Copper(II) and zinc(II) dinuclear enzymes model compounds: The nature of the metal ion in the biological function

2017 ◽  
Vol 1150 ◽  
pp. 316-328 ◽  
Author(s):  
L.G. Ferraresso ◽  
E.G.R. de Arruda ◽  
T.P.L. de Moraes ◽  
R.B. Fazzi ◽  
A.M. Da Costa Ferreira ◽  
...  
Keyword(s):  
Metal Ion ◽  
Biological Function ◽  
Model Compounds

scholarly journals Understanding Factors that Control the Structural (Dis)Assembly of Sulphur-Bridged Bimetallic Sites

Inorganics ◽  
2019 ◽  
Vol 7 (4) ◽  
pp. 42 ◽  
Author(s):  
Riyadh Alrefai ◽  
Henri Eggenweiler ◽  
Hartmut Schubert ◽  
Andreas Berkefeld
Keyword(s):  
Cyclic Voltammetry ◽  
Structure Function ◽  
General Type ◽  
Biological Function ◽  
Mechanism Of Formation ◽  
Model Compounds ◽  
Nickel Ions ◽  
Stereoelectronic Properties ◽  
Bimetallic Structures

Bimetallic structures of the general type [M2(µ-S)2] are omnipresent in nature, for biological function [M2(µ-S)2] sites interconvert between electronically distinct, but isostructural, forms. Different from structure-function relationships, the current understanding of the mechanism of formation and persistence of [M2(µ-S)2] sites is poorly developed. This work reports on bimetallic model compounds of nickel that interconvert between functional structures [Ni2(µ-S)2]+/2+ and isomeric congeners [2{κ-S–Ni}]2+/+, S = Aryl-S−, in which the nickel ions are geometrically independent. Interconversion of the two sets of structures was studied quantitatively by UV–VIS absorption spectroscopy and cyclic voltammetry. Assembly of the [Ni2(µ-S)2]+ core from [2{κ-S–Ni}]+ is thermodynamically and kinetically highly preferred over the disassembly of [Ni2(µ-S)2]2+ into [2{κ-S–Ni}]2+. Labile Ni-η2/3-bonding to aromatic π-systems of the primary thiophenol ligand is critical for modeling (dis)assembly processes. A phosphine coligand mimics the role of anionic donors present in natural sites that saturate metal coordination. Three parameters have been identified as critical for structure formation and persistence. These are, first, the stereoelectronic properties of the metals ions, second, the steric demand of the coligand, and, third, the properties of the dative bond between nickel and coligand. The energies of transition states connecting functional and precursor forms have been found to depend on these parameters.

There is no universal mechanism for the cleavage of RNA model compounds in the presence of metal ion catalysts

2013 ◽  
Vol 11 (48) ◽  
pp. 8324 ◽  
Author(s):  
Heidi Korhonen ◽  
Timo Koivusalo ◽  
Suvi Toivola ◽  
Satu Mikkola
Keyword(s):  
Metal Ion ◽  
Model Compounds ◽  
Universal Mechanism

Asymmetric α-alkylation of α-amino esters using pyridoxal model compounds with a chiral ionophore function; dependence of stereoselectivity on a chelated metal ion

1996 ◽  
pp. 1073-1074 ◽  
Author(s):  
Kazuyuki Miyashita ◽  
Hideto Miyabe ◽  
Kuninori Tai ◽  
Chiaki Kurozumi ◽  
Takeshi Imanishi
Keyword(s):  
Metal Ion ◽  
Model Compounds ◽  
Amino Esters

scholarly journals Chemistry and Some Biological Potential of Bismuth and Antimony Dithiocarbamate Complexes

Molecules ◽  
2020 ◽  
Vol 25 (2) ◽  
pp. 305 ◽  
Author(s):  
Jerry O. Adeyemi ◽  
Damian C. Onwudiwe
Keyword(s):  
Solid State ◽  
Binding Sites ◽  
Metal Ion ◽  
Antifungal Agents ◽  
Biological Function ◽  
Structural Diversity ◽  
Supramolecular Assemblies ◽  
Materials Chemistry ◽  
Interesting Application ◽  
Biological Potential

Interest in the synthesis of Bi(III) and Sb(III) dithiocarbamate complexes is on the rise, and this has been attributed to their wide structural diversity and their interesting application as biological agents and in solid state/materials chemistry. The readily available binding sites of the two sulphur atoms within the dithiocarbamate moiety in the complexes confers a wide variety of geometry and interactions that often leads to supramolecular assemblies. Although none of the bismuth or antimony metals are known to play any natural biological function, their dithiocarbamate complexes, however, have proven very useful as antibacterial, antileishmanial, anticancer, and antifungal agents. The dithiocarbamate ligands modulate the associated toxicity of the metals, especially antimony, since bismuth is known to be benign, allowing the metal ion to get to the targeted sites; hence, making it less available for side and other damaging reactions. This review presents a concise chemistry and some known biological potentials of their trivalent dithiocarbamate complexes.

scholarly journals New Perspectives on Thiamine Catalysis: From Enzymic to Biomimetic Catalysis

2007 ◽  
Vol 2007 ◽  
pp. 1-7 ◽  
Author(s):  
A. Stamatis ◽  
G. Malandrinos ◽  
M. Louloudi ◽  
N. Hadjiliadis
Keyword(s):  
Metal Ion ◽  
Enzymatic Reaction ◽  
Homogeneous System ◽  
Thiamine Pyrophosphate ◽  
Spectroscopic Techniques ◽  
Model Compounds ◽  
Bivalent Metal ◽  
X Ray ◽  
Structure Determinations ◽  
Heterogenous System

This paper is a brief review of the detailed mechanism of action of thiamine enzymes, based on metal complexes of bivalent transition and post-transition metals of model compounds, thiamine derivatives, synthesized and characterized with spectroscopic techniques and X-ray crystal structure determinations. It is proposed that the enzymatic reaction is initiated with a V conformation of thiamine pyrophosphate, imposed by the enzymic environment. Thiamine pyrophosphate is linked with the proteinic substrate through its pyrophosphate oxygens. In the course of the reaction, the formation of the “active aldehyde” intermediate imposes the S conformation to thiamine, while a bivalent metal ion may be linked through the N1' site of the molecule, at this stage. Finally, the immobilization of thiamine and derivatives on silica has a dramatic effect on the decarboxylation of pyruvic acid, reducing the time of its conversion to acetaldehyde from 330 minutes for the homogeneous system to less than 5 minutes in the heterogenous system.

scholarly journals Nucleases: diversity of structure, function and mechanism

2010 ◽  
Vol 44 (1) ◽  
pp. 1-93 ◽  
Author(s):  
Wei Yang
Keyword(s):  
Rna Splicing ◽  
Metal Ion ◽  
Catalytic Mechanism ◽  
Biological Function ◽  
Biological Process ◽  
Nutrient Regeneration ◽  
Phosphodiester Bonds ◽  
Recombination Repair ◽  
Cyclic Phosphate ◽  
Rna Maturation

AbstractNucleases cleave the phosphodiester bonds of nucleic acids and may be endo or exo, DNase or RNase, topoisomerases, recombinases, ribozymes, or RNA splicing enzymes. In this review, I survey nuclease activities with known structures and catalytic machinery and classify them by reaction mechanism and metal-ion dependence and by their biological function ranging from DNA replication, recombination, repair, RNA maturation, processing, interference, to defense, nutrient regeneration or cell death. Several general principles emerge from this analysis. There is little correlation between catalytic mechanism and biological function. A single catalytic mechanism can be adapted in a variety of reactions and biological pathways. Conversely, a single biological process can often be accomplished by multiple tertiary and quaternary folds and by more than one catalytic mechanism. Two-metal-ion-dependent nucleases comprise the largest number of different tertiary folds and mediate the most diverse set of biological functions. Metal-ion-dependent cleavage is exclusively associated with exonucleases producing mononucleotides and endonucleases that cleave double- or single-stranded substrates in helical and base-stacked conformations. All metal-ion-independent RNases generate 2′,3′-cyclic phosphate products, and all metal-ion-independent DNases form phospho-protein intermediates. I also find several previously unnoted relationships between different nucleases and shared catalytic configurations.

scholarly journals Recognition of Metal Ion Ligand-Binding Residues by Adding Correlation Features and Propensity Factors

2022 ◽  
Vol 12 ◽  
Author(s):  
Shuang Xu ◽  
Xiuzhen Hu ◽  
Zhenxing Feng ◽  
Jing Pang ◽  
Kai Sun ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Metal Ion ◽  
Biological Function ◽  
Structural Information ◽  
Basic Feature ◽  
Improved Method ◽  
Binding Residue ◽  
Protein Functions ◽  
Binding Residues ◽  
Correlation Information

The realization of many protein functions is inseparable from the interaction with ligands; in particular, the combination of protein and metal ion ligands performs an important biological function. Currently, it is a challenging work to identify the metal ion ligand-binding residues accurately by computational approaches. In this study, we proposed an improved method to predict the binding residues of 10 metal ion ligands (Zn2+, Cu2+, Fe2+, Fe3+, Co2+, Mn2+, Ca2+, Mg2+, Na+, and K+). Based on the basic feature parameters of amino acids, and physicochemical and predicted structural information, we added another two features of amino acid correlation information and binding residue propensity factors. With the optimized parameters, we used the GBM algorithm to predict metal ion ligand-binding residues. In the obtained results, the Sn and MCC values were over 10.17% and 0.297, respectively. Besides, the Sn and MCC values of transition metals were higher than 34.46% and 0.564, respectively. In order to test the validity of our model, another method (Random Forest) was also used in comparison. The better results of this work indicated that the proposed method would be a valuable tool to predict metal ion ligand-binding residues.

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