The Three-Dimensional Structure of 3′-Deoxycytidine

Abstract

Structural analysis of 3′-deoxycytidine and comparison with 2′-deoxynucleosides reveals no noticeable effect on the conformation of the molecule due to the lack of 3′-oxygen atom. There are two crystallographically independent molecules and both adopt the anti conformation with C3′-endo sugar puckering. A ‘head-to-tail’ packing of the molecules along the b axis results in a virtual ‘2′-5′ polycytidylic acid chain.     

C-peptide inhibitors of Ebola virus glycoprotein-mediated cell entry: Effects of conjugation to cholesterol and side chain–side chain crosslinking

We previously described potent inhibition of Ebola virus entry by a ‘C-peptide’ based on the GP2 C-heptad repeat region (CHR) targeted to endosomes (‘Tat-Ebo’). Here, we report the synthesis and evaluation of C-peptides conjugated to cholesterol, and Tat-Ebo analogs containing covalent side chain–side chain crosslinks to promote α-helical conformation. We found that the cholesterol-conjugated C-peptides were potent inhibitors of Ebola virus glycoprotein (GP)-mediated cell entry (～10³-fold reduction in infection at 40 μM). However, this mechanism of inhibition is somewhat non-specific because the cholesterol-conjugated peptides also inhibited cell entry mediated by vesicular stomatitis virus glycoprotein G. One side chain–side chain crosslinked peptide had moderately higher activity than the parent compound Tat-Ebo. Circular dichroism revealed that the cholesterol-conjugated peptides unexpectedly formed a strong α-helical conformation that was independent of concentration. Side chain–side chain crosslinking enhanced α-helical stability of the Tat-Ebo variants, but only at neutral pH. These result provide insight into mechanisms of C-peptide inhibiton of Ebola virus GP-mediated cell entry.     

Solvent effects on the conformational preferences of model peptoids. MP2 study

The influence of aqueous environment on the main‐chain conformation (ω₀, ?, and ψ dihedral angles) of two model peptoids: N‐acetyl‐N‐methylglycine N’‐methylamide (Ac‐N(Me)‐Gly‐NHMe) ( 1 ) and N‐acetyl‐N‐methylglycine N’,N’‐dimethylamide (Ac‐N(Me)‐Gly‐NMe₂) ( 2 ) was investigated by MP2/6‐311++G(d,p) method. The Ramachandran maps of both studied molecules with cis and trans configuration of the N‐terminal amide bond in the gas phase and in water environment were obtained and all energy minima localized. The polarizable continuum model was applied to estimate the solvation effect on conformation. Energy minima of the Ac‐N(Me)‐Gly‐NHMe and Ac‐N(Me)‐Gly‐NMe₂ have been analyzed in terms of the possible hydrogen bonds and C = O dipole attraction. To validate the theoretical results obtained, conformations of the similar structures gathered in the Cambridge Crystallographic Data Centre were analyzed. Obtained results indicate that aqueous environment in model peptoids 1 and 2 favors the conformation F (? and ψ = ?70º, 180º), and additionally significantly increases the percentage of structures with cis configuration of N‐terminal amide bond in studied compounds. Copyright © 2014 European Peptide Society and John Wiley & Sons, Ltd.     

Theoretical studies of phospholipid-glycophorin bilayer membranes using electron spin resonance and fluorescent probes

We have calculated the average value of the order parameter of a spin labelled lipid hydrocarbon chain in a DMPC bilayer containing a concentration c, of glycophorin, for a temperature above the main lipid phase transition temperature. We use the results of differential scanning calorimetry together with the results of other calculations to evaluate the parameters involved. To determine the orientation of the spin label, which is located near the glyceride backbone, we use the rotation isomeric model of hydrocarbon chains and allow for rocking and rotation of the chain. Our results are in good agreement with recent measurements and enable us to say that between about 200 and 1300 lipid molecules can be under the large glycophorin polar group ‘umbrella’ depending upon its conformation. In the case where this polar group adopts a ‘pancake’ conformation with about 1300 lipid molecules under it, we find that about 750–800 of them are perturbed and experience a reduced effective lateral pressure. We have calculated the average order parameter of a diphenylhexatriene (DPH) molecule under the same conditions as above, using the parameters determined there. We have used this calculation to predict the value of r_∞ that should be observed as a function of glycophorin concentration at T = 30°C. The predicted curve displays an unusual shape not observed in other lipid-protein bilayer membranes.     

Genetic trends of conformation traits and genetic correlations to osteochondrosis in boars

The objective of our study was to investigate the heritabilities and genetic correlations between traits from a linear exterior assessment system and osteochondrosis (OC) measured by computed tomography (CT), and in addition, to study the genetic trend in a population where the conformation traits have been included in the breeding goal. The data material consisted of phenotypes from a total of 4571 Norsvin Landrace test boars. At the end of the test period, all boars were subjected to a detailed exterior assessment system. Within 10 days of the assessment, the boars were CT scanned for measuring OC. The total score of osteochondrosis (OCT), used in this study, is the sum of phenotypes from the assessment on the medial and lateral condyles at the distal end of both the humerus and the femur of the right and the left leg of the boar based on images from CT. The exterior assessment traits included in the study were; ‘front leg knee’ (FKNE), ‘front leg pasterns’ (FPAS), ‘front leg stance’ (FSTA), ‘front leg twisted pasterns’ (FFLK), ‘hind leg stance’, ‘hind leg pasterns’ (HPAS), ‘hind leg standing under’ (HSTU), ‘hind leg small inner toe’, ‘dipped back’, ‘arched back’ (ARCH) and ‘waddling hindquarters’ (WADL). The estimation of (co)variance components and breeding values were performed using bivariate animal genetic models. Breeding values for HSTU, HPAS, FPAS, WADL and OCT traits were additional outputs from the same bivariate analyses. The lowest heritability was found for FFLK (h²_FFLK=0.05), whereas FPAS was estimated to have the highest heritability (h²_FPAS=0.36), and OCT demonstrating a heritability of 0.29. Significant genetic correlations were found between several traits; the strongest correlation was between FSTA and FFLK (0.94), which was followed by the correlation between FPAS and FKNE (0.69). The traits ARCH and FSTA had significant genetic correlations to OCT, whereas all other genetic correlations between OCT and the conformation traits were low and not significantly different from 0. Our study shows positive genetic trends for the conformation traits included in the breeding goal. In general, low genetic correlations between conformation traits and OC were observed in our study.     

Deuterium magnetic resonance of selectively deuterated cholesteryl esters in dipalmitoyl phosphatidylcholine dispersions

Dispersions (50 wt% water) containing 95 mol% dipalmitoyl phosphatidylcholine/5 mol% deuterated cholesteryl palmitate (or stearate) were studied using ²H-NMR. Incorporation of ester into the phospholipid bilayer was found to be 0.5 mol% at 50°C. From the profile of ²H quadrupolar splitting vs. chain position, support for an average conformation resembling a ‘horseshoe’ within the bilayer is obtained. Quadrupolar relaxation times $\text{T}{}_{2e}$ of approx. 250 μs and approx. 850 μs are measured for cholesteryl palmitate-2,2-d₂ and cholesteryl palmitate-16,16,16-d₃, respectively, which are less than one-half those obtained for the corresponding positions in dipalmitoyl-d₆₂ phosphatidylcholine. This is ascribed to a slower rate of motion of the ester chain and/or an extra, slow motion of the molecule.     

Conformational analysis of cytokinins and analogs

The conformational energy surfaces of 12 active cytokinins and analogs are studied with the aid of PCILO quantum mechanical calculations. The resulting conformational energy maps indicate that cytokinin activity is associated with the ability of the above molecules to attain a specific conformation, presumably related to their conformation at the active site of cytokinin receptor(s). The calculations locate the conformational energy minima and describe the flexibility of the studied molecules in terms of conformational barriers and transition paths. An approximate relation is found between cytokinin activity and the values of energy barriers to transitions between certain local minima. According to this relation, active compounds should have rotational barriers within 4–12 kcal/mol, besides the known hitherto constitutional requirements for high physiological activity.     

The crystal structure of D-glucaro-1,4-lactone monohydrate

In the crystal structure of D-glucaro-1,4-lactone monohydrate, C₆H₈O₇·H₂O, the molecules have the E₃ lactone-ring conformation, with a small distortion of the ring to ₃T². The α-hydroxycarboxylic acid side-chain is axial, with the HO---C---C=O torsion angle within 6° of cis-planar. The orientation of the side-chain is such that the hydroxyl group lies over the lactone ring, which is the same conformation as is reported to preponderate in solution. Calculations of non-bonding repulsion energy show that this conformation corresponds to an energy minimum, although comparable minima can also be obtained with the ring in the alternative ³E conformation. The lactone and water molecules are hydrogen-bonded to form layers two molecules,wide, separated by Van der Waals interactions. One of the water hydrogen atoms is involved in a weak, bifurcated hydrogen-bond.     

A novel form of vitamin B-12 and its derivatives

A new isomeric form of cobalamins is reported. The conversion of cobalamin to cobalamin′ (the new form) is achieved by substituting the benzimidazole base by a less bulky group like H₂O of CN^? and modest thermal treatment. The back conversion of adenosylcobalamin′ to the corresponding regular form occurs in the ‘base-off’ form at room temperature. It seems that the corrin ring becomes quite flexible in the ‘base-off’ form and the freer axial movement of the cobalt atom flips the corrin ring into a different conformation. The change in conformation is borne out by subtle changes in the proton magnetic resonances on the corrin ring and the base, and very marked variation in the emission Mössbauer spectra. The latter is indicative of appreciable changes in the spatial conformation in the immediate vicinity of the central metal atom.The ultraviolet-visible and infrared spectra of a cobalamin′ are indistinguishable from those of its corresponding regular form.The new conformational isomeric species is present as an impurity in all commercially available cobalamins (including pharmaceutical preparations). It raises the question whether the cobalamins′ constitute the real biologically active anti-anemic factor in humans     

Evidence for the presence of volume-sensitive KCl transport in ‘young’ human red cells

‘Young’ human red cells are shown to possess a specific K⁺ pathway which is dependent on Cl⁻ and sensitive to cell volume. This system was latent in ‘mature’ cells but was revealed by high hydrostatic pressure. This suggests the pathway is functionally active in ‘young’ cells but becomes masked with cell maturation.     

Conformational analysis of some phenethylamine molecules

A set of empirical potential functions (EPF), previously used in conformational energy calculations of polymers, was employed in the study of the conformational properties of a number of methyl-substituted phenethylmines, as well as phenylmethylamine, phenyl-n-propylamine, and 3,4,5-trimethoxyamphetamine. The conformational free energy was computed for each of these molecular species in four states: neutral charge-vacuo (I), neutral charge-aqueous solution (II), positive charge-vacuo (III), positive charge-aqueous solution (IV). The molecules generally adopt one of two stable conformations: a folded conformation with the amine chain perpendicular to the ring, and the amine group nearest to the ring; and an extended conformation with the amine chain perpendicular to the ring, and the amine group far from the ring. The folded conformation is usually preferred for states I, II and III, while the extended form is adopted for state IV. By using empirical potential functions it was also possible to calculate the conformational entropies associated with the minimum energy conformations, thereby allowing the Boltzmann probabilities to be determined. These probabilities are a measure of the population density of each of the various low energy regions. Some of the molecules studied have a steric “bulge” below the plane of the benzene ring. All of the compounds studied which possess this “bulge” are psychotropically inactive, and, in most cases, also pharmacologically inactive. All active compounds studied do not possess this “bulge”.     

Crystal structure of nonaquasamarium(III)bromide-l,4-dioxan adduct (1:3:2), Sm(H2O)9·Br3(C4H8O2)2

The title compound has been found to consist of tricapped trigonal prismatic Sm(H₂O)₉³⁺ ions in C_2v symmetry, sandwiched between expanded ‘close packed’ layers of bromide ions, with 1,4-dioxan molecules in chair conformation hydrogen bonding between the equatorial water molecules of adjacent cations.Orthorhombic, Amm2, a = 8.010(3), b = 19.848(4), c = 7.388(3) Å, R = 0.022 for 992 unique reflexions.     

Solid State and Solution Structure and Conformation of The Antiviral Acyclonucleoside 9-[4-Hydroxy-2-(hydroxymethyl)-butyl]guanine

Abstract

The title compound, 9-[4-hydroxy-2-(hydroxymethyl)-butyl]guanine (2HM-HBG), crystallizes in the triclinic space group P1 with two independent molecules and one water molecule in the asymmetric unit. The acyclic chain of one molecule is in the fully extended form, and the other partially folded. The orientation of this chain with respect to the base corresponds to the conformation syn in natural nucleosides. The conformations of the two molecules were compared with the solution conformation from an analysis of the ¹H-¹H vicinal coupling constants. The comportment of some acyclonucleosides in several enzyme systems is examined in relation to their existence in folded or extended forms.     

Molecular dynamics simulation of oligosaccharides containing N-acetyl neuraminic acid

αD -N-acetyl neuraminic acid (Neu5Ac, sialic acid) is a commonly occurring carbohydrate residue in various cell surface glycolipids and glycoproteins. This residue is linked terminally or internally to Gal residues via an α(2 → 3) or α(2 → 6) linkage. In the cell surface receptor, sialyl-Lewis^X, a terminal α(2 → 3) linkage is present. Previous studies from our laboratory have shown that in solution Lewis^X adopts a relatively rigid structure. In order to model the Neu5Ac residue, vacuum molecular dynamics of this monosaccharide were compared with simulations that explicitly include solvent water. The dynamical average of the monosaccharide conformation obtained from the two simulations was similar. Vacuum calculations for the disaccharide Neu5Ac α(2 → 3) Gal β-O-methyl show that a number of low energy minima are accessible to this disaccharide. Molecular dynamics simulations starting from the low energy minima show conformational transitions with a time scale of 10–50 ps among several of the minima while large barriers between other minima prevent transitions on the time scale studied. Simulations of this disaccharide in the presence of solvent show fewer conformational transitions, illustrating a dampening effect of the solvent that has been observed in some other studies. Our results are most consistent with an equilibrium among multiple conformations for the Neu5Ac α(2 → 3) Gal β linkage. © 1994 John Wiley & Sons, Inc.     

Re-entrant cholesteric phase in DNA liquid-crystalline dispersion particles

In this research, we observe and rationalize theoretically the transition from hexagonal to cholesteric packing of double-stranded (ds) DNA in dispersion particles. The samples were obtained by phase exclusion of linear ds DNA molecules from water-salt solutions of poly(ethylene glycol)—PEG—with concentrations ranging from 120 mg ml^?1 to 300 mg ml^?1. In the range of PEG concentrations from 120 mg ml^?1 to 220 mg ml^?1 at room temperature, we find ds DNA molecule packing, typical of classical cholesterics. The corresponding parameters for dispersion particles obtained at concentrations greater than 220 mg ml^?1 indicate hexagonal packing of the ds DNA molecules. However, slightly counter-intuitively, the cholesteric-like packing reappears upon the heating of dispersions with hexagonal packing of ds DNA molecules. This transition occurs when the PEG concentration is larger than 220 mg ml^?1. The obtained new cholesteric structure differs from the classical cholesterics observed in the PEG concentration range 120–220 mg ml^?1 (hence, the term ‘re-entrant’). Our conclusions are based on the measurements of circular dichroism spectra, X-ray scattering curves and textures of liquid-crystalline phases. We propose a qualitative (similar to the Lindemann criterion for melting of conventional crystals) explanation of this phenomenon in terms of partial melting of so-called quasinematic layers formed by the DNA molecules. The quasinematic layers change their spatial orientation as a result of the competition between the osmotic pressure of the solvent (favoring dense, unidirectional alignment of ds DNA molecules) and twist Frank orientation energy of adjacent layers (favoring cholesteric-like molecular packing).     

Interaction of meropenem with ‘N’ and ‘B’ isoforms of human serum albumin: a spectroscopic and molecular docking study

Carbapenems are used to control the outbreak of β-lactamases expressing bacteria. The effectiveness of drugs is influenced by its interaction with human serum albumin (HSA). Strong binding of carbapenems to HSA may lead to decreased bioavailability of the drug. The non-optimal drug dosage will provide a positive selection pressure on bacteria to develop resistance. Here, we investigated the interaction between meropenem and HSA at physiological pH 7.5 (N-isoform HSA) and non-physiological pH 9.2 (B-isoform HSA). Results showed that meropenem quenches the fluorescence of both ‘N’ and ‘B’ isoforms of HSA (ΔG < 0 and binding constant ~10⁴ M^?1). Electrostatic interactions and van der Waal interactions along with H-bonds stabilized the complex of meropenem with ‘N’ and ‘B’ isoforms of HSA, respectively. Molecular docking results revealed that meropenem binds to HSA near Sudlow’s site II (subdomain IIIA) close to Trp-214 with a contribution of a few residues of subdomain IIA. CD spectroscopy showed a change in the conformation of both the isoforms of HSA upon meropenem binding. The catalytic efficiency of HSA (only N-isoform) on p-nitrophenyl acetate was increased primarily due to a decrease in K_m and an increase in k_cat values. This study provides an insight into the molecular basis of interaction between meropenem and HSA.     

On the use of advanced modelling techniques to investigate the conformational discrepancy between two X-ray structures of the AppA BLUF domain

The conformation of the blue light utilising flavin domain of the signalling protein AppA in the dark state is a matter of intensive research, both experimental and theoretical, and has not yet unambiguously been determined. Two contradicting X-ray structures of the dark state have been published previously. We aim at resolving this seeming contradiction by exploring conformational pathways between the two X-ray structures using advanced modelling techniques, such as local-elevation searching and sampling, soft-core non-bonded interactions and protocols of successively biasing the sampling of sets of torsional angles which adopt different values in the two alternative X-ray structures. The results suggest a high energetic barrier for a change in the Trp104 side chain from a ‘Trp-in’ to a ‘Trp-out’ conformation or vice versa, and illustrate the complexity to model conformational transitions involving a large number of degrees of freedom.     

Inheritance of resistance to lettuce root aphid in the lettuce cultivars 'Avoncrisp' and 'Lakeland"

The inheritance of resistance in two lettuce cultivars to lettuce root aphid, Pemphigus bursarius, was studied in a series of laboratory and field experiments at Wellesbourne between 1989 and 1992. A source of total resistance in the cv. ‘Avoncrisp’ which is linked to the downy mildew resistance gene Dm6, was shown to be governed by a single dominant gene. There were no maternal effects evident in the inheritance of this resistance. The basis of the high level of resistance which exists in the cv. ‘Lakeland’ (formerly known as ‘Jubilee’) was also shown to be controlled by the same dominant gene. The linkage between Dm6 and root aphid resistance was broken in ‘Lakeland’ as this cultivar does not possess the Dm6 gene. The linkage was presumably broken when the original cross between the parents of cv. ‘Lakeland’, ‘Calmar’ and ‘Avoncrisp’ was made. Under laboratory conditions small numbers of aphids commence development on cv. ‘Lakeland’ but colonies fail to develop and under field conditions the resistance provides adequate Protectión against the pest. The resistance in both ‘Avoncrisp’ and ‘Lakeland’ was effective against a population of lettuce root aphid collected from an endive crop in southern France as well as being effective against the Wellesbourne population of this aphid.     

Molecular dynamics simulations of conformation and chain length dependent terahertz spectra of alanine polypeptides

Terahertz absorption spectra of alanine polypeptides in water were simulated with classical molecular dynamics at 310 K. Vibrational modes and oscillator strengths were calculated based on a quasi-harmonic approximation. Absorption spectra of Ala_n (n = 5, 15, 30) with different chain lengths and Ala₁₅ in coiled and helical conformations were studied in 10–40 cm^? 1 bandwidth. Simulation results indicated both the chain length and the conformation have significant influences on THz spectra of alanine polypeptides. With the increase of chain length, the average THz absorption intensity increases. Compared with the helical Ala₁₅ polypeptide, the THz spectra of coiled one shows stronger absorption peaks. These results were explained from different numbers of hydrogen bonds formed between polypeptides and the surrounding water molecules.