scholarly journals Identification of Molecular Fluorophore as a Component of Carbon Dots able to Induce Gelation in a Fluorescent Multivalent-Metal-Ion-Free Alginate Hydrogel

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Peter Kasak ◽  
Martin Danko ◽  
Sifani Zavahir ◽  
Miroslav Mrlik ◽  
Yuan Xiong ◽  
...  
Keyword(s):  
Optical Properties ◽  
Carbon Dots ◽  
Metal Ion ◽  
Divalent Metal ◽  
Simple Approach ◽  
Sodium Ions ◽  
Divalent Metal Ions ◽  
Alginate Hydrogel ◽  
Carboxylic Acid Groups ◽  
Multivalent Metal

Abstract We introduce a simple approach to fabricate fluorescent multivalent metal ion-free alginate hydrogels, which can be produced using carbon dots accessible from natural sources (citric acid and L-cysteine). Molecular fluorophore 5-oxo-2,3-dihydro-5H-[1,3]-thiazolo[3,2-a] pyridine-3,7-dicarboxylic acid (TPDCA), which is formed during the synthesis of carbon dots, is identified as a key segment for the crosslinking of hydrogels. The crosslinking happens through dynamic complexation of carboxylic acid groups of TPDCA and alginate cages along with sodium ions. The TPDCA derived hydrogels are investigated regarding to their thermal, rheological and optical properties, and found to exhibit characteristic fluorescence of this aggregated molecular fluorophore. Moreover, gradient hydrogels with tunable mechanical and optical properties and controlled release are obtained upon immersion of the hydrogel reactors in solutions of divalent metal ions (Ca2+, Cu2+, and Ni2+) with a higher affinity to alginate.

scholarly journals HK97 gp74 Possesses an α-Helical Insertion in the ββα Fold That Affects Its Metal Binding, cos Site Digestion, and In Vivo Activities

2020 ◽  
Vol 202 (8) ◽  
Author(s):  
Sasha A. Weiditch ◽  
Sarah C. Bickers ◽  
Diane Bona ◽  
Karen L. Maxwell ◽  
Voula Kanelis
Keyword(s):  
Metal Binding ◽  
Metal Ion ◽  
Divalent Metal ◽  
Metal Ion Binding ◽  
Divalent Metal Ions ◽  
Nmr Studies ◽  
Phage Dna ◽  
Divalent Metal Ion ◽  
Phage Morphogenesis

ABSTRACT The last gene in the genome of the bacteriophage HK97 encodes gp74, an HNH endonuclease. HNH motifs contain two conserved His residues and an invariant Asn residue, and they adopt a ββα structure. gp74 is essential for phage head morphogenesis, likely because gp74 enhances the specific endonuclease activity of the HK97 terminase complex. Notably, the ability of gp74 to enhance the terminase-mediated cleavage of the phage cos site requires an intact HNH motif in gp74. Mutation of H82, the conserved metal-binding His residue in the HNH motif, to Ala abrogates gp74-mediated stimulation of terminase activity. Here, we present nuclear magnetic resonance (NMR) studies demonstrating that gp74 contains an α-helical insertion in the Ω-loop, which connects the two β-strands of the ββα fold, and a disordered C-terminal tail. NMR data indicate that the Ω-loop insert makes contacts to the ββα fold and influences the ability of gp74 to bind divalent metal ions. Further, the Ω-loop insert and C-terminal tail contribute to gp74-mediated DNA digestion and to gp74 activity in phage morphogenesis. The data presented here enrich our molecular-level understanding of how HNH endonucleases enhance terminase-mediated digestion of the cos site and contribute to the phage replication cycle. IMPORTANCE This study demonstrates that residues outside the canonical ββα fold, namely, the Ω-loop α-helical insert and a disordered C-terminal tail, regulate the activity of the HNH endonuclease gp74. The increased divalent metal ion binding when the Ω-loop insert is removed compared to reduced cos site digestion and phage formation indicates that the Ω-loop insert plays multiple regulatory roles. The data presented here provide insights into the molecular basis of the involvement of HNH proteins in phage DNA packing.

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.

The Novel Two-Metal-Ion Mechanism for Type II Topoisomerases by the QM/MM and Free Energy Study

2019 ◽  
Author(s):  
Jingheng Wu ◽  
Hui Chao ◽  
Yong Shen
Keyword(s):  
Free Energy ◽  
Metal Ion ◽  
Divalent Metal ◽  
Free Energy Calculations ◽  
Nucleophilic Attack ◽  
Type Ii ◽  
Divalent Metal Ions ◽  
Dna Scission ◽  
Dna Strand ◽  
High Level

Catalysis of Type II topoisomerase employs a combination of nucleobase and divalent metal ions with a long discussing two-metal-ion mechanism. High-level quantum mechanics/molecular mechanics (QM/MM) and thermodynamics cycle perturbation (QTCP) free energy calculations support an associative novel two-metal-ion mechanism and elucidate the catalytic roles of metal ion, in which one divalent metal ion stabilizes the phosphoric pentacovalent transition state and the 3’‒OH leaving group while the secondary one facilitates to reorganize the nearby hydrogen network and residues. The DNA scission is fast and exothermic that a stepwise pathway proceeds for the nucleophilic attack by Y805 following by the protonation of the ribose alkoxide, inducing the formation of a bending DNA strand. These findings advance the fundamental knowledge on topoisomerases and the development of targeting anticancer drugs.

The Novel Two-Metal-Ion Mechanism for Type II Topoisomerases by the QM/MM and Free Energy Study

2019 ◽  
Author(s):  
Jingheng Wu ◽  
Hui Chao ◽  
Yong Shen
Keyword(s):  
Free Energy ◽  
Metal Ion ◽  
Divalent Metal ◽  
Free Energy Calculations ◽  
Nucleophilic Attack ◽  
Type Ii ◽  
Divalent Metal Ions ◽  
Dna Scission ◽  
Dna Strand ◽  
High Level

Catalysis of Type II topoisomerase employs a combination of nucleobase and divalent metal ions with a long discussing two-metal-ion mechanism. High-level quantum mechanics/molecular mechanics (QM/MM) and thermodynamics cycle perturbation (QTCP) free energy calculations support an associative novel two-metal-ion mechanism and elucidate the catalytic roles of metal ion, in which one divalent metal ion stabilizes the phosphoric pentacovalent transition state and the 3’‒OH leaving group while the secondary one facilitates to reorganize the nearby hydrogen network and residues. The DNA scission is fast and exothermic that a stepwise pathway proceeds for the nucleophilic attack by Y805 following by the protonation of the ribose alkoxide, inducing the formation of a bending DNA strand. These findings advance the fundamental knowledge on topoisomerases and the development of targeting anticancer drugs.

scholarly journals Ring-Cleaving Dioxygenases with a Cupin Fold

2012 ◽  
Vol 78 (8) ◽  
pp. 2505-2514 ◽  
Author(s):  
Susanne Fetzner
Keyword(s):  
Electron Transfer ◽  
Metal Ion ◽  
Direct Electron Transfer ◽  
Heterocyclic Ring ◽  
Divalent Metal ◽  
Ring Cleavage ◽  
Type I ◽  
Divalent Metal Ions ◽  
Canonical Type ◽  
Extradiol Dioxygenases

ABSTRACTRing-cleaving dioxygenases catalyze key reactions in the aerobic microbial degradation of aromatic compounds. Many pathways converge to catecholic intermediates, which are subject toorthoormetacleavage by intradiol or extradiol dioxygenases, respectively. However, a number of degradation pathways proceed via noncatecholic hydroxy-substituted aromatic carboxylic acids like gentisate, salicylate, 1-hydroxy-2-naphthoate, or aminohydroxybenzoates. The ring-cleaving dioxygenases active toward these compounds belong to the cupin superfamily, which is characterized by a six-stranded β-barrel fold and conserved amino acid motifs that provide the 3His or 2- or 3His-1Glu ligand environment of a divalent metal ion. Most cupin-type ring cleavage dioxygenases use an FeIIcenter for catalysis, and the proposed mechanism is very similar to that of the canonical (type I) extradiol dioxygenases. The metal ion is presumed to act as an electron conduit for single electron transfer from the metal-bound substrate anion to O2, resulting in activation of both substrates to radical species. The family of cupin-type dioxygenases also involves quercetinase (flavonol 2,4-dioxygenase), which opens up two C-C bonds of the heterocyclic ring of quercetin, a wide-spread plant flavonol. Remarkably, bacterial quercetinases are capable of using different divalent metal ions for catalysis, suggesting that the redox properties of the metal are relatively unimportant for the catalytic reaction. The major role of the active-site metal ion could be to correctly position the substrate and to stabilize transition states and intermediates rather than to mediate electron transfer. The tentative hypothesis that quercetinase catalysis involves direct electron transfer from metal-bound flavonolate to O2is supported by model chemistry.

Thermoelectric properties of Li-doped Cu0.95-xM0.05LixO (M=Mn, Ni, Zn)

2012 ◽  
Vol 1490 ◽  
pp. 69-73
Author(s):  
N. Yoshida ◽  
T. Naito ◽  
H. Fujishiro
Keyword(s):  
Thermal Conductivity ◽  
Electrical Resistivity ◽  
Thermoelectric Properties ◽  
Metal Ion ◽  
Figure Of Merit ◽  
Divalent Metal ◽  
Thermoelectric Figure Of Merit ◽  
Divalent Metal Ions ◽  
Thermoelectric Figure ◽  
Divalent Metal Ion

ABSTRACTThermoelectric properties of the Li-doped Cu0.95-xM0.05LixO (M=divalent metal ion; Mn, Ni, Zn) were investigated at the temperature up to 1273 K. In the doped divalent metal ions, Zn2+ ion was the most effective to reduce the thermal conductivity, and the Ni2+ substitution was preferable to decrease the electrical resistivity. For the Cu0.95-xNi0.05LixO sample at x=0.03, the maxima of the dimensionless thermoelectric figure of merit ZT and the power factor P at 1246 K were 4.2×10-2 and 1.6 ×10-4 W/K2m, respectively. The enhancement of the thermoelectric properties of the Li-doped Cu0.95-xM0.05LixO system was discussed.

An internal charge transfer-DNA platform for fluorescence sensing of divalent metal ions

2016 ◽  
Vol 52 (61) ◽  
pp. 9586-9588 ◽  
Author(s):  
Darian J. M. Blanchard ◽  
Richard A. Manderville
Keyword(s):  
Charge Transfer ◽  
Metal Ion ◽  
Divalent Metal ◽  
Ion Binding ◽  
Metal Ion Binding ◽  
Divalent Metal Ions ◽  
Fluorescence Sensing ◽  
Divalent Metal Ion ◽  
Internal Charge Transfer ◽  
Internal Charge

Utility of internal fluorescent guanine replacements for effective signaling of divalent metal ion binding.

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.

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