Design and catalytic studies of structural and functional models of the catechol oxidase enzyme

Terán, Aarón; Jaafar, Aida; Sánchez, Ana E.; Torralba, M. Carmen; Gutiérrez, Ángel

doi:10.1007/s00775-020-01791-2

Cited by 14 publications

(7 citation statements)

References 49 publications

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“…The evaluation criteria include: (1) sequence matching (aka sequence identity): the sequence identity between the designed sequence and native sequence of the target structure, (2) structure matching: the structure similarity (measured using TM-score) between the target structure and the predicted structure of the designed sequence. (3) sequencestructure matching: we further evaluated the fitness between the designed sequence and the target structure through building and assessing a threading structure.…”

Section: Resultsmentioning

confidence: 99%

“… (D, E, F) . We designed sequences for these proteins using FixBB, ProteinSolver, 3D-CNN, and ProDESIGN-LE and assessed the designed sequences using three metrics: (1) the sequence identity between the designed sequence and native sequence of the target structure ( C, F ), (2) the structure similarity (measured using TM-score) between the target structure and the predicted structure of the designed sequence ( A, D ), (3) we further built a threading structure through complementing the target backbone structure with the sidechains determined by designed sequences. The energy of the resultant threading structure is used as measurement of the fitness between the designed sequence and the target backbone structure ( B, E ).…”

Section: Resultsmentioning

confidence: 99%

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Accurate and efficient protein sequence design through learning concise local environment of residues

Huang

Fan

Wang

et al. 2022

Preprint

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Computational protein sequence design has been widely applied in rational protein engineering and increasing the design accuracy and efficiency is highly desired. Here we present an accurate and efficient design approach called ProDESIGNLE, which uses a concise but informative representation of residue’s local environment and trains a transformer to predict a residue’s amino acid type from its local environment. Using the trained transformer, ProDESIGN-LE iteratively selects an appropriate residue at a random position of the target structure, eventually acquiring a designed sequence with all residues fitting well with their own local environments.We assessed ProDESIGN-LE in silico by designing sequences for 68 naturally-occurring proteins used by the 14th critical assessment of protein structure prediction and 129 hallucinated structures. ProDESIGN-LE accomplished sequence design within 20 seconds per protein on average, and the predicted structures of these designed sequences perfectly resemble the target structures with state-of-the-art average TM-score (0.81 and 0.83 on these two datasets, respectively). We further experimentally validated ProDESIGN-LE by designing five sequences for an enzyme, chloramphenicol O-acetyltransferase type III (CAT III) and recombinantly expressing the designed proteins in E. coli. Of these designed proteins, three exhibited excellent solubility and one protein yielded monomeric species with circular dichroism spectra consistent with the natural CAT III protein. We anticipate that ProDESIGN-LE, with the improved accuracy and efficiency, would greatly facilitate rational protein engineering.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Accurate and efficient protein sequence design through learning concise local environment of residues

Huang

Fan

Wang

et al. 2022

Preprint

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“…In this regard, the nature of the atom donors, the flexibility of the ligand and, thus, the geometric features of the complex are of great interest in the synthesis of small molecules that can mimic the active sites of different metalloenzymes and are currently a focus in research studies. However, the majority of ligands reported have a five‐membered chelate ring and the influence of the number of members of the chelate ring around the copper(II) atoms has not been evaluated [7] …”

Section: Introductionmentioning

confidence: 99%

“…However, the majority of ligands reported have a five-membered chelate ring and the influence of the number of members of the chelate ring around the copper(II) atoms has not been evaluated. [7] Copper is also a bio-essential element and copper complexes can play several biological roles in vivo, such as: antibacterial, [8] antifungal, antimicrobial, and anticancer/antiproliferative activity. [9] Indeed, the study of the interaction of copper complexes with DNA is an important field of research since these complexes can cleave DNA under physiological conditions.…”

Section: Introductionmentioning

confidence: 99%

Effect of Chelate Ring Size of Binuclear Copper(II) Complexes on Catecholase Activity and DNA Cleavage

et al. 2021

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Catecholase activity of dicopper(II) complexes containing different numbers of chelate members in the pyridine groups of the ligand was studied to identify a functional model for copper enzyme catechol oxidase. Complexes [CuII(μ‐OH)CuII(L1)](ClO4) (1), [CuII(μ‐OH)CuII(L2)](ClO4) (2), and [CuII(μ‐OH)CuII(L3)](ClO4) (3) were synthesized and characterized by elemental analysis, FTIR, UV–Vis spectroscopy, mass spectrometry, and electrochemistry. Their catalytic activity in the oxidation of 3,5‐di‐tert‐butylcatechol was determined. Changing the number of members of the chelate rings altered the catalytic activity. Complex 2 showed the highest catalytic activity due to a high turnover rate, with efficiency of 3.40±0.61. Mechanistic investigations indicate that the catalytic reaction occurs through the reduction of Cu(II) to Cu(I) with formation of hydrogen peroxide. The spectroscopic and catecholase activity were further rationalized through DFT and TD‐DFT calculations. Interestingly, all three complexes also showed DNA binding properties, which were also corroborated via molecular docking studies.

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“…Catechol oxidase has been shown to be catalytically active between pH 4–pH 8. Low pH due to high ascorbic acid content could interfere with the binding of the enzyme to its active site copper 34 . Enzymatic browning of fruits not only affects the appearance of fruits but also their nutritional Quality.…”

Section: Discussionmentioning

confidence: 99%

Fabrication, characterization and antifungal evaluation of polyphenolic extract activated keratin starch coating on infected tomato fruits

Oluba

Obokare

Bayo-Olorunmeke

et al. 2022

Sci Rep

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In recent times, the application of protein-based bio-composite edible films in postharvest preservation of food and agricultural products is attracting increased attention due to their biodegradability, eco-friendliness and sustainability. In this study, an avocado pear peel polyphenolic extract enriched keratin-starch composite film was fabricated, characterized and evaluated for antimicrobial activity against fungal infected tomato fruits after 6 days of storage at room (25 ± 2 °C) temperature. The SEM/EDX and FTIR results revealed the successful film formation with high degree of compatibility and homogeneity. Following a 6-day post-coating loss in weight of the coated tomato fruits decreased significantly (p < 0.05) with increasing extract concentration while titratable acidity showed a significant (p < 0.05) increase with increasing extract load. Ascorbic acid and lycopene contents were significantly (p < 0.05) higher in the avocado pear peel polyphenolic extract-loaded films. No significant effect was observed in catechol oxidase activity of the tomato extract across the different treatment groups. In addition, fungal growth inhibition showed a dose dependent increase consistent with avocado pear peel polyphenolic load in coated tomato fruits compared to control. Results obtained in this study showed that polyphenolic activated keratin-starch coating was able to reduce spoilage-induce weight loss as well as conserve the overall quality (including titratable acid levels, lycopene and ascorbic acid contents) of fungal-infected tomato fruit and reduce microbial growth. Therefore polyphenolic activated keratin-starch coating could serve as a sustainable and ecofriendly postharvest preservation method to prolong the shelf life of tomato fruits.

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Design and catalytic studies of structural and functional models of the catechol oxidase enzyme

Cited by 14 publications

References 49 publications

Accurate and efficient protein sequence design through learning concise local environment of residues

Accurate and efficient protein sequence design through learning concise local environment of residues

Effect of Chelate Ring Size of Binuclear Copper(II) Complexes on Catecholase Activity and DNA Cleavage

Fabrication, characterization and antifungal evaluation of polyphenolic extract activated keratin starch coating on infected tomato fruits

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