Mg2+ and Ni2+ ion effect on stability and structure of triple poly I.poly A.poly I helix

The effects of Mg2+ and Ni2+ ions on the absorption spectra of IMP, single-stranded poly I and three-stranded A2I in solutions with 0.1 M Na+ (pH 7) have been studied. In contrast to Mg2+ ions, the Ni2+ ions affect the absorption spectra of these polynucleotides and IMP. The concentration dependences of the intensity at the extrema in the differential UV spectra suggest that in the region of high Ni2+ concentrations ionic complexes with poly I and A2I are formed, which are characterized by the association constants K'I = 2000 M(-1) and K'A2I = 550 M(-1), respectively. The shape of the DUV spectra prompts the conclusion that these complexes are formed due to the inner-sphere interaction of Ni2+ ions with N7 of poly I and A2I presumably due to the outer-sphere Ni2+-O6 interaction. The formation of the complexes leads to destruction of A2I triplexes. The dependences of the melting temperature (T(m)) of A2I on Mg2+ and Ni2+ concentrations have been measured. The thermal stability is observed to increase at the ionic contents up to 0.01 M Mg2+ and only to 2x10(-4) M Ni2+. At higher contents of Ni2+ ions, T(m) lowers and the cooperativity of A2I melting decreases continuously. In all the cases the melting process is the A2I-->A+I+I (3-->1) transition. According to the "ligand" theory, these effects are generated by the energy-advantageous Ni2+ binding to single-stranded poly I (K'A2I < K'I) and by the greater number of binding sites which appears during the 3-->1 transition and is entropy-advantageous.     

Conformational transitions and aggregation in poly(dA)-poly(dT) system induced by Na+ and Mg2+ ions

Effects of Mg²⁺ ions on thermally induced conformational transitions in the synthetic poly(dA)·poly(dT) and poly(dA)·2poly(dT) were studied in the buffered solutions (pH 6.9), containing 0.1 or 1 M NaCl at polynucleotide concentration of 0.1–0.3 mM (in nucleic bases). The experiments consist of measurements of the UV absorption and intensity of conventional visible static light scattering. The diagram of conformational transitions in the poly(dA)–poly(dT)–Mg²⁺ system was constructed on a basis of experimental data obtained. Anomalously strong light scattering, like critical opalescence, has been revealed at 0.1 M NaCl and [Mg²⁺]≥20 mM in the melting range of both polynucleotides, which eventually disappeared after the completion of polymer strands separation. The effect presumably is caused by a fluctuation process of polymer strands complexing which arises at a certain concentration of Mg²⁺ ions.     

Phase equilibrium in poly(rA).poly(rU) complexes with Cd2+ and Mg2+ ions, studied by ultraviolet, infrared, and vibrational circular dichroism spectroscopy

Ultraviolet (UV) and infrared (IR) absorption and vibrational circular dichroism (VCD) spectroscopy were used to study conformational transitions in the double-stranded poly(rA). poly(rU) and its components-single-stranded poly(rA) and poly(rU) in buffer solution (pH 6.5) with 0.1M Na+ and different Mg2+ and Cd2+ (10(-6) to 10(-2) M) concentrations. Transitions were induced by elevated temperature that changed from 10 up to 96 degrees C. IR absorption and VCD spectra in the base-stretching region were obtained for duplex, triplex, and single-stranded forms of poly(rA) . poly(rU) at [Mg2+],[Cd2+]/[P] = 0.3. For single-stranded polynucleotides, the kind of conformational transition (ordering --> disordering --> compaction, aggregation) is conditioned by the dominating type of Me2+-polymer complex that in turn depends on the ion concentration range. The phase diagram obtained for poly(rA) . poly(rU) has a triple point ([Cd2+] approximately 10(-4)M) at which the helix-coil (2 --> 1) transition is replaced with a disproportion transition 2AU --> A2U + poly(rA) (2 --> 3) and the subsequent destruction of the triple helix (3 --> 1). The 2 --> 1 transitions occur in the narrow temperature interval of 2 degrees -5 degrees . Unlike 2 --> 1 and 3 --> 1 melting, the disproportion 2 --> 3 transition is a slightly cooperative one and observed over a wide temperature range. At [Me2+] approximately 10(-3) M, the temperature interval of A2U stability is not less than 20 degrees C. In the case of Cd2+, it increases with the rise of ion concentration due to the decrease of T(m) (2-->3). The T(m) (3-->1) value is practically unchanged up to [Cd2+] approximately 10(-3)M. Differences between diagrams for Mg(2+) and Cd2+ result from the various kinds of ion binding to poly(rA).poly-(rU) and poly(rA).     

Partitioning behavior of group 1 and 2 cations in poly(ethylene glycol)-based aqueous biphasic systems

The partitioning behavior of several Group 1 and 2 cations was investigated in poly(ethylene glycol) (PEG)-based aqueous biphasic systems. All of these metal ions prefer the salt-rich phase over the PEG-rich phase with distribution ratios all well below one regardless of the system investigated. The relative salting-out ability of the individual cations can be directly correlated to their Gibbs free energy of hydration (ΔG_hyd). In addition, the relative magnitude of the distribution ratios for these metal ions can also be explained in terms of ΔG_hyd.     

Distinct roles of the active-site Mg2+ ligands, Asp882 and Asp705, of DNA polymerase I (Klenow fragment) during the prechemistry conformational transitions

DNA polymerases catalyze the incorporation of deoxynucleoside triphosphates into a growing DNA chain using a pair of Mg(2+) ions, coordinated at the active site by two invariant aspartates, whose removal by mutation typically reduces the polymerase activity to barely detectable levels. Using two stopped-flow fluorescence assays that we developed previously, we have investigated the role of the carboxylate ligands, Asp(705) and Asp(882), of DNA polymerase I (Klenow fragment) in the early prechemistry steps that prepare the active site for catalysis. We find that neither carboxylate is required for an early conformational transition, reported by a 2-aminopurine probe, that takes place in the open ternary complex after binding of the complementary dNTP. However, the subsequent fingers-closing step requires Asp(882); this step converts the open ternary complex into the closed conformation, creating the active-site geometry required for catalysis. Crystal structures indicate that the Asp(882) position changes very little during fingers-closing; this side chain may therefore serve as an anchor point to receive the dNTP-associated metal ion as the nucleotide is delivered into the active site. The Asp(705) carboxylate is not required until after the fingers-closing step, and we suggest that its role is to facilitate the entry of the second Mg(2+) into the active site. The two early prechemistry steps that we have studied take place normally at very low Mg(2+) concentrations, although higher concentrations are needed for covalent nucleotide addition, consistent with the second metal ion entering the ternary complex after fingers-closing.     

DNA conformational equilibrium in the presence of Zn2+ ions in neutral and alkaline solutions

Effect of Zn(2+) ions on DNA transition from B-form to a metallized form (m-DNA) in Tris and tetraborate buffers at pH 8.5 has been studied by visible and differential UV-spectroscopy and by thermal denaturation. The results have been compared to those obtained at pH 6.5 in cacodylate buffer. It was found that in alkaline solutions Zn(2+) ions induced a hypochromicity of the DNA absorption in the whole spectral range monitored, which was attributed to DNA transition from B- to the m-form. Complete metallization occurred only upon heating the DNA solutions containing more than ~2×10(-4) M of Zn(2+) ions. Phase diagrams of the DNA-zinc complexes at pH 6.5 and 8.5 have been obtained for the first time. The m-DNA form showed higher thermal stability compared to B-DNA.     

Functional Contribution of Ca2+ and Mg2+ to the Intermolecular Interaction of Visinin-like Proteins

The interaction of human visinin-like protein 1 (VILIP1) and visinin-like protein 3 (VILIP3) with divalent cations (Mg²⁺, Ca²⁺, Sr²⁺ and Ba²⁺) was explored using circular dichroism and fluorescence measurement. These results showed that the four cations each induced a different subtle change in the conformation of VILIPs. Moreover, VILIP1 and VILIP3 bound with Ca²⁺ or Mg²⁺ in a cooperative manner. Studies on the truncated mutants showed that the intact EF-3 and EF-4 were essential for the binding of VILIP1 with Ca²⁺ and Mg²⁺. Pull-down assay revealed that Ca²⁺ and Mg²⁺ enhanced the intermolecular interaction of VILIPs, and led to the formation of homo- and hetero-oligomer of VILIPs. Together with previous findings that Ca²⁺-dependent localization of VILIPs may be involved in the regulation of distinct cascades and deprivation of Ca²⁺-binding capacity of VILIPs did not completely eliminate their activity, it is likely to reflect that Mg²⁺-bound VILIPs may play a role in regulating the biological function of VILIPs in response to a concentration fluctuation of Ca²⁺ in cells.     

Thermodynamic analysis of conformational transitions in oligonucleotide complexes in presence of Na(+) and Mg(2+) ions, using "staggering zipper" model

Curves of transitions in double (2-->1 transition) and triple (3-->2 transition) complexes of oligonucleotides dA(N1)with dT(N2) in solutions with Na(+) and Mg(2+) are calculated for the case of oligomer lengths from 10 to 500 nucleotides in the wide range of ion concentrations. The calculated curves of transitions and their differential analogs reflect rather exactly the position and form of experimental curves and describe dependences of transition temperatures on the length of molecules, their concentration, and ionic conditions. Values of the nucleation parameter beta for the systems studied are determined by comparison of the calculated and experimental data obtained in a number of works. The average beta value equal to 10(-3) l/mole is in an agreement with values reported for similar systems earlier. It is shown that disordering of duplex and triplex ends ("end fraying") has an essential influence on the form of melting curves, their asymmetry and the increase of the transition interval.     

Lead ion effect on creatine kinase: equilibrium and kinetic studies of inactivation and conformational changes

The effects of lead ions on creatine kinase (CK) were studied by measuring activity changes, intrinsic fluorescence spectra and 8-anilo-1-naphthalenesulfonate (ANS)-binding fluorescence along with size-exclusion chromatography (SEC). Below 5 mM Pb(2+) concentration, there was nearly no change of the enzyme activity and a slight change of the ANS-binding fluorescence. The CK activity decreased significantly from 10 to 25 mM Pb(2+) concentrations. No residual activity was observed above 25 mM Pb(2+). The kinetic time courses of inactivity and unfolding were all mono-phase courses with the inactivation rate constants being greater than the unfolding rate constants for the same Pb(2+) concentration. The changes in fluorescence maximum and fluorescence intensity were relatively slow for 40-80 mM Pb(2+) as well as in the initial stage for less than 5 mM Pb(2+), showing that two transition states exist for Pb(2+) induced equilibrium-unfolding curves. The intrinsic fluorescence spectra and ANS-binding fluorescence measurements showed that even for high Pb(2+) concentrations, CK did not fully unfold. Additionally, the SEC results showed that the enzyme molecule still existed in an inactive dimeric state at 20 and 40 mM Pb(2+) solutions. All the results indicated the presence of at least one stable unfolding equilibrium intermediate of CK during Pb(2+) unfolding.     

A phosphorus-magnetic-resonance study of the interaction of Mg2+ with adenyl-5'-yl imidodiphosphate. Binding sites of Mg2+ ion on the phosphate chain.

The interaction of Mg2+ ions with adenyl-5'-yl imidodiphosphate, AMP-P(NH)P, has been studied at basic and acidic pH values by phosphorus magnetic resonance spectroscopy in aqueous solution. The results suggest that Mg2+ binds simultaneously to one (or both) of the two free oxygen atoms of the beta-phosphate moiety and to the nitrogen atom of the phosphate chain (P alpha-O-P beta-N-P gamma). The interaction arises from 1: 1 complexing of Mg2+ to AMP-P(NH)P. The mode of the Mg2+ binding on the phosphate chain remains the same at both basic and acidic pH values. As in the case of ATP and ADP, the association of Mg2+ reduces the pK by about 1.5 units. On the other hand phosphorus titration curves showed that when the phosphate chain does not possess the regular periodicity (O-P alpha-O-P beta-X-P gamma-O,X not equal to O) as in the case of ATP, protonation of the terminal phosphate group may induce a 31P chemical shift variation less important for this group than for the preceding one.     

Effect of Cu2+, Mn2+ and aromatic compounds on the production of laccase isoforms by Coprinus comatus

Six different extracellular laccase isoforms were identified in submerged cultures of the commercially important edible mushroom, Coprinus comatus. Although laccase activity (~55 IU/L) was readily detectable in unsupplemented control cultures containing 1.6 μM Cu²⁺ after 22-day incubation, mean enzyme levels (~150–185 IU/L) were 2.7–3.4-fold higher in cultures supplemented with 0.5–3.0 mM Cu²⁺. Laccase production was also stimulated by Mn supplementation over the range 0.05–0.8 mM Mn²⁺, and the peak value of ~225 IU/L recorded after 22 days in cultures containing 0.8 mM added Mn²⁺ was 4.5-fold higher compared with unsupplemented controls. Of 12 aromatic compounds tested for their effect on laccase isozyme production by C. comatus, highest laccase levels (~188 IU/L), equivalent to a 4.4-fold increase compared with unsupplemented controls (~43 IU/L), were recorded after 22 days in cultures supplemented with 3.0 mM caffeic acid. Other aromatic compounds tested all stimulated laccase production, with peak enzyme levels 1.3–3.3-fold higher compared with unsupplemented controls. Extracellular laccase levels in cultures supplemented with optimal concentrations of Mn²⁺ and caffeic acid together were 38% and 15% lower, respectively, compared with cultures containing the separate supplements. Lac1 was the most abundant laccase isoform produced under all the conditions tested, but marked differences were observed in the production patterns of Lac2–Lac6.     

Mg2+-induced conformational changes in the btuB riboswitch from E. coli

Mg²⁺ has been shown to modulate the function of riboswitches by facilitating the ligand-riboswitch interactions. The btuB riboswitch from Escherichia coli undergoes a conformational change upon binding to its ligand, coenzyme B₁₂ (adenosyl-cobalamine, AdoCbl), and down-regulates the expression of the B₁₂ transporter protein BtuB in order to control the cellular levels of AdoCbl. Here, we discuss the structural folding attained by the btuB riboswitch from E. coli in response to Mg²⁺ and how it affects the ligand binding competent conformation of the RNA. The btuB riboswitch notably adopts different conformational states depending upon the concentration of Mg²⁺. With the help of in-line probing, we show the existence of at least two specific conformations, one being achieved in the complete absence of Mg²⁺ (or low Mg²⁺ concentration) and the other appearing above ∼0.5 mM Mg²⁺. Distinct regions of the riboswitch exhibit different dissociation constants toward Mg²⁺, indicating a stepwise folding of the btuB RNA. Increasing the Mg²⁺ concentration drives the transition from one conformation toward the other. The conformational state existing above 0.5 mM Mg²⁺ defines the binding competent conformation of the btuB riboswitch which can productively interact with the ligand, coenzyme B₁₂, and switch the RNA conformation. Moreover, raising the Mg²⁺ concentration enhances the ratio of switched RNA in the presence of AdoCbl. The lack of a AdoCbl-induced conformational switch experienced by the btuB riboswitch in the absence of Mg²⁺ indicates a crucial role played by Mg²⁺ for defining an active conformation of the riboswitch.     

Characteristics of Ca2+ ion effect on the activity of Mg2+-dependent ATPase system in ghosts and reconstituted erythrocytes]

A good conformity if demonstrated of the kinetics of calcium ions effect on ATPase activity of human and rat erythrocyte ghosts. The increase of calcium concentration in the rat errythrocytes hemolysis medium (above 50-100 micrometer) results in a considerable aggregation of reconstructed vesicles. An activation of ouabaine-sensitive component of Mg2+-dependent ATPase under the increase of intracellular Ca2+ in reconstructed human erythrocytes is observed.     

Regulatory and structural EF-hand motifs of neuronal calcium sensor-1: Mg 2+ modulates Ca 2+ binding, Ca 2+ -induced conformational changes, and equilibrium unfolding transitions

Neuronal calcium sensor-1 (NCS-1) is a major modulator of Ca²⁺ signaling with a known role in neurotransmitter release. NCS-1 has one cryptic (EF1) and three functional (EF2, EF3, and EF4) EF-hand motifs. However, it is not known which are the regulatory (Ca²⁺-specific) and structural (Ca²⁺- or Mg²⁺-binding) EF-hand motifs. To understand the specialized functions of NCS-1, identification of the ionic discrimination of the EF-hand sites is important. In this work, we determined the specificity of Ca²⁺ binding using NMR and EF-hand mutants. Ca²⁺ titration, as monitored by [¹⁵N,¹H] heteronuclear single quantum coherence, suggests that Ca²⁺ binds to the EF2 and EF3 almost simultaneously, followed by EF4. Our NMR data suggest that Mg²⁺ binds to EF2 and EF3, thereby classifying them as structural sites, whereas EF4 is a Ca²⁺-specific or regulatory site. This was further corroborated using an EF2/EF3-disabled mutant, which binds only Ca²⁺ and not Mg²⁺. Ca²⁺ binding induces conformational rearrangements in the protein by reversing Mg²⁺-induced changes in Trp fluorescence and surface hydrophobicity. In a larger physiological perspective, exchanging or replacing Mg²⁺ with Ca²⁺ reduces the Ca²⁺-binding affinity of NCS-1 from 90 nM to 440 nM, which would be advantageous to the molecule by facilitating reversibility to the Ca²⁺-free state. Although the equilibrium unfolding transitions of apo-NCS-1 and Mg²⁺-bound NCS-1 are similar, the early unfolding transitions of Ca²⁺-bound NCS-1 are partially influenced in the presence of Mg²⁺. This study demonstrates the importance of Mg²⁺ as a modulator of calcium homeostasis and active-state behavior of NCS-1.     

Modeling conformational changes in cyclosporin A.

NMR and X-ray structures for the immunosuppressant cyclosporin A (CsA) reveal a remarkable difference between the unbound (free) conformation in organic solvents and the conformation bound to cyclophilin. We have performed computer simulations of the molecular dynamics of CsA under a variety of conditions and confirmed the stability of these two conformations at room temperature in water and in vacuum. However, when the free conformation was modeled in vacuum at 600 K, a transition pathway leading to the bound conformation was observed. This involved a change in the cis MeLeu-9 peptide bond to a trans conformation and the movement of the side chains forming the dominant hydrophobic cluster (residues MeBmt-1, MeLeu-4, MeLeu-6, and MeLeu-10) to the opposite side of the plane formed by the backbone atoms in the molecular ring. The final conformation had a backbone RMS deviation from the bound conformation of 0.53 A and was as stable in dynamics simulations as the bound conformation. Our calculations allowed us to make a detailed analysis of a transition pathway between the free and the bound conformations of CsA and to identify two distinct regions of coordinated movement in CsA, both of which underwent transitions independently.     

Mg2+ induces a sharp and reversible transition in U1 and U2 small nuclear ribonucleoprotein configurations.

When U1 and U2 small nuclear ribonucleoproteins (snRNPs) purified by a procedure which preserves their immunoprecipitability by autoimmune antibodies (Hinterberger et al., J. Biol. Chem. 258:2604-2613, 1983), were submitted to extensive digestion with micrococcal nuclease, we found that their degradation pattern was sharply dependent upon magnesium concentration, indicating that they undergo a profound structural modification. At low Mg2+ (less than or equal to 5 mM), both particles only exhibit a core-resistant structure previously identified as being common to all but U6 snRNAs (Liautard et al., J. Mol. Biol. 162: 623-643, 1982). At high Mg2+ (greater than or equal to 7 mM), U1 and U2 snRNPs behave differently from one another. In U1 snRNP, most U1 snRNA sequence is protected, except for the 10 5'-terminal nucleotides presumably involved in splicing and a short sequence between nucleotides 102 and 108. Another region spanning nucleotides 60 to 79 is only weakly protected. This structural modification was demonstrated to be reversible. In U2 snRNP, the U2 snRNA sequence remains exposed in its 5' part up to nucleotide 92, and the 3'-terminal hairpin located outside the core structure becomes protected.     

Ab initio conformational maps for disaccharides in gas phase and aqueous solution

Ab initio conformational maps for beta-lactose in both the gas phase and in aqueous solution have been constructed at the HF/6-31G(d,p) level of calculation. The results of the gas-phase ab initio calculations allow us to conclude that a rigid conformational map is able to predict the regions of the minima in the potential energy surface of beta-lactose, in full agreement with those found in the relaxed conformational map. The solvation effects do not give rise to any new local minimum in the potential energy surface of beta-lactose, but just change the relative Boltzmann populations of the conformers found in the gas-phase calculations. The values obtained for heteronuclear spin coupling constant (3J(H,C)), using the seven most stable conformers in solution are in good agreement with the available experimental values. This is a good indication that ab initio rigid conformational maps can be reliably used to sort the most stable conformers of beta-lactose.