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Sökning: WFRF:(Alavi Fatemeh)

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1.
  • Senanayake, Indunil C., et al. (författare)
  • Fungal diversity notes 1611–1716: taxonomic and phylogenetic contributions on fungal genera and species emphasis in south China
  • 2023
  • Ingår i: Fungal Diversity. - 1560-2745 .- 1878-9129. ; 122, s. 161-403
  • Tidskriftsartikel (refereegranskat)abstract
    • This article is the 15th contribution in the Fungal Diversity Notes series, wherein 115 taxa from three phyla, nine classes, 28 orders, 48 families, and 64 genera are treated. Fungal taxa described and illustrated in the present study include a new family, five new genera, 61 new species, five new combinations, one synonym, one new variety and 31 records on new hosts or new geographical distributions. Ageratinicolaceae fam. nov. is introduced and accommodated in Pleosporales. The new genera introduced in this study are Ageratinicola, Kevinia, Pseudomultiseptospora (Parabambusicolaceae), Marasmiellomycena, and Vizzinia (Porotheleaceae). Newly described species are Abrothallus altoandinus, Ageratinicola kunmingensis, Allocryptovalsa aceris, Allophoma yuccae, Apiospora cannae, A. elliptica, A. pallidesporae, Boeremia wisteriae, Calycina papaeana, Clypeococcum lichenostigmoides, Coniochaeta riskali-shoyakubovii, Cryphonectria kunmingensis, Diaporthe angustiapiculata, D. campylandrae, D. longipapillata, Diatrypella guangdongense, Dothiorella franceschinii, Endocalyx phoenicis, Epicoccum terminosporum, Fulvifomes karaiensis, F. pannaensis, Ganoderma ghatensis, Hysterobrevium baoshanense, Inocybe avellaneorosea, I. lucida, Jahnula oblonga, Kevinia lignicola, Kirschsteiniothelia guangdongensis, Laboulbenia caprina, L. clavulata, L. cobiae, L. cosmodisci, L. nilotica, L. omalii, L. robusta, L. similis, L. stigmatophora, Laccaria rubriporus, Lasiodiplodia morindae, Lyophyllum agnijum, Marasmiellomycena pseudoomphaliiformis, Melomastia beihaiensis, Nemania guangdongensis, Nigrograna thailandica, Nigrospora ficuum, Oxydothis chinensis, O. yunnanensis, Petriella thailandica, Phaeoacremonium chinensis, Phialocephala chinensis, Phytophthora debattistii, Polyplosphaeria nigrospora, Pronectria loweniae, Seriascoma acutispora, Setoseptoria bambusae, Stictis anomianthi, Tarzetta tibetensis, Tarzetta urceolata, Tetraploa obpyriformis, Trichoglossum beninense, and Tricoderma pyrrosiae. We provide an emendation for Urnula ailaoshanensis Agaricus duplocingulatoides var. brevisporus introduced as a new variety based on morphology and phylogeny.
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2.
  • Alavi, Fatemeh Sadat, et al. (författare)
  • A novel mechanism of heme degradation to biliverdin studied by QM/MM and QM calculations
  • 2018
  • Ingår i: Dalton Transactions. - : Royal Society of Chemistry (RSC). - 1477-9226 .- 1477-9234. ; 47:25, s. 8283-8291
  • Tidskriftsartikel (refereegranskat)abstract
    • Heme degradation by heme oxygenase enzymes is important for maintaining iron homeostasis and prevention of oxidative stress. Previous studies have reported that heme degradation proceeds through three consecutive steps of O2 activation: the regiospecific self-hydroxylation of heme, the conversion of hydroxyheme to verdoheme and CO, and the cleavage of the verdoheme macrocycle to release biliverdin and free ferrous iron. Our results indicate that in the second step of heme degradation, not only verdoheme is generated but ring opening and biliverdin production also occur. We have performed QM-cluster and QM/MM calculations, which show that calculations with H2O as the axial ligand of Fe give the lowest barrier. In the QM-cluster calculation, the reaction is exothermic by -85 kcal mol-1 and the rate-limiting barrier is 5 kcal mol-1, whereas the corresponding QM/MM calculations give a slightly lower barrier of 3 kcal mol-1, owing to strong hydrogen bonds and the protein environment.
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3.
  • Alavi, Fatemeh Sadat, et al. (författare)
  • QM/MM study of the conversion of biliverdin into verdoheme by heme oxygenase
  • 2019
  • Ingår i: Theoretical Chemistry Accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 138:5
  • Tidskriftsartikel (refereegranskat)abstract
    • It has been shown that after production of oxophlorin, the first step of intermediate, both production of biliverdin and production of verdoheme occur simultaneously (Alavi et al. in Dalton Trans 47:8283–8291, 2018). So the mechanism that converts biliverdin into verdoheme is the subject of some controversy. The detailed conversion of verdoheme to biliverdin was demonstrated before by the Jerusalem group, using combined quantum mechanical and molecular mechanical (QM/MM) calculations. Conversion of iron biliverdin to iron verdoheme in the presence of H + was investigated using the B3LYP method and the def2-QZVP basis set, considering dispersion effects with the DFT-D3 approach, obtaining accurate energies with large QM regions of almost 1000 atoms. Two spin states, singlet and triplet, were considered for the conversion of biliverdin to verdoheme. The reactant and product are triplet and singlet in their ground states, respectively. The potential energy surface suggests that a spin inversion takes place during the course of reaction after TS2. The ring closing process is exothermic by 5.8 kcal/mol with a kinetic barrier of 16.5 kcal/mol. The activation barrier for removing OH from the ring to produce iron verdoheme is estimated to be 23.2 kcal/mol.
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4.
  • Alavi, Fatemeh Sadat, et al. (författare)
  • QM/MM Study of the Conversion of Oxophlorin into Verdoheme by Heme Oxygenase
  • 2017
  • Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 121:51, s. 11427-11436
  • Tidskriftsartikel (refereegranskat)abstract
    • Heme oxygenase is an enzyme that degrades heme, thereby recycling iron in most organisms, including humans. Pervious density functional theory (DFT) calculations have suggested that iron(III) hydroxyheme, an intermediate generated in the first step of heme degradation by heme oxygenase, is converted to iron(III) superoxo oxophlorin in the presence of dioxygen. In this article, we have studied the detailed mechanism of conversion of iron(III) superoxo oxophlorin to verdoheme by using combined quantum mechanics and molecular mechanics (QM/MM) calculations. The calculations employed the B3LYP method and the def2-QZVP basis set, considering dispersion effects with the DFT-D3 approach, obtaining accurate energies with large QM regions of almost 1000 atoms. The reaction was found to be exothermic by -35 kcal/mol, with a rate-determining barrier of 19 kcal/mol in the doublet state. The protein environment and especially water in the enzyme pocket significantly affects the reaction by decreasing the reaction activation energies and changing the structures by providing strategic hydrogen bonds.
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5.
  • Jafari, Sonia, et al. (författare)
  • Quantum Mechanics/Molecular Mechanics Study of the Reaction Mechanism of Glyoxalase I
  • 2020
  • Ingår i: Inorganic Chemistry. - : American Chemical Society (ACS). - 1520-510X .- 0020-1669. ; 59, s. 2594-2603
  • Tidskriftsartikel (refereegranskat)abstract
    • Glyoxalase I (GlxI) is a member of the glyoxalasesystem, which is important in cell detoxification and convertshemithioacetals of methylglyoxal (a cytotoxic byproduct of sugarmetabolism that may react with DNA or proteins and introducenucleic acid strand breaks, elevated mutation frequencies, andstructural or functional changes of the proteins) and glutathioneinto D-lactate. GlxI accepts both the S and R enantiomers ofhemithioacetal, but converts them to only the S-D enantiomer oflactoylglutathione. Interestingly, the enzyme shows this unusualspecificity with a rather symmetric active site (a Zn ioncoordinated to two glutamate residues; Glu-99 and Glu-172),making the investigation of its reaction mechanism challenging.Herein, we have performed a series of combined quantummechanics and molecular mechanics calculations to study the reaction mechanism of GlxI. The substrate can bind to the enzyme in two different modes, depending on the direction of its alcoholic proton (H2; toward Glu-99 or Glu-172). Our results show that the S substrate can react only if H2 is directed toward Glu-99 and the R substrate only if H2 is directed toward Glu-172. In both cases, the reactions lead to the experimentally observed S-D enantiomer of the product. In addition, the results do not show any low- energy paths to the wrong enantiomer of the product from neither the S nor the R substrate. Previous studies have presented several opposing mechanisms for the conversion of R and S enantiomers of the substrate to the correct enantiomer of the product. Our results confirm one of them for the S substrate, but propose a new one for the R substrate.
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  • Resultat 1-5 av 5

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