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1.
Proc Natl Acad Sci U S A ; 121(33): e2405836121, 2024 Aug 13.
Artículo en Inglés | MEDLINE | ID: mdl-39116128

RESUMEN

The 2011 discovery of the first rare earth-dependent enzyme in methylotrophic Methylobacterium extorquens AM1 prompted intensive research toward understanding the unique chemistry at play in these systems. This enzyme, an alcohol dehydrogenase (ADH), features a La3+ ion closely associated with redox-active coenzyme pyrroloquinoline quinone (PQQ) and is structurally homologous to the Ca2+-dependent ADH from the same organism. AM1 also produces a periplasmic PQQ-binding protein, PqqT, which we have now structurally characterized to 1.46-Å resolution by X-ray diffraction. This crystal structure reveals a Lys residue hydrogen-bonded to PQQ at the site analogously occupied by a Lewis acidic cation in ADH. Accordingly, we prepared K142A- and K142D-PqqT variants to assess the relevance of this site toward metal binding. Isothermal titration calorimetry experiments and titrations monitored by UV-Vis absorption and emission spectroscopies support that K142D-PqqT binds tightly (Kd = 0.6 ± 0.2 µM) to La3+ in the presence of bound PQQ and produces spectral signatures consistent with those of ADH enzymes. These spectral signatures are not observed for WT- or K142A-variants or upon addition of Ca2+ to PQQ ⸦ K142D-PqqT. Addition of benzyl alcohol to La3+-bound PQQ ⸦ K142D-PqqT (but not Ca2+-bound PQQ ⸦ K142D-PqqT, or La3+-bound PQQ ⸦ WT-PqqT) produces spectroscopic changes associated with PQQ reduction, and chemical trapping experiments reveal the production of benzaldehyde, supporting ADH activity. By creating a metal binding site that mimics native ADH enzymes, we present a rare earth-dependent artificial metalloenzyme primed for future mechanistic, biocatalytic, and biosensing applications.


Asunto(s)
Methylobacterium extorquens , Methylobacterium extorquens/enzimología , Methylobacterium extorquens/metabolismo , Metaloproteínas/química , Metaloproteínas/metabolismo , Alcohol Deshidrogenasa/metabolismo , Alcohol Deshidrogenasa/química , Cristalografía por Rayos X , Cofactor PQQ/metabolismo , Cofactor PQQ/química , Materiales Biomiméticos/química , Materiales Biomiméticos/metabolismo , Metales de Tierras Raras/química , Metales de Tierras Raras/metabolismo , Modelos Moleculares , Lantano/química , Lantano/metabolismo
2.
ACS Synth Biol ; 13(8): 2600-2610, 2024 Aug 16.
Artículo en Inglés | MEDLINE | ID: mdl-39110689

RESUMEN

The engineering of enzymatic activity generally involves alteration of the protein primary sequences, which introduce structural changes that give rise to functional improvements. Mechanical forces have been used to interrogate protein biophysics, leading to deep mechanistic insights in single-molecule studies. Here, we use simple DNA springs to apply small pulling forces to perturb the active site of a thermostable alcohol dehydrogenase. Methods were developed to enable the study of different spring lengths and spring orientations under bulk catalysis conditions. Tension applied across the active site expanded the binding pocket volume and shifted the preference of the enzyme for longer chain-length substrates, which could be tuned by altering the spring length and the resultant applied force. The substrate specificity changes did not occur when the DNA spring was either severed or rotated by ∼90°. These findings demonstrate an alternative approach in protein engineering, where active site architectures can be dynamically and reversibly remodeled using applied mechanical forces.


Asunto(s)
Alcohol Deshidrogenasa , Biocatálisis , Dominio Catalítico , ADN , Ingeniería de Proteínas , Ingeniería de Proteínas/métodos , Alcohol Deshidrogenasa/genética , Alcohol Deshidrogenasa/metabolismo , Alcohol Deshidrogenasa/química , ADN/metabolismo , ADN/química , ADN/genética , Especificidad por Sustrato
3.
Molecules ; 29(16)2024 Aug 20.
Artículo en Inglés | MEDLINE | ID: mdl-39203012

RESUMEN

2,3-butanediol (2,3-BD) is a versatile bio-based platform chemical. An artificial four-enzyme synthetic biosystem composed of ethanol dehydrogenase, NADH oxidase, formolase and 2,3-butanediol dehydrogenase was designed for upgrading ethanol to 2,3-BD in our previous study. However, a key challenge in developing in vitro enzymatic systems for 2,3-BD synthesis is the relatively sluggish catalytic efficiency of formolase, which catalyzes the rate-limiting step in such systems. Herein, this study reports how engineering the tunnel and substrate binding pocket of FLS improved its catalytic performance. A series of single-point and combinatorial variants were successfully obtained which displayed both higher catalytic efficiency and better substrate tolerance than wild-type FLS. Subsequently, a cell-free biosystem based on the FLS:I28V/L482E enzyme was implemented for upgrading ethanol to 2,3-BD. Ultimately, this system achieved efficient production of 2,3-BD from ethanol by the fed-batch method, reaching a concentration of 1.39 M (124.83 g/L) of the product and providing both excellent productivity and yield values of 5.94 g/L/h and 92.7%, respectively. Taken together, this modified enzymatic catalysis system provides a highly promising alternative approach for sustainable and cost-competitive production of 2,3-BD.


Asunto(s)
Oxidorreductasas de Alcohol , Butileno Glicoles , Etanol , Butileno Glicoles/metabolismo , Butileno Glicoles/química , Etanol/metabolismo , Oxidorreductasas de Alcohol/metabolismo , Oxidorreductasas de Alcohol/química , NADH NADPH Oxidorreductasas/metabolismo , NADH NADPH Oxidorreductasas/química , Complejos Multienzimáticos/metabolismo , Complejos Multienzimáticos/química , Alcohol Deshidrogenasa/metabolismo , Alcohol Deshidrogenasa/química
4.
Int J Biol Macromol ; 275(Pt 2): 133707, 2024 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-38972651

RESUMEN

Alcohol dehydrogenase (ADH) is an important enzyme that catalyzes alcohol oxidation and/or aldehyde reduction. As one of NAD+-dependent ADH types, iron-containing/activated ADH (Fe-ADH) is ubiquitous in Bacteria, Archaea, and Eukaryotes, possessing a similar "tunnel-like" structure that is composed of a domain A in its N-terminus and a domain B in its C-terminus. A conserved "GGGS" sequence in the domain A of Fe-ADH associates with NAD+, and one conserved Asp residue and three conserved His residues in the domain B are its catalytic active sites by surrounding with Fe atom, suggesting that it might employ similar catalytic mechanism. Notably, all the biochemically characterized Fe-ADHs from hyperthermophiles that thrive in above 80 °C possess two unique characteristics that are absent in other Fe-ADHs: thermophilicity and thermostability, thereby demonstrating that they can oxidize alcohol and reduce aldehyde at high temperature. Considering these two unique characteristics, Fe-ADHs from hyperthermophiles are potentially industrial biocatalysts for alcohol and aldehyde biotransformation at high temperature. Herein, we reviewed structural and biochemical characteristics of Fe-ADHs from hyperthermophiles, focusing on similarity and difference between Fe-ADHs from hyperthermophiles and their homologs from non-hyperthermophiles, and between hyperthermophilic archaeal Fe-ADHs and bacterial homologs. Furthermore, we proposed future directions of Fe-ADHs from hyperthermophiles.


Asunto(s)
Alcohol Deshidrogenasa , Estabilidad de Enzimas , Hierro , Alcohol Deshidrogenasa/química , Alcohol Deshidrogenasa/metabolismo , Hierro/metabolismo , Hierro/química , Archaea/enzimología , Dominio Catalítico , Modelos Moleculares , Calor , Oxidación-Reducción
5.
J Org Chem ; 89(15): 11043-11047, 2024 Aug 02.
Artículo en Inglés | MEDLINE | ID: mdl-39042018

RESUMEN

Asymmetric reduction of 2-chloro-1-(6-fluorochroman-2-yl)ethan-1-one (NEB-7) into 2-chloro-1-(6-fluorochroman-2-yl)ethan-1-ol (NEB-8) is the crucial step for synthesis of liposoluble ß1 receptor blocker nebivolol. Four efficient and stereoselective alcohol dehydrogenases were identified, enabling the stereoselective synthesis of all enantiomers of NEB-8 at a substrate loading of 137 g·L-1 with ee values of >99% and high space-time yields. This study provides novel biocatalysts for the efficient synthesis of nebivolol precursors and uncovers the molecular basis for enantioselectivity manipulation by parametrization of Prelog's rule.


Asunto(s)
Biocatálisis , Nebivolol , Nebivolol/química , Estereoisomerismo , Estructura Molecular , Antagonistas de Receptores Adrenérgicos beta 1/química , Antagonistas de Receptores Adrenérgicos beta 1/síntesis química , Alcohol Deshidrogenasa/antagonistas & inhibidores , Alcohol Deshidrogenasa/metabolismo , Alcohol Deshidrogenasa/química
6.
Int J Biol Macromol ; 270(Pt 2): 132238, 2024 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-38729463

RESUMEN

Alcohol dehydrogenases (ADHs) mediated biocatalytic asymmetric reduction of ketones have been widely applied in the synthesis of optically active secondary alcohols with highly reactive hydroxyl groups ligated to the stereogenic carbon and divided into (R)- and (S)-configurations. Stereocomplementary ADHs could be applied in the synthesis of both enantiomers and are increasingly accepted as the "first of choice" in green chemistry due to the high atomic economy, low environmental factor, 100 % theoretical yield, and high environmentally friendliness. Due to the equal importance of complementary alcohols, development of stereocomplementary ADHs draws increasing attention. This review is committed to summarize recent advance in discovery of naturally evolved and tailor-made stereocomplementary ADHs, unveil the molecular mechanism of stereoselective catalysis in views of classification and functional basis, and provide guidance for further engineering the stereoselectivity of ADHs for the industrial biosynthesis of chiral secondary alcohol of industrial relevance.


Asunto(s)
Alcohol Deshidrogenasa , Alcoholes , Alcohol Deshidrogenasa/química , Alcohol Deshidrogenasa/metabolismo , Alcoholes/química , Alcoholes/metabolismo , Estereoisomerismo , Biocatálisis
7.
Food Chem ; 450: 139323, 2024 Aug 30.
Artículo en Inglés | MEDLINE | ID: mdl-38636386

RESUMEN

Radix puerariae thomsonii (RPT) contains many phenolics and exhibits various health benefits. Although the free phenolics in RPT have been identified, the composition and content of bound phenolics, which account for approximately 20% of the total phenolic content, remain unknown. In this study, 12 compounds were isolated and identified from RPT-bound phenolic extracts, of which 2 were novel and 6 were reported first in RPT. ORAC and PSC antioxidant activities of 12 compounds, as well as their effects on alcohol dehydrogenase (ADH), aldehyde dehydrogenase (ALDH), α-glucosidase, and α-amylase were evaluated. Genistein exhibited the highest ORAC activity, while daidzin demonstrated superior PSC activity. Five compounds, including two new compounds, exhibited the ability to activate both ADH and ALDH. All the compounds except 4-hydroxyphenylacetic acid methyl ester and 2,4,4'-trihydroxydeoxybenzoin demonstrated inhibitory effects on α-glucosidase and α-amylase. Alkaline hydrolysis and stepwise enzymatic hydrolysis revealed that bound phenolics in RPT mainly exist within starch.


Asunto(s)
Fenoles , Extractos Vegetales , Pueraria , alfa-Amilasas , alfa-Glucosidasas , Pueraria/química , Fenoles/química , Fenoles/farmacología , alfa-Amilasas/química , alfa-Amilasas/metabolismo , alfa-Amilasas/antagonistas & inhibidores , alfa-Glucosidasas/química , alfa-Glucosidasas/metabolismo , Extractos Vegetales/química , Extractos Vegetales/farmacología , Sitios de Unión , Alcohol Deshidrogenasa/química , Alcohol Deshidrogenasa/metabolismo , Aldehído Deshidrogenasa/química , Aldehído Deshidrogenasa/metabolismo , Antioxidantes/química , Antioxidantes/farmacología , Raíces de Plantas/química , Inhibidores Enzimáticos/química , Inhibidores Enzimáticos/farmacología , Estructura Molecular , Medicamentos Herbarios Chinos/química , Medicamentos Herbarios Chinos/farmacología
8.
Colloids Surf B Biointerfaces ; 238: 113917, 2024 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-38615391

RESUMEN

In this study, the encapsulation and structural characteristics of the self-assembled liposome formed by epigallocatechin gallate (EGCG) and alcohol dehydrogenase (ADH) were studied. According to the results, EGCG significantly increased the catalytic activity of ADH with a 33.33 % activation rate and the liposomes were able to entrap EGCG-ADH with an effectiveness of 88.94 %. The self-assembled monolayers had nanometer-sized particles, and the excellent self-assembled system was demonstrated by the low PDI value and high surface absolute potential. The scanning electron microscope showed that the self-assembled liposome was honeycomb, groove-shaped, and rough. The spectroscopic results showed that EGCG-ADH complex was formed through hydrogen bond, which changed the secondary structure of the liposome, and verified EGCG-ADH liposome system was successfully prepared. In vitro digestion experiments showed that the gastrointestinal tolerance and antioxidant activity of EGCG-ADH liposomes were significantly higher than those of free EGCG-ADH.


Asunto(s)
Alcohol Deshidrogenasa , Catequina , Liposomas , Liposomas/química , Catequina/química , Catequina/análogos & derivados , Alcohol Deshidrogenasa/química , Alcohol Deshidrogenasa/metabolismo , Antioxidantes/química , Antioxidantes/farmacología , Tamaño de la Partícula , Enlace de Hidrógeno
9.
Chem Biol Interact ; 394: 110992, 2024 May 01.
Artículo en Inglés | MEDLINE | ID: mdl-38579923

RESUMEN

Histidine residues 44 and 48 in yeast alcohol dehydrogenase (ADH) bind to the coenzymes NAD(H) and contribute to catalysis. The individual H44R and H48Q substitutions alter the kinetics and pH dependencies, and now the roles of other ionizable groups in the enzyme were studied in the doubly substituted H44R/H48Q ADH. The substitutions make the enzyme more resistant to inactivation by diethyl pyrocarbonate, modestly improve affinity for coenzymes, and substantially decrease catalytic efficiencies for ethanol oxidation and acetaldehyde reduction. The pH dependencies for several kinetic parameters are shifted from pK values for wild-type ADH of 7.3-8.1 to values for H44R/H48Q ADH of 8.0-9.6, and are assigned to the water or alcohol bound to the catalytic zinc. It appears that the rate of binding of NAD+ is electrostatically favored with zinc-hydroxide whereas binding of NADH is faster with neutral zinc-water. The pH dependencies of catalytic efficiencies (V/EtKm) for ethanol oxidation and acetaldehyde reduction are similarly controlled by deprotonation and protonation, respectively. The substitutions make an enzyme that resembles the homologous horse liver H51Q ADH, which has Arg-47 and Gln-51 and exhibits similar pK values. In the wild-type ADHs, it appears that His-48 (or His-51) in the proton relay systems linked to the catalytic zinc ligands modulate catalytic efficiencies.


Asunto(s)
Alcohol Deshidrogenasa , Dominio Catalítico , Histidina , Saccharomyces cerevisiae , Acetaldehído/metabolismo , Acetaldehído/química , Alcohol Deshidrogenasa/metabolismo , Alcohol Deshidrogenasa/genética , Alcohol Deshidrogenasa/química , Sustitución de Aminoácidos , Dietil Pirocarbonato/química , Dietil Pirocarbonato/farmacología , Etanol/metabolismo , Histidina/metabolismo , Histidina/química , Concentración de Iones de Hidrógeno , Cinética , NAD/metabolismo , Oxidación-Reducción , Saccharomyces cerevisiae/metabolismo , Saccharomyces cerevisiae/enzimología , Proteínas de Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/química , Proteínas de Saccharomyces cerevisiae/genética , Zinc/metabolismo , Zinc/química
10.
Chembiochem ; 25(12): e202400147, 2024 Jun 17.
Artículo en Inglés | MEDLINE | ID: mdl-38629211

RESUMEN

Chiral alcohols are not only important building blocks of various bioactive natural compounds and pharmaceuticals, but can serve as synthetic precursors for other valuable organic chemicals, thus the synthesis of these products is of great importance. Bio-catalysis represents one effective way to obtain these molecules, however, the weak stability and high cost of enzymes often hinder its broad application. In this work, we designed a biological nanoreactor by embedding alcohol dehydrogenase (ADH) and glucose dehydrogenase (GDH) in metal-organic-framework ZIF-8. The biocatalyst ADH&GDH@ZIF-8 could be applied to the asymmetric reduction of a series of ketones to give chiral alcohols in high yields (up to 99 %) and with excellent enantioselectivities (>99 %). In addition, the heterogeneous biocatalyst could be recycled and reused at least four times with slight activity decline. Moreover, E. coli containing ADH and GDH was immobilized by ZIF-8 to form biocatalyst E. coli@ZIF-8, which also exhibits good catalytic behaviours. Finally, the chiral alcohols are further converted to marketed drugs (R)-Fendiline, (S)-Rivastigmine and NPS R-568 respectively.


Asunto(s)
Alcohol Deshidrogenasa , Biocatálisis , Enzimas Inmovilizadas , Escherichia coli , Glucosa 1-Deshidrogenasa , Cetonas , Estructuras Metalorgánicas , Alcohol Deshidrogenasa/metabolismo , Alcohol Deshidrogenasa/química , Estructuras Metalorgánicas/química , Estructuras Metalorgánicas/metabolismo , Cetonas/química , Cetonas/metabolismo , Enzimas Inmovilizadas/metabolismo , Enzimas Inmovilizadas/química , Escherichia coli/enzimología , Escherichia coli/metabolismo , Glucosa 1-Deshidrogenasa/metabolismo , Glucosa 1-Deshidrogenasa/química , Oxidación-Reducción , Estereoisomerismo
11.
Angew Chem Int Ed Engl ; 63(22): e202403539, 2024 05 27.
Artículo en Inglés | MEDLINE | ID: mdl-38556813

RESUMEN

The design and orderly layered co-immobilization of multiple enzymes on resin particles remain challenging. In this study, the SpyTag/SpyCatcher binding pair was fused to the N-terminus of an alcohol dehydrogenase (ADH) and an aldo-keto reductase (AKR), respectively. A non-canonical amino acid (ncAA), p-azido-L-phenylalanine (p-AzF), as the anchor for covalent bonding enzymes, was genetically inserted into preselected sites in the AKR and ADH. Employing the two bioorthogonal counterparts of SpyTag/SpyCatcher and azide-alkyne cycloaddition for the immobilization of AKR and ADH enabled sequential dual-enzyme coating on porous microspheres. The ordered dual-enzyme reactor was subsequently used to synthesize (S)-1-(2-chlorophenyl)ethanol asymmetrically from the corresponding prochiral ketone, enabling the in situ regeneration of NADPH. The reactor exhibited a high catalytic conversion of 74 % and good reproducibility, retaining 80 % of its initial activity after six cycles. The product had 99.9 % ee, which that was maintained in each cycle. Additionally, the double-layer immobilization method significantly increased the enzyme loading capacity, which was approximately 1.7 times greater than that of traditional single-layer immobilization. More importantly, it simultaneously enabled both the purification and immobilization of multiple enzymes on carriers, thus providing a convenient approach to facilitate cascade biocatalysis.


Asunto(s)
Alcohol Deshidrogenasa , Biocatálisis , Enzimas Inmovilizadas , Enzimas Inmovilizadas/química , Enzimas Inmovilizadas/metabolismo , Alcohol Deshidrogenasa/metabolismo , Alcohol Deshidrogenasa/química , Alcohol Deshidrogenasa/genética , Ingeniería de Proteínas , Aldo-Ceto Reductasas/metabolismo , Aldo-Ceto Reductasas/química , Aldo-Ceto Reductasas/genética , Fenilalanina/química , Fenilalanina/metabolismo , Fenilalanina/análogos & derivados , Azidas/química
12.
Angew Chem Int Ed Engl ; 63(27): e202404024, 2024 07 01.
Artículo en Inglés | MEDLINE | ID: mdl-38641561

RESUMEN

Here we demonstrate the preparation of enzyme-metal biohybrids of NAD+ reductase with biocatalytically-synthesised small gold nanoparticles (NPs, <10 nm) and core-shell gold-platinum NPs for tandem catalysis. Despite the variety of methods available for NP synthesis, there remains a need for more sustainable strategies which also give precise control over the shape and size of the metal NPs for applications in catalysis, biomedical devices, and electronics. We demonstrate facile biosynthesis of spherical, highly uniform, gold NPs under mild conditions using an isolated enzyme moiety, an NAD+ reductase, to reduce metal salts while oxidising a nicotinamide-containing cofactor. By subsequently introducing platinum salts, we show that core-shell Au@Pt NPs can then be formed. Catalytic function of these enzyme-Au@Pt NP hybrids was demonstrated for H2-driven NADH recycling to support enantioselective ketone reduction by an NADH-dependent alcohol dehydrogenase.


Asunto(s)
Biocatálisis , Oro , Nanopartículas del Metal , NAD , Platino (Metal) , Nanopartículas del Metal/química , NAD/química , NAD/metabolismo , Oro/química , Platino (Metal)/química , Hidrógeno/química , Hidrógeno/metabolismo , Alcohol Deshidrogenasa/metabolismo , Alcohol Deshidrogenasa/química , Oxidación-Reducción
13.
Chembiochem ; 25(11): e202400108, 2024 Jun 03.
Artículo en Inglés | MEDLINE | ID: mdl-38567504

RESUMEN

Detailed insights into protein structure/function relationships require robust characterization methodologies. Free-solution capillary electrophoresis (CE) is a unique separation technique which is sensitive to the conformation and/or composition of proteins, and therefore provides information on the heterogeneity of these properties. Three unrelated, conformationally/compositionally-altered proteins were separated by CE. An electrophoretic mobility distribution was determined for each protein along with its conformational and/or compositional heterogeneity. The CE results were compared with molar mass distributions obtained from size-exclusion chromatography coupled to light scattering (SEC-MALS). Bovine serum albumin multimers and two monomeric species were separated, highlighting variations in conformational/compositional heterogeneity among the multimers. Analysis of yeast alcohol dehydrogenase resolved two monomeric conformers and various tetrameric species, illustrating the impact of zinc ion removal and disulfide bond reduction on the protein's heterogeneity. The apo (calcium-free) and holo forms of bovine α-lactalbumin were separated and differences in the species' heterogeneity were measured; by contrast, the SEC-MALS profiles were identical. Comparative analysis of these structurally unrelated proteins provided novel insights into the interplay between molar mass and conformational/compositional heterogeneity. Overall, this study expands the utility of CE by demonstrating its capacity to discern protein species and their heterogeneity, properties which are not readily accessible by other analytical techniques.


Asunto(s)
Electroforesis Capilar , Conformación Proteica , Bovinos , Animales , Alcohol Deshidrogenasa/química , Alcohol Deshidrogenasa/metabolismo , Albúmina Sérica Bovina/química , Lactalbúmina/química
14.
Chemistry ; 30(32): e202400454, 2024 Jun 06.
Artículo en Inglés | MEDLINE | ID: mdl-38568868

RESUMEN

Rivastigmine is one of the several pharmaceuticals widely prescribed for the treatment of Alzheimer's disease. However, its practical synthesis still faces many issues, such as the involvement of toxic metals and harsh reaction conditions. Herein, we report a chemo-enzymatic synthesis of Rivastigmine. The key chiral intermediate was synthesized by an engineered alcohol dehydrogenase from Lactobacillus brevis (LbADH). A semi-rational approach was employed to improve its catalytic activity and thermal stability. Several LbADH variants were obtained with a remarkable increase in activity and melting temperature. Exploration of the substrate scope of these variants demonstrated improved activities toward various ketones, especially acetophenone analogs. To further recycle and reuse the biocatalyst, one LbADH variant and glucose dehydrogenase were co-immobilized on nanoparticles. By integrating enzymatic and chemical steps, Rivastigmine was successfully synthesized with an overall yield of 66 %. This study offers an efficient chemo-enzymatic route for Rivastigmine and provides several efficient LbADH variants with a broad range of potential applications.


Asunto(s)
Alcohol Deshidrogenasa , Enzimas Inmovilizadas , Levilactobacillus brevis , Rivastigmina , Rivastigmina/química , Levilactobacillus brevis/enzimología , Alcohol Deshidrogenasa/metabolismo , Alcohol Deshidrogenasa/química , Enzimas Inmovilizadas/química , Enzimas Inmovilizadas/metabolismo , Biocatálisis , Acetofenonas/química , Acetofenonas/metabolismo , Ingeniería de Proteínas
15.
J Chem Inf Model ; 64(8): 3400-3410, 2024 Apr 22.
Artículo en Inglés | MEDLINE | ID: mdl-38537611

RESUMEN

Lactobacillus kefir alcohol dehydrogenase (LkADH) and ketoreductase from Chryseobacterium sp. CA49 (ChKRED12) exhibit different chemoselectivity and stereoselectivity toward a substrate with both keto and aldehyde carbonyl groups. LkADH selectively reduces the keto carbonyl group while retaining the aldehyde carbonyl group, producing optically pure R-alcohols. In contrast, ChKRED12 selectively reduces the aldehyde group and exhibits low reactivity toward ketone carbonyls. This study investigated the structural basis for these differences and the role of specific residues in the active site. Molecular dynamics (MD) simulations and quantum chemical calculations were used to investigate the interactions between the substrate and the enzymes and the essential cause of this phenomenon. The present study has revealed that LkADH and ChKRED12 exhibit significant differences in the structure of their respective active pockets, which is a crucial determinant of their distinct chemoselectivity toward the same substrate. Moreover, residues N89, N113, and E144 within LkADH as well as Q151 and D190 within ChKRED12 have been identified as key contributors to substrate stabilization within the active pocket through electrostatic interactions and van der Waals forces, followed by hydride transfer utilizing the coenzyme NADPH. Furthermore, the enantioselectivity mechanism of LkADH has been elucidated using quantum chemical methods. Overall, these findings not only provide fundamental insights into the underlying reasons for the observed differences in selectivity but also offer a detailed mechanistic understanding of the catalytic reaction.


Asunto(s)
Aldehídos , Cetonas , Simulación de Dinámica Molecular , Cetonas/química , Cetonas/metabolismo , Aldehídos/química , Aldehídos/metabolismo , Especificidad por Sustrato , Teoría Cuántica , Lactobacillus/enzimología , Lactobacillus/metabolismo , Dominio Catalítico , Alcohol Deshidrogenasa/metabolismo , Alcohol Deshidrogenasa/química
16.
Protein Sci ; 33(4): e4933, 2024 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-38501647

RESUMEN

Alcohol dehydrogenases (ADHs) are synthetically important biocatalysts for the asymmetric synthesis of chiral alcohols. The catalytic performance of ADHs in the presence of organic solvents is often important since most prochiral ketones are highly hydrophobic. Here, the organic solvent tolerance of KpADH from Kluyveromyces polyspora was semi-rationally evolved. Using tolerant variants obtained, meticulous experiments and computational studies were conducted to explore properties including stability, activity and kinetics in the presence of various organic solvents. Compared with WT, variant V231D exhibited 1.9-fold improvement in ethanol tolerance, while S237G showed a 6-fold increase in catalytic efficiency, a higher T 50 15 $$ {\mathrm{T}}_{50}^{15} $$ , as well as 15% higher tolerance in 7.5% (v/v) ethanol. Based on 3 × 100 ns MD simulations, the increased tolerance of V231D and S237G against ethanol may be ascribed to their enhanced ability in retaining water molecules and repelling ethanol molecules. Moreover, 6.3-fold decreased KM value of V231D toward hydrophilic ketone substrate confirmed its capability of retaining hydration shell. Our results suggest that retaining hydration shell surrounding KpADH is critical for its tolerance to organic solvents, as well as catalytic performance. This study provides useful guidance for engineering organic solvent tolerance of KpADH and other ADHs.


Asunto(s)
Alcohol Deshidrogenasa , Etanol , Alcohol Deshidrogenasa/genética , Alcohol Deshidrogenasa/química , Solventes/química , Agua , Catálisis , Cetonas
17.
Plant J ; 118(4): 1054-1070, 2024 May.
Artículo en Inglés | MEDLINE | ID: mdl-38308388

RESUMEN

Alcohol dehydrogenases (ADHs) are a group of zinc-binding enzymes belonging to the medium-length dehydrogenase/reductase (MDR) protein superfamily. In plants, these enzymes fulfill important functions involving the reduction of toxic aldehydes to the corresponding alcohols (as well as catalyzing the reverse reaction, i.e., alcohol oxidation; ADH1) and the reduction of nitrosoglutathione (GSNO; ADH2/GSNOR). We investigated and compared the structural and biochemical properties of ADH1 and GSNOR from Arabidopsis thaliana. We expressed and purified ADH1 and GSNOR and determined two new structures, NADH-ADH1 and apo-GSNOR, thus completing the structural landscape of Arabidopsis ADHs in both apo- and holo-forms. A structural comparison of these Arabidopsis ADHs revealed a high sequence conservation (59% identity) and a similar fold. In contrast, a striking dissimilarity was observed in the catalytic cavity supporting substrate specificity and accommodation. Consistently, ADH1 and GSNOR showed strict specificity for their substrates (ethanol and GSNO, respectively), although both enzymes had the ability to oxidize long-chain alcohols, with ADH1 performing better than GSNOR. Both enzymes contain a high number of cysteines (12 and 15 out of 379 residues for ADH1 and GSNOR, respectively) and showed a significant and similar responsivity to thiol-oxidizing agents, indicating that redox modifications may constitute a mechanism for controlling enzyme activity under both optimal growth and stress conditions.


Asunto(s)
Alcohol Deshidrogenasa , Proteínas de Arabidopsis , Arabidopsis , Oxidación-Reducción , Arabidopsis/enzimología , Arabidopsis/genética , Alcohol Deshidrogenasa/metabolismo , Alcohol Deshidrogenasa/genética , Alcohol Deshidrogenasa/química , Proteínas de Arabidopsis/metabolismo , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/química , Especificidad por Sustrato , S-Nitrosoglutatión/metabolismo , Secuencia de Aminoácidos , Etanol/metabolismo
18.
Biochem Biophys Res Commun ; 691: 149298, 2024 Jan 08.
Artículo en Inglés | MEDLINE | ID: mdl-38011820

RESUMEN

Alcohol dehydrogenases (ADHs) are popular catalysts for synthesizing chiral synthons a vital step for active pharmaceutical intermediate (API) production. They are grouped into three superfamilies namely, medium-chain (MDRs), short-chain dehydrogenase/reductases (SDRs), and iron-containing alcohol dehydrogenases. The former two are used extensively for producing various chiral synthons. Many studies screen multiple enzymes or engineer a specific enzyme for catalyzing a substrate of interest. These processes are resource-intensive and intricate. The current study attempts to decipher the ability to match different ADHs with their ideal substrates using machine learning algorithms. We explore the catalysis of 284 antibacterial ketone intermediates, against MDRs and SDRs to demonstrate a unique pattern of activity. To facilitate machine learning we curated a dataset comprising 33 features, encompassing 4 descriptors for each compound. Subsequently, an ensemble of machine learning techniques viz. Partial Least Squares (PLS) regression, k-Nearest Neighbors (kNN) regression, and Support Vector Machine (SVM) regression, was harnessed. Moreover, the assimilation of Principal Component Analysis (PCA) augmented precision and accuracy, thereby refining and demarcating diverse compound classes. As such, this classification is useful for discerning substrates amenable to diverse alcohol dehydrogenases, thereby mitigating the reliance on high-throughput screening or engineering in identifying the optimal enzyme for specific substrate.


Asunto(s)
Alcohol Deshidrogenasa , Algoritmos , Alcohol Deshidrogenasa/química , Catálisis , Aprendizaje Automático , Máquina de Vectores de Soporte
19.
Phys Chem Chem Phys ; 25(45): 31292-31300, 2023 Nov 22.
Artículo en Inglés | MEDLINE | ID: mdl-37955422

RESUMEN

Alcohol dehydrogenases (ADH) are a family of enzymes that catalyse the interconversion between ketones/aldehydes and alcohols in the presence of NADPH cofactor. It is challenging to desymmetrise the substituted cyclopentane-1,3-dione by engineering an ADH, while the reaction mechanism of the metal independent ADH remains elusive. Here we measured the conversion of a model substrate 2-benzyl-2-methylcyclopentane-1,3-dione by LbADH and found it predominately gave the (2R,3R) product. Binding mode analysis of the substrate in LbADH from molecular dynamics simulations disclosed the origin of the enantioselectivity of the enzyme; the opening and closing of the loop 191-205 above the substrate are responsible for shaping the binding pocket to orientate the substrate, so as to give different stereoisomer products. Using QM/MM calculations, we elucidated the reaction mechanism of LbADH. Furthermore, we demonstrated the reaction profile corresponding to the production of different stereoisomers, which is in accordance with our experimental observations. This research here will shed a light on the rational engineering of ADH to achieve stereodivergent stereoisomer products.


Asunto(s)
Alcohol Deshidrogenasa , Alcoholes , Alcohol Deshidrogenasa/química , Aldehídos , Catálisis , Cetonas/química , Especificidad por Sustrato
20.
Protein Eng Des Sel ; 362023 01 21.
Artículo en Inglés | MEDLINE | ID: mdl-37306945

RESUMEN

Gene fusion or co-immobilization are key tools to optimize enzymatic reaction cascades by modulating catalytic features, stability and applicability. Achieving a defined spatial organization between biocatalysts by site-specific applications is complicated by the involvement of oligomeric enzymes. It can lead to activity losses due to disturbances of the quaternary structures and difficulties in stoichiometric control. Thus, a toolkit of active and robust monomeric enzymes is desirable for such applications. In this study, we engineered one of the rare examples of monomeric alcohol dehydrogenases for improved catalytic characteristics by site-directed mutagenesis. The enzyme from the hyperthermophilic archaeon Thermococcus kodakarensis naturally exhibits high thermostability and a broad substrate spectrum, but only low activity at moderate temperatures. The best enzyme variants showed an ~5-fold (2-heptanol) and 9-fold (3-heptanol) higher activity while preserving enantioselectivity and good thermodynamic stability. These variants also exhibited modified kinetic characteristics regarding regioselectivity, pH dependence and activation by NaCl.


Asunto(s)
Alcohol Deshidrogenasa , Alcohol Deshidrogenasa/genética , Alcohol Deshidrogenasa/química , Alcohol Deshidrogenasa/metabolismo , Heptanol , Mutagénesis Sitio-Dirigida , Temperatura , Termodinámica , Estabilidad de Enzimas , Cinética
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