Machine Learning: A Suitable Method for Biocatalysis

Catalysts, Journal Year: 2023, Volume and Issue: 13(6), P. 961 - 961

Published: June 1, 2023

Biocatalysis is currently a workhorse used to produce wide array of compounds, from bulk fine chemicals, in green and sustainable manner. The success biocatalysis largely thanks an enlargement the feasible chemical reaction toolbox. This materialized due major advances enzyme screening tools methods, together with high-throughput laboratory techniques for biocatalyst optimization through engineering. Therefore, enzyme-related knowledge has significantly increased. To handle large number data now available, computational approaches have been gaining relevance biocatalysis, among them machine learning methods (MLMs). MLMs use algorithms learn improve experience automatically. review intends briefly highlight contribution within biochemical engineering bioprocesses present key aspects scope related fields, mostly readers non-skilled mind. Accordingly, brief overview basic concepts underlying are presented. complemented steps build model followed by insights into types intelligently analyse data, identify patterns develop realistic applications bioprocesses. Notwithstanding, given this review, some recent illustrative examples protein engineering, production, formulation provided, future developments suggested. Overall, it envisaged that will provide how these assets more efficient biocatalysis.

Language: Английский

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Sub-micro- and nano-sized polyethylene terephthalate deconstruction with engineered protein nanopores

Nature Catalysis, Journal Year: 2023, Volume and Issue: 6(12), P. 1174 - 1185

Published: Oct. 19, 2023

Abstract The identification or design of biocatalysts to mitigate the accumulation plastics, including sub-micro- and nano-sized polyethylene terephthalate (nPET), is becoming a global challenge. Here we computationally incorporated two hydrolytic active sites with geometries similar that Idionella sakaiensis PET hydrolase, fragaceatoxin C (FraC), membrane pore-forming protein. FraC m1/m2 could be assembled into octameric nanopores (7.0 nm high × 1.6–6.0 entry), which deconstructed (40 °C, pH 7.0) nPET from GoodFellow, commodities plastic bottles. m1 m2 degrade by endo- exo-type chain scission. While produces bis(2-hydroxyethyl) as main product, yields diversity oligomers terephthalic acid. Mechanistic biochemical differences benchmark hydrolases, along pore dynamics, suggest these protein catalytic nanoreactors do not deconstruct macro-PET but are promising in nanotechnology for filtering, capturing breaking down nPET, example, wastewater treatment plants.

Language: Английский

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A Plurizyme with Transaminase and Hydrolase Activity Catalyzes Cascade Reactions

Angewandte Chemie International Edition, Journal Year: 2022, Volume and Issue: 61(37)

Published: June 23, 2022

Engineering dual-function single polypeptide catalysts with two abiotic or biotic catalytic entities (or combinations of both) supporting cascade reactions is becoming an important area enzyme engineering and catalysis. Herein we present the development a PluriZyme, TR2 E2 , efficient native transaminase (kcat : 69.49±1.77 min-1 ) artificial esterase 3908-0.41 activities integrated into scaffold, evaluate its utility in reaction. (pHopt 8.0-9.5; Topt 60-65 °C) efficiently converts methyl 3-oxo-4-(2,4,5-trifluorophenyl)butanoate 3-(R)-amino-4-(2,4,5-trifluorophenyl)butanoic acid, crucial intermediate for synthesis antidiabetic drugs. The reaction proceeds through conversion β-keto ester acid at hydrolytic site subsequently β-amino (e.e. >99 %) site. power PluriZyme was proven set esters, demonstrating potential such designs to address bioinspired reactions.

Language: Английский

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Biosynthesis of alkanes/alkenes from fatty acids or derivatives (triacylglycerols or fatty aldehydes)

Biotechnology Advances, Journal Year: 2022, Volume and Issue: 61, P. 108045 - 108045

Published: Sept. 29, 2022

This review summarizes the most relevant advances in biological transformation of fatty acids (or derivatives) into hydrocarbons to be used as biofuels (biogasoline, green diesel and jet biofuel). Among enzymes, acid decarboxylase from Jeotgalicoccus sp. ATCC 8456 (OleTJE) stands out a promising enzyme. OleTJE may coupled cascade reactions with metalloenzymes or reductases Old Yellow Enzymes (OYE) family perform hydrogenation α-olefins paraffins. The photodecarboxylase Chlorella variabilis NC64A (CvFAP) is an example coupling biocatalysis photocatalysis produce alkanes. Besides (photo)decarboxylation free and/or triacyclglycerols alkanes/alkenes, by enzymes has also been employed. cyanobacterial aldehyde decarbonylase (cAD) Nostoc punctiforme outstanding this kind Overall, these kinds open up new possibilities production renewable sources, even if they have many limitations on current situation. improving features via immobilization coimmobilization, well utilization whole cells haves reviewed.

Language: Английский

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Immobilization of Lipase B from Candida antarctica in Octyl-Vinyl Sulfone Agarose: Effect of the Enzyme-Support Interactions on Enzyme Activity, Specificity, Structure and Inactivation Pathway

International Journal of Molecular Sciences, Journal Year: 2022, Volume and Issue: 23(22), P. 14268 - 14268

Published: Nov. 17, 2022

Lipase B from Candida antarctica was immobilized on heterofunctional support octyl agarose activated with vinyl sulfone to prevent enzyme release under drastic conditions. Covalent attachment established, but the blocking step using hexylamine, ethylenediamine or amino acids glycine (Gly) and aspartic acid (Asp) altered results. The activities were lower than those observed biocatalyst, except when as reagent p-nitrophenol butyrate (pNPB) substrate. stability increased these new biocatalysts at pH 7 9 all agents (much more significantly 9), while it decreased 5 Gly agent. stress inactivation of activity versus three different substrates (pNPB, S-methyl mandelate triacetin) in a relatively similar fashion. tryptophane (Trp) fluorescence spectra for biocatalysts, suggesting conformations. However, changes during not too biocatalyst blocked Asp, that, this pathways may be so different.

Language: Английский

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Enhancing the Hydrolytic Activity of a Lipase towards Larger Triglycerides through Lid Domain Engineering

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(18), P. 13768 - 13768

Published: Sept. 6, 2023

Lipases have valuable potential for industrial use, particularly those mostly active against water-insoluble substrates, such as triglycerides composed of long-carbon chain fatty acids. However, in most cases, engineered variants often need to be constructed achieve optimal performance substrates. Protein engineering techniques been reported strategies improving lipase characteristics by introducing specific mutations the cap domain esterases or lid lipases through swapping. Here, we improved activity a (WP_075743487.1, LipMRD) retrieved from Marine Metagenomics MarRef Database and assigned Actinoalloteichus genus. The improvement was achieved site-directed mutagenesis substituting its (FRGTEITQIKDWLTDA) with that Rhizopus delemar (previously R. oryzae; UniProt accession number, I1BGQ3) (FRGTNSFRSAITDIVF). results demonstrated redesigned mutants gain bulkier triglycerides, glyceryl tridecanoate tridodecanoate, olive oil, coconut palm oil. Residue W89 (LipMRD numbering) appears key increase activity, an also This study reinforces importance domains their amino acid compositions determining substrate specificity lipases, but generalization swapping between introduction improve may require further investigation.

Language: Английский

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AsiteDesign: a Semirational Algorithm for an Automated Enzyme Design

The Journal of Physical Chemistry B, Journal Year: 2023, Volume and Issue: 127(12), P. 2661 - 2670

Published: March 21, 2023

With advances in protein structure predictions, the number of available high-quality structures has increased dramatically. In light these advances, structure-based enzyme engineering is expected to become increasingly important for optimizing biocatalysts industrial processes. Here, we present AsiteDesign, a Monte Carlo-based protocol active sites. AsiteDesign provides framework introducing new catalytic residues given binding pocket either create activity or alter existing one. implemented using pyRosetta and incorporates enhanced sampling techniques efficiently explore search space. The was tested by designing an alternative triad site Pseudomonas fluorescens esterase (PFE). designed variant experimentally verified be active, demonstrating that can find triads. Additionally, employed enhance hydrolysis bulky chiral substrate (1-phenyl-2-pentyl acetate) PFE. experimental verification variants demonstrated F158L/F198A F125A/F158L mutations 1-phenyl-2-pentyl acetate from 8.9 66.7 23.4%, respectively, reversed enantioselectivity (R) (S)-enantiopreference, with 32 55% enantiomeric excess (ee), respectively.

Language: Английский

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The effects of the chemical modification on immobilized lipase features are affected by the enzyme crowding in the support

Biotechnology Progress, Journal Year: 2023, Volume and Issue: 40(1)

Published: Oct. 12, 2023

In this article, we have analyzed the interactions between enzyme crowding on a given support and its chemical modification (ethylenediamine via carbodiimide route picryl sulfonic (TNBS) of primary amino groups) activity stability. Lipase from Thermomyces lanuginosus (TLL) lipase B Candida antarctica (CALB) were immobilized octyl-agarose beads at two very different loadings, one them exceeding capacity support, well under capacity. Chemical modifications highly loaded lowly biocatalysts gave results in terms stability, which could increase or decrease depending loading. For example, both increased their after while effect was opposite for biocatalysts. Additionally, with TNBS CALB biocatalyst stability activity.

Language: Английский

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Chemoenzymatic synthesis

Communications Chemistry, Journal Year: 2025, Volume and Issue: 8(1)

Published: March 13, 2025

Communications Chemistry is pleased to introduce a Collection of research works focused on recent developments within the interdisciplinary field chemoenzymatic synthesis. Here, Guest Editors highlight key themes and look towards future this field.

Language: Английский

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The nature of the buffer alters the effects of the chemical modification on the stability of immobilized lipases

Process Biochemistry, Journal Year: 2023, Volume and Issue: 133, P. 20 - 27

Published: Aug. 9, 2023

The objective of this paper was to analyze whether an interaction between the effects buffer nature and chemical modification on enzyme stability exists. For this, lipase B from Candida antarctica (CALB) Thermomyces lanuginosus (TLL) were immobilized octyl agarose beads modified with picryl sulfonic acid (TNBS) ethylenediamine via carbodiimide route. obtained biocatalysts them inactivated in different buffers (2-amino-2-(hydroxymethyl)propane-1,3-diol (Tris)-HCl, N-(2-hydroxyethyl)piperazine-N′-(2-ethanesulfonic acid) (HEPES) or phosphate). A significant found surfaces their stabilities these buffers. While phosphate where lowest for both unmodified enzymes, differences become much smaller after some modifications. In many instances, improves when using a negative other one (e.g., TNBS TLL positive Tris-HCl buffers, amination CALB decreased its HEPES while it almost had no effect phosphate).Thus, clear co-interactions established.

Language: Английский

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