Absence Of Divalent Metal Ions Research Articles

Comparative study of substrate and product binding to the human ABO(H) blood group glycosyltransferases

The first comparative thermodynamic study of the human blood group glycosyltransferases, alpha-(1-->3)-N-acetylgalactosaminyltransferase (GTA) and alpha-(1-->3)-galactosyltransferase (GTB), interacting with donor substrates, donor and acceptor analogs, and trisaccharide products in vitro is reported. The binding constants, measured at 24 degrees C with the direct electrospray ionization mass spectrometry (ES-MS) assay, provide new insights into these model GTs and their interactions with substrate and product. Notably, the recombinant forms of GTA and GTB used in this study are shown to exist as homodimers, stabilized by noncovalent interactions at neutral pH. In the absence of divalent metal ion, neither GTA nor GTB exhibits any appreciable affinity for its native donors (UDP-GalNAc, UDP-Gal). Upon introduction of Mn(2+), both donors undergo enzyme-catalyzed hydrolysis in the presence of either GTA or GTB. Hydrolysis of UDP-GalNAc in the presence of GTA proceeds very rapidly under the solution conditions investigated and a binding constant could not be directly measured. In contrast, the rate of hydrolysis of UDP-Gal in the presence of GTB is significantly slower and, utilizing a modified approach to analyze the ES-MS data, a binding constant of 2 x 10(4) M(-1) was established. GTA and GTB bind the donor analogs UDP-GlcNAc, UDP-Glc with affinities similar to those measured for UDP-Gal and UDP-GalNAc (GTB only), suggesting that the native donors and donor analogs bind to the GTA and GTB through similar interactions. The binding constant determined for GTA and UDP-GlcNAc (approximately 1 x 10(4) M(-1)), therefore, provides an estimate for the binding constant for GTA and UDP-GalNAc. Binding of GTA and GTB with the A and B trisaccharide products was also investigated for the first time. In the absence of UDP and Mn(2+), both GTA and GTB recognize their respective trisaccharide products but with a low affinity approximately 10(3) M(-1); the presence of UDP and Mn(2+) has no effect on A trisaccharide binding but precludes B-trisaccharide binding.

Molecular crowding effect on metal ion binding properties of the hammerhead ribozyme

Although metal ion is essential for the DNA and RNA folding, there are a limited number of reports describing the influence of molecular environments on the metal ion binding. Here, we investigated the binding properties of Mg(2+) and Na(+) toward the hammerhead ribozyme in the presence of PEG [poly(ethylene glycol)] as a cosolute that changes the solvent property of the reaction. PEG8000 (PEG with the average molecular weight of 8000) increased the reaction rate at lower Mg(2+) concentrations but not at higher concentrations. We also found that PEG8000 unchanged the number of Mg(2+) bound while the binding cooperativity of Na(+) in the reaction without divalent metal ion was altered. The change of Na(+) condensation by cosolute has also been reported for diffusely bound Na(+) to Watson-Crick base pairs. It is thus supposed that diffusely bound Na(+) stabilizes the ribozyme active form in the absence of divalent metal ion. This study provides insights into the RNA-metal ion interaction and the hammerhead ribozyme activity under the molecular crowding condition occurred in a cell and on biosensor devices.

R.KpnI, an HNH superfamily REase, exhibits differential discrimination at non-canonical sequences in the presence of Ca2+ and Mg2+

KpnI REase recognizes palindromic sequence, GGTAC↓C, and forms complex in the absence of divalent metal ions, but requires the ions for DNA cleavage. Unlike most other REases, R.KpnI shows promiscuous DNA cleavage in the presence of Mg2+. Surprisingly, Ca2+ suppresses the Mg2+-mediated promiscuous activity and induces high fidelity cleavage. To further analyze these unique features of the enzyme, we have carried out DNA binding and kinetic analysis. The metal ions which exhibit disparate pattern of DNA cleavage have no role in DNA recognition. The enzyme binds to both canonical and non-canonical DNA with comparable affinity irrespective of the metal ions used. Further, Ca2+-imparted exquisite specificity of the enzyme is at the level of DNA cleavage and not at the binding step. With the canonical oligonucleotides, the cleavage rate of the enzyme was comparable for both Mg2+- and Mn2+-mediated reactions and was about three times slower with Ca2+. The enzyme discriminates non-canonical sequences poorly from the canonical sequence in Mg2+-mediated reactions unlike any other Type II REases, accounting for the promiscuous behavior. R.KpnI, thus displays properties akin to that of typical Type II REases and also endonucleases with degenerate specificity in its DNA recognition and cleavage properties.

Crystallization and preliminary X-ray analysis of a protease inhibitor from the latex of Carica papaya.

A Kunitz-type protease inhibitor purified from the latex of green papaya (Carica papaya) fruits was crystallized in the presence and absence of divalent metal ions. Crystal form I, which is devoid of divalent cations, diffracts to a resolution of 2.6 A and belongs to space group P3(1) or P3(2). This crystal form is a merohedral twin with two molecules in the asymmetric unit and unit-cell parameters a = b = 74.70, c = 78.97 A. Crystal form II, which was grown in the presence of Co2+, diffracts to a resolution of 1.7 A and belongs to space group P2(1)2(1)2(1), with unit-cell parameters a = 44.26, b = 81.99, c = 140.89 A.

The Hammerhead Ribozyme Structure Brought in Line

RNA catalysis seems to be considerably more wide spread than originally thought, with the most prominent example being the ribosome, where RNA catalyses the peptidyl-transferase reaction. Among the most and longest studied catalytic RNAs are the small nucleolytic ribozymes, such as the hairpin, VS, HDV and hammerhead ribozymes. They all catalyse the site-specific cleavage of their own phosphodiester backbone in cis or that of a substrate RNA in trans through a transesterification reaction involving the 2’-OH. A novel crystal structure of the hammerhead ribozyme has just been reported, and this should help to clarify a long-standing debate on the mechanism of catalysis. First identified in the 1980s as a catalytically active element in the replication cycle of certain viroids and the satellite RNA of plant viruses, the hammerhead ribozyme is the smallest naturally occurring RNA endonuclease. The motif has also been found in transcripts from the satellite DNA of amphibians, schistosomes, cave cricket and, most recently, encoded in the genomes of other eukaryotic organisms. The hammerhead ribozyme consists of a catalytic core of 11 conserved nucleotides that are flanked by three helices (Figure 1A). In the absence of divalent metal ions, the structure is extended, but upon addition of Mg , the RNA folds in two well-defined steps into a Y-shaped structure (Figure 1B), as deduced by Lilley and coworkers in studies using comparative gel electrophoresis, FRET, NMR and calorimetry. In this active conformation, a reversible transesterification reaction is catalysed by the hammerhead ribozyme (Scheme 1). 9] During cleavage, the 2’OH of nucleotide C17 is deprotonated and attacks the scissile 3’,5’ phosphodiester bond. Of the two cleavage products one carries a 2’,3’-cyclic phosphate, the other a 5’-hydroxy terminus. In the reverse (ligation) reaction, the 5’-oxygen attacks the cyclic phosphate. For the hammerhead ribozyme, however, the ligation does not proceed as efficiently as seen for the hairpin ribozyme. Both reactions proceed through the same, trigonal-bipyramidal pentacoordinated transition state (Scheme 1), thus meeting the principle of microscopic reversibility. This transition state was deduced from the observation that the chirality of the scissile phosphate, when exchanged for a phosphorothioate, was inverted during the course of the reaction, a hallmark of the SN2 mechanism. In the transition state, the 2’-OH of C17 has to be in line with the adjacent phosphorus and the 5’-oxygen of nucleotide 1.1 (Scheme 1). This requirement and other data detailed below gave rise to presumably the longest-standing debate in the ribozyme field. The first hammerhead ribozyme crystal structures showed a maximal deviation from the ACHTUNGTRENNUNGrequired in-line orientation of the three atoms, at 908. Hammerhead cleavage, however, could be achieved by soaking all RNA crystals with divalent metal ions. While the first observation argued for a ground-state structure to be present in the crystal, the second would indicate that no major rearrangements were necessary to reach the tran[a] R. Przybilski, Dr. C. Hammann AG Molecular Interactions Department of Genetics, University of Kassel Heinrich-Plett-Strasse 40 34132 Kassel (Germany) Fax: (+49)561-804-4800 E-mail : c.hammann@uni-kassel.de Figure 1. The hammerhead ribozyme. A) Secondary structure with stems I, II and III and the 11 conserved nucleotides (bold). Cleavage takes place between nucleotides 17 and 1.1, as indicated by an arrow. Numbers are given according to the conventional scheme. In minimal versions of the ribozyme, either stem I or II is closed by loops (dashed lines). B) Y-shaped conformation of the minimal version of the ribozyme upon addition of magnesium. Naturally occurring ribozymes are endowed with tertiary stabilising structures formed between C) loops L1 and L2 or D) loop L1 and bulge B2 in stem II. The ribozyme format shown in (D) was used for crystallisation.

EPR Spectroscopic Analysis of U7 Hammerhead Ribozyme Dynamics during Metal Ion Induced Folding

Electron paramagnetic resonance (EPR) spectroscopy was used to examine changes in internal structure and dynamics of the hammerhead ribozyme upon metal ion induced folding, changes in pH, and the presence and absence of ribozyme inhibitors. A nitroxide spin-label was attached to nucleotide U7 of the HH16 catalytic core, and this modified ribozyme was observed to retain catalytic activity. U7 was shown by EPR spectroscopy to be more mobile in the ribozyme-product complex than in either the unfolded ribozyme or the ribozyme-substrate complex. A two-step divalent metal ion dependent folding pathway was observed for the ribozyme-substrate complex with a weak first transition observed at 0.25 mM Mg2+ and a strong second transition observed around 10 mM Mg2+, in agreement with studies using other biophysical and biochemical techniques. Previously, ribozyme activity was observed in the absence of divalent metal ions and the presence of high concentrations of monovalent metal ions, although the activity was less than that observed in the presence of divalent metal ions. Here, we observed similar dynamics for U7 in the presence of 4 M Na+ or Li+, which were distinctively different than that observed in the presence of 10 mM Mg2+, indicating that U7 of the catalytic core forms a different microenvironment under monovalent versus divalent metal ion conditions. Interestingly, the catalytically efficient microenvironment of U7 was similar to that observed in a solution containing 1 M Na+ upon addition of one divalent metal ion per ribozyme. In summary, these results demonstrate that changes in local dynamics, as detected by EPR spectroscopy, can be used to study conformational changes associated with RNA folding and function.

Calcium‐ and magnesium‐dependent interactions between calcium‐ and integrin‐binding protein and the integrin αIIb cytoplasmic domain

Calcium- and integrin-binding protein (CIB) is a small EF-hand calcium-binding protein that is involved in hemostasis through its interaction with the alphaIIb cytoplasmic domain of integrinalphaIIbbeta(3). We have previously demonstrated that CIB lacks structural stability in the absence of divalent metal ions but that it acquires a well-folded conformation upon addition of Ca(2+) or Mg(2+). Here, we have used fluorescence spectroscopy, NMR spectroscopy, and isothermal titration calorimetry to demonstrate that both Ca(2+)-bound CIB (Ca(2+)-CIB) and the Mg(2+)-bound protein (Mg(2+)-CIB) bind with high affinity and through a similar mechanism to alphaIIb cytoplasmic domain peptides, but that metal-free CIB (apo-CIB) binds in a different manner. The interactions are thermodynamically distinct for Ca(2+)-CIB and Mg(2+)-CIB, but involve hydrophobic interactions in each case. Since the Mg(2+) concentration inside the cell is sufficient to saturate CIB at all times, our results imply that CIB would be capable of binding to the alphaIIb cytoplasmic domain independent of an intracellular Ca(2+) stimulus in vivo. This raises the question of whether CIB can act as a Ca(2+) sensor in alphaIIbbeta(3) signaling or if other regulatory mechanisms such as fibrinogen-induced conformational changes in alphaIIbbeta(3), post-translational modifications, or the binding of other accessory proteins mediate the interactions between CIB and alphaIIbbeta(3). Differences in NMR spectra do suggest, however, that Ca(2+)-binding to the Mg(2+)- CIB-alphaIIb complex induces subtle structural changes that could further modulate the activity of alphaIIbbeta(3).

Binding Stoichiometry and Kinetics of the Interaction of a Human Anthrax Toxin Receptor, CMG2, with Protective Antigen

The protective antigen (PA) moiety of anthrax toxin binds to cellular receptors and mediates entry of the two enzymatic moieties of the toxin into the cytosol. Two PA receptors, anthrax toxin receptor (ATR)/tumor endothelial marker 8 (TEM8) and capillary morphogenesis protein 2 (CMG2), have been identified. We expressed and purified the von Willebrand A (VWA) domain of CMG2 and examined its interactions with monomeric and heptameric forms of PA. Monomeric PA bound a stoichiometric equivalent of CMG2, whereas the heptameric prepore form bound 7 eq. The Kd of the VWA domain-PA interaction is 170 pm when liganded by Mg2+, reflecting a 1000-fold tighter interaction than most VWA domains with their endogenous ligands. The dissociation rate constant is extremely slow, indicating a 30-h lifetime for the CMG2.PA monomer complex. CMG2 metal ion-dependent adhesion site (MIDAS) was studied kinetically and thermodynamically. The association rate constant (approximately 10(5) m(-1) s(-1)) is virtually identical in the presence or absence of Mg2+ or Ca2+ , but the dissociation rate of metal ion liganded complex is up to 4 orders of magnitude slower than metal ion free complex. Residual affinity (Kd approximately 960 nm) in the absence of divalent metal ions allowed the free energy for the contribution of the metal ion to be calculated as 5 kcal mol(-1), demonstrating that the metal ion-dependent adhesion site is directly coordinated by CMG2 and PA in the binding interface. The high affinity of the VWA domain for PA supports its potency in neutralizing anthrax toxin, demonstrating its potential utility as a novel therapeutic for anthrax.

Sequence-specific cleavage of RNA in the absence of divalent metal ions by a DNAzyme incorporating imidazolyl and amino functionalities.

Two modified 2'-deoxynucleoside 5'-triphosphates have been used for the in vitro selection of a modified deoxyribozyme (DNAzyme) capable of the sequence-specific cleavage of a 12 nt RNA target in the absence of divalent metal ions. The modified nucleotides, a C5-imidazolyl-modified dUTP and 3-(aminopropynyl)-7-deaza-dATP were used in place of TTP and dATP during the selection and incorporate two extra protein-like functionalities, namely, imidazolyl (histidine analogue) and primary amino (lysine analogue) into the DNAzyme. The functional groups are analogous to the catalytic Lys and His residues employed during the metal-independent cleavage of RNA by the protein enzyme RNaseA. The DNAzyme requires no divalent metal ions or other cofactors for catalysis, remains active at physiological pH and ionic strength and can recognize and cleave a 12 nt RNA substrate with sequence specificity. This is the first example of a functionalized, metal-independent DNAzyme that recognizes and cleaves an all-RNA target in a sequence-specific manner. The selected DNAzyme is two orders of magnitude more efficient in its cleavage of RNA than an unmodified DNAzyme in the absence of metal ions and represents a rate enhancement of 10(5) compared with the uncatalysed hydrolysis of RNA.

Template‐Directed Assembly of Metallosalen–DNA Hairpin Conjugates

Encoded assembly: Hairpin metallosalen–DNA was assembled from two salicylaldehyde-modified, complementary oligonucleotides by DNA template-directed synthesis. Assembly reactions in the absence of divalent metal ions produced a new class of metal-free salen–DNA hairpin constructs. Metallosalen–DNA hairpin conjugates demonstrated high B-form duplex stability, which may facilitate structural studies of metallosalen–DNA conjugates. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2268/2004/z776_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.

Novel biomaterials derived from deoxyribozyme and NAPzyme

AbstractWe report the potential of a small Ca2+‐dependent deoxyribozyme as a novel biomaterial to distinguish RNA foldings. It is found that an immobilized deoxyribozyme using avidin‐biotin interaction cleaves the target site within only single‐stranded RNAs. The RNA cleavage reaction is also detected using the deoxyribozyme SPR sensor chip. Furthermore, we develop a novel NAPzyme (nucleic acid peptide deoxyribozyme) with its RNA cleavage function in the absence of divalent metal ions.

The dynamic nature of the four-way junction of the hepatitis C virus IRES.

Translation is initiated within the RNA of the hepatitis C virus at the internal ribosome entry site (IRES). The IRES is a 341-nucleotide element that contains a four-way helical junction (IIIabc) as a functionally important element of the secondary structure. The junction has three additional, nonpaired nucleotides at the point of strand exchange on one diagonal. We have studied the global conformation and folding of this junction in solution, using comparative gel electrophoresis and steady-state and time-resolved fluorescence resonance energy transfer. In the absence of divalent metal ions, the junction adopts an extended-square structure, in contrast to perfect four-way RNA junctions, which retain coaxial helical stacking under all conditions. The IIIabc junction is induced to fold on addition of Mg(2+), by pairwise coaxial stacking of arms, into the conformer in which the unpaired bases are located on the exchanging strands. Fluorescence lifetime measurements indicate that in the presence of Mg(2+) ions, the IIIabc junction exists in a dynamic equilibrium comprising approximately equal populations of antiparallel and parallel species. These dynamic properties may be important in mediating interactions between the IRES and the ribosome and initiation factors.

Catalytic and structural role of the metal ion in dUTP pyrophosphatase.

The metal ion dependence of the catalytic activity of recombinant Escherichia coli dUTP pyrophosphatase (dUTPase), an essential enzyme preventing incorporation of uracil into DNA, has been investigated by steady-state kinetic, electron paramagnetic resonance, and electron nuclear double resonance methods. Values of k(cat) and k(cat)K(m) were 4.5 +/- 0.1 s(-1) and 0.49 +/- 0.1 x 10(6) M(-1).s(-1) in the absence of divalent metal ions, 14.7 +/- 2.2 s(-1) and 25.1 +/- 7.4 x 10(6) M(-1).s(-1) in the presence of Mg(2+) or Mn(2+), and 24.2 +/- 3.6 s(-1) and 2.4 +/- 0.7 x 10(6) M(-1).s(-1) when supported by VO(2+) or bis(acetylacetonato)oxovanadium(IV). Binding of VO(2+) to the enzyme in the presence of dUDP, a nonhydrolyzable substrate analog, was specific and competitive with Mg(2+). Electron paramagnetic resonance spectra of the ternary enzyme-VO(2+)-chelate-dUDP complex revealed a pattern of (31)P superhyperfine coupling specifying two structurally equivalent phosphate groups equatorially coordinated to the VO(2+) ion. Proton electron nuclear double resonance spectra revealed an equatorial acetylacetonate ligand, indicating that one of the organic ligands had been displaced. By molecular graphics modeling, we show that the diphosphate group of enzyme-bound dUDP is sterically accessible to a hemi-chelate form of VO(2+). We propose a similar location compatible with all kinetic and spectroscopic results to account for the reactivity of VO(2+) and the VO(2+)-chelate in dUTP hydrolysis. In this location the metal ion could promote an ordered conformation of the C-terminal fragment that is obligatory for catalysis but dynamically flexible in the free enzyme.

Transformation of the plant growth regulator daminozide (Alar) and structurally related compounds with CuII ions: oxidation versus hydrolysis.

As part of a study of metal ion effects on chemical transformations of nitrogen-containing agrochemicals, conversion of daminozide to succinate via cleavage of the hydrazide C-N bond was examined in the presence and absence of divalent metal ions. No conversion was observed in metal ion-free solutions or in the presence of 1.0 mM NiII, ZnII, and PbII. CuII, in contrast, markedly increased rates of daminozide to succinate conversion. Halide ions (CI-, Br-) had no effect on daminozide conversion in the absence of metal ions but markedly increased conversion rates observed in the presence of CuII. The nitrogen-donor ligands ethylenediamine, N-(2-hydroxyethyl)ethylenediamine, and 1,4,7,10-tetraazacyclododecane decreased rates of CuII-facilitated conversion, while 1,5,9-triazacyclododecane actually increased rates of conversion. H NMR and UV spectroscopy provide evidence for the formation of 1:1 CuII-daminozide complexes. Halide ion effects and nitrogen-donor ligand effects point to an oxidative mechanism for CuII-facilitated daminozide breakdown, rather than hydrolysis. The structurally related compound butyric acid 2,2-dimethylhydrazide (BH) is subject to the same CuII-facilitated breakdown via an oxidative mechanism. N,N-Dimethylsuccinamic acid (SA), in contrast, breaks down via a hydrolytic mechanism.

Metal-free MIRAS phasing: structure of apo-S100A3.

S100 proteins are involved in metal-dependent intracellular signalling. Metal-free S100A3, a cysteine-rich Ca(2+)- and Zn(2+)-binding protein, has been crystallized by vapour diffusion under the strict exclusion of oxygen and in the absence of divalent metal ions. Metal binding induces large conformational changes, rendering the apo-S100A3 crystals very sensitive to various metal compounds. Therefore, the structure was solved by MIRAS phasing using potassium iodide and xenon derivatives. Iodide replaces a water molecule at the surface of the S100A3 protein, whereas xenon binds in a hydrophobic cavity at the dimer interface. Despite significant non-isomorphism, the combination of both derivatives was sufficient for structure determination. The overall apo-S100A3 structure resembles the structures of metal-free S100B and S100A6 solution structures. In contrast to the NMR structures, the EF-hand loops are well ordered in the apo-S100A3 crystal structure. In the N-terminal pseudo-EF-hand loop a water molecule occupies the position of the Ca(2+) ion. The C-terminal canonical EF-hand loop shows an extended conformation and a different helix arrangement to other S100/metal complex crystal structures.

Distortion of DNA junctions imposed by the binding of resolving enzymes: a fluorescence study

Junction-resolving enzymes are nucleases that are specific for the structure of the four-way DNA junction. The binding of RuvC of Escherichia coli and Hjc of Sulfolobus solfataricus can be followed by an increase in the fluorescence anisotropy of Cy3 terminally attached to one of the helical arms of a four-way junction. By contrast, there was no change in fluorescein anisotropy with the binding of single dimers of these proteins. Fluorescence resonance energy transfer has therefore been used between fluorescein and Cy3 fluorophores attached to the ends of helical arms to analyse the global structure of the junction on protein binding. The results indicate that both enzymes induce a marked change in the global DNA conformation on the binding of a single dimer. The structure of the protein-junction complexes is independent of the presence or absence of divalent metal ions, unlike that of the protein-free junction. The structures of the RuvC and Hjc complexes are different, but both represent a significant opening of the structure compared to the stacked X-structure of the protein-free junction in the presence of magnesium ions. This protein-induced opening is likely to be important in the function of these enzymes.

Mg2+ Is Not Catalytically Required in the Intrinsic and Kirromycin-stimulated GTPase Action of Thermus thermophilus EF-Tu

The influence of divalent metal ions on the intrinsic and kirromycin-stimulated GTPase activity in the absence of programmed ribosomes and on nucleotide binding affinity of elongation factor Tu (EF-Tu) from Thermus thermophilus prepared as the nucleotide- and Mg(2+)-free protein has been investigated. The intrinsic GTPase activity under single turnover conditions varied according to the series: Mn(2+) (0.069 min(-1)) > Mg(2+) (0.037 min(-1)) approximately no Me(2+) (0.034 min(-1)) > VO(2+) (0.014 min(-1)). The kirromycin-stimulated activity showed a parallel variation. Under multiple turnover conditions (GTP/EF-Tu ratio of 10:1), Mg(2+) retarded the rate of hydrolysis in comparison to that in the absence of divalent metal ions, an effect ascribed to kinetics of nucleotide exchange. In the absence of added divalent metal ions, GDP and GTP were bound with equal affinity (K(d) approximately 10(-7) m). In the presence of added divalent metal ions, GDP affinity increased by up to two orders of magnitude according to the series: no Me(2+) < VO(2+) < Mn(2+) approximately Mg(2+) whereas the binding affinity of GTP increased by one order of magnitude: no Me(2+) < Mg(2+) < VO(2+) < Mn(2+). Estimates of equilibrium (dissociation) binding constants for GDP and GTP by EF-Tu on the basis of Scatchard plot analysis, together with thermodynamic data for hydrolysis of triphosphate nucleotides (Phillips, R. C., George, P., and Rutman, R. J. (1969) J. Biol. Chem. 244, 3330-3342), showed that divalent metal ions stabilize the EF-Tu.Me(2+).GDP complex over the protein-free Me(2+).GDP complex in solution, with the effect greatest in the presence of Mg(2+) by approximately 10 kJ/mol. These combined results show that Mg(2+) is not a catalytically obligatory cofactor in intrinsic and kirromycin-stimulated GTPase action of EF-Tu in the absence of programmed ribosomes, which highlights the differential role of Mg(2+) in EF-Tu function.

14] Purification and characterization of Saccharomyces cerevisiae Rnt1p nuclease

In this article, we have described methods used to purify Rnt1p and study its biochemical properties. Rnt1p can be easily purified from bacteria as N-terminal His6-tagged protein and its activity may be monitored in vitro. Rnt1p cleaves the RNA by binding to a cleavage site followed by hydrolysis and product release. The kinetic parameters of Rnt1p are similar to those of other nucleases, including bacterial RNase III. The ability of Rnt1p to bind substrate without cleaving it in the absence of divalent metal ions provides a convenient means to study RNA recognition and binding independent of catalysis. The gel mobility shift and in-the-gel cleavage assays described here reveal the formation of two Rnt1p-RNA complexes with different cleavage activities, suggesting that the protein may bind the substrate in two different forms or through a two-step binding reaction.

The NMR solution structure of the NMDA receptor antagonist, conantokin-T, in the absence of divalent metal ions

The solution conformation of conantokin-T, a Gla-containing 21-residue peptide, (G 1EγγY 5QKMLγ 10NLRγA 15EVKKN 20A-amide), in the absence of divalent metal ions, was studied by use of two-dimensional proton NMR spectroscopy. The peptide is helical from the N-terminus to the C-terminus, as defined by upfield-shifted α-proton resonances and by characteristic NOE connectivities. Extensive interactions among the amino acid side-chains were identified from the NOESY spectra of this peptide in a buffered aqueous solution. Four hydrophobic residues Tyr 5, Met 8, Leu 9, and Leu 12 contact one another in a stable cluster, even in the presence of 6 M urea. The solution structure of conantokin-T is a well-defined α-helix, having RMSD values for the backbone and all heavy atoms of 0.40 Å and 0.77 Å, respectively. Potential repulsion between the negatively-charged side chains of Gla 10 and Gla 14 is minimized by a Gln 6-Gla 10 hydrogen bond and by an Arg 13-Gla 14 ion-pair interaction. The C-terminal amide and the Asn 20 side-chain amide both interact with the backbone and minimize fraying at the C-terminal end of the α-helix. This study provides a basis to evaluate the changes in peptide conformation concomitant upon the binding of divalent metal ions. In addition, this investigation demonstrates that apo-conantokin-T has almost all of the favorable interactions that are known to contribute to helical stabilization in proteins and monomeric helices.

Characterization and divalent metal-ion dependence of in vitro selected deoxyribozymes which cleave DNA/RNA chimeric oligonucleotides

By in vitro selection, a variety of catalytic DNA oligonucleotides were obtained which cleave chimeric oligonucleotides at a single ribonucleotide position embedded within a deoxyribonucleotide context in the presence or absence of divalent metal ions. After several cycles of selection/amplification in the absence and in the presence of low amounts of Mg 2+ two different types of catalysts emerged: one type depended strongly on Mg 2+ or other divalent metal ions, the other type performed cleavage reactions independently of Mg 2+ in the presence of spermine. Experimental analysis of the secondary structure of some of the selected deoxyribozymes was carried out by chemical probing. The ribonucleotide in the selected catalysts is unpaired and presents the cleavage site to the attacking nucleophile. Our results suggest that the main selection criterion under metal-free conditions was a favourable arrangement of the attacking nucleophile and the phosphate leaving group. The cleavage rates of the selected divalent metal independent catalysts are within the same order of magnitude as the rate of metal independent substrate hydrolysis in the hammerhead ribozyme. One of the metal dependent catalysts showed an unexpected preference for Ca 2+ instead of Mg 2+. In this deoxyribozyme binding of Ca 2+ ocurred co-operatively whereas binding of Mg 2+ did not. Comparison of the secondary structure and reactivity of this catalyst with Mg 2+ and Ca 2+ suggests that here a special binding pocket for Ca 2+ was selected. This deoxyribozyme achieved a rate acceleration of substrate cleavage in the order of at least 10 4 compared to the uncatalysed reaction performing a cleavage mechanism similar to that of the hammerhead or hairpin ribozyme.