Sequence dependence and role of 5'-phosphate in the B to Z transition

Spectroscopic studies on pd(CG)3 and pd(GC)3 have been carried out to elucidate the sequence dependence and effect of free 5'-phosphate on the B to Z transition. Unlike d(CG)3, pd(CG)3 fails to undergo salt-induced B to Z transition at ambient temperature. Model building studies have been carried out to determine the inhibitory role of the 5'-phosphate group, but have been unsuccessful.

Undecaprenyl phosphate recycling comes out of age

The recycling of the lipid carrier undecaprenyl-phosphate (Und-P) requires the dephosphorylation of Und-PP, a reaction proposed to occur at the external or periplasmic side of the bacterial cell membrane. In this issue of Molecular Microbiology, experiments based on the analysis of lipopolysaccharide modifications in Escherichia coli demonstrate that the phosphorylation of lipid A at position 1 is catalysed by the membrane enzyme LpxT (formerly YeiU). This enzyme specifically transfers the distal phosphate group from Und-PP to lipid A 1-phosphate to produce lipid A 1-diphosphate. Furthermore, this reaction requires a functionally intact MsbA protein, which catalyses the transfer of lipid A across the membrane, confirming that the LpxT-mediated lipid A modification occurs on the periplasmic side of the membrane. These observations provide a novel and unexpected link between periplasmic lipid A modifications and the Und-PP recycling pathway.

Histomorphometric evaluation of human sinus floor augmentation healing responses to placement of calcium phosphate or Ricinus communis polymer associated with autogenous bone

Background: Prosthetic rehabilitation of the posterior maxilla with dental implants is often difficult because of proximity to the maxillary sinus and insufficient bone height. Maxillary sinus floor augmentation procedures aim to obtain enough bone with an association between biomaterials and autogenous bone.Purpose: the purpose of this study was to evaluate histomorphometrically two grafting materials (calcium phosphate and Ricinus communis polymer) used in maxillary sinus floor augmentation associated with autogenous bone.Materials and Methods: Biopsies were taken from 10 consecutive subjects (mean age 45 years) 10 months after maxillary sinus floor augmentation. The sinus lift was performed with a mixture of autogenous bone and R. communis polymer or calcium phosphate in a 1:2 proportion. Routine histologic processing and staining with hernatoxylin and eosin were performed.Results: the histomorphometric analysis indicated satisfactory regenerative results in both groups for a mean of bone tissue in the grafted area (44.24 +/- 13.79% for the calcium phosphate group and 38.77 +/- 12.85% for the polymer group). Histologic evaluation revealed the presence of an inflammatory infiltrate of mononuclear prevalence that, on average, was nonsignificant. The histologic sections depicted mature bone with compact and cancellous areas in both groups.Conclusion: the results indicated that both graft materials associated with the autogenous bone were biocompatible, although both were still present after 10 months.

Phosphate functionalization of spongiolite surface

Spongiolite from Mato Grosso do Sul (Brazil), natural inorganic composite constituted of silica needles, was treated with concentrated phosphoric acid at high temperatures. Superficial coating of the needles was proved to be constituted of silicon diphosphate, a compound offering six-coordinated silicon sites. Owing to the affinity of three charged ions to phosphate groups, this coating acts as specific adsorbent for the rare earth elements which prefer octahedral coordination (starting from samarium, yttrium included). The uptake of lanthanum and neodymium are significantly lower due to different coordination tendencies. Lanthanide fixation upon silica with PO4 groups anchored on its surface may be useful in the manufacturing of special phosphate-silicate glasses. (C) 2003 Elsevier B.V. All rights reserved.

Role of a ribosomal RNA phosphate oxygen during the EF-G–triggered GTP hydrolysis

Elongation factor-catalyzed GTP hydrolysis is a key reaction during the ribosomal elongation cycle. Recent crystal structures of G proteins, such as elongation factor G (EF-G) bound to the ribosome, as well as many biochemical studies, provide evidence that the direct interaction of translational GTPases (trGTPases) with the sarcin-ricin loop (SRL) of ribosomal RNA (rRNA) is pivotal for hydrolysis. However, the precise mechanism remains elusive and is intensively debated. Based on the close proximity of the phosphate oxygen of A2662 of the SRL to the supposedly catalytic histidine of EF-G (His87), we probed this interaction by an atomic mutagenesis approach. We individually replaced either of the two nonbridging phosphate oxygens at A2662 with a methyl group by the introduction of a methylphosphonate instead of the natural phosphate in fully functional, reconstituted bacterial ribosomes. Our major finding was that only one of the two resulting diastereomers, the SP methylphosphonate, was compatible with efficient GTPase activation on EF-G. The same trend was observed for a second trGTPase, namely EF4 (LepA). In addition, we provide evidence that the negative charge of the A2662 phosphate group must be retained for uncompromised activity in GTP hydrolysis. In summary, our data strongly corroborate that the nonbridging proSP phosphate oxygen at the A2662 of the SRL is critically involved in the activation of GTP hydrolysis. A mechanistic scenario is supported in which positioning of the catalytically active, protonated His87 through electrostatic interactions with the A2662 phosphate group and H-bond networks are key features of ribosome-triggered activation of trGTPases.

Role of a ribosomal RNA phosphate oxygen during the EF-G-triggered hydrolysis

Elongation factor-catalyzed GTP hydrolysis is a key reaction during the ribosomal elongation cycle. Recent crystal structures of G proteins, such as elongation factor G (EF-G) bound to the ribosome, as well as many biochemical studies, provide evidence that the direct interaction of translational GTPases (trGTPases) with the sarcin-ricin loop (SRL) of ribosomal RNA (rRNA) is pivotal for hydrolysis. However, the precise mechanism remains elusive and is intensively debated. Based on the close proximity of the phosphate oxygen of A2662 of the SRL to the supposedly catalytic histidine of EF-G (His87), we probed this interaction by an atomic mutagenesis approach. We individually replaced either of the two nonbridging phosphate oxygens at A2662 with a methyl group by the introduction of a methylphosphonate instead of the natural phosphate in fully functional, reconstituted bacterial ribosomes. Our major finding was that only one of the two resulting diastereomers, the SP methylphosphonate, was compatible with efficient GTPase activation on EF-G. The same trend was observed for a second trGTPase, namely EF4 (LepA). In addition, we provide evidence that the negative charge of the A2662 phosphate group must be retained for uncompromised activity in GTP hydrolysis. (1) In summary, our data strongly corroborate that the nonbridging proSP phosphate oxygen at the A2662 of the SRL is critically involved in the activation of GTP hydrolysis. A mechanistic scenario is supported in which positioning of the catalytically active, protonated His87 through electrostatic interactions with the A2662 phosphate group and H-bond networks are key features of ribosome-triggered activation of trGTPases.

Role of a ribosomal RNA phosphate oxygen during the EF-G-triggered hydrolysis

Elongation factor-catalyzed GTP hydrolysis is a key reaction during the ribosomal elongation cycle. Recent crystal structures of G proteins, such as elongation factor G (EF-G) bound to the ribosome, as well as many biochemical studies, provide evidence that the direct interaction of translational GTPases (trGTPases) with the sarcin-ricin loop (SRL) of ribosomal RNA (rRNA) is pivotal for hydrolysis. However, the precise mechanism remains elusive and is intensively debated. Based on the close proximity of the phosphate oxygen of A2662 of the SRL to the supposedly catalytic histidine of EF-G (His87), we probed this interaction by an atomic mutagenesis approach. We individually replaced either of the two nonbridging phosphate oxygens at A2662 with a methyl group by the introduction of a methylphosphonate instead of the natural phosphate in fully functional, reconstituted bacterial ribosomes. Our major finding was that only one of the two resulting diastereomers, the SP methylphosphonate, was compatible with efficient GTPase activation on EF-G. The same trend was observed for a second trGTPase, namely EF4 (LepA). In addition, we provide evidence that the negative charge of the A2662 phosphate group must be retained for uncompromised activity in GTP hydrolysis. (1) In summary, our data strongly corroborate that the nonbridging proSP phosphate oxygen at the A2662 of the SRL is critically involved in the activation of GTP hydrolysis. A mechanistic scenario is supported in which positioning of the catalytically active, protonated His87 through electrostatic interactions with the A2662 phosphate group and H-bond networks are key features of ribosome-triggered activation of trGTPases.

Purified inositol hexakisphosphate kinase is an ATP synthase: diphosphoinositol pentakisphosphate as a high-energy phosphate donor.

Diphosphoinositol pentakisphosphate (PP-IP5) and bis(diphospho)inositol tetrakisphosphate (bis-PP-IP4) are recently identified inositol phosphates that possess pyrophosphate bonds. We have purified an inositol hexakisphosphate (IP6) kinase from rat brain supernatants. The pure protein, a monomer of 54 kDa, displays high affinity (Km = 0.7 microM) and selectivity for inositol hexakisphosphate as substrate. It can be dissociated from bis(diphospho)inositol tetrakisphosphate synthetic activity. The purified enzyme transfers a phosphate from PP-IP5 to ADP to form ATP. This ATP synthase activity indicates the high phosphate group transfer potential of PP-IP5 and may represent a physiological role for PP-IP5.

Biochemical and structural characterization of residue 96 mutants of Plasmodium falciparum triosephosphate isomerase: active-site loop conformation, hydration and identification of a dimer-interface ligand-binding site

Plasmodium falciparum TIM (PfTIM) is unique in possessing a Phe residue at position 96 in place of the conserved Ser that is found in TIMs from the majority of other organisms. In order to probe the role of residue 96, three PfTIM mutants, F96S, F96H and F96W, have been biochemically and structurally characterized. The three mutants exhibited reduced catalytic efficiency and a decrease in substrate-binding affinity, with the most pronounced effects being observed for F96S and F96H. The k(cat) values and K-m values are (2.54 +/- 0.19) x 10(5) min(-1) and 0.39 +/- 0.049 mM, respectively, for the wild type; (3.72 +/- 0.28) x 10(3) min(-1) and 2.18 +/- 0.028 mM, respectively, for the F96S mutant;(1.11 +/- 0.03) x 10(4) min(-1) and 2.62 +/- 0.042 mM, respectively, for the F96H mutant; and (1.48 +/- 0.05) x 10(5) min(-1) and 1.20 +/- 0.056 mM, respectively, for the F96W mutant. Unliganded and 3-phosphoglycerate (3PG) complexed structures are reported for the wild-type enzyme and the mutants. The ligand binds to the active sites of the wild-type enzyme (wtPfTIM) and the F96W mutant, with a loop-open state in the former and both open and closed states in the latter. In contrast, no density for the ligand could be detected at the active sites of the F96S and F96H mutants under identical conditions. The decrease in ligand affinity could be a consequence of differences in the water network connecting residue 96 to Ser73 in the vicinity of the active site. Soaking of crystals of wtPfTIM and the F96S and F96H mutants resulted in the binding of 3PG at a dimer-interface site. In addition, loop closure at the liganded active site was observed for wtPfTIM. The dimer-interface site in PfTIM shows strong electrostatic anchoring of the phosphate group involving the Arg98 and Lys112 residues of PfTIM.

ESR study of metal ion-guanosine monophosphate interaction

The addition of guanosine 5-monophosphate (5′-GMP) to an aqueous solution of Mn2+ ions results in a decrease in ESR signal intensity and an increase in line-width of Mn2+ ions. This can be interpreted in terms of stepwise formation of outersphere and inner-sphere complexes as When Mg2+ is added to a mixture of Mn2+ and 5′-GMP, ESR signal intensity increases, presumably due to the replacement of Mn2+ by Mg2+ in the complex. From the variation of ESR signal intensity as a function of concentration of Mg2+, the product K1K2 for the magnesium complex i s calculated as 125 M−1. This difference in stability constants may indicate that both phosphate group and guanine base are involved in the formation of Mn2+-5′-GMP complex.

Interaction of DNA with anti-cancer drugs: copper-thiosemicarbazide system

The interaction of copper-thiosemicarbazide complexes with DNA was investigated using ultraviolet and infrared spectroscopy. Evidence for the interaction of the complexes with nucleic acid bases and with the phosphate group is presented.

Metal-Nucleotide Interactions: Crystal Structures of Alkali (Li+, Na+, K+) and Alkaline Earth (Ca2+, Mg2+) Metal Complexes of Adenosine 2'-Monophosphate

Crystal structures of lithium, sodium, potassium, calcium and magnesium salts of adenosine 2'-monophosphate (2'-AMP) have been obtained at atomic resolution by X-ray crystallographic methods. 2'-AMP.Li belongs to the monoclinic space group P21 with a = 7.472(3)Å, b = 26.853(6) Å, c = 9.184(1)Å, b = 113.36(1)Å and Z= 4. 2'-AMP.Na and 2'-AMP.K crystallize in the trigonal space groups P31 and P3121 with a = 8.762(1)Å, c = 34.630(5)Å, Z= 6 and a = 8.931(4), Åc = 34.852(9)Å and Z= 6 respectively while 2'-AMP.Ca and 2'-AMP.Mg belong to space groups P6522 and P21 with cell parameters a = 9.487(2), c = 74.622(13), Z = 12 and a = 4.973(1), b = 10.023(2), c = 16.506(2), beta = 91.1(0) and Z = 2 respectively. All the structures were solved by direct methods and refined by full matrix least-squares to final R factors of 0.033, 0.028, 0.075, 0.069 and 0.030 for 2'-AMP.Li, 2'-AMP.Na, 2'- AMP.K, 2'-AMP.Ca and 2'-AMP.Mg, respectively. The neutral adenine bases in all the structures are in syn conformation stabilized by the O5'-N3 intramolecular hydrogen bond as in free acid and ammonium complex reported earlier. In striking contrast, the adenine base is in the anti geometry (cCN = -156.4(2)°) in 2'-AMP.Mg. Ribose moieties adopt C2'-endo puckering in 2'-AMP.Li and 2'-AMP.Ca, C2'-endo-C3'-exo twist puckering in 2'-AMP.Na and 2'-AMP.K and a C3'-endo-C2'-exo twist puckering in 2'-AMP.Mg structure. The conformation about the exocyclic C4'-C5' bond is the commonly observed gauche-gauche (g+) in all the structures except the gauche- trans (g-) conformation observed in 2'-AMP.Mg structure. Lithium ions coordinate with water, ribose and phosphate oxygens at distances 1.88 to 1.99Å. Na+ ions and K+ ions interact with phosphate and ribose oxygens directly and with N7 indirectly through a water oxygen. A distinct feature of 2'-AMP.Na and 2'-AMP.K structures is the involvement of ribose O4' in metal coordination. The calcium ion situated on a two-fold axis coordinates directly with three oxygens OW1, OW2 and O2 and their symmetry mates at distances 2.18 to 2.42Å forming an octahedron. A classic example of an exception to the existence of the O5'-N3 intramolecular hydorgen bond is the 2'-AMP.Mg strucure. Magnesium ion forms an octahedral coordination with three water and three phosphate oxygens at distances ranging from 2.02 to 2.11Å. A noteworthy feature of its coordination is the indirect link with N3 through OW3 oxygen resulting in macrochelation between the base and the phosphate group. Greater affnity of metal clays towards 5' compared to 2' and 3' nucleotides (J. Lawless, E. Edelson, and L. Manring, Am. Chem. Soc. Northwest Region Meeting, Seattle. 1978) due to macrochelation infered from solution studies (S. S. Massoud, H. Sigel, Eur. J. Biochem. 179, 451-458 (1989)) and interligand hydrogen bonding induced by metals postulated from metal-nucleotide structures in solid state (V. Swaminathan and M. Sundaralingam, CRC. Crit. Rev. Biochem. 6, 245-336 (1979)) are borne out by our structures also. The stacking patterns of adenine bases of both 2'-AMP.Na and 2'-AMP.K structures resemble the 2'-AMP.NH4 structure reported in the previous article. 2'-AMP.Li, 2'-AMP.Ca and 2'-AMP.Mg structures display base-ribose O4' stacking. An overview of interaction of monovalent and divalent cations with 2' and 5'-nucleotides has been presented.

Synthesis of BaSO4 nanoparticles by precipitation method using sodium hexa metaphosphate as a stabilizer

We describe the synthesis and structure of Barium sulfate nanoparticles by precipitation method in the presence of water soluble inorganic stabilizing agent, sodium hexametaphosphate, (NaPO3)(6). The structural parameters were refined by the Rietveld refinement method using powder X-ray diffraction data. Barium sulfate nanoparticles were crystallized in the orthorhombic structure with space group Pbnm (No. 62) having the lattice parameters a = 7.215(1) (angstrom), b = 8.949(1) (angstrom) and c = 5.501 (1) (angstrom) respectively. Transmission electron microscopy study reveals that the nanoparticles are size range, 30-50 nm. Fourier transform infrared spectra showed distinct absorption due to the SO42- moiety at 1115 and 1084 cm(-1) indicating formation of barium sulfate nanoparticles free from the phosphate group from the stabilizer used in the synthesis. (C) 2009 Elsevier Ltd. All rights reserved.

Studies on the enzyme hydrolysing flavin mononucleotide in plants: II. Phosphotransferase activity of the partially purified enzyme from Phaseolus radiatus

The preparation of the enzyme hydrolysing FMN whose partial purification from green-gram extracts is described in the preceding paper, has been shown to possess phosphotransferase activity. The enzyme could transfer the phosphate group cleaved from FMN to acceptors like thiamine, pyridoxal, pyridoxamine and nucleosides resulting in the formation of their corresponding phosphate esters and nucleotides. The properties of the enzyme hydrolysing FMN and the phosphotransferase activity of the preparation are compared.

On self-interacting oligoribonucleotides. I. Absorption and optical rotatory dispersion of 2′-5′- and 3′-5′-oligoguanylic acids

A series of 2′-5′-oligoguanylic acids are prepared by reacting G(cyclic)p with takadiastase T1 ribonuclease and separating the products chromatographically. The 3′-5′-oligoguanylic acids are obtained by separating the products of alkaline degradation of 3′-5′-poly(G). The optical rotatory dispersion and hypochromism of both 2′-5′- and 3′-5′-oligoguanylic acids are studied at two different pH. The optical rotatory dispersion spectrum of 2′-5′-GpG is significantly different from that of 3′-5′-GpG. The magnitude of rotation of the long-wavelength peak of 2′-5′-GpG is larger than that of 3′-5′-GpG. This finding contradicts the explanation that the extra stability and more intense circular dichroism band of other 3′-5′-dinucleoside monophosphates is due to H-bond formation between 2′-OH and either the base or the phosphate oxygen. The end phosphate group has a marked effect on the spectrum of GpG between 230 and 250 mμ. In addition the optical rotatory dispersion spectra of 2′-5′ exhibit strong pH, temperature, and solvent dependence between 230 and 250 mμ. ΔH and AS for order ⇌ disorder transition is estimated to be 9.7 kcal/mole and 35.2 eu, respectively. The optical rotatory dispersion spectra of guanine-rich oligoribonucleotides, GpGpC, GpGpU, GpGpGpC, and GpGpGpU are compared to the calculated optical rotatory dispersion from the semiempirical expression of Cantor and Tinoco, using measured optical rotatory dispersion of dimers. Contrary to previous studies, agreement is found not at all satisfactory. However, optical rotatory dispersion of 3′-5′-GpGpGpC and GpGpGpU can be estimated from the semiempirical expression, if a next-nearest interaction parameter is introduced empirically. Such interaction parameter can be calculated from the measured properties of trinucleotide sequences like GpGpG, GpGpC, and GpGpU, assuming that only the nearest-neighbor interaction is important. The optical rotatory dispersion of single-stranded poly(G) is also predicted. The importance of syn-anti equilibrium and next-nearest-neighbor interaction in oligoguanylic acids is suggested as a probable explanation.