adopts the three-dimensional structure of the aldo/keto reductase superfamily. The aldo/keto reductase fold is structurally distinct from all known ketoreductases of fatty acid biosynthesis, which instead belong to the short-chain dehydrogenase/reductase superfamily. The results presented here provide structural support for convergent functional evolution of these two ketoreductases that share similar roles in the biosynthesis of fatty acids/polyketides. In addition, the chalcone reductase structure represents the first protein structure of a member of the aldo/ketoreductase 4 family. Therefore, the chalcone reductase structure serves as a template for the homology modeling of other aldo/keto-reductase 4 family members, including the reductase involved in morphine biosynthesis, namely codeinone reductase.     

Structural elucidation of low abundant metabolites in complex sample matrices

Identification of metabolites is a major challenge in biological studies and relies in principle on mass spectrometry (MS) and nuclear magnetic resonance (NMR) methods. The increased sensitivity and stability of both NMR and MS systems have made dereplication of complex biological samples feasible. Metabolic databases can be of help in the identification process. Nonetheless, there is still a lack of adequate spectral databases that contain high quality spectra, but new developments in this area will assist in the (semi-)automated identification process in the near future. Here, we discuss new developments for the structural elucidation of low abundant metabolites present in complex sample matrices. We describe how a recently developed combination of high resolution MS multistage fragmentation (MS ⁿ ) and high resolution one dimensional (1D)-proton (¹H)-NMR of liquid chromatography coupled to solid phase extraction (LC–SPE) purified metabolites can circumvent the need for isolating extensive amounts of the compounds of interest to elucidate their structures. The LC–MS–SPE–NMR hardware configuration in conjunction with high quality databases facilitates complete structural elucidation of metabolites even at sub-microgram levels of compound in crude extracts. However, progress is still required to optimally exploit the power of an integrated MS and NMR approach. Especially, there is a need to improve and expand both MS ⁿ and NMR spectral databases. Adequate and user-friendly software is required to assist in candidate selection based on the comparison of acquired MS and NMR spectral information with reference data. It is foreseen that these focal points will contribute to a better transfer and exploitation of structural information gained from diverse analytical platforms.     

Structural elucidation of polymethoxyflavones from shift reagent proton NMR measurements

The quantitative shift reagent behavior of polymethoxylated flavones in the presence of Pr(fod)₃ shows that for structural elucidation of these molecules the degree of substitution in the neighborhood of the carbonyl group can be determined from the number of signals that are strongly shifted and broadened. The induced shifts of the remaining signals are of complementary help and even the resonances of individual methoxyl groups can be ascribed.     

Structural and vibrational spectroscopic elucidation of sulpiride in solid state

The study on the conformational and vibrational behaviors of sulpiride molecule which is known as a neuroleptic or antipsychotic drug that is widely used clinically in the treatment of schizophrenic or depressive disorders is an important scientific and practical task. In here, a careful enough study of monomer and dimeric forms of sulpiridine {5-(aminosulfonyl)-N-[(1-ethyl-2-pyrrolidinyl) ethyl]-2-methoxy-benzamide (C₁₅H₂₃N₃O₄S)} is undertaken by density functional theory (DFTB3LYP) method with the B3LYP/6-31G(d,p) basis set. The conformations of free molecule were searched by means of torsion potential energy surfaces scan studies through dihedral angles D₁ (8?N, 18C, 20C, 23?N), D₂ (18C, 20C, 23?N, 25C) and D₃ (28C, 30C, 41S, 44?N) in electronically ground state, employing 6-31G basic set. The final geometrical parameters for the obtained stable conformers were determined by means of geometry optimization, carried out at DFT/B3LYP/6-31G(d,p) theory level. Afterwards, the possible dimer forms of the molecule were formed and their energetically preferred conformations were investigated. Moreover, the effect of basis set superposition error on the structure and energy of the three energetically favourable sulpiride dimers has been determined. The optimized structural parameters of the most stable monomer and three low energy dimer forms were used in the vibrational wavenumber calculations. Raman and IR (4000–400?cm^?1) spectra of sulpiride have been recorded in the solid state. The assignment of the bands was performed based on the potential energy distribution data. The natural bond orbital analysis has been performed on both monomer and dimer geometries in order to elucidate delocalization of electron density within the molecule. The predicted frontier molecular orbital energies at DFT/B3LYP/6-31G(d,p) theory level show that charge transfer occurs within the molecule. The first-order hyperpolarizability (β₀) and related properties (μ and α) of the title molecule were also calculated.     

Structural elucidation of the capsular polysaccharide isolated from Kaistella flava

The Gram-negative bacterium under study belongs to the genus Kaistella. It was isolated from a soil sample of the Haian Island in China, and it produces a lipophilic polysaccharide characterised by a branched hexasaccharide repeating unit, counting four 6-deoxy-alpha-l-mannose (Rha) residues, one 2-acetamido-2-deoxy-beta-d-glucose (GlcNAc) and a 2-acetamido-2,6-dideoxy-beta-d-galactose (FucNAc) unit. The structure of the repeating unit, assigned through 2D-NMR spectroscopy, is herein reported for the first time: [carbohydrate structure: see text]