QM study of carbon dioxide (CO2) and carbonyl sulfide (COS) degradation by cluster model of Carbonic anhydrase enzyme

Ghiasi, Mina; Gholami, Samira; Nasiri, Samira

doi:10.1016/j.comptc.2021.113188

Cited by 2 publications

(2 citation statements)

References 77 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Historical differences in opinion arise in part from the advancement of computational resources over time. Initial studies from the 1990s were limited to minimal 18-33 atom quantum mechanical-cluster (QM-cluster) models of only the metal-coordinated atoms and CO 2 [26,35,36], but modeling capabilities have since grown to include simulating the surrounding protein and water environment through both larger QM-cluster models [19,24,37,38] and hybrid quantum mechanical/molecular mechanics (QM/MM) models [27,34,38,39]. Although many QM-only and recent QM/MM models propose the Lindskog path to be the energetically favored mechanism, thermodynamic differences between the two paths are frequently noted to be miniscule and that both paths may be competitive with each other [26,27,[35][36][37]39].…”

Section: Introductionmentioning

confidence: 99%

QM-cluster model study of CO₂ hydration mechanisms in metal-substituted human carbonic anhydrase II

Summers¹,

DeYonker²

2023

Electron. Struct.

View full text Add to dashboard Cite

Human carbonic anhydrase (CA) metalloenzymes utilize a Zn2+-containing active site to catalyze the interconversion of carbon dioxide to bicarbonate. The Zn2+ may be replaced with other divalent transition metals, though the catalytic efficiency of the enzyme will be reduced. In this work, quantum mechanical cluster models of the active site are used to map the reaction profile for the hydration mechanism of carbon dioxide. The Lipscomb proton transfer and Lindskog rotation mechanisms were examined for the native Zn2+-enzyme along with variants where the metal was substituted with Cd2+, Ni2+, Fe2+, and Fe3+. The findings highlight the impact the metal coordination geometry has on the reaction profile. The results also suggest Fe2+, which is the functional metal for a prototypical CA of an anaerobic bacterium, might also be functional for human CA if cultured within an anaerobic environment.

show abstract

Section: Introductionmentioning

confidence: 99%

QM-cluster model study of CO₂ hydration mechanisms in metal-substituted human carbonic anhydrase II

Summers¹,

DeYonker²

2023

Electron. Struct.

View full text Add to dashboard Cite

show abstract

“…Carbonic anhydrase (EC 4.2.1.1., CA) is a PH regulator and metabolic enzyme in all forms of life which catalyzes the reversible hydration of carbon dioxide to bicarbonate and a proton, Eq. 1 and 2 [1][2][3][4][5].…”

Section: Introductionmentioning

confidence: 99%

QM and QM/MM study on inhibition mechanism of polyphenolic compounds as non-classical inhibitors of α-human carbonic anhydrase (II)

et al. 2021

Self Cite

View full text Add to dashboard Cite

Phenolic and polyphenolic compounds are distributed in plant tissues as a secondary metabolite which are compromised in multiple and imperative physiological phenomena. Herein, inhibition mechanism of human carbonic anhydrase isoform II, hCAII, with seven phenolic compounds including phenol, catechol, resorcinol, 4-methyl catechol, vanillic acid, trans-cinnamic acid and ortho-coumaric acid has been investigated using quantum mechanical and ONIOM calculations. B3LYP-D3/6-311++G** method has been employed to calculate the electronic structure and electronic energy of different species through the reaction mechanism path. The model system of hCAVII has been used that includes the core of the catalytic center, Zn 2+ , binds to three histidine residues and a hydroxide ion or water molecule forming a first coordination shell. Thr199 and Glu106 were considered as neighboring residues to the ones binding zinc. All thermodynamic functions through the reaction path are evaluated in different phases. The calculated results indicate that all phenolic inhibitors do not directly interact with the zinc ion in the CA active center, and the presence of aromatic moieties was associated with more effective inhibition. In addition, the implicit and explicit solvent effect has been considered for water solvent using QM and ONIOM (QM/MM) calculations.

show abstract

QM study of carbon dioxide (CO2) and carbonyl sulfide (COS) degradation by cluster model of Carbonic anhydrase enzyme

Cited by 2 publications

References 77 publications

QM-cluster model study of CO₂ hydration mechanisms in metal-substituted human carbonic anhydrase II

QM-cluster model study of CO₂ hydration mechanisms in metal-substituted human carbonic anhydrase II

QM and QM/MM study on inhibition mechanism of polyphenolic compounds as non-classical inhibitors of α-human carbonic anhydrase (II)

Contact Info

Product

Resources

About

QM study of carbon dioxide (CO2) and carbonyl sulfide (COS) degradation by cluster model of Carbonic anhydrase enzyme

Cited by 2 publications

References 77 publications

QM-cluster model study of CO2 hydration mechanisms in metal-substituted human carbonic anhydrase II

QM-cluster model study of CO2 hydration mechanisms in metal-substituted human carbonic anhydrase II

QM and QM/MM study on inhibition mechanism of polyphenolic compounds as non-classical inhibitors of α-human carbonic anhydrase (II)

Contact Info

Product

Resources

About

QM-cluster model study of CO₂ hydration mechanisms in metal-substituted human carbonic anhydrase II

QM-cluster model study of CO₂ hydration mechanisms in metal-substituted human carbonic anhydrase II