958 results on '"Enzyme model"'
Search Results
2. Modeling Type‐1 Iodothyronine Deiodinase with Peptide‐Based Aliphatic Diselenides: Potential Role of Highly Conserved His and Cys Residues as a General Acid Catalyst.
- Author
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Arai, Kenta, Toba, Haruka, Yamamoto, Nozomi, Ito, Mao, and Mikami, Rumi
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ACID catalysts , *CHEMICAL properties , *SULFHYDRYL group , *SCISSION (Chemistry) , *ATOMS - Abstract
Type‐1 iodothyronine deiodinase (ID‐1) catalyzes the reductive elimination of 5'‐I and 5‐I on the phenolic and tyrosyl rings of thyroxine (T4), respectively. Chemically verifying whether I atoms with different chemical properties undergo deiodination through a common mechanism is challenging. Herein, we report the modeling of ID‐1 using aliphatic diselenide (Se‐Se) and selenenylsulfide (Se‐S) compounds. Mechanistic investigations of deiodination using the ID‐1‐like reagents suggested that the 5'‐I and 5‐I deiodinations proceed via the same mechanism through an unstable intermediate containing a Se⋅⋅⋅I halogen bond between a selenolate anion, reductively produced from Se‐Se (or Se‐S) in the compound, and an I atom in T4. Moreover, imidazolium and thiol groups, which may act as general acid catalysts, promoted the heterolytic cleavage of the C‐I bond in the Se⋅⋅⋅I intermediate, which is the rate‐determining step, by donating a proton to the C atom. [ABSTRACT FROM AUTHOR]
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- 2023
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3. Synthesis of Poly(aromatic)s II: Enzyme-Model Complexes as Catalyst
- Author
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Higashimura, Hideyuki, He, Liang-Nian, Series Editor, Rogers, Robin D., Series Editor, Su, Dangsheng, Series Editor, Tundo, Pietro, Series Editor, Zhang, Z. Conrad, Series Editor, Kobayashi, Shiro, editor, Uyama, Hiroshi, editor, and Kadokawa, Jun-ichi, editor
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- 2019
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4. A Facially Coordinating Tris‐Benzimidazole Ligand for Nonheme Iron Enzyme Models.
- Author
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Gunasekera, Parami S., Abhyankar, Preshit C., MacMillan, Samantha N., and Lacy, David C.
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IRON , *ENZYMES , *OXYGENASES - Abstract
Herein, we report a new tripodal tris‐benzimidazole ligand (Tbim) that structurally mimics the 3‐His coordination environment of certain nonheme mononuclear iron oxygenases. The coordination chemistry of Tbim was explored with iron(II) revealing a diverse set of coordination modes. The aerobic oxidation of biomimetic model substrate diethyl‐2‐phenylmalonate was studied using the Tbim−Fe and Fe(OTf)2. [ABSTRACT FROM AUTHOR]
- Published
- 2021
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5. A new structural model for NiFe hydrogenases: an unsaturated analogue of a classic hydrogenase model leads to more enzyme-like Ni—Fe distance and interplanar fold
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Daniel J. Harrison, Alan J. Lough, and Ulrich Fekl
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crystal structure ,NiFe hydrogenase ,enzyme model ,bioinorganic ,sulfur ligand ,Crystallography ,QD901-999 - Abstract
The complex cation in the title compound, (carbonyl-1κC)(1η5-pentamethylcyclopentadienyl)(μ-2,3,9,10-tetramethyl-1,4,8,11-tetrathiaundeca-2,9-diene-1,11-diido-1κ2S,S′′′:2κ4S,S′,S′′,S′′′)ironnickel(Fe—Ni) hexafluorophosphate, [FeNi(C10H15)(C11H18S4)(CO)]PF6 or [Ni(L′)FeCp*(CO)]PF6, is composed of the nickel complex fragment [Ni(L′)] coordinated as a metalloligand (using S1 and S4) to the [FeCp*(CO)]+ fragment, where (L′)2− is [S—C(Me)=C(Me)—S—(CH2)3—S—C(Me)=C(Me)—S]2− and where Cp*− is cyclo-C5(Me)5− (pentamethylcyclopentadienyl). The ratio of hexafluorophosphate anion per complex cation is 1:1. The structure at 150 K has orthorhombic (Pbcn) symmetry. The atoms of the complex cation are located on general positions (multiplicity = 8), whereas there are two independent hexafluorophosphate anions, each located on a twofold axis (Wyckoff position 4c; multiplicity = 4). The structure of the new dimetallic cation [Ni(L′)FeCp*(CO)]+ can be described as containing a three-legged piano-stool environment for iron [Cp*Fe(CO)`S2'] and an approximately square-planar `S4' environment for Ni. The NiS2Fe diamond-shaped substructure is notably folded at the S—S hinge: the angle between the NiS2 plane and the FeS2 plane normals is 64.85 (6)°. Largely because of this fold, the nickel–iron distance is relatively short, at 2.9195 (8) Å. The structural data for the complex cation, which contains a new unsaturated `S4' ligand (two C=C double bonds), provide an interesting comparison with the known NiFe hydrogenase models containing a saturated `S4'-ligand analogue having the same number of carbon atoms in the ligand backbone, namely with the structures of [Ni(L)FeCp(CO)]+ (as the PF6− salt, CH2Cl2 solvate) and [Ni(L)FeCp*(CO)]+ (as the PF6− salt), where (L)2− is [S—CH2—CH2—S—(CH2)3—S—CH2—CH2—S]2− and Cp− is cyclopentadienyl. The saturated analogues [Ni(L)FeCp(CO)]+ and [Ni(L)FeCp*(CO)]+ have similar Ni—Fe distances: 3.1727 (6), 3.1529 (7) Å (two independent molecules in the unit cell) and 3.111 (5) Å, respectively, for the two complexes, whereas [Ni(L′)FeCp*(CO)]+ described here stands out with a much shorter Ni—Fe distance [2.9196 (8) Å]. Also, [Ni(L)FeCp(CO)]+ and [Ni(L)FeCp*(CO)]+ show interplanar fold angles that are similar between the two: 39.56 (5), 41.99 (5) (independent molecules in the unit cell) and 47.22 (9) °, respectively, whereas [Ni(L′)FeCp*(CO)]+ possesses a much more pronounced fold [64.85 (6)°]. Given that larger fold angles and shorter Ni—Fe distances are considered to be structurally closer to the enzyme, unsaturation in an `S4'-ligand of the type (S—C2—S—C3—S—C2—S)2− seems to increase structural resemblance to the enzyme for structural models of the type [Ni(`S4')FeCpR(CO)]+ (CpR = Cp or Cp*).
- Published
- 2018
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6. Basic Amino Acid Conjugates of 1,2‐Diselenan‐4‐amine with Protein Disulfide Isomerase‐like Functions as a Manipulator of Protein Quality Control.
- Author
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Tsukagoshi, Shunsuke, Mikami, Rumi, and Arai, Kenta
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ISOMERASES , *AMINO acids , *PROTEIN disulfide isomerase , *QUALITY control , *AMINO acid sequence , *PROTEINS , *HISTIDINE - Abstract
Protein disulfide isomerase (PDI) can assist immature proteins to correctly fold by controlling cysteinyl disulfide (SS)‐relating reactions (i. e. SS‐formation, SS‐cleavage, and SS‐isomerization). PDI controls protein quality by suppressing protein aggregation, as well as functions as an oxidative folding catalyst. Following the amino acid sequence of the active center in PDI, basic amino acid conjugates of 1,2‐diselenan‐4‐amine (1), which show oxidoreductase‐ and isomerase‐like activities for SS‐relating reactions, were designed as a novel PDI model compound. By conjugating the amino acids, the diselenide reduction potential of compound 1 was significantly increased, causing improvement of the catalytic activities for all SS‐relating reactions. Furthermore, these compounds, especially histidine‐conjugated one, remarkably suppressed protein aggregation even at low concertation (0.3 mM∼). Thus, it was demonstrated that the conjugation of basic amino acids into 1 simultaneously achieves the enhancement of the redox reactivity and the capability to suppress protein aggregation. [ABSTRACT FROM AUTHOR]
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- 2020
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7. Abnormal Enhancement of Protein Disulfide Isomerase-like Activity of a Cyclic Diselenide Conjugated with a Basic Amino Acid by Inserting a Glycine Spacer
- Author
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Rumi Mikami, Shunsuke Tsukagoshi, and Kenta Arai
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oxidative folding ,enzyme model ,selenium ,aggregation ,chaperone ,catalyst ,Biology (General) ,QH301-705.5 - Abstract
In a previous study, we reported that (S)-1,2-diselenane-4-amine (1) catalyzes oxidative protein folding through protein disulfide isomerase (PDI)-like catalytic mechanisms and that the direct conjugation of a basic amino acid (Xaa: His, Lys, or Arg) via an amide bond improves the catalytic activity of 1 by increasing its diselenide (Se–Se) reduction potential (E′°). In this study, to modulate the Se–Se redox properties and the association of the compounds with a protein substrate, new catalysts, in which a Gly spacer was inserted between 1 and Xaa, were synthesized. Exhaustive comparison of the PDI-like catalytic activities and E′° values among 1, 1-Xaa, and 1-Gly-Xaa showed that the insertion of a Gly spacer into 1-Xaa either did not change or slightly reduced the PDI-like activity and the E′° values. Importantly, however, only 1-Gly-Arg deviated from this generality and showed obviously increased E°′ value and PDI-like activity compared to the corresponding compound with no Gly spacer (1-Arg); on the contrary, its catalytic activity was the highest among the diselenide compounds employed in this study, while this abnormal enhancement of the catalytic activity of 1-Gly-Arg could not be fully explained by the thermodynamics of the Se–Se bond and its association ability with protein substrates.
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- 2021
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8. Nanoenzymes as Selenoprotein Mimics
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Huang, Xin, Yin, Xianzhen, Xu, Jiayun, Liu, Junqiu, Liu, Junqiu, Luo, Guimin, and Mu, Ying
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- 2012
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9. Oxido-alcoholato/thiolato-molybdenum(VI) complexes with a dithiolene ligand generated by oxygen atom transfer to the molybdenum(IV) complexes.
- Author
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Sugimoto, Hideki, Sato, Masanori, Asano, Kaoru, Suzuki, Takeyuki, Ogura, Takashi, and Itoh, Shinobu
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MOLYBDENUM , *OXYGEN atom transfer reactions , *X-ray crystallography , *STEREOCHEMISTRY , *SULFOXIDES - Abstract
Graphical abstract Oxido-alcoholato- and oxido-thiolato-molybdenum(VI) complexes are prepared by oxygen atom transfer reaction to the molybdenum(IV) complexes. The reactivity of the thiolate complex is higher than that of the alcoholate complex. Abstract Oxido-alcoholato- and oxido-thiolato-molybdenum(VI) complexes bearing two ene-1,2-dithiolate ligands (cyclohexene-1,2-dithiolate) are prepared as synthetic models of molybdenum(VI) reaction centers of dimethyl sulfoxide reductase family of molybdenum enzymes. These complexes are prepared by oxygen atom transfer from tertiary amine N -oxide (trimethylamine N -oxide and N,N -dimethylaniline N -oxide) to the five-coordinate alcoholato- and thiolato-molybdenum(IV) complexes, and are characterized by UV–vis, cold-spray-ionization mass, resonance Raman, and 1H NMR spectroscopies. The oxygen atom transfer reactions are studied kinetically at a low temperature (−40 °C) to demonstrate that the reactivity of the thiolato-molybdenum(IV) complex is higher than that of alcoholato-molybdenum(IV) complex by about 7 times, and that the oxygen atom transfer reactivity increases with increasing the electron withdrawing ability of the p -substituent of N , N -dimethylaniline N -oxide derivatives. Mechanistic details are discussed based on the reactivity studies. [ABSTRACT FROM AUTHOR]
- Published
- 2019
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10. Bifurcation Analysis and Chaos Control for a Discrete-Time Enzyme Model.
- Author
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Din, Qamar and Iqbal, Muhammad Asad
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ENZYMES , *MATHEMATICAL models , *FEEDBACK control systems , *CATALYSTS , *AUTOMATIC control systems - Abstract
Basically enzymes are biological catalysts that increase the speed of a chemical reaction without undergoing any permanent chemical change. With the application of Euler's forward scheme, a discrete-time enzyme model is presented. Further investigation related to its qualitative behaviour revealed that discrete-time model shows rich dynamics as compared to its continuous counterpart. It is investigated that discrete-time model has a unique trivial equilibrium point. The local asymptotic behaviour of equilibrium is discussed for discrete-time enzyme model. Furthermore, with the help of the bifurcation theory and centre manifold theorem, explicit parametric conditions for directions and existence of flip and Hopf bifurcations are investigated. Moreover, two existing chaos control methods, that is, Ott, Grebogi and Yorke feedback control and hybrid control strategy, are implemented. In particular, a novel chaos control technique, based on state feedback control is introduced for controlling chaos under the influence of flip and Hopf bifurcations in discrete-time enzyme model. Numerical simulations are provided to illustrate theoretical discussion and effectiveness of newly introduced chaos control method. [ABSTRACT FROM AUTHOR]
- Published
- 2019
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11. Catalyzed and Electrocatalyzed Oxidation of l-Tyrosine and l-Phenylalanine to Dopachrome by Nanozymes.
- Author
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Jianwen Hou, Vázquez-González, Margarita, Fadeev, Michael, Xia Liu, Lavi, Ronit, and Willner, Itamar
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TYROSINE , *PHENYLALANINE , *CATALYSIS , *AQUEOUS solutions , *OXIDATION - Abstract
Catalyzed oxygen insertion into C-H bonds represents a continuous challenge in chemistry. Particularly, driving this process at ambient temperature and aqueous media represents a "holy grail" in catalysis. We report on the catalyzed cascade transformations of l-tyrosine or l-phenylalanine to dopachrome in the presence of l-ascorbic acid/H2O2 as oxidizing mixture and CuFe-Prussian Blue-like nanoparticles, Fe3O4 nanoparticles or Au nanoparticles as catalysts. The process involves the primary transformation of l-tyrosine to l-DOPA that is further oxidized to dopachrome. The transformation of l-phenylalanine to dopachrome in the presence of CuFe-Prussian Blue-like nanoparticles and l-ascorbic acid/H2O2 involves in the first step the formation of l-tyrosine and, subsequently, the operation of the catalytic oxidation cascade of l-tyrosine to l-DOPA and dopachrome. Electron spin resonance experiments demonstrate that ascorbate radicals and hydroxyl radicals play cooperative functions in driving the different oxygen-insertion processes. In addition, the aerobic elecrocatalyzed oxidation of l-tyrosine to dopachrome in the presence of naphthoquinone-modified Fe3O4 nanoparticles and l-ascorbic acid is demonstrated. In this system, magnetic-field attraction of the naphthoquinone-modified Fe3O4 nanoparticles onto the electrode allows the quinone-mediated electrocatalyzed reduction of O2 to H2O2 (bias potential -0.5 V vs SCE). The electrogenerated H2O2 is then utilized to promote the transformation of l-tyrosine to dopachrome in the presence of l-ascorbic acid and Fe3O4 catalyst. [ABSTRACT FROM AUTHOR]
- Published
- 2018
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12. Challenges in the Synthesis of Active Site Mimics for [NiFe]-Hydrogenases
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Thomas B. Rauchfuss, Giuseppe Zampella, Federica Arrigoni, Danielle L. Gray, Debashis Basu, Toby J. Woods, Basu, D, Gray, D, Woods, T, Rauchfuss, T, Arrigoni, F, and Zampella, G
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Ni ,CHIM/03 - CHIMICA GENERALE ED INORGANICA ,Hydrogenase ,biology ,Stereochemistry ,Chemistry ,Organic Chemistry ,Active site ,Fe ,DFT ,Inorganic Chemistry ,nickel ,iron ,hydrogen ,biology.protein ,enzyme model ,organometallic compound ,Physical and Theoretical Chemistry - Abstract
One of the more active areas in bioorganometallic chemistry is the preparation and reactivity studies of active site mimics of the [NiFe]-hydrogenases. One area of particular recent progress involves reactions that interconvert Ni(μ-X)Fe centers for X = OH, H, CO, as described by Song et al. Such reactions illustrate new ways to access intermediates related to the Ni-R and Ni-SI states of the enzyme. Most models are derivatives of the type (diphosphine)Ni(SR)2Fe(CO)3-n(PR′3)n. In recent work, the methodology has been generalized to include FeII(diphosphine) derivatives of Ni(N2S2), where N2S22- is the tetradentate diamine-dithiolate (CH2N(CH3)CH2CH2S-)2. Indeed, models based on Ni(N2S2) have proven valuable, but these studies also highlight challenges in working with heterobimetallic complexes, specifically the tendency of some such Ni-Fe complexes to convert to homometalliic Ni-Ni derivatives. This kind of problem is not readily detected by X-ray crystallography. With this caution in mind, we argue that one series of complexes recently described in this journal are almost certainly misassigned.
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- 2021
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13. Cheminformatic quantum mechanical enzyme model design: A catechol-O-methyltransferase case study
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Diem-Trang Pham, Qianyi Cheng, Thomas J. Summers, Nathan J. DeYonker, Dudley K. Kelso, Manuel A. Palma, and Charles Edwin Webster
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biology ,Chemistry ,Cheminformatics ,Biophysics ,Active site ,Articles ,Crystal structure ,Catechol O-Methyltransferase ,Residue (chemistry) ,Computational chemistry ,Interaction network ,Catalytic Domain ,Enzyme model ,Convergence (routing) ,Solvents ,biology.protein ,Quantum Theory ,Quantum - Abstract
To accurately simulate the inner workings of an enzyme active site with quantum mechanics (QM), not only must the reactive species be included in the model but also important surrounding residues, solvent, or coenzymes involved in crafting the microenvironment. Our lab has been developing the Residue Interaction Network Residue Selector (RINRUS) toolkit to utilize interatomic contact network information for automated, rational residue selection and QM-cluster model generation. Starting from an x-ray crystal structure of catechol-O-methyltransferase, RINRUS was used to construct a series of QM-cluster models. The reactant, product, and transition state of the methyl transfer reaction were computed for a total of 550 models, and the resulting free energies of activation and reaction were used to evaluate model convergence. RINRUS-designed models with only 200–300 atoms are shown to converge. RINRUS will serve as a cornerstone for improved and automated cheminformatics-based enzyme model design.
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- 2021
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14. Dioxygen Activation and Pyrrole α‐Cleavage with Calix[4]pyrrolato Aluminates: Enzyme Model by Structural Constraint
- Author
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Lukas M. Sigmund, Markus Enders, Lutz Greb, Jürgen Graf, Christopher Ehlert, and Ganna Gryn'ova
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Models, Molecular ,intersystem crossing ,Cooperativity ,O2 Activation | Hot Paper ,dioxygen activation ,010402 general chemistry ,Photochemistry ,01 natural sciences ,Catalysis ,chemistry.chemical_compound ,Phenols ,Pyrroles ,Singlet state ,Triplet state ,Bond cleavage ,Research Articles ,Density Functional Theory ,Pyrrole ,Flavoproteins ,Molecular Structure ,010405 organic chemistry ,Ligand ,Chemistry ,metal–ligand cooperativity ,General Chemistry ,0104 chemical sciences ,Oxygen ,structural constraint ,Intersystem crossing ,Enzyme model ,aluminum ,Calixarenes ,Research Article - Abstract
The present work describes the reaction of triplet dioxygen with the porphyrinogenic calix[4]pyrrolato aluminates to alkylperoxido aluminates in high selectivity. Multiconfigurational quantum chemical computations disclose the mechanism for this spin‐forbidden process. Despite a negligible spin–orbit coupling constant, the intersystem crossing (ISC) is facilitated by singlet and triplet state degeneracy and spin–vibronic coupling. The formed peroxides are stable toward external substrates but undergo an unprecedented oxidative pyrrole α‐cleavage by ligand aromatization/dearomatization‐initiated O−O σ‐bond scission. A detailed comparison of the calix[4]pyrrolato aluminates with dioxygen‐related enzymology provides insights into the ISC of metal‐ or cofactor‐free enzymes. It substantiates the importance of structural constraint and element–ligand cooperativity for the functions of aerobic life., The reaction of triplet dioxygen with closed shell molecules is formally spin‐forbidden. Nature overcomes this prohibition by a variety of enzymes. The surprising reactivity of calix[4]pyrrolato aluminate with O2 is described and the spin‐inversion process is analyzed. The square‐planar aluminates transpire as enzyme models that substantiate the critical role of metal–ligand cooperativity and structural constraint for the functions of aerobic life.
- Published
- 2021
15. Toward Diiron Dithiolato Biomimetics with Rotated Conformation of the [FeFe]-Hydrogenase Active Site: A DFT Case Study on Electron-Rich, Isocyanide-Based Scaffolds
- Author
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Arrigoni, F, Rizza, F, Bertini, L, De Gioia, L, Zampella, G, Arrigoni F., Rizza F., Bertini L., De Gioia L., Zampella G., Arrigoni, F, Rizza, F, Bertini, L, De Gioia, L, Zampella, G, Arrigoni F., Rizza F., Bertini L., De Gioia L., and Zampella G.
- Abstract
The electron rich Fe2(pdt)(RNC)6 1 (pdt=CH2(CH2S−)2) has been used as starting point for a DFT multi-functional study to assess the feasibility of designing a stable inverted (or rotated) disposition of the two FeL3 pyramidal moieties in the dimetallic core, a key feature of [FeFe]-hydrogenase cofactor. The choice of 1 was motivated by the presence of a rotated form in solution, slightly less stable than the unrotated stereoisomer. Aimed to find an upgraded version of 1, featuring the rotated isomer as ground state, various combinations of factors have been tested, for their effect on the relative stability of rotated vs unrotated isomers. The general result is that combining coordination asymmetry, electron donor presence and isocyanides R substituents able to establish intramolecular interactions is effective in stabilizing the rotated isomer. Our DFT study may inspire the design of synthetic biomimetics, with improved resemblance to the natural system.
- Published
- 2022
16. Glutathione Peroxidase-Like Activity of Amino-Substituted Water-Soluble Cyclic Selenides: A Shift of the Major Catalytic Cycle in Methanol.
- Author
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Kenta Arai, Ayako Tashiro, Yuui Osaka, and Michio Iwaoka
- Subjects
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GLUTATHIONE peroxidase , *WATER-soluble polymers , *SELENIDES , *CATALYTIC activity , *METHANOL , *PROTON sources - Abstract
We previously reported that water-soluble cyclic selenides can mimic the antioxidative function of glutathione peroxidase (GPx) in water through a simple catalytic cycle, in which the selenide (>Se) is oxidized by H2O2 to the selenoxide (>Se=O) and the selenoxide is reduced by a thiol back to the selenide. In methanol, however, the GPx-like activity could not be explained by this simple scenario. To look into the reasons for the unusual behaviors in methanol, monoamino-substituted cyclic selenides with a variable ring size were synthesized, and the intermediates of the catalytic cycle were characterized by means of 77Se-NMR and LC-MS spectroscopies. In water, it was confirmed that the selenide and the selenoxide mainly contribute to the antioxidative function, though a slight contribution from the dihydroxy selenane (>Se(OH)2) was also suggested. In methanol, on the other hand, other active species, such as hydroxyselenonium (>Se+-OH) and hydroxy perhydroxy selenane (>Se(OH)(OOH)), could be generated to build another catalytic cycle. This over-oxidation would be more feasible for amino-substituted cyclic selenides, probably because the ammonium (NH3+) group would transfer a proton to the selenoxide moiety to produce a hydroxyselenonium species in the absence of an additional proton source. Thus, a shift of the major catalytic cycle in methanol would make the GPx-like antioxidative function of selenides perplexing. [ABSTRACT FROM AUTHOR]
- Published
- 2017
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17. Thiamine-Appended Cyclodextrin Dimer as a Ligase Model
- Author
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Ikeda, H., Horimoto, Y., Nakata, M., Ueno, A., Labandeira, J. J. Torres, editor, and Vila-Jato, J. L., editor
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- 1999
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18. An Enzyme Model Which Mimics Chymotrypsin and N-Terminal Hydrolases
- Author
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Luis Simón, Francisca Sanz, M.M. Iglesias Aparicio, Á.L. Fuentes De Arriba, Joaquín R. Morán, José J. Garrido-González, and M.M. García
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chemistry.chemical_classification ,Chymotrypsin ,biology ,010405 organic chemistry ,General Chemistry ,010402 general chemistry ,01 natural sciences ,Combinatorial chemistry ,Catalysis ,0104 chemical sciences ,Enzyme ,chemistry ,Transition state analog ,Organocatalysis ,Enzyme model ,biology.protein ,Enzyme mimic ,Oxyanion hole - Abstract
Enzymes are the most efficient and specific catalysts to date. Although they have been thoroughly studied for years, building a true enzyme mimic remains a challenging and necessary task. Here, we show how a three-dimensional geometry analysis of the key catalytic residues in natural hydrolases has been exploited to design and synthesize small-molecule artificial enzymes which mimic the active centers of chymotrypsin and N-terminal hydrolases. The optimized prototype catalyzes the methanolysis of the acyl enzyme mimic with a half-life of only 3.7 min at 20 °C, and it is also able to perform the transesterification of vinyl acetate at room temperature. DFT studies and X-ray diffraction analysis of the catalyst bound to a transition state analogue proves the similarity with the geometry of natural hydrolases.
- Published
- 2020
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19. Bio-PEDOT: Modulating Carboxyl Moieties in Poly(3,4-ethylenedioxythiophene) for Enzyme-Coupled Bioelectronic Interfaces
- Author
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Wing Cheung Mak, Panote Thavarungkul, Lingyin Meng, Warakorn Limbut, Kiattisak Promsuwan, Proespichaya Kanatharana, and Phachara Suklim
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Materials science ,Polymers ,Biosensing Techniques ,02 engineering and technology ,010402 general chemistry ,01 natural sciences ,Tricarboxylate ,chemistry.chemical_compound ,PEDOT:PSS ,Limit of Detection ,Humans ,General Materials Science ,Lactic Acid ,Carboxylate ,Electrodes ,Conductive polymer ,Bioelectronics ,L-Lactate Dehydrogenase ,Reproducibility of Results ,Electrochemical Techniques ,Bridged Bicyclo Compounds, Heterocyclic ,Enzymes, Immobilized ,021001 nanoscience & nanotechnology ,0104 chemical sciences ,chemistry ,Chemical engineering ,Enzyme model ,0210 nano-technology ,Biosensor ,Poly(3,4-ethylenedioxythiophene) - Abstract
Modulation of chemical functional groups on conducting polymers (CPs) provides an effective way to tailor the physicochemical properties and electrochemical performance of CPs, as well as serves as a functional interface for stable integration of CPs with biomolecules for organic bioelectronics (OBEs). Herein, we introduced a facile approach to modulate the carboxylate functional groups on the PEDOT interface through a systematic evaluation on the effect of a series of carboxylate-containing molecules as counterion dopant integrated into the PEDOT backbone, including acetate as monocarboxylate (mono-COO-), malate as dicarboxylate (di-COO-), citrate as tricarboxylate (tri-COO-), and poly(acrylamide-co-acrylate) as polycarboxylate (poly-COO-) bearing different amounts of molecular carboxylate moieties to create tunable PEDOT:COO- interfaces with improved polymerization efficiency. We demonstrated the modulation of PEDOT:COO- interfaces with various granulated morphologies from 0.33 to 0.11 μm, tunable surface carboxylate densities from 0.56 to 3.6 μM cm-2, and with improved electrochemical kinetics and cycling stability. We further demonstrated the effective and stable coupling of an enzyme model lactate dehydrogenase (LDH) with the optimized PEDOT:poly-COO- interface via simple covalent chemistry to develop biofunctionalized PEDOT (Bio-PEDOT) as a lactate biosensor. The biosensing mechanism is driven by a sequential bioelectrochemical signal transduction between the bio-organic LDH and organic PEDOT toward the concept of all-polymer-based OBEs with a high sensitivity of 8.38 μA mM-1 cm-2 and good reproducibility. Moreover, we utilized the LDH-PEDOT biosensor for the detection of lactate in spiked serum samples with a high recovery value of 91-96% and relatively small RSD in the range of 2.1-3.1%. Our findings provide a new insight into the design and optimization of functional CPs, leading to the development of new OBEs for sensing, biosensing, bioengineering, and biofuel cell applications.
- Published
- 2020
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20. Penambatan Molekuler dan Simulasi Dinamika Molekuler Senyawa Dari Genus Nigella Terhadap Penghambatan Aktivitas Enzim Protease HIV-1
- Author
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Muhammad Zubair, Alwiyah Mukaddas, and Saipul Maulana
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chemistry.chemical_classification ,Protease ,biology ,Chemistry ,Stereochemistry ,medicine.medical_treatment ,Active site ,biology.organism_classification ,Ligand (biochemistry) ,Nigella ,Protease inhibitor (biology) ,Amino acid ,Amprenavir ,Enzyme model ,medicine ,biology.protein ,medicine.drug - Abstract
Nigella plant genus has potential as anti-HIV. One species of Nigella, Nigella sativa has been reported to have HIV-1 protease enzyme inhibitory activity. This research aims to determine the compounds of the Nigella genus that have activity as HIV-1 protease enzyme inhibitory activity through molecular docking method by Autodock Vina and to compare interaction stability through molecular dynamics simulations by AMBER. The metabolite of the Nigella genus was obtained from the KnapSack website, and enzyme model was obtained from the Protein Data Bank (3NU3). The results of molecular docking found the lowest affinity energy of Nigella compound is Nigellidine 4-O-sulfite (-13.4 kcal/mol). Meanwhile, the affinity energy of the ligand native (Amprenavir) was -12.1 kcal/mol. The lowest affinity energy of Nigellidine 4-O-sulfite might be predicted to have potency as an HIV-1 Protease inhibitor. Molecular dynamics simulation showed Root Mean Square Fluctuation (RMSF) value of Nigellidine 4-O-sulfite with the amino acid active site is 0.4064 Å for ASP:25 and 0.5667 Å for ASP: 125. Whereas RMSF ligand native with the amino acid active site, ASP: 25 is 0.3647 Å and ASP: 125 is 0.3639 Å. The higher RMSF value of Nigellidine 4-O-sulfite describes the lower interaction stability than the ligand native.
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- 2020
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21. The Monod Model and Its Alternatives
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Koch, Arthur L., Reddy, C. A., editor, Chakrabarty, A. M., editor, Demain, Arnold L., editor, Tiedje, James M., editor, Koch, Arthur L., editor, Robinson, Joseph A., editor, and Milliken, George A., editor
- Published
- 1998
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22. Glycolipid Hydrolase Models D, L-Stereorecognition of Amino Acids
- Author
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Ohkatsu, Yasukazu, Ozawa, Miho, and Coleman, A. W., editor
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- 1998
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23. Enzyme Models
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Dugas, Hermann, Cantor, Charles R., editor, and Dugas, Hermann
- Published
- 1996
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24. Cyclodextrin Homo- and Hetero-Dimers as Enzyme Models
- Author
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Ikeda, H., Nishikawa, S., Takaoka, J., Akiike, T., Yamamoto, Y., Ueno, A., Toda, F., Szejtli, J., editor, and Szente, L., editor
- Published
- 1996
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25. Toward Diiron Dithiolato Biomimetics with Rotated Conformation of the [FeFe]-Hydrogenase Active Site: A DFT Case Study on Electron-Rich, Isocyanide-Based Scaffolds
- Author
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Federica Arrigoni, Fabio Rizza, Luca Bertini, Luca De Gioia, Giuseppe Zampella, Arrigoni, F, Rizza, F, Bertini, L, De Gioia, L, and Zampella, G
- Subjects
Inorganic Chemistry ,Computational chemistry ,Hydrogenase ,Biomimetic model ,Enzyme model ,Density functional calculation ,Isocyanide ligand - Abstract
The electron rich Fe2(pdt)(RNC)6 1 (pdt=CH2(CH2S−)2) has been used as starting point for a DFT multi-functional study to assess the feasibility of designing a stable inverted (or rotated) disposition of the two FeL3 pyramidal moieties in the dimetallic core, a key feature of [FeFe]-hydrogenase cofactor. The choice of 1 was motivated by the presence of a rotated form in solution, slightly less stable than the unrotated stereoisomer. Aimed to find an upgraded version of 1, featuring the rotated isomer as ground state, various combinations of factors have been tested, for their effect on the relative stability of rotated vs unrotated isomers. The general result is that combining coordination asymmetry, electron donor presence and isocyanides R substituents able to establish intramolecular interactions is effective in stabilizing the rotated isomer. Our DFT study may inspire the design of synthetic biomimetics, with improved resemblance to the natural system.
- Published
- 2022
26. Polymer Assisted Molecular Recognition: The Current Understanding of the Molecular Imprinting Procedure
- Author
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Wulff, Günter, Pandit, Upendra K., editor, and Alderweireldt, Frank C., editor
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- 1991
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27. S ‐Denitrosylase‐Like Activity of Cyclic Diselenides Conjugated with Xaa‐His Dipeptide: Role of Proline Spacer as a Key Activity Booster
- Author
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Rumi Mikami, Kenta Arai, Shunsuke Tsukagoshi, and Yoshiki Oda
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chemistry.chemical_classification ,Dipeptide ,Proline ,Chemistry ,Stereochemistry ,Oxidative folding ,Organic Chemistry ,Selenol ,Proteins ,Dipeptides ,Conjugated system ,Biochemistry ,Diselenide ,chemistry.chemical_compound ,Catalytic cycle ,Enzyme model ,Thiol ,Molecular Medicine ,Sulfhydryl Compounds ,Oxidation-Reduction ,Molecular Biology - Abstract
This study developed dipeptide-conjugated 1,2-diselenan-4-amine (1), i. e., 1-Xaa-His, as a new class of S-denitrosylase mimic. The synthesized compounds, especially 1-Pro-His, remarkably promoted S-denitrosylation of nitrosothiols (RSNO) via a catalytic cycle involving the reversible redox reaction between the diselenide and its corresponding diselenol ([SeH,SeH]) form with coexisting reductant thiols (R'SH), during which the [SeH,SeH] form as a key reactive species reduces RSNO to the corresponding thiol (RSH). Structural analyses of 1-Pro-His suggested that the peptide backbone of [SeH,SeH] is rigidly bent to form a γ-turn, possibly including an NH⋅⋅⋅Se hydrogen bond between the imidazole ring of His and selenol group, thus stabilizing the [SeH,SeH] form thermodynamically, and dramatically enhancing the catalytic activity. Furthermore, the synthetic compounds were found to prohibit S-nitrosylation-induced protein misfolding in the presence of RSNO, eventually implying their potential as a drug seed for misfolding diseases caused by the dysregulation of the S-denitrosylation system.
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- 2021
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28. Increase in the Thermal Stability of Phytase from Citrobacter freundii by Site-Directed Saturation Mutagenesis
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S. P. Sineoky, S. P. Voronin, A. N. Kalinina, T. L. Gordeeva, M. D. Kashirskaya, and L. N. Borshchevskaya
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0301 basic medicine ,chemistry.chemical_classification ,biology ,Chemistry ,Mutant ,biology.organism_classification ,Applied Microbiology and Biotechnology ,Biochemistry ,Citrobacter freundii ,Pichia pastoris ,03 medical and health sciences ,030104 developmental biology ,Enzyme ,Enzyme model ,Thermal stability ,Phytase ,Saturated mutagenesis - Abstract
Phytases are widely used to improve the properties of mixed fodder. Due to its high specific activity, PhyА-Cf phytase from Citrobacter freundii is of special interest for agrobiotechnology. In order to decrease the thermal sensitivity of the enzyme during fodder granulation at 60–80°C, the thermal stability of phytase was enhanced by site-directed saturation mutagenesis. The mutant genes were cloned in a pP10 vector under the control of the GAP promoter and expressed in Pichia pastoris yeast cells. A mutant variant of the enzyme, K46M/K138E, showed a 35% increase in the thermal stability (10 min at 80°C) as compared to phytase from the wild-type strain. Analysis of the 3D enzyme model showed that the substitution of K138E located on the enzyme surface in the region of a loop with a highly irregular structure (a so-called coil) exerted a significant effect on the change in the protein thermal stability. It was shown that the introduced mutations did not noticeably affect the industrially valuable enzyme characteristics, including the specific activity, temperature, and pH profile.
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- 2019
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29. Lock and key-based nanozyme model to understand the substituent effect on the hydrolysis of organophosphate-based nerve agents by Zr-incorporated cerium oxide
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Kritika Khulbe and Govindasamy Mugesh
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Cerium oxide ,010405 organic chemistry ,Organophosphate ,Substituent ,010402 general chemistry ,01 natural sciences ,Combinatorial chemistry ,0104 chemical sciences ,Inorganic Chemistry ,chemistry.chemical_compound ,Hydrolysis ,chemistry ,Enzyme model ,Materials Chemistry ,medicine ,Degradation (geology) ,Physical and Theoretical Chemistry ,Selectivity ,Nerve agent ,medicine.drug - Abstract
Nanozymes are efficient class of synthetic enzymes capable of performing multi-step redox sensitive enzyme mimetic reactions on their surface with high turnover frequency and recyclability. It has been shown that the introduction of vacancies on the CeO2 surface transforms it into phosphotriesterase-like mimetic nanozyme, which can be used for the hydrolysis of neurotoxic organophosphate-based nerve agents. Further, the introduction of Zr in CeO2 nanozyme provides structural stability along with generating vacancies in the surface which can perform simultaneously two-step hydrolysis of the nerve agents. Herein, we describe the reasons for the difference in the degradation pathways used for various substituted organophosphate substrates and the selectivity involved by Zr-incorporated CeO2 nanozyme resembling a lock-and-key fit enzyme model.
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- 2019
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30. Influence of reaction parameters in the polymerization between genipin and chitosan for enzyme immobilization
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Tania Maria Haas Costa, Elí Emanuel Esparza Flores, Rafael C. Rodrigues, Manuela P. Klein, Plinho Francisco Hertz, Fernanda Dias Cardoso, Natália Carminatti Ricardi, and Larissa Bertoldo Siqueira
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0106 biological sciences ,chemistry.chemical_classification ,0303 health sciences ,Immobilized enzyme ,biology ,Bioengineering ,biology.organism_classification ,01 natural sciences ,Applied Microbiology and Biotechnology ,Biochemistry ,law.invention ,Chitosan ,03 medical and health sciences ,chemistry.chemical_compound ,Enzyme ,Magazine ,Aspergillus oryzae ,chemistry ,Polymerization ,law ,010608 biotechnology ,Enzyme model ,Genipin ,030304 developmental biology ,Nuclear chemistry - Abstract
In this work, we studied the effect of some variables in the reaction between genipin and chitosan, to prepare a support for enzyme immobilization. Reaction temperature, pH, time and genipin concentration were evaluated for support activation and β-galactosidase from Aspergillus oryzae was used as the enzyme model. The immobilized enzyme was characterized by immobilization properties and kinetic parameters and by thermal and operational stability. It was found that support activation at alkaline pH (9.0), at 60 °C for 1 h, resulted in an activity recovery of 37.5%. The immobilized enzyme had a stabilization factor of 2.0 at 50 °C compared with the free enzyme. In batch process, the immobilized preparation kept 100% of its relative initial activity during 40 batches. This research shows, for the first time, a complete study about the parameters that affect the support activation process and the possible structure formed between genipin and chitosan.
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- 2019
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31. Modeling Thioredoxin Reductase‐Like Activity with Cyclic Selenenyl Sulfides: Participation of an NH⋅⋅⋅Se Hydrogen Bond through Stabilization of the Mixed Se−S Intermediate
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Haruhito Ueno, Gaurango Chakrabarty, Yuumi Sato, Nozomi Akahoshi, Michio Iwaoka, Kenta Arai, Takahiko Matsunaga, and Govindasamy Mugesh
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chemistry.chemical_classification ,biology ,010405 organic chemistry ,Chemistry ,Hydrogen bond ,Stereochemistry ,Thioredoxin reductase ,Organic Chemistry ,Active site ,Dithiol ,General Chemistry ,010402 general chemistry ,01 natural sciences ,Redox ,Catalysis ,0104 chemical sciences ,chemistry.chemical_compound ,Catalytic cycle ,Enzyme model ,biology.protein ,Thiol - Abstract
At the redox-active center of thioredoxin reductase (TrxR), a selenenyl sulfide (Se-S) bond is formed between Cys497 and Sec498, which is activated into the thiolselenolate state ([SH,Se- ]) by reacting with a nearby dithiol motif ([SHCys59 ,SHCys64 ]) present in the other subunit. This process is achieved through two reversible steps: an attack of a cysteinyl thiol of Cys59 at the Se atom of the Se-S bond and a subsequent attack of a remaining thiol at the S atom of the generated mixed Se-S intermediate. However, it is not clear how the kinetically unfavorable second step progresses smoothly in the catalytic cycle. A model study that used synthetic selenenyl sulfides, which mimic the active site structure of human TrxR comprising Cys497, Sec498, and His472, suggested that His472 can play a key role by forming a hydrogen bond with the Se atom of the mixed Se-S intermediate to facilitate the second step. In addition, the selenenyl sulfides exhibited a defensive ability against H2 O2 -induced oxidative stress in cultured cells, which suggests the possibility for medicinal applications to control the redox balance in cells.
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- 2019
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32. Selective cytotoxicity and antifungal properties of copper(II) and cobalt(II) complexes with imidazole-4-acetate anion or 1-allylimidazole
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Michał Arabski, Katarzyna Gałczyńska, Łukasz Madej, Karol Ciepluch, Barbara Maciejewska, Krystyna Kurdziel, Anna Lankoff, Aneta Wegierek-Ciuk, and Zuzanna Drulis-Kawa
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Models, Molecular ,0301 basic medicine ,Circular dichroism ,Antifungal Agents ,Stereochemistry ,Chemical structure ,Molecular Conformation ,lcsh:Medicine ,Microbial Sensitivity Tests ,Toxicology ,Article ,Coordination complex ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Coordination Complexes ,Cell Line, Tumor ,Humans ,Imidazole ,lcsh:Science ,chemistry.chemical_classification ,Multidisciplinary ,Molecular Structure ,lcsh:R ,Fungi ,Imidazoles ,Cobalt ,DNA ,030104 developmental biology ,Enzyme ,chemistry ,Metals ,Enzyme model ,lcsh:Q ,Lysozyme ,Copper ,030217 neurology & neurosurgery ,Macromolecule - Abstract
The physicochemical properties of metal complexes determine their potential applications as antitumor agents. In this study, the antitumor properties of mononuclear cobalt(II) and copper(II) coordination compounds (stoichiometry: [Co(iaa)2(H2O)2]·H2O (iaa = imidazole-4-acetate anion), [Co(1-allim)6](NO3)2 (1-allim = 1-allylimidazole), [Cu(iaa)2H2O] and [Cu(1-allim)4(NO3)2]) and their ligands have been evaluated on human lung carcinoma A549 cells and normal bronchial BEAS-2B cells. Designing the chemical structure of new antitumor agents the possible interactions with macromolecules such as DNA or proteins should be take into account. PCR gene tlr4 product served as DNA model, whereas lysozyme and phage-derived endolysin (both peptidoglycan degrading enzymes) were applied as protein/enzyme model. The interactions were analysed using PCR-HRM and circular dichroism, FT-IR, spectrophotometry, respectively. Additionally, the antimicrobial properties of the complexes at a non-cytotoxic concentration were analyzed against S. aureus, E. coli, P. aeruginosa and C. albicans strains. The results obtained in this study showed the selective cytotoxicity of metal complexes, mainly [Cu(1-allim)4(NO3)2] towards tumor cells. From all tested compounds, only [Co(iaa)2(H2O)2].H2O non-covalently interacts with DNA. Cu(II) and Co(II) complexes did not affect the secondary conformation of tested proteins but modified the hydrolytic activity of enzymes (lysozyme and endolysin). Moreover, only [Co(iaa)2(H2O)2].H2O exhibited the antifungal properties. In conclusion, Co(II) and Cu(II) metal complexes bearing two imidazole-4-acetate ligands seemed to be promising antitumor and antifungal agents for future drug design and application.
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- 2019
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33. Highly enhanced activity and stability via affinity induced immobilization β-glucosidase from Aspergillus niger onto amino-based silica for the biotransformation of ginsenoside Rb1
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Xingxuan Ren, Xiuhong Wu, Boquan Qu, Yongkang Liu, Shaoyan Wang, and Yanling Quan
- Subjects
Immobilized enzyme ,Ginsenosides ,Biochemistry ,Michaelis–Menten kinetics ,Analytical Chemistry ,Hydrolase ,Enzyme Stability ,Enzyme kinetics ,Biotransformation ,Thermostability ,chemistry.chemical_classification ,Chromatography ,biology ,Chemistry ,beta-Glucosidase ,Organic Chemistry ,Aspergillus niger ,Temperature ,General Medicine ,Hydrogen-Ion Concentration ,biology.organism_classification ,Enzymes, Immobilized ,Silicon Dioxide ,Enzyme ,Enzyme model - Abstract
In this study, an enzyme immobilization method for the effective biotransformation of ginsenoside Rb1 to impart activity and stability was developed. Using a hydrolase enzyme model, β-glucosidase from Aspergillus niger, immobilization within chemically affinity-linked amino-based silica provided an immobilization efficiency 5.86-fold higher than that of free enzyme. Compared with the free enzyme, the immobilized enzyme functioned optimally at a wider pH range and had higher thermostability. The optimum pH for the free and immobilized enzymes was 5.5. The optimal reaction temperature of the immobilized enzyme was 45 °C, which was 5 °C higher than that of the free enzyme. The Michaelis constant (Km) values before and after immobilization were 0.482 mmol•L−1 and 0.387 mmol•L−1, respectively. The catalytic rate (Kcat) for the immobilized and free enzymes was 22.269 mmol•L−1and 8.800 mmol•L−1, respectively, and the catalytic efficiency (Kcat/Km) activity of the immobilized enzyme was 3.30-fold higher than that of the free enzyme. The immobilized enzyme could preserve 97 % of the activity after 45 cycles of repeated use. The high catalytic activity and significant operational stability are beneficial for industrial applications.
- Published
- 2021
34. Catecholase activity of a self-assembling dimeric Cu(II) complex with distant Cu(II) centers.
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Sarkar, Shuranjan, Sim, Arum, Kim, Sunghwan, and Lee, Hong-In
- Subjects
- *
CATECHOLASE , *DIMERIC ions , *LIGANDS (Chemistry) , *X-ray crystallography , *X-ray imaging - Abstract
Catecholase activity and its mechanistic investigation of a self-assemblying dimeric Cu(II) complex, Cu 2 L 2 , where L is N , N ′-(ethane-1,2-diyldi- o -phenylene)-bis(pyridine-2-carboxamidide), is presented. The complex was constructed by a spontaneous self-assembly of the organic ligand and Cu(II) ion. X-ray crystallography of Cu 2 L 2 (CH 3 OH) 2 ·2CH 3 OH, found that the coordination geometry of the Cu(II) site was a distorted square pyramid and two Cu(II) ions were apart by 6.992 Å. Though the metal centers are distant, Cu 2 L 2 showed high catecholase activity when 3,5-di- tert -butylcatechol (3,5-H 2 dtbc) was treated with Cu 2 L 2 in the presence of air at basic condition with k cat of 720 h −1 in Michaelis–Menten model. Information collected from the UV–vis kinetic, electron paramagnetic resonance (EPR), and high-resolution electrospray ionization mass spectrometry (ESI MS) measurements on the reaction mixtures could lead the suggestion of the mechanistic pathway of the catecholase activity of Cu 2 L 2 in which each Cu(II) site oxidized 3,5-H 2 dtbc to 3,5-di- tert -butyl-1,2-benzosemiquinonate anion radical (3,5-dtbq − ). Subsequently, 3,5-di- tert -butyl- o -quinone (3,5-dtbq) was formed via both disproportionation and air oxidation of 3,5-dtbq − . Cu 2 L 2 could be reduced to either one- or two-electron reduced state. The reduced complexes were reoxidized by dioxygen molecule accompanying with the generation of hydrogen peroxide. [ABSTRACT FROM AUTHOR]
- Published
- 2015
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35. Enzyme kinetic parameters estimation: A tricky task?
- Author
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Juan Carlos Aledo
- Subjects
Propagation of uncertainty ,Models, Statistical ,Kinetic energy ,beta-Galactosidase ,Biochemistry ,Models, Biological ,Standard deviation ,Task (project management) ,Substrate Specificity ,Enzyme model ,Linear regression ,Statistics ,Range (statistics) ,Humans ,Learning ,Laboratory experiment ,Laboratories ,Students ,Molecular Biology ,Mathematics - Abstract
We are living in the Big Data era, and yet we may have serious troubles when dealing with a handful of kinetic data if we are not properly instructed. The aim of this paper, related to enzyme kinetics, is to illustrate how to determine the Km and Vmax of a michaelian enzyme avoiding the pitfalls in which we often fall. To this end, we will resort to kinetic data obtained by second-year Biochemistry students during a laboratory experiment using β-galactosidase as an enzyme model, assayed at different concentrations of its substrate. When these data were analyzed using conventional linear regression of double-reciprocal plots, the range of Km and Vmax values obtained by different students varied widely. Even worse, some students obtained negative values for the kinetic parameters. Although such a scenario could make us think of a wide inter-student variability regarding their skills to obtain reliable data, the reality was quite different: when properly analyzed (accounting for error propagation) the data obtained by all the students were good enough to allow a correct estimation of the Km (2.8 ± 0.3 mM) and Vmax (179 ± 27 mM/min) with a reduced intergroup standard deviation. A student-accessible discussion of the importance of weighted linear regression in biochemical sciences is provided.
- Published
- 2021
36. Why the Enzyme Model of Modularity Fails to Explain Higher Cognitive Processes.
- Author
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Tzu-Wei Hung
- Subjects
MODULARITY (Psychology) ,COGNITION ,INFORMATION processing ,PROBLEM solving ,SEMANTICS ,SYNTAX (Grammar) - Abstract
The enzyme model (EM), inspired by biological enzyme catalysis, is a computational-functional description of information processing and distribution in modular cognitive systems. It has been argued that EM offers advantages in solving both the allocation problem and global computation and thus may play a role in upholding the massive modularity hypothesis (MMH). This paper, however, argues that EM solutions are untenable, as EM avoids the infinite regress of allocation problem only at a high cost and with several critical drawbacks. Moreover, to clarify global processes, EM needs to satisfy two necessary conditions: first to demonstrate that the EM allows cross module communication, and second to be sensitive to not only the syntax but also the semantics of representations. I argue that EM only satisfies the first condition and thus fails to hold. [ABSTRACT FROM AUTHOR]
- Published
- 2014
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37. Basic Amino Acid Conjugates of 1,2-Diselenan-4-amine with Protein Disulfide Isomerase-like Functions as a Manipulator of Protein Quality Control
- Author
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Kenta Arai, Rumi Mikami, and Shunsuke Tsukagoshi
- Subjects
chemistry.chemical_classification ,Quality Control ,010405 organic chemistry ,Stereochemistry ,Oxidative folding ,Amino Acids, Basic ,Organic Chemistry ,Molecular Conformation ,Protein Disulfide-Isomerases ,General Chemistry ,Protein aggregation ,010402 general chemistry ,01 natural sciences ,Biochemistry ,0104 chemical sciences ,Amino acid ,Protein Aggregates ,chemistry ,Enzyme model ,Humans ,Protein folding ,Protein disulfide-isomerase ,Peptide sequence ,Protein quality - Abstract
Protein disulfide isomerase (PDI) can assist immature proteins to correctly fold by controlling cysteinyl disulfide (SS)-relating reactions (i. e., SS-formation, SS-cleavage, and SS-isomerization). PDI controls protein quality by suppressing protein aggregation, as well as functions as an oxidative folding catalyst. Following the amino acid sequence of the active center in PDI, basic amino acid conjugates of 1,2-diselenan-4-amine (1), which show oxidoreductase- and isomerase-like activities for SS-relating reactions, were designed as a novel PDI model compound. By conjugating the amino acids, the diselenide reduction potential of compound 1 was significantly increased, causing improvement of the catalytic activities for all SS-relating reactions. Furthermore, these compounds, especially histidine-conjugated one, remarkably suppressed protein aggregation even at low concertation (0.3 mM∼). Thus, it was demonstrated that the conjugation of basic amino acids into 1 simultaneously achieves the enhancement of the redox reactivity and the capability to suppress protein aggregation.
- Published
- 2020
38. Preparation and characterization of 0D Au NPs@3D BiOI nanoflower/2D NiO nanosheet array heterostructures and their application as a self-powered photoelectrochemical biosensing platform
- Author
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Qingzhi Han, Qin Wei, Yanting Qi, Dan Wu, and Hanyu Wang
- Subjects
Materials science ,biology ,Non-blocking I/O ,General Engineering ,Bioengineering ,General Chemistry ,Nanoflower ,Atomic and Molecular Physics, and Optics ,Chemical engineering ,Enzyme model ,biology.protein ,General Materials Science ,Glucose oxidase ,Surface plasmon resonance ,Biosensor ,Chemical bath deposition ,Nanosheet - Abstract
In this work, we demonstrate that zero-dimensional Au nanoparticles (0D Au NPs)-decorated three-dimensional bismuth oxyiodide (BiOI) nanoflower (3D BiOI NFs)/two-dimensional nickel oxide (NiO) nanosheet array (2D NiO NSAs) hybrid nanostructures can be used as a self-powered cathodic photoelectrochemical (PEC) biosensing platform. The in situ formation of 3D BiOI NFs on 2D NiO NSAs was carried out by a chemical bath deposition method, while 0D Au NPs were coated on 3D BiOI NFs/2D NiO NSAs through a dip-coating method. Subsequently, glucose oxidase (GOD) as an enzyme model was immobilized on the surface of a Au@BiOI/NiO electrode via the adhesion of poly-(diallyldimethylammonium chloride) (PDDA). The proposed heterostructure exhibited excellent PEC properties because the unique structure of the Au NPs@BiOI NFs/NiO NSAs increased the specific surface area, light harvesting ability and the surface plasmon resonance effect of the Au NPs. The system displayed high sensitivity toward glucose in the presence of an air-saturated electrolyte. At the optimum conditions, the biosensor showed a promising application for the self-powered cathodic PEC biosensing of glucose, with a dynamic linear range of 1 × 10−7 M to 5 × 10−2 M and a low limit of detection of 8.71 × 10−8 M. Moreover, the proposed self-powered PEC biosensor was evaluated for the determination of diluted glucose injections, with the results indicating the potential of the proposed biosensor for bioanalysis applications.
- Published
- 2019
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39. α-Glucosidase inhibitory effects of polyphenols from Geranium asphodeloides: Inhibition kinetics and mechanistic insights through in vitro and in silico studies
- Author
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Arzu Özel, Suat Sari, İshak Erik, Gülin Renda, Didem Şöhretoğlu, Michal Šoral, Burak Barut, Büşra Korkmaz, and Tibor Liptaj
- Subjects
Hydrolysable tannin ,Saccharomyces cerevisiae Proteins ,Geranium ,Flavonoid ,Ethyl acetate ,Saccharomyces cerevisiae ,01 natural sciences ,Biochemistry ,chemistry.chemical_compound ,Drug Discovery ,medicine ,Glycoside Hydrolase Inhibitors ,Enzyme kinetics ,Molecular Biology ,IC50 ,Acarbose ,chemistry.chemical_classification ,biology ,Plant Extracts ,010405 organic chemistry ,Organic Chemistry ,Polyphenols ,alpha-Glucosidases ,biology.organism_classification ,0104 chemical sciences ,Molecular Docking Simulation ,010404 medicinal & biomolecular chemistry ,chemistry ,Enzyme model ,medicine.drug - Abstract
Some Geranium species have been used to treat diabetes. To evaluate the scientific basis of this ethnopharmacological use, we aimed to isolate potent α-glucosidase inhibitory metabolites of Geranium asphodeloides Burm. through in vitro bioactivity-guided fractionation. All the tested extracts showed high α-glucosidase inhibitory effect compared to acarbose. Among the tested extracts, the ethyl acetate subextract showed the highest activity with an IC50 value of 0.85 ± 0.01 µM. A hydrolysable tannin, 1,2,4-tri-O-galloyl-β- d -glucopyranose (1), and five flavonoid glycosides, kaempferol-3-O-α-rhamnopyranoside (2), kaempferol-3-O-α-arabinofuranoside (3), quercetin-3-O-β-glucopyranoside (4), quercetin-3-O-α-rhamnopyranoside (5), and quercetin-3-O-α-rhamnofuranoside (6), were isolated from the ethyl acetate subextract. Their structures were identified by 1D- and 2D-NMR experiments. 1 exhibited the highest α-glucosidase inhibitory effect, approximately 61 times more potent than positive control, acarbose, with an IC50 value of 0.95 ± 0.07 µM. Also, 2 was more potent than acarbose. An enzyme kinetics analysis revealed that compounds 2, 3 and 4 were competitive, whereas 1 and 6 uncompetitive inhibitors. Molecular docking studies were performed to get insights into inhibition mechanisms of the isolated compounds in the light of the enzyme kinetic studies using various binding sites of the enzyme model.
- Published
- 2018
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40. Identification of Adjacent NNRTI Binding Pocket in Multi-mutated HIV1- RT Enzyme Model: An in silico Study
- Author
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Utsab Debnath, R F Kamil, Saroj Verma, and Yenamandra S. Prabhakar
- Subjects
Models, Molecular ,0301 basic medicine ,Protein Conformation ,In silico ,Mutant ,Quantitative Structure-Activity Relationship ,Computational biology ,Molecular Dynamics Simulation ,01 natural sciences ,03 medical and health sciences ,Virology ,Drug Discovery ,Humans ,Computer Simulation ,Homology modeling ,Amino Acids ,Tyrosine ,Binding site ,Binding Sites ,010405 organic chemistry ,Chemistry ,Wild type ,Hydrogen Bonding ,HIV Reverse Transcriptase ,0104 chemical sciences ,Molecular Docking Simulation ,030104 developmental biology ,Infectious Diseases ,Docking (molecular) ,Enzyme model ,HIV-1 ,Reverse Transcriptase Inhibitors - Abstract
Introduction: A possible strategy to combat mutant strains is to have a thorough structural evaluation before and after mutations to identify the diversity in the non-nucleoside inhibitor binding pocket and their effects on enzyme-ligand interactions to generate novel NNRTI’s accordingly. Objective: The primary objective of this study was to find effects of multiple point mutations on NNRTI binding pocket. This study included the contribution of each individual mutation in NNIBP that propose an adjacent binding pocket which can be used to discover novel NNRTI derivatives. Methods: An in Silico model of HIV-1 RT enzyme with multiple mutations K103N, Y181C and Y188L was developed and evaluated. Two designed NNRTI pyridinone derivatives were selected as ligands for docking studies with the homology model through alignment based docking and residue based docking approaches. Binding pockets of wild type HIV-1 RT and multi-mutated homology model were compared thoroughly. Result and Discussion: K103N mutation narrowed the entrance of NNRTI binding pocket and forbade electrostatic interaction with α amino group of LYS103. Mutations Y181C and Y188L prevented NNRTI binding by eliminating aromatic π interactions offered by tyrosine rings. Docking study against new homology model suggested an adjacent binding pocket with combination of residues in palm and connection domains. This pocket is approximately 14.46Å away from conventional NNRTI binding site. Conclusion: Increased rigidity, steric hindrance and losses of important interactions cumulatively prompt ligands to adapt adjacent NNRTI binding pocket. The proposed new and adjacent binding pocket is identified by this study which can further be evaluated to generate novel derivatives.
- Published
- 2018
- Full Text
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41. Redox‐Controlled Stabilization of an Open‐Shell Intermediate in a Bioinspired Enzyme Model
- Author
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Christoph Förster, Kristina Hanauer, and Katja Heinze
- Subjects
Inorganic Chemistry ,chemistry ,010405 organic chemistry ,Molybdenum ,Enzyme model ,chemistry.chemical_element ,010402 general chemistry ,Photochemistry ,01 natural sciences ,Redox ,Open shell ,0104 chemical sciences - Published
- 2018
- Full Text
- View/download PDF
42. Cell Membrane-Based Nanoreactor To Mimic the Bio-Compartmentalization Strategy of a Cell
- Author
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Hongbo Zhang, Hélder A. Santos, Andrea Poillucci, Alexandra Correia, Vimalkumar Balasubramanian, Christian Celia, Faculty of Pharmacy, Division of Pharmaceutical Chemistry and Technology, Drug Research Program, Preclinical Drug Formulation and Analysis group, and Nanomedicines and Biomedical Engineering
- Subjects
ta221 ,Cell ,Biomedical Engineering ,ENZYMATIC-REACTIONS ,LIPOSOMES ,enzyme reaction ,self-assembled membrane vesicles ,02 engineering and technology ,Nanoreactor ,010402 general chemistry ,01 natural sciences ,Horseradish peroxidase ,Article ,VESICLES ,Biomaterials ,Cell membrane ,RED-BLOOD-CELLS ,colloidal nanoparticles ,BIODISTRIBUTION ,Organelle ,medicine ,ta318 ,DRUG-DELIVERY ,nanoerythrosomes ,biology ,CATALYSIS ,Chemistry ,Vesicle ,HORSERADISH-PEROXIDASE ,021001 nanoscience & nanotechnology ,PARTICLE-SIZE ,POLYMERIC NANOPARTICLES ,0104 chemical sciences ,medicine.anatomical_structure ,Membrane ,317 Pharmacy ,Enzyme model ,Biophysics ,biology.protein ,1182 Biochemistry, cell and molecular biology ,0210 nano-technology ,nanoparticle reactors - Abstract
Organelles of eukaryotic cells are structures made up of membranes, which carry out a majority of functions necessary for the surviving of the cell itself. Organelles also differentiate the prokaryotic and eukaryotic cells, and are arranged to form different compartments guaranteeing the activities for which eukaryotic cells are programmed. Cell membranes, containing organelles, are isolated from cancer cells and erythrocytes and used to form biocompatible and long circulating ghost nanoparticles delivering payloads or catalyzing enzymatic reactions as nanoreactors. In this attempt, red blood cell membranes were isolated from erythrocytes, and engineered to form nanoerythrosomes (NERs) of 150 nm. The horseradish peroxidase, used as an enzyme model, was loaded inside the aqueous compartment of NERs, and its catalytic reaction with Resorufm was monitored. The resulting nanoreactor protected the enzyme from proteolytic degradation, and potentiated the enzymatic reaction in situ as demonstrated by maximal velocity (V-max) and Michaelis constant (K-m), thus suggesting the high catalytic activity of nanoreactors compared to the pure enzymes.
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- 2018
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43. Synthetic and structural study on some new porphyrin or metalloporphyrin macrocycle-containing model complexes for the active site of [FeFe]-hydrogenases.
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Song, Li-Cheng, Wang, Liang-Xing, Li, Chang-Gong, Li, Fengyu, and Chen, Zhongfang
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PORPHYRINS , *METALLOPORPHYRINS , *MACROCYCLIC compounds , *CHEMICAL models , *COMPLEX compounds synthesis , *BINDING sites , *HYDROGENASE - Abstract
Abstract: To mimick the natural enzymes [FeFe]-hydrogenases, some new porphyrin and metalloporphyrin moiety-containing model complexes, namely 5-[p-Fe2(CO)6(μ-SCH2)2CHO2CC6H4],10,15,20-triphenylporphyrin (2), 5-[p-Fe2(CO)6(μ-SCH2)2CHO2CC6H4],10,15,20-triphenylporphyrinozinc (3), 5-[p-Fe2(CO)6(μ-SCH2)2NC2H4SC6H4],10,15,20-triphenylporphyrin (7), and 5-[p-Fe2(CO)5(μ-SCH2)2NC2H4SC6H],10,15,20-triphenylporphyrin (8), have been successfully prepared by our designed synthetic routes involving the corresponding precursor compounds [(μ-SCH2)2CHO2CC6H4CHO-p]Fe2(CO)6 (1), p-Boc-NHC2H4SC6H4CHO (4), 5-(p-Boc-NHC2H4SC6H4),10,15,20-triphenylporphyrin (5), and 5-(p-NH2C2H4 SC6H4),10,15,20-triphenylporphyrin (6). All these new compounds 1–8 have been characterized by elemental analysis and various spectroscopic methods, and particularly for 1–3 and 7 by X-ray crystallography. In addition, the density functional theory computations on 8 were performed to assist its structural characterization. [Copyright &y& Elsevier]
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- 2014
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44. Preparative and Structural Studies on [NiII(L)(N(CH2CH2S)2(CH2CH2SH))]0/1−1 (L = PEt3, SePh): A Thiol in the Secondary Coordination Sphere.
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Chen, Chien-Hong, Yen, Shih-Ying, Huang, Tzu-Ting, Lee, Gene-Hsiang, Kuo, Ting-Shen, and Lee, Chien-Ming
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CHEMICAL structure , *THIOLS , *COORDINATION compounds , *CARBONYL compounds , *MOLECULAR structure of enzymes , *X-ray diffraction - Abstract
A Ni(II)-mixed-chalcogenolate carbonyl complex, [PPN][Ni(CO)(SePh)2(S- p-C6H4-Cl)] ( 1) was obtained from the treatment of [CpNi(μ-S- p-C6H4-Cl)]2 and fac-[PPN][Fe(CO)3(SePh)3]. Using 1 as a precursor, two four-coordinated square planar Ni(II)-chalcogenolate/chalcogenol complexes, [PPN][Ni-(SePh)(N(CH2CH2S)2(CH2CH2SH))] ( 2) and [Ni(PEt3)(N(CH2CH2S)2(CH2CH2SH))] ( 4) containing the thiol in the secondary coordination sphere have been synthesized and identified by single-crystal X-ray diffraction. Analyses of structural data and vibrational energy (νSH = 2431 cm−1 for 4) reveal that the pendant thiol in complexes 2 and 4, respectively do not form intramolecular interaction with the nickel and thiolato sulfur. Compared to previously reported analogues coordinated by [P( o-C6H4S)2( o-C6H4SH)]2−ligand (Chen, C.-H.; Lee, G.-H.; Liaw, W.-F. Inorg. Chem. 2006, 45, 2307), the lack of intramolecular interaction in complexes 2 and 4 may be attributed to the rotatable C-S and C-C bonds of [N(CH2CH2S)2(CH2CH2SH)]2− ligand, precluding the pendant thiol from pointing a direction to the nickel and thiolato sulfur. [ABSTRACT FROM AUTHOR]
- Published
- 2013
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45. Synthetic Diversity and Catalytic Mechanism of Peptide Dendrimers
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Estelle Delort, Tamis Darbre, and Jean-Louis Reymond
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Dendrimer ,Enzyme model ,Ester hydrolysis ,Peptide ,Solid-phase synthesis ,Chemistry ,QD1-999 - Abstract
Peptide dendrimers composed of alternating sequences of natural amino acids and branching diamino acids are investigated as synthetic enzyme models. The dendrimers can be prepared by solid-phase peptide synthesis and are obtained pure in yields of 5–35%. Peptide dendrimers with surface histidine residues catalyze ester hydrolysis reaction with enzyme-like kinetics, including substrate binding (KM), catalytic turnover (kcat), and rate acceleration kcat/kuncat = 1000–20'000. Mechanistic investigation by substrate variation, pH-profile, and isothermaltitration calorimetry show that the catalytic effect is caused by positive interaction between the histidine side-chains and creation of a hydrophobic microenvironment for substrate binding.
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- 2005
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46. Homogeneous catalytic O2 reduction to water by a cytochrome c oxidase model with trapping of intermediates and mechanistic insights.
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Halime, Zakaria, Kotani, 0Hiroaki, Yuqi Li, Fukuzumi, Shunichi, and Karlin, Kenneth D.
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CYTOCHROME oxidase , *ACETONE , *COPPER ions , *WATER , *RHEOLOGY , *SCISSION (Chemistry) , *IRON - Abstract
An efficient and selective four-electron plus four-proton (4e-/4H+) reduction of O2 to water by decamethylferrocene and trifluoroacetic acid can be catalyzed by a synthetic analog of the heme a3/CuB site in cytochrome c oxidase (6LFeCu) or its Cu-free version (6LFe) in acetone. A detailed mechanistic-kinetic study on the homogeneous catalytic system reveals spectroscopically detectable intermediates and that the rate-determining step changes from the O2-binding process at 25?°C room temperature (RT) to the O-O bond cleavage of a newly observed FeIII-OOH species at lower temperature (-60 °C). At RT, the rate of O2-binding to 6LFeCu is significantly faster than that for 6LFe, whereas the rates of the O-O bond cleavage of the FeIII-OOH species observed (-60 °C) with either the 6LFeCu or 6LFe catalyst are nearly the same. Thus, the role of the Cu ion is to assist the heme and lead to faster O2-binding at RT. However, the proximate Cu ion has no effect on the O-O bond cleavage of the FeIII-OOH species at low temperature. [ABSTRACT FROM AUTHOR]
- Published
- 2011
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47. Studies of 4-arylthiazolylhydrazones derived from 1-indanones as Trypanosoma cruzi squalene epoxidase inhibitors by molecular simulations
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Liliana M. Finkielsztein, Lucas Fabian, Guido J. Noguera, and Elisa Lombardo
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Models, Molecular ,0301 basic medicine ,Protein Conformation ,Squalene monooxygenase ,Trypanosoma cruzi ,MOLECULAR SIMULATIONS ,Molecular Dynamics Simulation ,01 natural sciences ,Biochemistry ,03 medical and health sciences ,Squalene ,chemistry.chemical_compound ,4-ARYLTHIAZOLYLHYDRAZONES ,parasitic diseases ,0103 physical sciences ,Amino Acid Sequence ,Homology modeling ,Enzyme Inhibitors ,Physical and Theoretical Chemistry ,chemistry.chemical_classification ,010304 chemical physics ,biology ,Organic Chemistry ,Hydrazones ,Ciencias Químicas ,TRYPANOSOMA CRUZI ,biology.organism_classification ,Molecular Docking Simulation ,Química Orgánica ,030104 developmental biology ,Enzyme ,Squalene Monooxygenase ,chemistry ,Docking (molecular) ,Drug Design ,Enzyme model ,Indans ,SQUALENE EPOXIDASE ,Thermodynamics ,Pharmacophore ,CIENCIAS NATURALES Y EXACTAS - Abstract
Chagas disease or American trypanosomiasis is a parasitic disease caused by the protozoan Trypanosoma cruzi. Its squalene epoxidase (SE) is a target for drug design and development because it is a key enzyme in the biosynthetic pathway of ergosterol, which is essential for the life cycle of the parasite. Previously, we reported that some 4-arylthiazolylhydrazones derived from 1-indanones (TZHs) active against T. cruzi are able to accumulate squalene probably by SE inhibition. In this work, we performed a series of theoretical studies to verify that TZHs act as inhibitors of this enzyme. Since the crystal structure of SE is unknown for all species, we built a 3D enzyme model of T. cruzi SE by homology modeling. Based on this model, we carried out docking, molecular dynamics, and MM/PBSA calculations and the results were compared with those found for the reference inhibitor compound terbinafine (Tbf). The binding free energy values allowed the discrimination between accumulators and non-accumulators of squalene compounds, in agreement with the experimental findings. Pairwise residue free energy decomposition showed that the key amino acids involved in inhibitor binding for TZHs and Tbf were the same. Also, molecular superposition analysis between these compounds revealed high structural similarity. In addition, we proposed a pharmacophore model for T. cruzi SE inhibitors, which confirmed that TZHs and Tbf share chemical features with respect to their biochemical interaction characteristics at similar positions in 3D space. All theoretical calculations suggest that the experimentally observed squalene accumulation is produced by T. cruzi SE inhibition. Fil: Noguera, Guido Julian. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Farmacología. Cátedra de Química Medicinal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Química y Metabolismo del Fármaco. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Química y Metabolismo del Fármaco; Argentina Fil: Fabian, Lucas Emanuel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Química y Metabolismo del Fármaco. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Química y Metabolismo del Fármaco; Argentina Fil: Lombardo, Maria Elisa. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Centro de Investigaciones sobre Porfirinas y Porfirias. Universidad de Buenos Aires. Centro de Investigaciones sobre Porfirinas y Porfirias; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Química Biológica; Argentina Fil: Finkielsztein, Liliana M.. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Química y Metabolismo del Fármaco. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Química y Metabolismo del Fármaco; Argentina. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Farmacología. Cátedra de Química Medicinal; Argentina
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- 2018
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48. Deciphering the mechanism of O2 reduction with electronically tunable non-heme iron enzyme model complexes
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Rupal Gupta, Alexander A D'Arpino, Bao Y Sciscent, Roshaan Surendhran, Anthony F. Cannella, Alan E. Friedman, Samantha N. MacMillan, and David C. Lacy
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010405 organic chemistry ,Chemistry ,General Chemistry ,Rate equation ,Crystal structure ,010402 general chemistry ,01 natural sciences ,0104 chemical sciences ,3. Good health ,Reduction (complexity) ,Homologous series ,chemistry.chemical_compound ,Crystallography ,Hammett equation ,Enzyme model ,Non heme iron ,Structural motif - Abstract
A homologous series of electronically tuned 2,2',2''-nitrilotris(N-arylacetamide) pre-ligands (H3LR ) were prepared (R = NO2, CN, CF3, F, Cl, Br, Et, Me, H, OMe, NMe2) and some of their corresponding Fe and Zn species synthesized. The iron complexes react rapidly with O2, the final products of which are diferric mu-oxo bridged species. The crystal structure of the oxidized product obtained from DMA solutions contain a structural motif found in some diiron proteins. The mechanism of iron mediated O2 reduction was explored to the extent that allowed us to construct an empirically consistent rate law. A Hammett plot was constructed that enabled insightful information into the rate-determining step and hence allows for a differentiation between two kinetically equivalent O2 reduction mechanisms.
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- 2018
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49. Synthesis and structural characterization of the mono- and diphosphine-containing diiron propanedithiolate complexes related to [FeFe]-hydrogenases. Biomimetic H2 evolution catalyzed by (μ-PDT)Fe2(CO)4[(Ph2P)2N(n-Pr)]
- Author
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Song, Li-Cheng, Li, Chang-Gong, Ge, Jian-Hua, Yang, Zhi-Yong, Wang, Hu-Ting, Zhang, Juan, and Hu, Qing-Mei
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- *
HYDROGENASE , *ENZYMES , *PHOSPHINE , *IRON compounds , *BIOMIMETIC chemicals , *LIGANDS (Biochemistry) , *XYLENE - Abstract
Abstract: As the new H-cluster models, six diiron propanedithiolate (PDT) complexes with mono- and diphosphine ligands have been prepared and structurally characterized. The monophosphine model complex (μ-PDT)Fe2(CO)5[Ph2PNH(t-Bu)] (1) was prepared by reaction of parent complex (μ-PDT)Fe2(CO)6 (A) with 1 equiv of Ph2PNH(t-Bu) in refluxing xylene, whereas A reacted with 1 equiv of Me3NO·2H2O in MeCN at room temperature followed by 1 equiv of Ph2PH to give the corresponding monophosphine model complex (μ-PDT)Fe2(CO)5(Ph2PH) (2). Further treatment of 2 with 1 equiv of n-BuLi in THF at −78°C followed by 1 equiv of CpFe(CO)2I from −78°C to room temperature afforded monophosphine model complex (μ-PDT)Fe2(CO)5[Ph2PFe(CO)2Cp] (3), whereas the diphosphine model complexes (μ-PDT)Fe2(CO)4(Ph2PC2H4PPh2) (4), (μ-PDT)Fe2(CO)4[(Ph2P)2N(n-Pr)] (5) and (μ-PDT)Fe2(CO)4[(Ph2P)2N(n-Bu)] (6) were obtained by reactions of A with ca.1 equiv of the corresponding diphosphines in refluxing xylene. All the new model complexes were characterized by elemental analysis, spectroscopy and particularly for 1 and 3–6 by X-ray crystallography. On the basis of electrochemical and spectroelectrochemical studies, model 5 was found to be a catalyst for HOAc proton reduction to H2, and for this electrocatalytic reaction an ECCE mechanism was proposed. [Copyright &y& Elsevier]
- Published
- 2008
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50. Artificial enzymes, “Chemzymes”: current state and perspectives.
- Author
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Bjerre, Jeannette, Rousseau, Cyril, Marinescu, Lavinia, and Bols, Mikael
- Subjects
- *
ENZYMES , *ORGANIC chemistry , *CATALYSTS , *CATALYSIS , *MOLECULES , *HYDROGEN-ion concentration , *CYCLODEXTRINS , *GLYCOSIDASES , *OXIDASES , *ESTERASES , *MOLECULAR models - Abstract
Enzymes have fascinated scientists since their discovery and, over some decades, one aim in organic chemistry has been the creation of molecules that mimic the active sites of enzymes and promote catalysis. Nevertheless, even today, there are relatively few examples of enzyme models that successfully perform Michaelis–Menten catalysis under enzymatic conditions (i.e., aqueous medium, neutral pH, ambient temperature) and for those that do, very high rate accelerations are seldomly seen. This review will provide a brief summary of the recent developments in artificial enzymes, so called “Chemzymes”, based on cyclodextrins and other molecules. Only the chemzymes that have shown enzyme-like activity that has been quantified by different methods will be mentioned. This review will summarize the work done in the field of artificial glycosidases, oxidases, epoxidases, and esterases, as well as chemzymes that catalyze conjugate additions, cycloadditions, and self-replicating processes. The focus will be mainly on cyclodextrin-based chemzymes since they have shown to be good candidate structures to base an enzyme model skeleton on. In addition hereto, other molecules that encompass binding properties will also be presented. [ABSTRACT FROM AUTHOR]
- Published
- 2008
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- View/download PDF
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