Atropisomerism in Rilpivirine hydrochloride: Spectroscopic characterization of Rilpivirine and related impurities

Nuclear magnetic resonance (NMR) technique has been used to find the property of atropisomerism in Rilpivirine hydrochloride by variable temperature analysis and various 2D techniques. Both the Rilpivirine hydrochloride (E‐isomer) and Impurity‐A (Z‐isomer) isomers have been differentiated and confirmed by NMR and ultraviolet techniques. Preparative high‐performance liquid chromatography isolation for Impurity‐A is followed by spectroscopic (NMR, mass spectra, and infrared) investigation that provides a perfect solution for determination of the structure of Rilpivirine and related impurities.     

Extreme heat- and pressure-resistant 7-kDa protein P2 from the archaeon Sulfolobus solfataricus is dramatically destabilized by a single-point amino acid substitution

This study reports the characterization of the recombinant 7-kDa protein P2 from Sulfolobus solfataricus and the mutants F31A and F31Y with respect to temperature and pressure stability. As observed in the NMR, FTIR, and CD spectra, wild-type protein and mutants showed substantially similar structures under ambient conditions. However, midpoint transition temperatures of the denaturation process were 361, 334, and 347 K for wild type, F31A, and F31Y mutants, respectively: thus, alanine substitution of phenylalanine destabilized the protein by as much as 27 K. Midpoint transition pressures for wild type and F31Y mutant could not be accurately determined because they lay either beyond (wild type) or close to (F31Y) 14 kbar, a pressure at which water undergoes a phase transition. However, a midpoint transition pressure of 4 kbar could be determined for the F31A mutant, implying a shift in transition of at least 10 kbar. The pressure-induced denaturation was fully reversible; in contrast, thermal denaturation of wild type and mutants was only partially reversible. To our knowledge, both the pressure resistance of protein P2 and the dramatic pressure and temperature destabilization of the F31A mutant are unprecedented. These properties may be largely accounted for by the role of an aromatic cluster where Phe31 is found at the core, because interactions among aromatics are believed to be almost pressure insensitive; furthermore, the alanine substitution of phenylalanine should create a cavity with increased compressibility and flexibility, which also involves an impaired pressure and temperature resistance. Proteins 29:381–390, 1997. © 1997 Wiley-Liss, Inc.     

Monensin A methyl ester complexes with Li+, Na+, and K+ cations studied by ESI-MS, 1H- and 13C-NMR, FTIR, as well as PM5 semiempirical method

Monensin A methyl ester (MON1) was synthesized by a new method and its ability to form complexes with Li+, Na+, and K+ cations was studied by electrospray ionization-mass spectroscopy (ESI-MS), 1H and 13C nuclear magnetic resonance (NMR), Fourier transform infrared (FTIR), and PM5 semiempirical methods. It is shown that MON1 with monovalent metal cations forms stable complexes of 1:1 stoichiometry. The structures of the complexes are stabilized by intramolecular hydrogen bonds in which the OH groups are always involved. In the structure of MON1, the oxygen atom of the C=O ester group is involved in very weak bifurcated intramolecular hydrogen bonds with two hydroxyl groups, whereas in the complexes of MON1 with monovalent metal cations the C=O ester group is not engaged in any intramolecular hydrogen bonds. Furthermore, it is demonstrated that the strongest intramolecular hydrogen bonds are formed within the MON1-Li+ complex structure. The structures of the MON1 and its complexes with Li+, Na+, and K+ cations are visualized and discussed in detail.     

Studies on canthaxanthin in lipid membranes

Polar carotenoid pigment - canthaxanthin - has been found to interfere with the organization of biological membranes, in particular of the retina membranes of an eye of primates. The organization of lipid membranes formed with dipalmitoylphosphatidylcholine (DPPC) and egg yolk phosphatidylcholine containing canthaxanthin was studied by means of several techniques including: electronic absorption spectroscopy, linear dichroism, X-ray diffractometry, ¹H-NMR spectroscopy and FTIR spectroscopy. It appears that canthaxanthin present in the lipid membranes at relatively low concentration (below 1 mol% with respect to lipid) modifies significantly physical properties of the membranes. In particular, canthaxanthin (i) exerts restrictions to the segmental molecular motion of lipid molecules both in the headgroup region and in the hydrophobic core of the bilayer, (ii) promotes extended conformation of alkyl lipid chains, (iii) modifies the surface of the lipid membranes (in particular in the gel state, L_β´) and promotes the aggregation of lipid vesicles. It is concluded that canthaxanthin incorporated into lipid membranes is distributed among two pools: one spanning the lipid bilayer roughly perpendicularly to the surface of the membrane and one parallel to the membrane, localized in the headgroup region. The population of the horizontal fraction increases with the increase in the concentration of the pigment in the lipid phase. Such a conclusion is supported by the linear dichroism analysis of the oriented lipid multibilayers containing canthaxanthin: The mean angle between the dipole transition moment and the axis normal to the plane of the membrane was determined as 20 ± 3° at 0.5 mol% and 47 ± 3° at 2 mol% canthaxanthin. The analysis of the absorption spectra of canthaxanthin in the lipid phase and ¹H-NMR spectra of lipids point to the exceptionally low aggregation threshold of the pigment in the membrane environment (∼1 mol%). All results demonstrate a very strong modifying effect of canthaxanthin with respect to the dynamic and structural properties of lipid membranes.     

The hydration of amides in helices; a comprehensive picture from molecular dynamics,IR, and NMR

We examined the hydration of amides of alpha(3)D, a simple, designed three-helix bundle protein. Molecular dynamics calculations show that the amide carbonyls on the surface of the protein tilt away from the helical axis to interact with solvent water, resulting in a lengthening of the hydrogen bonds on this face of the helix. Water molecules are bonded to these carbonyl groups with partial occupancy ( approximately 50%-70%), and their interaction geometries show a large variation in their hydrogen bond lengths and angles on the nsec time scale. This heterogeneity is reflected in the carbonyl stretching vibration (amide I' band) of a group of surface Ala residues. The surface-exposed amides are broad, and shift to lower frequency (reflecting strengthening of the hydrogen bonds) as the temperature is decreased. By contrast, the amide I' bands of the buried (13)C-labeled Leu residues are significantly sharper and their frequencies are consistent with the formation of strong hydrogen bonds, independent of temperature. The rates of hydrogen-deuterium exchange and the proton NMR chemical shifts of the helical amide groups also depend on environment. The partial occupancy of the hydration sites on the surface of helices suggests that the interaction is relatively weak, on the order of thermal energy at room temperature. One unexpected feature that emerged from the dynamics calculations was that a Thr side chain subtly disrupted the helical geometry 4-7 residues N-terminal in sequence, which was reflected in the proton chemical shifts and the rates of amide proton exchange for several amides that engage in a mixed 3(10)/alpha/pi-helical conformation.     

The Three-Dimensional Structure of [NiFeSe] Hydrogenase from Desulfovibrio vulgaris Hildenborough: A Hydrogenase without a Bridging Ligand in the Active Site in Its Oxidised, “as-Isolated” State

Hydrogen is a good energy vector, and its production from renewable sources is a requirement for its widespread use. [NiFeSe] hydrogenases (Hases) are attractive candidates for the biological production of hydrogen because they are capable of high production rates even in the presence of moderate amounts of O₂, lessening the requirements for anaerobic conditions. The three-dimensional structure of the [NiFeSe] Hase from Desulfovibrio vulgaris Hildenborough has been determined in its oxidised “as-isolated” form at 2.04-Å resolution. Remarkably, this is the first structure of an oxidised Hase of the [NiFe] family that does not contain an oxide bridging ligand at the active site. Instead, an extra sulfur atom is observed binding Ni and Se, leading to a SeCys conformation that shields the NiFe site from contact with oxygen. This structure provides several insights that may explain the fast activation and O₂ tolerance of these enzymes.     

Local structural preferences and dynamics restrictions in the urea-denatured state of SUMO-1: NMR characterization

We have investigated by multidimensional NMR the structural and dynamic characteristics of the urea-denatured state of activated SUMO-1, a 97-residue protein belonging to the growing family of ubiquitin-like proteins involved in post-translational modifications. Complete backbone amide and 15N resonance assignments were obtained in the denatured state by using HNN and HN(C)N experiments. These enabled other proton assignments from TOCSY-HSQC spectra. Secondary Halpha chemical shifts and 1H-1H NOE indicate that the protein chain in the denatured state has structural preferences in the broad beta-domain for many residues. Several of these are seen to populate the (phi,psi) space belonging to polyproline II structure. Although there is no evidence for any persistent structures, many contiguous stretches of three or more residues exhibit structural propensities suggesting possibilities of short-range transient structure formation. The hetero-nuclear 1H-15N NOEs are extremely weak for most residues, except for a few at the C-terminal, and the 15N relaxation rates show sequence-wise variation. Some of the regions of slow motions coincide with those of structural preferences and these are interspersed by highly flexible residues. The implications of these observations for the early folding events starting from the urea-denatured state of activated SUMO-1 have been discussed.     

Phycocolloid chemistry as a taxonomic indicator of phylogeny in the Gigartinales, Rhodophyceae: A review and current developments using Fourier transform infrared diffuse reflectance spectroscopy

The taxonomic significance of the polysaccharide structures of algal cell walls has been underscored several times over the past few decades but has never been pursued systematically. Many changes in red algal systematics and the biochemical analyses of phycocolloids have occured in recent years. The cell-wall composi-tion of representatives of 167 (24.7%) genera and 470 (11.5%) species of red algae has been documented.The method developed by Chopin and Whalen for carrageenan identification by Fourier transform infrared diffuse reflectance spectroscopy is extended to the study of phycocolloids for diverse species in many red algal orders. This paper focuses on the Gigartinales in which representatives of 28 (68.3%) families, 88 (50.6%) genera and 224 (27.9%) species have been analyzed. In light of recent molecular phylogenies, some patterns of distribution of key phycocolloid attributes, corresponding to familial and ordinal level groupings, are emerging; however, more species remain to be analyzed. The well-documented biochemical alternation of generations in the Phyllophoraceae, Petrocelidaceae and Gigartinaceae still holds (with two exceptions), but this pattern was not recorded in other families of Gigartinales.     

Synthesis and in vitro biological evaluation of new pyrimidines as glucagon-like peptide-1 receptor agonists

The therapeutic success of peptide glucagon-like peptide-1 (GLP-1) receptor agonists for the treatment of type 2 diabetes mellitus has inspired discovery efforts aimed at developing orally available small-molecule GLP-1 receptor agonists. In this study, two series of new pyrimidine derivatives were designed and synthesized using an efficient route, and were evaluated in terms of GLP-1 receptor agonist activity. In the first series, novel pyrimidines substituted at positions 2 and 4 with groups varying in size and electronic properties were synthesized in a good yield (78–90%). In the second series, the designed pyrimidine templates included both urea and Schiff base linkers, and these compounds were successfully produced with yields of 77–84%. In vitro experiments with cultured cells showed that compounds 3a and 10a (10^?15–10^?9 M) significantly increased insulin secretion compared to that of the control cells in both the absence and presence of 2.8 mM glucose; compound 8b only demonstrated significance in the absence of glucose. These findings represent a valuable starting point for the design and discovery of small-molecule GLP-1 receptor agonists that can be administered orally.     

Molecular resolution visualization of a pore formed by trichogin,an antimicrobial peptide,in a phospholipid matrix

Electrochemical scanning tunneling microscopy (EC-STM) was employed to study the aggregation of trichogin OMe (TCG), an antimicrobial peptide, incorporated into a lipid monolayer. High-resolution EC-STM images show that trichogin molecules aggregate to form channels in the lipid monolayer. Two types of aggregates were observed in the images. The first consisted of a bundle of six TCG molecules surrounding a central pore. The structure and dimensions of this channel are similar to aggregates that in bilayers are described by the barrel-stave model. The EC-STM images also reveal that channels aggregate further to form a hexagonal lattice of a two dimensional (2D) nanocrystal. The model of 2D lattice was built from trimers of TCG molecules that alternatingly are oriented with either hydrophilic or hydrophobic faces to each other. In this way each TCG molecule is oriented partially with its hydrophilic face towards the hexameric pore allowing the formation of the column of water inside this pore.     

Novel seed coat lignins in the Cactaceae: structure,distribution and implications for the evolution of lignin diversity

We have recently described a hitherto unsuspected catechyl lignin polymer (C‐lignin) in the seed coats of Vanilla orchid and in cacti of one genus, Melocactus (Chen et al., Proc. Natl. Acad. Sci. USA. 2012, 109, 1772‐1777.). We have now determined the lignin types in the seed coats of 130 different cactus species. Lignin in the vegetative tissues of cacti is of the normal guaiacyl/syringyl (G/S) type, but members of most genera within the subfamily Cactoidae possess seed coat lignin of the novel C‐type only, which we show is a homopolymer formed by endwise β–O–4‐coupling of caffeyl alcohol monomers onto the growing polymer resulting in benzodioxane units. However, the species examined within the genera Coryphantha, Cumarinia, Escobaria and Mammillaria (Cactoideae) mostly had normal G/S lignin in their seeds, as did all six species in the subfamily Opuntioidae that were examined. Seed coat lignin composition is still evolving in the Cactaceae, as seeds of one Mammillaria species (M. lasiacantha) possess only C‐lignin, three Escobaria species (E. dasyacantha, E. lloydii and E. zilziana) contain an unusual lignin composed of 5‐hydroxyguaiacyl units, the first report of such a polymer that occurs naturally in plants, and seeds of some species contain no lignin at all. We discuss the implications of these findings for the mechanisms that underlie the biosynthesis of these newly discovered lignin types.     

The dynamic duo: Combining NMR and small angle scattering in structural biology

Structural biology provides essential information for elucidating molecular mechanisms that underlie biological function. Advances in hardware, sample preparation, experimental methods, and computational approaches now enable structural analysis of protein complexes with increasing complexity that more closely represent biologically entities in the cellular environment. Integrated multidisciplinary approaches are required to overcome limitations of individual methods and take advantage of complementary aspects provided by different structural biology techniques. Although X‐ray crystallography remains the method of choice for structural analysis of large complexes, crystallization of flexible systems is often difficult and does typically not provide insights into conformational dynamics present in solution. Nuclear magnetic resonance spectroscopy (NMR) is well‐suited to study dynamics at picosecond to second time scales, and to map binding interfaces even of large systems at residue resolution but suffers from poor sensitivity with increasing molecular weight. Small angle scattering (SAS) methods provide low resolution information in solution and can characterize dynamics and conformational equilibria complementary to crystallography and NMR. The combination of NMR, crystallography, and SAS is, thus, very useful for analysis of the structure and conformational dynamics of (large) protein complexes in solution. In high molecular weight systems, where NMR data are often sparse, SAS provides additional structural information and can differentiate between NMR‐derived models. Scattering data can also validate the solution conformation of a crystal structure and indicate the presence of conformational equilibria. Here, we review current state‐of‐the‐art approaches for combining NMR, crystallography, and SAS data to characterize protein complexes in solution.     

Peptides and Gd complexes containing colloidal assemblies as tumor-specific contrast agents in MRI: physicochemical characterization

The aggregation behavior of an amphiphilic supramolecular system, with potential application as a tumor-specific magnetic resonance imaging contrast agent, has been studied in detail by dynamic light scattering, small-angle neutron scattering and cryotransmission electron microscopy. The system was constituted of mixed aggregates formed by an anionic unimer containing the DTPAGlu, a chelating agent for the paramagnetic Gd(3+) ion, and an uncharged unimer containing the bioactive peptide CCK8, capable of directing the assembly toward tumor cells. Mixed aggregates formed by both unimers, and in the case of the DTPAGlu unimer with the chelating agent as free base or as Gd(3+) complex, have been investigated. A number of interesting features of the aggregation behavior were revealed: at physiological pH, micelles and bilayer structures were present, whereas upon decreasing solution pH or increasing ionic strength, the formation of bilayer structures was favored. On the basis of the above observations, the aggregating mechanism has been elucidated by considering the screening effect on intra- and interaggregate electrostatic repulsions.     

Short Communication: The potential of portable near infrared spectroscopy for assuring quality and authenticity in the food chain,using Iberian hams as an example

This communication assesses the use of a portable near infrared (NIR) instrument to measure quantitative (fatty acid profile) properties and qualitative (‘Premium’ and ‘Non-premium’) categories of individual Iberian pork carcasses at the slaughterhouse. Acorn-fed Iberian pigs have more unsaturated fats than pigs fed conventional compound feed. Recent advances in miniaturisation have led to a number of handheld NIR devices being developed, allowing processing decisions to be made earlier, significantly reducing time and costs. The most common methods used for assessing quality and authenticity of Iberian hams are analysis of the fatty acid composition of subcutaneous fat using gas chromatography and DNA analysis. In this study, NIR calibrations for fatty acids and classification as premium or non-premium ham, based on carcass fat measured in situ, were developed using a portable NIR spectrometer. The accuracy of the quantitative equations was evaluated through the standard error of cross validation or standard error of prediction of 0.84 for palmitic acid (C16:0), 0.94 for stearic acid (C18:0), 1.47 for oleic acid (C18:1) and 0.58 for linoleic acid (C18:2). Qualitative calibrations provided acceptable results, with up to 98% of samples (n = 234) correctly classified with probabilities ⩾0.9. Results indicated a portable NIR instrument has the potential to be used to measure quality and authenticity of Iberian pork carcasses.     

Algal chemodiversity and bioactivity: sources of natural variability and implications for commercial application

There has been significant recent interest in the commercial utilisation of algae based on their valuable chemical constituents many of which exhibit multiple bioactivities with applications in the food, cosmetic, agri- and horticultural sectors and in human health. Compounds of particular commercial interest include pigments, lipids and fatty acids, proteins, polysaccharides and phenolics which all display considerable diversity between and within taxa. The chemical composition of natural algal populations is further influenced by spatial and temporal changes in environmental parameters including light, temperature, nutrients and salinity, as well as biotic interactions. As reported bioactivities are closely linked to specific compounds it is important to understand, and be able to quantify, existing chemical diversity and variability. This review outlines the taxonomic, ecological and chemical diversity between, and within, different algal groups and the implications for commercial utilisation of algae from natural populations. The biochemical diversity and complexity of commercially important types of compounds and their environmental and developmental control are addressed. Such knowledge is likely to help achieve higher and more consistent levels of bioactivity in natural samples and may allow selective harvesting according to algal species and local environmental conditions for different groups of compounds.     

Methods for structural characterization of prefibrillar intermediates and amyloid fibrils

Protein fibrillation is first and foremost a structural phenomenon. Adequate structural investigation of the central conformational individuals of the fibrillation process is however exceedingly difficult. This is due to the nature of the process, which may be described as a dynamically evolving equilibrium between a large number of structural species. These are furthermore of highly diverging sizes and present in very uneven amounts and timeframes. Different structural methods have different strengths and limitations. These, and in particular recent advances within solution analysis of the undisturbed equilibrium using small angle X-ray scattering, are reviewed here.     

Neocarzinostatin chromophore: Presence of a cyclic carbonate subunit and its modification in the structure of other biologically active forms

On the basis of spectroscopic evidence, opening of a five-membered cyclic carbonate ring (1,3-dioxolan-2-one) in the C₁₅-subunit of the previously determined partial structure $\text{1}$ (Fig. 1) of the major neocarzinostatin chromophore (NCS-Chrom $\text{A}$), is proposed to account for its base-catalyzed methanolysis to NCS-Chrom $\text{C}$. NCS-Chrom $\text{B}$, apparently an authentic natural product present as a minor component in all preparations of NCS studied, was found to be formally equivalent to the hydrolysis/decarboxylation product of the cyclic carbonate functionality in NCS-Chrom $\text{A}$. The mercaptan-dependent DNA strand-scission activity, equivalent for NCS-Chrom $\text{A}$, $\text{B}$ and $\text{C}$, is independent of the integrity of the cyclic carbonate ring system and implicates a secondary site in the C₁₅-substructure for mercaptan activation.