Main-chain Dynamics of a Partially Folded Protein:15N NMR Relaxation Measurements of Hen Egg White Lysozyme Denatured in Trifluoroethanol

¹⁵N NMR relaxation measurements have been used to study the dynamic behaviour of the main-chain of hen lysozyme in a partially folded state, formed in a 70% (v/v) trifluoroethanol (TFE)/30% water mixture at 37°C and pH 2. This state is characterised by helical secondary structure in the absence of extensive tertiary interactions. The NMR relaxation data were interpreted by mapping of spectral density functions and by derivation of segmental as well as global order parameters. The results imply that the dynamics of lysozyme in TFE can, at least for the great majority of residues, be adequately described by internal motions which are superimposed on an overall isotropic tumbling of the molecule. Although the dynamic behaviour shows substantial variations along the polypeptide chain, it correlates well with the conformational preferences identified in the TFE state by other NMR parameters. Segments of the polypeptide chain which are part of persistent helical structures are highly restricted in their motion (S²> 0.8, with effective internal correlation times τ_e< 200 ps) but are also found to experience conformational exchange on a millisecond timescale. Regions which are stabilised in less persistent helical structure possess greater flexibility (0.6 <S²< 0.8, 200 ps < τ_e< 1 ns) and those which lack defined conformational preferences are highly flexible (S²< 0.6, τ_e∼1 ns). The dynamic behaviour of the main-chain was found to be correlated with other local features of the polypeptide chain, including hydrophobicity and the position of the disulphide bridges. Despite the absence of extensive tertiary interactions, preferential stabilisation of native-like secondary structure by TFE results in a pattern of main-chain dynamics which is similar to that of the native state.     

Molecular states in single-stranded adenylate chains by relaxation analysis

The single-strand helix-coil transition in various oligo- and polyadenylates is characterized by means of an improved cable temperature-jump technique. In all the polymers studied {poly(rA), poly(dA), poly[A(m^2′)] and poly[A(e^2′)]} helix-coil relaxation is observed in the time range from 30 to 1000 nsec. Relaxation-time constants observed at wavelengths λ<280 nm (τ_α) are different from those found at λ >280 nm (τβ), indicating the presence of more than two conformational states. The time constants τ_α increase in the series poly(dA), poly[A(m^2′)], constants τ_β/τ_α is approximately 2.5, except in poly(dA) where τ_β/τ_α ≈ 9. Relaxation measurements with r(A)_n- oligomers show a decrease in conformational mobility with increasing chain length. The relaxation curves also demonstrate that “internal” residues have lower reaction rates than residues at the ends of the oligomer chain. Measurement in D₂O reveal a solvent isotope effect for τ_α of +87% for poly(rA), and of +53% for poly(dA), whereas no isotope effect is found in τ_β. The absence of “slow” relaxation processes in the model compound 9,9′ -trimethylenebisadenine shows that the relatively low rate of the single-strand helix-coil transitions is due to the coupling of base stacking with the folding of the sugar–phosphate chain. The absence of a seprate relaxation process (corresponding to τ_β) in 9,9′-trimethylenebisadenine, as well as in the dinucleotides ApC and CpA, suggests that this relaxation process is dependent upon the presence of both the sugar–phosphate chain and of adjacent adenine bases. The experimental data provide evidence that there is more than one ordered conformation in various single-stranded oligo- and polyadenylates and that the transition between these conformations is influenced by the sugar conformation.     

Adducts from mercury(I) and mercury(II) compounds with Bispyrazolylalkanes.X-Ray crystal structure of Bis(3,5-dimethylpyrazol-l-yl)methane(dicyano)-mercury(II)

The 1:1 adducts between thebis(3,5-dimethylpyrazol-1-yl)methane (L′-L′) or 2,2′-bis(pyrazol- 1-yl)propane (L″L″) ligand and HgX₂ (with X = Cl, CN or CO₂CF₃) have been obtained as well as [(L′L′)₂]Hg(ClO₄)₂ and the mercury(I) derivative (ligand)₂Hg₂(ClO₄)₂. The adducts have been characterized from analytical and spectral data (IR, proton and ¹³C NMR). Four-coordinated mercury is present in (L′L′)Hg(CN)₂, in which the metal-(NN)₂C ring adopts an asymmetric boat form. The molecular parameters are significantly different for the two independent molecules, the CHgC angles and the two Hg-N distances being 163.1(9)°and 2.55(1) plus 2.70(1) Å in the one case, and 148.2(8)° and 2.40(1) plus 2.51(1) Å, in the other; correspondingly the N-Hg-N angle, the ‘bite’ of the ligand, ranges from 79.0(5)° to 71.7(4)°, a value outside the range previously reported.     

Active Species for Ce(IV)-Induced Hydrolysis of Phosphodiester Linkage in cAMP AND DNA

The hydrolysis of cyclic adenosine 3′,5′-monophosphate and 2′-deoxythymidylyl(3′-5′)2′-deoxythymidine by Ce(NH₄)₂(NO₃)₆ was kinetically studied. The rate of hydrolysis was fairly proportional to the concentration of [Ce ^IV ₂ (OH)₄]⁴⁺, showing that this is the catalytically active species. According to quantum-chemical calculation, the two Ce(IV) ions in this [Ce^IV ₂(OH)₄]⁴⁺ cluster are bridged by two OH residues. Upon the complex formation with H₂ PO₄ ^? (a model compound for the phosphodiesters), these two Ce(IV) ions bind the two oxygen atoms of the substrate and enhance the electrophilicity of the phosphorus atom. The catalytic mechanism of Ce(IV)-induced hydrolysis of phosphodiesters has been proposed on the basis these results.     

Nuclear magnetic resonance study of the impact of ribose 2′-O-methylation on the aqueous solution conformation of cytidylyl-(3′ → 5′)-cytidine

In order to obtain information about the conformational characteristics at the nearestneighbor level in the 2′-O-methylated region of t-RNA, as well as in the bizarre 5′-terminus of eucaryotic mRNA, a detailed nuclear magnetic resonance study of 2′-O-methyl-cytidylyl-(3′ → 5′)-cytidine (CmpC) was conducted. Proton spectra were recorded at 270 MHz in the Fourier mode in D₂O solutions, 0.01M, pD 7.3 in the temperature range 5–80°C. Complete accurate sets of nmr parameters were derived for each of the nucleotidyl units by a combination of homo-nuclear decouplings and simulation iteration methods. The data were translated into conformational parameters using procedures developed in earlier studies from these laboratories. It is shown that the ribofuranose ring exists at a ²E ? ³E equilibrium with clear preference [(75–80)%] for the ³E mode. The C(4′)-C(5′) and C(5′)-O(5′) bonds form a stable conformational network with outspoken preference for conformers in which Ψ₁, Ψ₂ ? 60° and ?₂ ? 180°. The orientation of the 3′-phosphate and 2′-O-methyl groups is such that ?₁′ ? 210° and ?″ ? 60°. The phosphodiester bonds are flexible and shift trends for base, H(1′), and H(5″) suggest the existence of a conformational blend of right-handed stack (g^?g^?), left-handed stack (g⁺g⁺), and unstacked arrays (tg^? and tg⁺). Elevation of temperature perturbs the ²E ? ³E equilibrium accompanied with modest depopulation of ψ₁, ψ₂ ? 60° and ?₂ ? 180° conformers. The major effect of elevation of temperature is in the increase of unstacked arrays at the expense of g^?g^? and g⁺g⁺ conformers. The shift trend of Cmp-H(3′) with temperature shows that torsional variation about O(3′)-P is facilitated by increase in temperature and the preferred rotamer about O(3′)-P in the unstacked form is t (ω₁′ = 180°). A detailed comparison of the aqueous solution conformations of CpC and CmpC reveals that 2′-O-methylation causes: (i) a reduction in the magnitude of _χ1; (ii) an increase in the population of ³E pucker at the 3′-nucleotidyl unit; and (iii) modest perturbations in the O(3′)-P and P-O(5′) bond conformations. Comparison of the aqueous solution conformations of AmpA and CmpC makes clear that the conformational properties of pyrimidine-pyrimidine and purine-purine dimers which carry a 2′-O-methylated 3′-nucleotidyl unit are significantly different.     

The Telomeric dG(GT)4G Sequence Can Adopt a Parallel-Stranded Double Helical Conformation

Abstract

Oligonucleotides 3′-d(GTGTGTGTGG)-L-d(GGTGTGTGTG)-3′ (hp-GT) and 3′- d(G^4STG^4STG^4STG^4STGG)-L-d(GGTGTGTGTG)-3′ (hp-SGT), (L=(CH₂CH₂O)₃), were shown by use of several optical techniques to form a novel parallel-stranded (ps) intramolecular double helix with purine-purine and pyrimidine-pyrimidine base pairing. The rotational relaxation time of hp-GT was similar to that of a 10-bp reference duplex, and the fraction of unpaired bases was determined to be ～ 7%, testifying to the formation of an intramolecular double helical hairpin by the sequence under the given experimental conditions. A quasi-two- state mode of ps-double helix formation was validated, yielding a helix-coil transition enthalpy of ?135±5 kJ/mol. The G-G and T·T (or ^4ST·T) base pair configurations and conformational parameters of the double helix were derived with molecular modeling by force field techniques. Repetitive d(GT) sequences are abundant in telomers of different genomes and in the regulatory regions of genes. Thus, the observed conformational potential of the repetitive d(GT) sequence may be of importance in the regulation of cell processes.     

Studies on Synthesis and Structure of O-β-D-Ribofuranosyl(1″→2′)-ribonucleosides and Oligonucleotides♣

Abstract

Minor nucleosides found in several eukaryotic initiator tRNAs_i ^Met, O-β-D-ribofuranosyl(1″→2′)adenosine and -guanosine (Ar and Gr), as well as their pyrimidine analogues, were obtained from N-protected 3′,5′-O-(1,1,3,3-tetraisopropyldisiloxane-1,3-diyl)ribonucleosides and 1-O-acetyl-2,3,5-tri-O-benzoyl-β-D-ribofuranose in the presence of tin tetrachloride in 1,2-dichloroethane. A crystal structure has been solved for 2′-O-ribosyluridine. The 3′-phosphoramidites of protected 2′-O-ribosylribonucleosides were prepared as the reagents for 2′-O-ribofuranosyloligonucleotides synthesis. O-β-D-Ribofuranosyl(1″→2′)adenylyl(3′→5′)guanosine (ArpG) was obtained and its structure was analysed by NMR spectroscopy.

     

Purification of spermidine synthase from rat ventral prostate by affinity chromatography on immobilized S-adenosyl(5′)-3-thiopropylamine

A novel affinity chromatographic adsorbent was developed for purification of spermidine synthase from rat prostate. The adsorbent (S-adenosyl(5′)-3-thiopropylamine-Sepharose) possesses a ligand structurally similar to S-adenosyl(5′)-3-methylthiopropylamine (decarboxy AdoMet), a substrate of spermidine synthase. The S-adenosyl(5′)-3-thiopropylamine-Sepharose was prepared by an alkylation on sulfur of S-adenosyl-3-thiopropylamine by bromoacetamidohexyl-Sepharose under mild acidic conditions. The enzyme has been purified to homogeneity in 40% yield by using DEAE-cellulose, affinity chromatography employing S-adenosyl(5′)-3-thiopropylamine-Sepharose, and gel filtration. The enzyme had a molecular weight of approximately 73,000 and was composed of two subunits of equal size. The specificity of the reaction was rather strict, but cadaverine could replace putrescine as the aminopropyl acceptor, and the rate was 1/20th of the rate for spermidine formation. Apparent K_m values for putrescine and decarboxy AdoMet were 0.1 mm and 1.1 μm, respectively. Inhibition by decarboxy AdoMet and 5′-deoxy-5′-methylthioadenosine was observed. The inhibition by 5′-deoxy-5′-methylthioadenosine was partially noncompetitive with respect to decarboxy AdoMet.     

Thermodynamic and Structural Properties of r(ACC) as Revealed by Ultraviolet Electronic Absorption,Circular Dichroism, 1H-NMR Spectroscopy and Monte Carlo Simulations

Abstract

UV absorption, circular dichroïsm (CD) and ¹H NMR, associated with Monte Carlo (MC) molecular structure simulations have been applied to the study of the trinucleoside diphosphate: r(ACC).

The MC study which has been conducted as a function of temperature, is based on random variations of the nucleotide conformational angles, i.e. phosphodiester chain torsional angles and sugar pucker pseudorotational angles. All of the chemical bond lengths and valence angles remained fixed during the structural simulation, except those of the sugar pucker. Six different initial structures have been selected in order to explore the molecular conformational space as completely as possible. This simulation procedure led to distinct families of equilibrium conformations at 283,298 and 318 K.

The thermodynamical parameters such as variations in entropy, enthalpy and also melting temperature (ΔS⁰ _x, ΔH⁰ _x and T_m) of the stacking (X) equilibrium were obtained from UV absorption and circular dichroïsm (CD) spectra recorded over a 80K temperature range. Chemical shifts (δ), vicinal coupling constants(³J _k) and cross-relaxation rates (σ_k,l) of trimers were measured at 400.13 MHz over a range of concentrations (2–13mM) and temperatures (283–333K). Least-squares fitting of the experimental chemical shifts to simple models of association (A) and stacking equilibria allowed separation of the variations in the δ values (Δδ_x and Δδ_A) due to either phenomenon. The three NMR data sets (Δδ_x, ³J^k,l and σ_k.l) were then evaluated for the minima conformers obtained with the MC simulations. Theoretical values of Δδ_x were estimated using the results of an ab initio study while the coupling constant data were simulated with Karplus-type equations. Finally, the relaxation data were simulated from the distance matrices using treatment for cases of both slow conformational exchange accompanied by rapid small-amplitude fluctuations about the minima structures.

A consistent picture of the large amplitude deformations (torsional angle variation) of these trimers has emerged from the present study. Optimized conformational blends at 283, 296 and 318K were obtained by least-squares fitting of the experimental data to the theoretical ones, while considering the populations as adjustable parameters. As it would be expected, the right-handed helical conformation (A-RNA type) is found to be the major stacked species, in the temperature range of 283 to 318K. Limited evidence for bulged structures has been obtained, whereas novel reverse-stacked and half-stacked conformers also presented theoretical data compatible with the NMR observables of aqueous r(ACC).     

An unusual porosin type neolignan from Licaria chrysophylla

The trunk wood of Licaria chrysophylla contains rel-(7S, 8R, 1′S, 5′S)-Δ^8′-3,3′,5′-trimethoxy-4,5-methylenedioxy-1′,4′,5′,6′- tetrahydro-4′-oxo-7.1′,8.0.2′-neolignan (chrysophyllin A), which differs from all other known benzofuranoid neolignans by showing 7.1′ (rather than 8.1′) and 8.0.2′ (rather than 7.0.2′) linkages between the propenylphenol and allylphenol derived moieties.     

Conformation and dynamic structure of poly(inosinic acid) in neutral aqueous solution by 1H-, 2H-, 13C-, and 31P-NMR spectroscopy

The conformation and dynamic structure of single-stranded poly(inosinic acid), poly(I), in aqueous solution at neutral pH have been investigated by nmr of four nuclei at different frequencies: ¹H (90 and 250 MHz), ²H (13.8 MHz), ¹³C (75.4 MHz), and ³¹P (36.4 and 111.6 MHz). Measurements of the proton-proton coupling constants and of the ¹H and ¹³C chemical shifts versus temperature show that the ribose is flexible and that base-base stacking is not very significant for concentrations varying from 0.04 to 0.10M in the monomer unit. On the other hand, the proton T₁ ratios between the sugar protons, T₁ (H₁′)/T₁ (H₃′), indicate a predominance of the anti orientation of the base around the glycosidic bond. The local motions of the ribose and the base were studied at different temperatures by measurements of nuclear Overhauser enhancement (NOE) of protonated carbons, the ratio of the proton relaxation times measured at two frequencies (90 and 250 MHz), and the deuterium quadrupolar transverse relaxation time T₂. For a given temperature between 22 and 62°C, the ¹³C-{¹H} NOE value is practically the same for seven protonated carbons (C₂, C₈, C_1′, C_2′, C_3′, C_4′, C_5′). This is also true for the T₁ ratio of the corresponding protons. Thus, the motion of the ribose–base unit can be considered as isotropic and characterized by a single correlation time, τ_c, for all protons and carbons. The τ_c values determined from either the ¹³C-{¹H} NOE or proton T₁ ratios, T₁(90 MHz)/T₁(250 MHz), and/or deuterium transverse relaxation time T₂ agree well. The molecular motion of the sugar-phosphate backbone (O-P-O) and the chemical-shift anisotropy (CSA) were deduced from T₁ (³¹P) and ³¹P-{¹H} NOE measurements at two frequencies. The CSA contribution to the phosphorus relaxation is about 12% at 36.4 MHz and 72% at 111.6 MHz, corresponding to a value of 118 ppm for the CSA (σ = σ∥ ? σ?). Activation energies of 2–6 kcal/mol for the motion of the ribose–base unit and the sugarphosphate backbone were evaluated from the proton and phosphorus relaxation data.     

Crystal Structure and Molecular Conformation of 4-Thiouracil-2′-Trifluorothioacetamide -3′, 5′-Diacetyl-β-D-Riboside

Abstract

4-thiouracil-2′-trifluorothioacetamide-3′, 5′-diacetyl-β-D-riboside is one of the modified thiouracil analogs synthesized in our institute. The determination of the crystal and molecular structure of this compound was carried out with a view to study the conformation of the molecule in the solid state as well as to investigate the conformations of the trifluoroacetamide and the acetyl substituents of the ribose and their effects on the conformation of the ribose ring. Crystals of 4-thiouracil-2′-trifluorothioacetamide-3′,5′- diacetyl-β-D-riboside are orthorhombic, space group P2₁ 2₁ 2₁, with cell dimensions a= 15.351 (2), b= 15.535 (1), c= 8.307 (1) Å, V=1981.0 (7) ų, Z=4, D_m= 1.53, D_c=1.527 g/c.c. and μ=30.1cm -¹. The structure was determined using CuKα (λ, =1.5418 Å) at a temperature T of 297K, with 2333 reflections, which were collected on a Enraf-Nonius CAD-4 diffactometer, out of which 2249 (I ≥20) were considered observed. The structure was determined by direct methods using MULTAN and refined by full matrix least squares method to a final reliability factor of 0.054 and a weighted R factor of 0.079. The nucleoside is in the anti conformation [X_CN =51.4 (5)°], the ribose has the unusual C (2′) endo -C (1′) exo (²T₁), and a g+ conformation [ψ=47.5 (4)] across C(4′)-C(5′) bond. The pseudorotation angle P is 152.8 (4) ° and the amplitude of pucker τ_m of 42.7 (3)°. The average C-F bond distance is 1.308 Å. There is no base pairing and the typical base-base hydrogen bonded interactions are not present in this structure. On the other hand, a hydrogen bonded dimer is formed involving C(3′) - H(3′)… O (2) and N(3) -H (N3) … O (Al) hydrogen bonds joining the base, ribose ring and the acetyl group. The trend towards longer exocyclic bonds at the acetyl centers in compounds with strongly electronegative aglycones, is also exhibited in this compound, with C(3′)-O(3′) and C(5′)-0(5′) being much longer than C(1′)-O(4′). The acetyl groups also take part in C-H…O hydrogen bonding with the acetyl oxygen atom OA2.     

Frequency dependence of the proton magnetic relaxation in aqueous solutions iof haemoproteins

The longitudinal proton magnetic relaxation times T₁ were measured for ferri (met)-and carbonmonoxy-bovine haemoglobin and equine myoglobin in 0.1 M KH₂PO₄ aqueous solutions near pH 6 at 5°C and 35°C from 1.5- to 60-MHz Larmor frequencies. It is concluded that the correlation time τ_C for the dipole–dipole interaction of electron and nuclear spins is in fact the electron (ferric) spin relaxation time τ_S being close to 1.5 × 10^?10 sec for both metHb and metMb at 5°C. At 35°C the paramagnetic relaxation rates are not determined solely by the relaxation of protons exchanging from the haem pocket with bulk solvent. Hence, τC at 35°C cannot be calculated from the dispersion data obtained at this temperature. The relevance of this for the determination of interspin distances r is discussed.     

A comparison of 15N NMR relaxation measurements with a molecular dynamics simulation: Backbone dynamics of the glucocorticoid receptor DNA-binding domain

The rapid motions of the backbone of the DNA-binding domain of the glucocorticoid receptor (GR DBD) have been investigated using proton-detected heteronuclear NMR experiments on ¹⁵N-labeled protein at pH 6.0 and with a 200 psec molecular dynamics simulation of hydrated GR DBD. The experimental data were interpreted in terms of a generalized order parameter (S²) and an effective correlation time (τ_e) for the internal motion of each amide bond. A back calculation, using the same model, yielded the {¹H}-¹⁵N nuclear Overhauser effects (NOEs) and the ¹⁵N spin-lattice relaxation times (T₁) from the simulated data. The rapid motions of the backbone turned out to be rather limited and uniform throughout the protein, with a somewhat reduced mobility in the two major α-helical regions and a slightly enhanced flexibility for some residues in the first zinc coordinating region. The agreement between the experimental and simulated S²-values was as good as quantitative for most of the residues, except for some residues that were subject to a more large-scale, and in the simulation thus poorly sampled, motion. Examples of such motions that were found in the simulation include jumps of the amide bond of Ile-487 between the charged oxygens of the side chain of Asp-485 and less distinct large scale motions for some of the residues in the extended regions, that were shown to give rise to noisy and/or fast decaying internal reorientational correlation functions. For these residues large differences in the simulated and experimental τ_e-values were found, indicating that motions on different time scales were dominating in the experimental and simulated values. The lower (<0.7) experimental NOEs for these residues could not be reproduced in the simulation and were shown to be a consequence of the lower τ_e-values estimated in the simulation. By combining information from the simulation and the experiment a more complete picture of the motions for these residues can be obtained as is illustrated with an estimation of the jump angle and jump frequency for the amide bond of Ile-487. © 1993 Wiley-Liss, Inc.     

Theoretical drug design: 6-azauridine-5'-phosphate--its X-ray crystal structure, potential energy maps, and mechanism of inhibition of orotidine-5'-phosphate decarboxylase.

The cytostatic drug 6-azauridine is converted in vivo to 6-azauridine-5′-phosphate (z⁶Urd-5′-P), which blocks the enzyme orotidine-5′-phosphate decarboxylase (Ord-5′-Pdecase) and therefore inhibits the de novo production of uridine-5′-phosphate (Urd-5′-P). In order to relate the structure and function of z⁶Urd-5′-P, it was crystallized as trihydrate, space group P2₁2₁2₁ with a = 20.615 Å, b = 6.265 Å, c = 11.881 Å, and the structure established by Patterson methods. Atomic parameters were refined by full-matrix least-squares methods to R = 0.066 using 1638 counter measured x-ray data. The ribose of z⁶Urd-5′-P is in a twisted C(2′)-exo, C(3′)endo conformation, the heterocycle is in extreme anti position with angle N(6)-N(1)-C(1′)-O(4′) at 86.3°, and the orientation about the C(4′)-C(5′) bond is gauche, trans in contrast to gauche, gauche found for all the other 5′-ribonucleotides. Conformational energy calculations show that z⁶Urd-5′-P may adopt an extreme anti conformation not allowed to Urd-5′-P, and they also predict the same unusual trans, gauche conformation about the C(4′)-C(5′) bond in orotidine-5′-phosphate (Ord-5′-P) and in z⁶Urd-5′-P, which renders the distances O(2)…O(5′) in z⁶Urd-5′-P and O(7)…O(5′) in Ord-5′-P comparable. On this basis the function of z⁶Urd-5′-P as an Ord-5′-Pdecase inhibitor can be explained as being due to its structural similarity with the substrate Ord-5′-P and further clarifies the inhibitory action of 5′-nucleotides bearing the heterocycles oxipurinol, xanthine, or allopurinol [J. A. Fyfe, R. L. Miller, and T. A. Krenitsky, J. Biol. Chem. 248 , 3801 (1973)]. With this in mind, new inhibitors for Ord-5′-Pdecase may be designed.     

Syn–anti equilibrium of purine bases in dinucleoside monophosphates as studied by proton longitudinal relaxation

The preferential orientations of the purine bases in dinucleoside monophosphates such as ApA, ApG, and GpA in 10^?2M neutral aqueous solutions have been investigated by proton relaxation at 250 MHz. These orientations are deduced from computer simulations of the magnetization recovery curves following a 180° nonselective pulse. The distances between the H(8) proton of a base and the ribose ring protons which are used in these calculations are obtained by minimization as a function of the glycosyl torsion angle ? of the standard deviation between the isotropic reorientation correlation times τ_R derived from the relaxation rates of these protons. The average H(1′) – H(8) distance obtained by this procedure may be readily verified from the reduction of the H(1′) relaxation rate when H(8) is substituted by a deuteron. The limits of validity of the assumption of a single correlation time τ_R governing the proton relaxation have been estimated, taking into account several possible internal motions, e.g., the rotation of the base, of the methylene exocyclic group and the N ? S interconversion of the ribose ring. For 10^?10 < τ_R < 2 × 10^?10 sec, it appears that the influence of these motions on the proton relaxation becomes perceptible when the jump rates among equilibrium positions exceed ca. 10⁹ sec^?1. The whole of the experimental results show that for the ribose ring N conformer, the orientation of the bases is found in the ranges 60° < ? < 80° (syn) and 180° < ? < 210° (anti). For ribose S conformer, it is observed that this orientation is mainly syn with 5° < ? < 90°. The average H(1′) – H(8) distance provides semiquantitative information on the overall syn or anti orientations of the base in each nucleoside moiety. At 298 K the population of the anti conformer is found to increase in the order A- pG < Ap -G ～ Gp -A < Ap -A < A-pA < G-pA . A more detailed analysis of relaxation data shows that the maximum possible fraction of the stacked form of dinucleotides, due to the occurrence of N-anti conformers in both nucleoside moieties, is in the order ApG < GpA < ApA, in agreement with previous works, with however smaller values. Lastly the deuteron linewidth in position 8 of the bases indicates a syn–anti transition rate of the order of 10⁹ sec^?1 at room temperature, without noticeable effects therefore on the proton relaxation.     

Cytldlne Cyclic (3′, 5′) Monophosphate: Cyclic Nucleotide With a Non-Characteristic Ribose Ring Conformation

Abstract

Cytidine 3′,-5′-cyclic phosphate (cCMP) occurs in nature and has growth stimulatory activity on L-1210 cells. The initiation of cell growth by cCMP, under conditions where CAMP, cGMP and cUMP delay the onset of proliferation suggests that cCMP may play a regulatory role in the cell metabolism. It has been reported that in 3′,5′-cyclic nucleotides, the phosphate ring fused to the furanose ring resuicts the conformation of the furanose ring to the twist form C(3′) endo C(4′) exo (³T₄), in contrast to the C(2′) endo C(3′) endo (²T₃) and C(3′) endo C(2′) exo (³T₂) twist forms normally found in nucleotides and nucleosides. We have carried out an accurate crystal structure of cCMP and found that the furanose ring in cCMP has the C(3′) endo C(2′) exo conformation (³T₂), with a pseudo rotation amplitude (P) of 44° and phase angle τ_m of 12°. cCMP is in low anti conformation (X_CN = 15.4°) and O(5′) has the fixed g conformation. The phosphate ring is constrained to the chair conformation, as in other cyclic nucleotides. The two exocyclic P-O bond distances are short (1.489, 1.476Å) and the ring angle at N(3) is large (125.2°) suggesting that the molecule in the solid state is a zwitterion with a plus charge on N(3). The crystals are hydrated and highly unstable. The three water molecules are highly disordered in ten locations. The crystals of cCMP 3H₂O are hexagonal, a = 16.294(3), b = c = 11.099(4)Å, space group P6₁, final R value is 0.067 for 1620 reflections 230.     

Photochemistry of the O-Nitrobenzyl Protecting Group in RNA Synthesis

Abstract

UV irradiation of 2′-O (o-nitrobenzyl)adenylyl(3′-5′)uridine in the presence of O₂ yields the corresponding nitrobenzoyl derivative in addition to the expected A-U. A mechanism proposed for this oxidation involves the successive removal of the two benzylic protons with a hydroperoxide as the intermediate between the two steps.     

Multinuclear NMR of cis-dicarbonylbis(dithiocarbamato)iron(II) complexes in chloroform solution

The ¹³C and ¹⁵SN NMR spectra of eleven cis-Fe(S₂CNRR′)₂(CO)₂ complexes, where R and R′ are organic substituents, have been measured at ambient temperature in CDCl₃ (0.08–0.16 M). The ¹³C absorptions for the carbonyl ligands correlate well with the force constants for the CO stretching vibrations in CHCl₃ solution. Each of the parameters (¹³CO absorption and k_cis for CO) correlate well with the aqueous solution pK_a for⁺H₂NRR′, corrected for the phenyl-containing substituents, high pK_a values corresponding to high ¹³CO absorptions and low k_cis CO force constants. [p ]Evidence was found in the ¹³C NMR spectra for hindered rotation about the CN bond in S₂CNC₂ in complexes with higher pK_a(corr) values and in the ¹³C spectra of the corresponding thiuram disulfides. [p ]The ¹⁵N (natural abundance) NMR spectra for each of the complexes was determined. Each revealed a single sharp absorption in a region of the ¹⁵N NMR spectrum which indicates substantial CN double bond character, as one would expect for coordinated dithiocarbamate ligands.     

Hydrolysis of some mRNA 5′-Cap Analogs Catalyzed by the Human Fhit Protein - and Lupin ApppA Hydrolases

Abstract

Hydrolysis of the following four cap analogs: m⁷G(5′)ppp(5′)A, m⁷G(5′)ppp(5′)m⁶A, m⁷G(5′)ppp(5′)m^2′OG and m⁷G(5′)ppp(5′)2′dG catalyzed by homogeneous human Fhit protein and yellow lupin Ap₃A hydrolase has been investigated. The hydrolysis products were identified by HPLC analysis and the K_m and V_max values calculated based on the data obtained by the fluorimetric method.