Spatial configurations of polynucleotide chains. 3. Polydeoxyribonucleotides

The virtual bond scheme set forth in preceding papers for treating the average properties of polyriboadenylic acid (poly rA) is here applied to the calculation of the unperturbed mean-square end-to-end distance of polydeoxyriboadenylic acid (poly dA). The modifications in structure and in charge distribution resulting from the replacement of the hydroxyl group at C_2′ in the ribose residue by hydrogen in deoxyribose produce only minor modifications in the conformational energies associated with the poly dA chain as compared to those found for poly rA. The main difference is manifested in the energy associated with rotations about the C_3′–O_3′ bond of the deoxyribose residue in the C_2′-endo conformation; accessible rotations are confined to the range between 0° and 30° relative to the trans conformation, whereas in the ribose unit the accessible regions comprise two ranges centered at approximately 35° and 85°. The characteristic ratio 〈r²〉0/nl² calculated on the basis of the conformational energy estimates is ≈9 for the poly dA chain with all deoxyribose residues in the C_3′-endo conformation and ≈21 with all residues in the C_2′-endo form. Satisfactory agreement is achieved between the theoretical values and experimental results on apurinic acid by treating the poly dA chain as a random copolymer of C_3′-endo and C_2′-endo conformational isomers present in a ratio of ～1 to 9.     

A vibrational spectroscopic study of the self-association of polyinosinic acid and polyguanylic acid in aqueous solution

We have studied by Raman and ir spectroscopy the structure of self-associated polyinosinic acid and polyguanylic acid in aqueous solution. The results are consistent with the formation of a four-stranded complex, which melts cooperatively near 60°C in the case of poly (I) in the presence of K⁺ ions. The conformation of the ribose in both systems is mixed C2′-endo/C3′-endo, giving a structure that is intermediate between the extremes proposed previously from x-ray diffraction studies. Characteristic Raman bands for the C2′-endo ribose conformation in polyribonucleotides are identified. The four-stranded structure of poly (I) appears to be very flexible, with ≈15% of the tetrameric segments being disrupted and ≈30% of the ribose units adopting a disordered conformation prior to melting. This disordering process increases to ≈75% above the melting transition, with the remaining ≈25% of the ribose units keeping an ordered C2′-endo or C3′-endo conformation. © 1994 John Wiley & Sons, Inc.     

Different domain organization of two main conformational states of Na<Superscript>+</Superscript>/K<Superscript>+</Superscript>-ATPase

The Na⁺/K⁺-ATPase generates an electrochemical gradient of Na⁺ and K⁺, which is necessary for the functioning of animal cells. During the catalytic act, the enzyme passes through two principal conformational states, E₁ and E₂. To assess the domain organization of the protein in these conformations, thermal denaturation of Na⁺/K⁺-ATPases from duck salt gland and from rabbit kidney has been studied in the absence and in the presence of Na⁺ or K⁺, which induce the transition to E₁ or E₂. The melting curves for the ion-free forms of the two ATPases have different shapes: the rabbit protein shows one transition at 56.1°C, whereas the duck protein shows two transitions, at 49.8 and 56.9°C. Addition of Na⁺ or K⁺ ions abolishes the difference in thermal behavior between these enzymes, but through opposite effects. The melting curves for the E₂ conformation (K⁺ bound) in both cases exhibit a single peak of heat absorption at ∼63°C. For the E₁ conformation (Na⁺ bound), each melting curve has three peaks, indicating denaturation of three domains. The difference in the domain organization of Na⁺/K⁺-ATPase in the E1 and E2 states may account for the different sensitivity to temperature, proteolysis, and oxidative stress observed for the two enzyme conformations.     

A vibrational spectroscopic study of the metastable form of associated polyinosinic acid

We have studied by Raman and ir spectroscopy the metastable complex formed by the self-association of polyinosinic acid in aqueous solution. The complex is easily prepared by quickly cooling to ca. 0°C a warm solution of the polyribonucleotide to which a small amount of rubidium salt has been added. Upon heating, this metastable form melts cooperatively near 13°C, well below the dissociation temperature of a stable four-stranded complex, which occurs at 47°C in the same conditions. The presence of several components in the stretching-mode region of the carbonyl groups in the vibrational spectra of the metastable complex suggests that it also has a parallel four-stranded structure. The difference in structure between the two forms is believed to be caused by the presence of fewer metal ions in the central channel of the metastable complex, in agreement with conclusions reached in previous investigations. The Raman spectra further show that the ribose units in the metastable form have a C3′-endo conformation, in contrast with the stable form, for which we have previously suggested a mixed C2′-endo/C3′-endo conformation. © 1996 John Wiley & Sons, Inc.     

Structural and Conformational Studies on Deoxyguanosyl-3′,5′-Deoxyadenosine Monophosphate and Its Ethyl Phosphotriester Analogs - Left-Handed Dimers

Abstract

The mode of base-base stacking, the handedness and the sugar(dGpA)phosphate backbone conformation of deoxyguanosyl 3′-5′ deoxyadenosine and its diastereomeric ethyl phosphotriester analogs were studied by ¹H NMR, UV and CD spectroscopy. The results indicate the three dimers are left-handed, while the sugar phosphate backbone is comprised predominantly of C_2′-endo, gg (C_4′-C_5′) and g′g′ (C_5′-O) conformers. The two bases are extensively stacked and interact about 90° along the dyad axes. The extent of base overlap in dGpA is slightly greater than in either ethyl phosphotriester analog. The absolute configurations of the two ethyl phosphotriester diastereoisomers of dGpA can be assigned by one-dimensional and two-dimensional ¹H NMR nuclear Overhauser enhancement experiments.     

The effect of monovalent cations on the association behavior of guanosine 5'-monophosphate, cytidine 5'-monophosphate, and their equimolar mixture in aqueous solution

¹H- and ³¹P-nmr spectroscopy have been used to investigate the self-association of M₂(5′-CMP) [M = Li⁺, Na⁺, K⁺, Rb⁺, or (CH₃)₄ N⁺; 5′-CMP = cytidine 5′-monophosphate], the self-association of Li₂(5′-GMP) (5′-GMP = guanosine 5′-monophosphate), and the heteroassociation of 5′-GMP and 5′-CMP (1 : 1 mole ratio) in aqueous solution as a function of the nature of the monovalent cation. Proton spectral differences for the different 5′-CMP salts exhibit a cation-size dependence and have been ascribed to a change in the stacking geometry. An average stacking association constant of 0.63 ± 0.24M^?1 at 1°C, consistent with the weak stacking interactions of the cytosine bases, was determined for the 5′-CMP salts. Heteroassociation of 5′-GMP and 5′-CMP follows the reverse of the cation order for the formation of ordered aggregates of 5′-GMP. Heteroassociation occurs in the presence of Li⁺, Na⁺, and Rb⁺ ions, but only self-association occurs for the K⁺ nucleotides. Li₂(5′-GMP), which does not form ordered species, self-associates to form disordered base stacks with a stacking constant of 1.63 ± 0.11M^?1 at 1°C.     

Kinetic Studies of a (Na++ K++ Mg2+) ATPase in Sugar Beet Roots

Kinetic studies of a dithiothreitol treated membrane ATPase fraction from sugar beet roots led to the following conclusions: 1) In the presence of MgATP, Na⁺ and K⁺ stimulate the ATPase activity in different ways following simple Michaelis-Menten kinetics. Thus separate sites for Na⁺ and K⁺ are suggested. 2) In the absence of K⁺, Na⁺ acts as an uncompetitive modifier raising the apparent K_m and V_max for MgATP. 3) In the absence of Na⁺, K⁺ activates non-competitively with respect to MgATP. Thus K⁺ increases V_max but does not affect the apparent affinity constant. 4) K⁺ and Na⁺ double the rate constants. 5) In the presence of Na⁺ or K⁺, Mg²⁺ in excess acts as a weak inhibitor to Na⁺ and/or K⁺ activity. 6) The temperature-activity dependence in the 5–40°C interval shows biphasic Arrhenius plots with the transition point between 15–18°C. The activation energy is lowered at temperatures > 18°C.     

Interaction of Purine Nucleotides with Cobalt-Hexammine,Cobalt-Pentammine and Cobalt- Tetrammine Cations. Evidence for the Rigidity of Adenosine and Flexibility of Guanosine and Deoxyguanosine Sugar Conformations

Abstract

The interaction of adenosine-5′-monophosphate (5′-AMP), guanosine-5′-monophosphate (5′-GMP) and 2′-deoxyguanosine-5′-monophosphate (5′-dGMP) with the [Co(NH₃)₆]³⁺, [CO(NH₃)₅C1]²⁺ and [CO(NH₃)₄C1₂]⁺ cations has been investigated in aqueous solution with metal/nucleotide ratios (r) of 1/2, 1 and 2 at neutral pH. The solid complexes have been isolated and characterized by FT-IR and ¹H-NMR spectroscopy.

The complexes are polymeric in nature both in the crystalline solid and aqueous solution. The binding of the cobalt-hexammine cation is indirectly (via NH₃) through the N-7 and the PO₃ ^2- groups of the AMP and via O-6, N-7 and the PO₃ ^2- of the GMP and dGMP anions (outer-sphere). The cobalt-pentammine and cobalt-tetrammine bindings are through the phosphate groups (inner-sphere) and the N-7 site (outer-sphere) of these nucleotide anions. The ribose moiety shows C2′-endo/anti conformation, in the free AMP and GMP anions as well as in the cobalt-ammine - AMP complexes, whereas a mixture of the C2′-endo/anti and C3′-endo/anti sugar puckers were observed for the Co(NH₃)₆-GMP, Co(NH₃)₅-GMP and a C3′-endo/anti conformer for the Co(NH₃)₄-GMP complexes. The deoxyribose showed an O4′-endo/anti conformation for the free dGMP anion and a C3′-endo/anti for the Co(NH₃)₆-dGMP, Co(NH₃)₅-dGMP and Co(NH₃)₄-dGMP complexes.     

Solubilization, purification, and reconstitution of α2β1 isozyme of Na+/K+-ATPase from caveolae of pulmonary smooth muscle plasma membrane: comparative studies with DHPC, C12E8, and Triton X-100

We identified α₂, α₁, and β₁ isoforms of Na⁺/K⁺-ATPase in caveolae vesicles of bovine pulmonary smooth muscle plasma membrane. The biochemical and biophysical characteristics of the α₂β₁ isozyme of Na⁺/K⁺-ATPase from caveolae vesicles were studied during solubilization and purification using the detergents 1,2-heptanoyl-sn-phosphatidylcholine (DHPC), poly(oxy-ethylene)8-lauryl ether (C₁₂E₈), and Triton X-100, and reconstitution with the phospholipid dioleoyl-phosphatidylcholine (DOPC). DHPC was determined to be superior to C₁₂E₈, whereas C₁₂E₈ was better than Triton X-100 in the active enzyme yields and specific activity. Fluorescence studies with DHPC-purified α₂β₁ isozyme of Na⁺/K⁺-ATPase elicited higher E1Na?E2 K transition compared with that of the C₁₂E₈- and Triton X-100-purified enzyme. The rate of Na⁺ efflux in DHPC–DOPC-reconstituted isozyme was higher compared to the C₁₂E₈–DOPC- and Triton X100–DOPC-reconstituted enzyme. Circular dichroism analysis suggests that the DHPC-purified α₂β₁ isozyme of Na⁺/K⁺-ATPase possessed more organized secondary structure compared to the C₁₂E₈- and Triton X-100-purified isozyme.     

Proton magnetic resonance study of 8-(6-aminohexyl)-aminoadenosine 5′-monophosphate

The nucleotide 8-(6-aminohexyl)-amino adenosine 5′-monophosphate (8-AHA-AMP) has been investigated by 220-MHz proton magnetic resonance spectroscopy. The conformation and ionization state of the nucleotide have been determined. The anti-conformation about the glycosyl bond is the preferred form. The interaction between the hexyldiamino chain and the ribose moiety in this conformation gives rise to unusual ribosyl conformation results. The distribution of conformations about the glycosyl bond has little influence on the effectiveness of this nucleotide analog in the purification of dehydrogenases by affinity chromatography. The chemical shift dependence on pH has been carried out on 8-methylaminoadenosine 5′-monophosphate. The 8-aminoadenine ring is protonated at N1 (pK_α 5.0) and at N7 (pK_α 1.5) in acidic solutions. The protonation at N7 is apparently stabilized by a delocalization of charge onto the 8-amino group. The neutrality of the 8-aminoadenine ring at physiological pH is consistent with the effcient binding of the nucleotide by dehydrogenases. An improved method for the preparation of the 8-AHA-AMP is described.     

A critical temperature transition of K+-Na+ exchange in human lymphocytes

Human lymphocytes were equilibrated for 48 hours at 5-6 mM K⁺_ex over a range of temperatures between 0 and 37°C, and at 5°C over a range of external K⁺ levels between 0 and 32 mM. Cell K⁺ and Na⁺ contents are normal between 37 and 10′. Below 10′ there is a critical thermal transition in ion contents centering around 3°C. This and the steep sigmoidal isotherms of K⁺ and Na⁺ at 5°C confirm the cooperative nature of ion exchange. At 0′, cell K⁺ is maintained at a concentration that is seven to eight times that of the external medium. Isotopic K⁺ influx shows smaller, rapidly-exchanging, and larger, slowly-exchanging fractions. The latter, which correspond to the saturable, sigmoidal components of cell K⁺, are slowed by decreasing temperature. Although there is a critical temperature transition of K⁺-Na⁺ exchange, there is no corresponding transition for isotopic K⁺ exchange, which has an activation energy of 11.6 kcal/mole. The combined ion content and flux data are readily understood by reference to two major concepts of the association-induction hypothesis: that of rapid solute exclusion from cell water existing in a state of polarized multilayers, and that of solute accumulation limited by adsorption onto and desorption from fixed anionic sites that interact with one another in a critical, cooperative fashion.     

Temperature Dependence of the Sodium Pump is Altered in the Cerebral Cortex of CCK<Subscript>2</Subscript> Receptor-Deficient Mice

Previously we have shown that the temperature dependence of the sodium pump (Na⁺,K⁺-ATPase) is altered under different neuropathological conditions. In this study we compared temperature dependence of the Na⁺,K⁺-ATPase in the fronto-parietal cortex of CCK₂ receptor-deficient (homo- and heterozygous) and normal (wild-type) mice. The Arrhenius plot for Na⁺,K⁺-ATPase from wild-type brain is non-linear with a breakpoint at 20.3 ± 0.4°C. In case of the brain cell membrane of CCK₂ receptor-deficient mice (homo- and heterozygous) the breakpoint on Arrhenius plot was detected at 26.0 ± 1.1°C and 25.4 ± 0.4°C, respectively. The shift of the breakpoint on the Arrhenius plot established in CCK₂ receptor-deficiency as well as in case of some other pathological conditions confirms that such kind of alteration in the Na⁺,K⁺-ATPase temperature dependence is likely related to the homeostatic adjustment of altered function of the sodium pump.     

Changes in the polyelectrolyte-amphiphile interaction due to helix-coil transition induced by specific counterions or variations in temperature

For the system κ-carrageenan/amitriptyline it is shown that the degree of binding of amitriptyline is closely related to the carrageenan conformation as regulated by the counterions (Na⁺ or K⁺). The adsorption becomes much more pronounced when the carrageenan molecule is in the helix form (counterion K⁺) than when it has a coil conformation (counterion Na⁺). Furthermore, for the helical state the adsorption becomes strongly cooperative. It is also shown experimentally that the release from the adsorbed state has a conversion temperature at about 42°C (helix-coil transition). The effect is also related to the linear charge density. For κ-carrageenan with a higher charge density the adsorption is strong and cooperative both in the presence of Na⁺ and K⁺ ions. © 1996 John Wiley & Sons, Inc.     

Intracellular free sodium concentrations in GH4C1 cells

In the present investigation, intracellular sodium ([Na⁺]_i) levels were determined in GH₄C₁ cells using the fluorescent probe SBFI. Fluorescence was determined by excitation at 340 nm and 385 nm, and emission was measured at 500 nm. Intracellular free sodium ([Na⁺]_i) was determined by comparing the ratio 340/385 to a calibration curve. The ratio was linear between 10 and 60 mM Na⁺. Resting [Na⁺]_i in GH₄C₁ cells was 26 ± 6.2 mM (mean ± SD). In cells incubated in Na⁺-buffer [Na⁺]_i decreased to 3 ± 3.6 mM. If Na⁺/K⁺ ATPase was inhibited by incubating the cells with 1 mM ouabain, [Na⁺]_i increased to 47 ± 12.8 mM in 15 min. Stimulating the cells with TRH, phorbol myristyl acetete, or thapsigargin had no effect on [Na⁺]_i. Incubating the cells in Ca²⁺-buffer rapidly increased [Na⁺]_i. The increase was not inhibited by tetrodotoxin. Addition of extracellular Ca²⁺, nimodipine, or Ni²⁺ to these cells immediately decreased [Na⁺]_i, whereas Bay K 8644 enhanced the influx of Na⁺. In cells where [Na⁺]_i was increased the TRH-induced increase in intracellular free calcium ([Ca²⁺]_i) was decreased compared with control cells. Our results suggest that Na⁺ enters the cells via Ca²⁺ channels, and [Na⁺]_i may attenuate TRH-induced changes in [Ca²⁺]_i in GH₄C₁ cells. © 1993 Wiley-Liss, Inc.     

RNA Modified Uridines VI: Conformations of 3-[3-(S)-Amino-3-Carboxypropyl]Uridine (acp3U) from tRNA and 1-Methyl-3-[3-(S)-Amino-3-Carboxypropyl]Pseudouridine (m1acp3Ψ) from rRNA

Abstract

The conformation of chemically synthesized acp³U is 60& 3′-endo, gauche⁺, whereas that of m¹acp³Ψ is 60& 2′-endo, gauche⁺. We conclude that the difference in conformation probably imparts important local structures to their respective tRNA and rRNA.     

Secondary structure in polyuridylic acid: Non-classical hydrogen bonding and the function of the ribose 2′-hydroxyl group

The role of non-classical hydrogen bonding in RNA structure has been investigated using polyuridylic acid, which has a labile ordered structure at temperatures near 0 °C, as a model system. By comparing the proton nuclear magnetic resonance spectrum of poly(U) in the transition region with that of uridine and the dimer UpU we find evidence that both the imino N(₃)-H and the ribosyl 2′-OH protons are hydrogen bonded. The characteristics of the former are consistent with participation in N(₃)-HOC bonding primarily between residues in the same strand. As yet we cannot unambiguously assign the acceptor for the 2′-OH in ordered poly(U): because of its apparent stability and the acceptable stereochemistry, we presently favor a bond between ribose 2′-OH and O(1′) connecting adjacent nucleotides of the same strand. This arrangement could contribute to the co-operativity of the poly(U) helix formation. The recently proposed 2′-OHO(1′) interactions in crystalline yeast transfer RNA^Phe suggest similar interactions might play a role in the conformational stability of natural RNAs. A second conformational transition below the major transition in the ultraviolet can be detected in poly(U) by monitoring the H(₆) proton of uracil.     

Cultured cells from renal cortex of hibernators and nonhibernators. Regulation of cell K+ at low temperature

Cells were grown as primary monolayer cultures from kidney cortex of guinea pigs (nonhibernators), hamsters and ground squirrels (both hibernating species). When plates of cells were placed at 5 °C, cells of guinea pigs lost 37% of their K⁺ in 2 h and those of the hibernator lost about 10%.Uptake of ⁴²K into the cells exhibited a simple, single exponential time course at both temperatures. Unidirectional efflux of K⁺ was equal to K⁺ influx in all cultures at 37 °C and, within limits of error, in hibernator cells at 5 °C. Efflux was 3- to 5-fold greater than influx in guinea pig cells at 5 °C.After 2 h in the cold the ouabain-sensitive K⁺ influx remaining (7–15% of that at 37 °C) was about the same in the cells of the 3 species. Cells from active hamsters and from hibernating ground squirrels, however, exhibited significantly greater pump activity after 45 min in the cold (19 and 14%, respectively). The stimulation of K⁺ influx by increasing [K⁺]_o did not show an increase in K_m⁺ at 5 °C in cells of guinea pigs and ground squirrels. Lowering [K⁺]_c and/or raising [Na⁺]_c by treatment in low- and high-K⁺ media caused only slight stimulation of K⁺ influx, except in cells of ground squirrels at 5 °C in which the stimulation was at least 11-times greater than at 37 °C or in cells of guinea pigs at either temperature.This altered kinetic response of K⁺ transport to cytoplasmic ion stimulation with cooling accounted for about one-third of the improved regulation of K⁺ at 5 °C in ground squirrel cells; the other two-thirds was attributable to a greater decrease in K⁺ leak with cooling. The inhibition of active transport by cold in all 3 species was much less severe than that previously seen in any (Na⁺ + K⁺)-ATPase of mammalian cells.     

Hydrolysis of adenylyl imidodiphosphate in the presence of Na+ + Mg+ by (Na+ + K+)-activated ATPase

(1) Contrary to what has usually been assumed, (Na⁺ + K⁺)-ATPase slowly hydrolyses AdoPP[NH]P in the presence of Na⁺ + Mg²⁺ to ADP-NH₂ and P_i. The activity is ouabain-sensitive and is not detected in the absence of either Mg²⁺ or Na²⁺. The specific activity of the Na⁺ + Mg²⁺ dependent AdoPP[NH]P hydrolysis at 37°C and pH 7.0 is 4% of that for ATP under identical conditions and only 0.07% of that for ATP in the presence of K⁺. The activity is not stimulated by K⁺, nor can K⁺ replace Na⁺ in its stimulatory action. This suggests that phosphorylation is rate-limiting. Stimulation by Na⁺ is positively cooperative with a Hill coefficient of 2.4; half-maximal stimulation occurs at 5–9 mM. The K_m value for AdoPP[NH]P is 17 μM. At 0°C and 21°C the specific activity is 2 and 14%, respectively, of that at 37°C. AMP, ADP and AdoPP[CH₂]P are not detectably hydrolysed by (Na⁺ + K⁺)-ATPase in the presence of Na⁺ + Mg²⁺. (2) In addition, AdoPP[NH]P undergoes spontaneous, non-enzymatic hydrolysis at pH 7.0 with rate constants at 0, 21 and 37°C of 0.0006, 0.006 and 0.07 h^?1, respectively. This effect is small compared to the effect of enzymatic hydrolysis under comparable conditions. Mg²⁺ present in excess of AdoPP[NH]P reduces the rate constant of the spontaneous hydrolysis to 0.005 h^?1 at 37°C, indicating that the MgAdoPP[NH]P complex is virtually stable to spontaneous hydrolysis, as is also the case for its enzymatic hydrolysis. (3) A practical consequence of these findings is that AdoPP[NH]P binding studies in the presence of Na⁺ + Mg²⁺ with enzyme concentrations in the mg/ml range are not possible at temperatures above 0°C. On the other hand, determination of affinity in the (Na⁺ + K⁺)-ATPase reaction by competition with ATP at low protein concentrations (μg/ml range) remains possible without significant hydrolysis of AdoPP[NH]P even at 37°C.     

A comparison of the subcellular distribution of 5′-nucleotidase, (Na+K+)-ATPase and adenyl cyclase in beef thyroid gland

The validity of 5′-nucleotidase as a plasma membrane marker enzyme in beef thyroid has been tested by comparing the subcellular distribution of its activity to that of (Na⁺K⁺)-activated ATPase and adenyl cyclase. The specific activity and total activity of (Na⁺K⁺)-ATPase and adenyl cyclase were greatest in the 1000 × g (“nuclear”) and 33 000 × g (“mitochondrial and lysosomal”) fractions. In contrast, 5′-nucleotidase activity was concentrated in the 165 000 × g (“microsomal”) pellet and supernatant. Partially purified plasma membranes were separated from the 1000 (N₂), 30 000 (M₂) and 165 000 × g (P₂) pellets by discontinuous sucrose gradient centrifugation. Again a discordant distribution of these enzyme activities was observed. (Na⁺K⁺)-ATPase specific activity was increased approximately 30-fold over the homogenate in Fractions N₂ and M₂. Basal, thyroid-stimulating hormone-and fluoride-stimulated adenyl cyclase activities were concentrated in the same fractions. 5′-Nucleotidase activity was preferentially located in M₂ and P₂. These differences in distribution pattern suggest that 5′-nucleotidase activity is not uniquely located in the plasma membrane in the thyroid.