Electronic structures and energetic of metal(II)-superoxo species: a DFT exploration

Monika, .; Ansari, Azaj

doi:10.1007/s11224-022-02030-x

Cited by 7 publications

(2 citation statements)

References 69 publications

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“…In this way, the electronic energies, Eel, of the optimized systems were obtained. According to previous studies, the B3LYP/6-31G(3d,p) level of theory represents a good balance between accuracy and computational resources for obtaining the necessary structural and thermodynamic parameters for the systems representing biological systems with metal dications, such as Zn 2+ , Cu 2+ , Co 2+ , and Mn 2+ and metal-ion hydration [ 48 , 53 , 54 , 55 , 56 , 57 ]. Each metal complex was optimized in the gas phase, with the methyl groups capping the models of constrained amino acid residues.…”

Section: Methodsmentioning

confidence: 99%

Identification of an Additional Metal-Binding Site in Human Dipeptidyl Peptidase III

Matić

Šupljika

Brkić

et al. 2023

IJMS

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Dipeptidyl peptidase III (DPP III, EC 3.4.14.4) is a monozinc metalloexopeptidase that hydrolyzes dipeptides from the N-terminus of peptides consisting of three or more amino acids. Recently, DPP III has attracted great interest from scientists, and numerous studies have been conducted showing that it is involved in the regulation of various physiological processes. Since it is the only metalloenzyme among the dipeptidyl peptidases, we considered it important to study the process of binding and exchange of physiologically relevant metal dications in DPP III. Using fluorimetry, we measured the Kd values for the binding of Zn2+, Cu2+, and Co2+ to the catalytic site, and using isothermal titration calorimetry (ITC), we measured the Kd values for the binding of these metals to an additional binding site. The structure of the catalytic metal’s binding site is known from previous studies, and in this work, the affinities for this site were calculated for Zn2+, Cu2+, Co2+, and Mn2+ using the QM approach. The structures of the additional binding sites for the Zn2+ and Cu2+ were also identified, and MD simulations showed that two Cu2+ ions bound to the catalytic and inhibitory sites exchanged less frequently than the Zn2+ ions bound to these sites.

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Section: Methodsmentioning

confidence: 99%

Identification of an Additional Metal-Binding Site in Human Dipeptidyl Peptidase III

Matić

Šupljika

Brkić

et al. 2023

IJMS

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“…We selected this ligand for our study because several metal complexes have been reported with TMC ligands. [71][72][73] O⋯O bond cleavage in metal hydroperoxo species leads to the formation of metal-oxo species. 66 In this work, the formation of 3d metal-oxo (Cr-Cu) species and a comparative study among them have been carried out, and we have tried to figure out what are the driving factors for the formation of the "Oxo Wall".…”

Section: Introductionmentioning

confidence: 99%

Theoretical study of the formation of metal–oxo species of the first transition series with the ligand 14-TMC: driving factors of the “Oxo Wall”

Monika,

Kumar,

Somi

et al. 2023

Dalton Trans.

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DFT and TDDFT exploration on the role of pyridyl ligands with copper toward bonding aspects and light harvesting

Ahmed,

Gupta,

Ansari

2023

J Mol Model

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Electronic structures and energetic of metal(II)-superoxo species: a DFT exploration

Cited by 7 publications

References 69 publications

Identification of an Additional Metal-Binding Site in Human Dipeptidyl Peptidase III

Identification of an Additional Metal-Binding Site in Human Dipeptidyl Peptidase III

Theoretical study of the formation of metal–oxo species of the first transition series with the ligand 14-TMC: driving factors of the “Oxo Wall”

DFT and TDDFT exploration on the role of pyridyl ligands with copper toward bonding aspects and light harvesting

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