Hydrated metal ion as a general acid in the catalytic mechanism of the 8-17 DNAzyme

2021 ◽  
Author(s):  
Marjorie Cepeda Plaza ◽  
Francisca Rojas-Hernández ◽  
Romina Paillao-Bustos ◽  
Catalina Cortés-Guajardo
Keyword(s):  
Metal Ions ◽  
Metal Ion ◽  
Catalytic Mechanism ◽  
Divalent Metal ◽  
Divalent Metal Ions ◽  
General Acid ◽  
Catalytic Dna

The RNA-cleaving 8-17 DNAzyme, which is a metalloenzyme that depends on divalent metal ions for function, is the most studied catalytic DNA in terms of its mechanism. By the end...

scholarly journals Structure of New Binary and Ternary DNA Polymerase Complexes From Bacteriophage RB69

2021 ◽  
Vol 8 ◽  
Author(s):  
Jongseo Park ◽  
Hyung-Seop Youn ◽  
Jun Yop An ◽  
Youngjin Lee ◽  
Soo Hyun Eom ◽  
...  
Keyword(s):  
Metal Ions ◽  
Dna Polymerase ◽  
Metal Ion ◽  
Ternary Complex ◽  
Critical Role ◽  
Divalent Metal ◽  
Binary Complex ◽  
Divalent Metal Ions ◽  
Divalent Metal Ion ◽  
Initial Binding

DNA polymerase plays a critical role in passing the genetic information of any living organism to its offspring. DNA polymerase from enterobacteria phage RB69 (RB69pol) has both polymerization and exonuclease activities and has been extensively studied as a model system for B-family DNA polymerases. Many binary and ternary complex structures of RB69pol are known, and they all contain a single polymerase-primer/template (P/T) DNA complex. Here, we report a crystal structure of the exonuclease-deficient RB69pol with the P/T duplex in a dimeric form at a resolution of 2.2 Å. The structure includes one new closed ternary complex with a single divalent metal ion bound and one new open binary complex in the pre-insertion state with a vacant dNTP-binding pocket. These complexes suggest that initial binding of the correct dNTP in the open state is much weaker than expected and that initial binding of the second divalent metal ion in the closed state is also much weaker than measured. Additional conformational changes are required to convert these complexes to high-affinity states. Thus, the measured affinities for the correct incoming dNTP and divalent metal ions are average values from many conformationally distinctive states. Our structure provides new insights into the order of the complex assembly involving two divalent metal ions. The biological relevance of specific interactions observed between one RB69pol and the P/T duplex bound to the second RB69pol observed within this dimeric complex is discussed.

scholarly journals Modeling of neotame and fructose thermochemistry: Comparison with mono and divalent metal ions by Computational and experimental approach

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Deepali Sharma ◽  
Suvardhan Kanchi ◽  
Ayyappa Bathinapatla ◽  
Inamuddin ◽  
Abdullah M. Asiri
Keyword(s):  
Metal Ions ◽  
Metal Ion ◽  
Density Functional ◽  
Divalent Metal ◽  
Basis Set ◽  
Hydroxyl Groups ◽  
Specific Cell ◽  
Water Medium ◽  
Artificial Sweetener ◽  
Divalent Metal Ions

AbstractThe metal complexes can demonstrate various interesting biological activities in the human body. However, the role of certain metal ions for specific cell activities is still subject to debate. This study is aimed at comparing the thermochemical properties of neotame (artificial sweetener) and α, β-fructose in gas phase and water medium. The interaction of α and β-fructose, neotame with monovalent and divalent metal ions was studied and comprehended by density functional theory (DFT) using B3LYP functional, 6–311 + G (d, p) and D3 basis set. Metal ion affinities (MIA) values depicted that ionic radius of metal ions played an important role in the interaction of α, β-fructose and neotame. The ∆G parameter was calculated to predict and understand the interaction of metal ions with α and β-fructose, neotame. The results suggested that the presence of hydroxyl groups and oxygen atoms in sugar molecules acted as preferred sites for the binding and interaction of mono and divalent ions. For the first time computational study has been introduced in the present study to review the progress in the application of metal binding with sugar molecules especially with neotame. Moreover, voltammetric behaviour of neotame-Zn2+ was studied using cyclic and differential pulse voltammetry. The obtained results suggest that the peak at −1.13 V is due to the reduction of Zn2+ in 0.1 M phosphate buffer medium at pH 5.5. Whereas, addition of 6-fold higher concentration of neotame to the ZnCl2.2H2O resulted in a new irreversible cathodic peak at −0.83, due to the reduction of neotame-Zn2+ complex. The Fourier transform infrared spectroscopy (FTIR) results indicates that the β-amino group (-NH) and carboxyl carbonyl (-C = O) groups of neotame is participating in the chelation process, which is further supported by DFT studies. The findings of this study identify the efficient chelation factors as major contributors into metal ion affinities, with promising possibilities to determine important biological processes in cell wall and glucose transmembrane transport.

scholarly journals Complementary Metal Ion Specificity of the Metal-Citrate Transporters CitM and CitH of Bacillus subtilis

2000 ◽  
Vol 182 (22) ◽  
pp. 6374-6381 ◽  
Author(s):  
Bastiaan P. Krom ◽  
Jessica B. Warner ◽  
Wil N. Konings ◽  
Juke S. Lolkema
Keyword(s):  
Bacillus Subtilis ◽  
Metal Ions ◽  
Metal Ion ◽  
Physiological Function ◽  
Divalent Metal ◽  
Uptake System ◽  
Divalent Metal Ions ◽  
Ion Specificity ◽  
Citrate Transporter ◽  
Wide Range

ABSTRACT Citrate uptake in Bacillus subtilis is stimulated by a wide range of divalent metal ions. The metal ions were separated into two groups based on the expression pattern of the uptake system. The two groups correlated with the metal ion specificity of two homologousB. subtilis secondary citrate transporters, CitM and CitH, upon expression in Escherichia coli. CitM transported citrate in complex with Mg2+, Ni2+, Mn2+, Co2+, and Zn2+ but not in complex with Ca2+, Ba2+, and Sr2+. CitH transported citrate in complex with Ca2+, Ba2+, and Sr2+ but not in complex with Mg2+, Ni2+, Mn2+, Co2+, and Zn2+. Both transporters did not transport free citrate. Nevertheless, free citrate uptake could be demonstrated in B. subtilis, indicating the expression of at least a third citrate transporter, whose identity is not known. For both the CitM and CitH transporters it was demonstrated that the metal ion promoted citrate uptake and, vice versa, that citrate promoted uptake of the metal ion, indicating that the complex is the transported species. The results indicate that CitM and CitH are secondary transporters that transport complexes of divalent metal ions and citrate but with a complementary metal ion specificity. The potential physiological function of the two transporters is discussed.

Divalent metal ion-mediated assembly of spherical nucleic acids: the case study of Cu2+

2015 ◽  
Vol 17 (45) ◽  
pp. 30292-30299 ◽  
Author(s):  
Jang Ho Joo ◽  
Jae-Seung Lee
Keyword(s):  
Nucleic Acids ◽  
Metal Ions ◽  
Metal Ion ◽  
Divalent Metal ◽  
Divalent Metal Ions ◽  
New Strategy ◽  
Divalent Metal Ion ◽  
Spherical Nucleic Acids

A new strategy for reversibly assembling spherical nucleic acids (SNAs) is demonstrated based on the coordinative binding of divalent metal ions, particularly Cu2+, to nucleobases.

scholarly journals Effect of divalent metal ions on annexin-mediated aggregation of asolectin liposomes.

2000 ◽  
Vol 47 (3) ◽  
pp. 675-683 ◽  
Author(s):  
V I Mel'gunov ◽  
E I Akimova ◽  
K S Krasavchenko
Keyword(s):  
Metal Ions ◽  
Metal Ion ◽  
Relative Concentration ◽  
Toxic Metal ◽  
Transition Metal Ions ◽  
Divalent Metal ◽  
Divalent Metal Ions ◽  
Large Unilamellar Vesicles ◽  
Protein Molecules ◽  
Divalent Metal Ion

Annexins belong to a family of Ca2+- and phospholipid-binding proteins that can mediate the aggregation of granules and vesicles in the presence of Ca2+. We have studied the effects of different divalent metal ions on annexin-mediated aggregation of liposomes using annexins isolated from rabbit liver and large unilamellar vesicles prepared from soybean asolectin II-S. In the course of these studies, we have found that annexin-mediated aggregation of liposomes can be driven by various earth and transition metal ions other than Ca2+. The ability of metal ions to induce annexin-mediated aggregation decreases in the order: Cd2+ > Ba2+, Sr2+ > Ca2+ > Mn2+ > Ni2+ > Co2+. Annexin-mediated aggregation of vesicles is more selective to metal ions than the binding of annexins to membranes. We speculate that not every type of divalent metal ion can induce conformational change sufficient to promote the interaction of annexins either with two opposing membranes or with opposing protein molecules. Relative concentration ratios of metal ions in the intimate environment may be crucial for the functioning of annexins within specialized tissues and after treatment with toxic metal ions.

Alginate Polyelectrolyte Ionotropic Gels-XII. Chromatographic Separation of Divalent Transition Metal Ions using Alginates as Ion Exchangers

1992 ◽  
Vol 4 (1) ◽  
pp. 49-54 ◽  
Author(s):  
Refat M. Hassan ◽  
S. A. El-Shatoury ◽  
M. Th. Makhlouf
Keyword(s):  
Ion Exchange ◽  
Metal Ions ◽  
Metal Ion ◽  
Transition Metal Ions ◽  
Selectivity Coefficient ◽  
Divalent Metal ◽  
Divalent Metal Ions ◽  
Ion Exchangers ◽  
Calcium Alginate Gel ◽  
Exchange Selectivity

The separation of divalent metal ion mixtures has been investigated chromatographically on columns of either gel or sol forms of alginate polyelectrolyte. Separation was obtained in the form of narrow sharp zones for the metal ions. Ion exchange selectivity indicated that Cu2+ ions were most strongly retained among the divalent metal ions studied. The factors which affect the ion exchange selectivity, such as the strength of chelation and the mobility and radii of the metal ions, are discussed. The selectivity coefficient for the separation of a mixture of Cu2+ and Co2+ ions on columns of calcium alginate gel or sodium alginate sol was determined and found to be 1.9 ± 0.1 in both ion exchangers at 25°C.

Suppressive Effects on Filamentous Bulking by Addition of Corn Cob Flour and Divalent Metal Ions

1992 ◽  
Vol 26 (9-11) ◽  
pp. 2493-2496 ◽  
Author(s):  
T. Iyo ◽  
T. Yoshino ◽  
S. Ohno
Keyword(s):  
Metal Ions ◽  
Metal Ion ◽  
Continuous Process ◽  
Divalent Metal ◽  
Volume Index ◽  
Main Element ◽  
Corn Cob ◽  
Divalent Metal Ions ◽  
Filamentous Bulking ◽  
Filamentous Microorganisms

We investigated the suppressive effects on filamentous bulking by addition of grinding flour of corn cob (corn cob flour abbreviated to CCF), agriculture waste, and the divalent metal ions. When 1000 mg.L−1 of activated sludge loading with 30 % of CCF was operated by a continuous process, we obtained a microbial coagulation of which nucleus was formed by CCF with good settling character and high density in spite of use the substrate of which the main element was glucose caused easily the filamentous bulking. This effect, further, was increased with addition of Ca2+ ion. From SEM observation, we found few filamentous microorganisms but cocci and short rods dominant on this surface of CCF which possessed good settling character, i.e., 20-30 ml·g−1 of sludge volume index (SVI) and 2-6 cnrmin.−1 of the interfacial settling velocity. It was characteristic that many Arcellasp., Protozoa, adhered to the surface of CCF with Ca2+. From these results, it was estimated that Ca2+, divalent metal ion, promoted the cross-linking act among cytoplasmic membranes charged negative and increased the affinity between CCF and microorganisms.

scholarly journals Platonic Relationships in Metal Phosphonate Chemistry: Ionic Metal Phosphonates

Crystals ◽  
2019 ◽  
Vol 9 (6) ◽  
pp. 301 ◽  
Author(s):  
Konstantinos Xanthopoulos ◽  
Zafeiria Anagnostou ◽  
Sophocles Chalkiadakis ◽  
Duane Choquesillo-Lazarte ◽  
Gellert Mezei ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Metal Ions ◽  
Metal Ion ◽  
Divalent Metal ◽  
Divalent Metal Ions ◽  
Charge Balance ◽  
Phosphonic Acids ◽  
Metal Phosphonates ◽  
Metal Phosphonate ◽  
Phosphonate Ligands

Phosphonate ligands demonstrate strong affinity for metal ions. However, there are several cases where the phosphonate is found non-coordinated to the metal ion. Such compounds could be characterized as salts, since the interactions involved are ionic and hydrogen bonding. In this paper we explore a number of such examples, using divalent metal ions (Mg2+, Ca2+, Sr2+ and Ni2+) and the phosphonic acids: p-aminobenzylphosphonic acid (H2PABPA), tetramethylenediamine-tetrakis(methylenephosphonic acid) (H8TDTMP), and 1,2-ethylenediphosphonic acid (H4EDPA). The compounds isolated and structurally characterized are [Mg(H2O)6]·[HPABPA]2·6H2O, [Ca(H2O)8]·[HPABPA]2, [Sr(H2O)8]·[HPABPA]2, [Mg(H2O)6]·[H6TDTMP], and [Ni(H2O)6]·[H2EDPA]·H2O. Also, the coordination polymer {[Ni(4,4’-bpy)(H2O)4]·[H2EDPA]·H2O}n was synthesized and characterized, which contains a bridging 4,4’-bipyridine (4,4’-bpy) ligand forming an infinite chain with the Ni2+ cations. All these compounds contain the phosphonate anion as the counterion to charge balance the cationic charge originating from the metal cation.

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