Enzyme-substrate Interactions Research Articles

S-acylation of Sprouty and SPRED proteins by the S-acyltransferase zDHHC17 involves a novel mode of enzyme–substrate interaction

S-acylation is an essential post-translational modification, which is mediated by a family of 23 zDHHC enzymes in humans. Several thousand proteins are modified by S-acylation; however, we lack a detailed understanding of how enzyme-substrate recognition and specificity is achieved. Previous work showed that the ankyrin repeat domain of zDHHC17 (ANK17) recognizes a short linear motif, known as the zDHHC ANK binding motif (zDABM) in substrate protein SNAP25, as a mechanism of substrate recruitment prior to S-acylation. Here, we investigated the S-acylation of the Sprouty and SPRED family of proteins by zDHHC17. Interestingly, although Sprouty-2 (Spry2) contains a zDABM that interacts with ANK17, this mode of binding is dispensable for S-acylation, and indeed removal of the zDABM does not completely ablate binding to zDHHC17. Furthermore, the related SPRED3 protein interacts with and is efficiently S-acylated by zDHHC17, despite lacking a zDABM. We undertook mutational analysis of SPRED3 to better understand the basis of its zDABM-independent interaction with zDHHC17. This analysis found that the cysteine-rich SPR domain of SPRED3, which is the defining feature of all Sprouty and SPRED proteins, interacts with zDHHC17. Surprisingly, the interaction with SPRED3 was independent of ANK17. Our mutational analysis of Spry2 was consistent with the SPR domain of this protein containing a zDHHC17-binding site, and Spry2 also showed detectable binding to a zDHHC17 mutant lacking the ANK domain. Thus, zDHHC17 can recognize its substrates through zDABM-dependent and/or zDABM-independent mechanisms, and some substrates display more than one mode of binding to this enzyme.

Comparing the effect of several pretreatment steps, selected to steer (bio)chemical reactions, on the volatile profile of leek (Allium ampeloprasum var. porrum)

Volatile compounds in foods can witness the occurrence of (bio)chemical reactions, comprising both enzymatic and non-enzymatic reactions, which can be influenced by processing. This study investigated the effect of different pretreatments aimed at either minimizing, realized by a heat treatment, or inducing, realized by a tissue disruptive treatment, enzymatic reactivities, on the volatile profile of leek. The volatile profiles obtained were then linked to possible (bio)chemical reactions that could have occurred during the treatments. The study showed that different pretreatments led to markedly different volatile profiles, characterized by different (abundances of) volatile compounds. Partial and extensive tissue disruption was achieved by pulsed electric fields at low electric field strength and mixing, respectively. After these tissue disruptive treatments, the volatile compounds could mainly be related to the occurrence of several enzyme-substrate interactions, including conversions of alk(en)yl cysteine sulfoxides by alliinase and of unsaturated fatty acids by lipoxygenase and hydroperoxide lyase. Thermally-induced reactions were also observed to impact the resultant volatile profile. Present study revealed that targeted (pre)treatment allows to steer (bio)chemical reactions towards specific volatile compounds in leek products.

Modification of nitrile hydratase from Rhodococcus erythropolis CCM2595 by semirational design to enhance its substrate affinity.

Nitrile hydratase (NHase, EC 4.2.1.84) is an excellent biocatalyst that catalyzes the hydration of nitrile substances to their corresponding amides. Given its catalytic specificity and eco-friendliness, NHase has extensive applications in the chemical, pharmaceutical, and cosmetic industries. To improve the affinity between Rhodococcus erythropolis CCM2595-derived NHase (ReNHase) and adiponitrile, this study used a semirational design to improve the efficiency of ReNHase in catalyzing the generation of 5-cyanopentanamide from adiponitrile. Enzyme kinetics analysis showed that Km of the mutant ReNHaseB:G196Y was 3.265 mmol l-1, which was lower than that of the wild-type NHase. The affinity of the mutant ReNHaseB:G196Y to adiponitrile was increased by 36.35%, and the efficiency of the mutant ReNHaseB:G196Y in catalyzing adiponitrile to 5-cyanopentamide was increased by 10.11%. The analysis of the enzyme-substrate interaction showed that the hydrogen bond length of the mutant ReNHaseB:G196Y to adiponitrile was shortened by 0.59 Å, which enhanced the interaction between the mutant and adiponitrile and, thereby, increased the substrate affinity. Similarly, the structural analysis showed that the amino acid flexibility near the mutation site of ReNHaseB:G196Y was increased, which enhanced the binding force between the enzyme and adiponitrile. Our work may provide a new theoretical basis for the modification of substrate affinity of NHase and increase the possibility of industrial applications of the enzyme.

Highly catalytic supramolecular host–guest complex for high value directional conversion of lignin to syringyl monomer

In order to meet the challenge of enzyme catalysis of waste lignin, laccase (LAC)- guaiacyl(G)-type monomers noncovalent supramolecular system (LGS) were constructed for conversion of lignin. In this contribution, the catalytic effect of LGS formed by LAC and G-type monomers was studied. LAC changes the secondary structure conformation of its binding site to accommodate the G-type monomer, which is bound by hydrogen bonding and hydrophobic interactions. A mechanistic study highlights that the non-covalent complexation accelerates the internal electron transfer rate of LGS and syringol substrate for subsequent coupling reactions. In the presence of guaiacol/4-ethylguaiacol/vanillin-LAC, the conversion of dealkali lignin were 16.44, 29.12 and 22.72, respectively, higher than that in the presence of LAC alone. And the product of syringyl monomer was significantly increased in the actual lignin catalysis. Our work explains the mechanisms underlying existing enzyme-substrate interactions and enhanced catalytic system can be used for efficient utilization of waste.

Enzyme-substrate interface targeting by imidazole-based γ-secretase modulators activates γ-secretase and stabilizes its interaction with APP.

Alzheimer's disease (AD) pathogenesis has been linked to the accumulation of longer, aggregation-prone amyloid β (Aβ) peptides in the brain. Γ-secretases generate Aβ peptides from the amyloid precursor protein (APP). Γ-secretase modulators (GSMs) promote the generation of shorter, less-amyloidogenic Aβs and have therapeutic potential. However, poorly defined drug-target interactions and mechanisms of action have hampered their therapeutic development. Here, we investigate the interactions between the imidazole-based GSM and its target γ-secretase-APP using experimental and in silico approaches. We map the GSM binding site to the enzyme-substrate interface, define a drug-binding mode that is consistent with functional and structural data, and provide molecular insights into the underlying mechanisms of action. In this respect, our analyses show that occupancy of a γ-secretase (sub)pocket, mediating binding of the modulator's imidazole moiety, is sufficient to trigger allosteric rearrangements in γ-secretase as well as stabilize enzyme-substrate interactions. Together, these findings may facilitate the rational design of new modulators of γ-secretase with improved pharmacological properties.

Combinatorial treatment with β-glucanase enzyme and chlorhexidine induces cysticidal effects in Acanthamoeba cyst.

Acanthamoeba cysts have a cellulose cell wall made up of a solid layer of β-glucan, which confers resistance to the dormant phase of this microorganism. The ability of Acanthamoeba to change to this dormant phase causes difficulties in treating its infection at the cyst stage as compared to the trophozoite stage. Therefore, targeting cyst total mortality can help to prevent re-infection in patients. To ensure cysticidal treatment, a β-glucanase enzyme was introduced in vitro to the Acanthamoeba cyst, followed by a chlorhexidine solution treatment. β-glucanase enzyme and chlorhexidine dose-response analysis was performed based on cell wall integrity measurement. The treatment was also performed on human corneal epithelial cells to confirm the safety of the treatment in vitro. The surface morphology of the cysts was observed using scanning electron microscopy (SEM), while the protein alterations were determined using 1D protein analysis. The interaction of the β-glucanase enzyme with cellulose linkages was investigated based on molecular dosimetry. Incubation of the cyst for 24h at 8.75 units/ml of β-glucanase followed by 0.88μg/ml of chlorhexidine resulted in a substantial reduction in the total chlorhexidine used, which made it safer for human corneal epithelial cells. Ultrastructural changes revealed the reduction of the thickness in ectocyst and endocyst layers with the loss of the internal structure of the cyst. After combination treatment of chlorhexidine and β-glucanase, a decrease in the cyst protein from the size of 37 to 25kDa was observed. The enzyme-substrate interaction validated these results based on molecular docking between 1,4-β-D-glucan and 1,4- β-D-xylan with the β-glucanase enzyme. In silico analysis revealed that two catalytic glutamate residues (Glu160 and Glu267) are essential to catalysing the hydrolytic reaction. Molecular dynamic simulation analysis revealed that both ligands formed stable interactions throughout the simulation. This work concludes that the enzymatic approach combined with chlorhexidine is a novel and effective technique for ensuring the cysticidal effects against the Acanthamoeba cyst. The interaction of the chlorhexidine and β-glucanase enzyme on the surface of the cyst of amoeba resulted in the ecto-and endo cyst layer being damaged and confirmed the cysticidal effects.

Effects of terminal modification on the catalytic efficiency and thermostability of Brucella melitensis 7α-hydroxysteroid dehydrogenase

Brucella melitensis 7α-hydroxysteroid dehydrogenase (Bm7α-HSDH) catalyzes the oxidation of chenodeoxycholic acid to 7-oxolithocholic acid. In this work, we investigated the effects of terminal modification (His-tags location and terminal truncation) on its catalytic efficiency and thermostability. Compared with C-terminal His-tagged Bm7α-HSDH (C-Bm7α-HSDH), N-Bm7α-HSDH showed a 3.6-fold higher kcat and a 1.3-fold lower Km, resulting in a 7.0-fold higher kcat/Km value toward chenodeoxycholic acid. Circular dichroism spectroscopy indicated that the melting temperature of N-Bm7α-HSDH (46.13 °C) was 3.0 °C lower than that of C-Bm7α-HSDH (49.13 °C). N-Bm7α-HSDH produced 7-oxolithocholic acid in the highest yield of 96.7% in 4 h, whereas the C-Bm7α-HSDH gave 96.4% in 10 h. Moreover, amino acids truncation and His-tag cleave experiments confirmed the C-terminal residues played key roles in catalytic functions. Molecular dynamics simulations further indicated C-terminal His-tagged modification could deform the substrate-binding region to disrupt the enzyme–substrate interactions and catalytic motion. However, the N-terminal His-tag hardly affected the catalytic efficiency due to its location far from the active site of the enzyme. This study provides structural insights into the terminus modifications of hydroxysteroid dehydrogenase on steroid substrate recognition and stabilization, thus affecting its catalytic functions.

Exploring the expression patterns of palmitoylating and de-palmitoylating enzymes in the mouse brain using the curated RNA-seq database BrainPalmSeq.

Protein S-palmitoylation is a reversible post-translational lipid modification that plays a critical role in neuronal development and plasticity, while dysregulated S-palmitoylation underlies a number of severe neurological disorders. Dynamic S-palmitoylation is regulated by a large family of ZDHHC palmitoylating enzymes, their accessory proteins, and a small number of known de-palmitoylating enzymes. Here, we curated and analyzed expression data for the proteins that regulate S-palmitoylation from publicly available RNAseq datasets, providing a comprehensive overview of their distribution in the mouse nervous system. We developed a web-tool that enables interactive visualization of the expression patterns for these proteins in the nervous system (http://brainpalmseq.med.ubc.ca/), and explored this resource to find region and cell-type specific expression patterns that give insight into the function of palmitoylating and de-palmitoylating enzymes in the brain and neurological disorders. We found coordinated expression of ZDHHC enzymes with their accessory proteins, de-palmitoylating enzymes and other brain-expressed genes that included an enrichment of S-palmitoylation substrates. Finally, we utilized ZDHHC expression patterns to predict and validate palmitoylating enzyme-substrate interactions.

Elucidating the Role of O2 Uncoupling in the Oxidative Biodegradation of Organic Contaminants by Rieske Non-heme Iron Dioxygenases.

Oxygenations of aromatic soil and water contaminants with molecular O2 catalyzed by Rieske dioxygenases are frequent initial steps of biodegradation in natural and engineered environments. Many of these non-heme ferrous iron enzymes are known to be involved in contaminant metabolism, but the understanding of enzyme–substrate interactions that lead to successful biodegradation is still elusive. Here, we studied the mechanisms of O2 activation and substrate hydroxylation of two nitroarene dioxygenases to evaluate enzyme- and substrate-specific factors that determine the efficiency of oxygenated product formation. Experiments in enzyme assays of 2-nitrotoluene dioxygenase (2NTDO) and nitrobenzene dioxygenase (NBDO) with methyl-, fluoro-, chloro-, and hydroxy-substituted nitroaromatic substrates reveal that typically 20–100% of the enzyme’s activity involves unproductive paths of O2 activation with generation of reactive oxygen species through so-called O2 uncoupling. The 18O and 13C kinetic isotope effects of O2 activation and nitroaromatic substrate hydroxylation, respectively, suggest that O2 uncoupling occurs after generation of FeIII-(hydro)peroxo species in the catalytic cycle. While 2NTDO hydroxylates ortho-substituted nitroaromatic substrates more efficiently, NBDO favors meta-substituted, presumably due to distinct active site residues of the two enzymes. Our data implies, however, that the O2 uncoupling and hydroxylation activity cannot be assessed from simple structure–reactivity relationships. By quantifying O2 uncoupling by Rieske dioxygenases, our work provides a mechanistic link between contaminant biodegradation, the generation of reactive oxygen species, and possible adaptation strategies of microorganisms to the exposure of new contaminants.

Functionalisation of organosolv lignin by enzymatic demethylation for bioadhesive formulation

Bio-based adhesives offer a sustainable alternative to formaldehyde-based adhesives, which is the most common product applied in wood-based panel manufacturing. Despite the undeniable interest in lignin as a bulk chemical for the synthesis of bio-based adhesives, the main problem is its low reactivity. Therefore, it is crucial to study techniques to increase their reactivity, such as demethylation. One of the parameters to monitor the success of the demethylation is the methanol concentration measured in the reaction medium and complementing these results with the use of non-quantitative analyses such as FT-IR, MALDI-ToF and SEC. In order to maximize the action of the enzyme, a preliminary screening was performed with laccases with different redox potentials, which were added to organosolv lignin in the form of purified enzymes and cocktails. Trametes versicolor laccase was selected as the best candidate for the demethylation of organosolv lignin, with a methanol released concentration of 107 mg/L. Based on these results, parameters affecting both enzyme action and enzyme-substrate interaction were evaluated. Optimal working conditions were strongly defined by the use of surfactants that enhanced lignin solubility (Tween-80) and mediators that favored enzyme catalysis to participate directly in the enzyme catalytic cycle (HBT). However, it was also observed that factors such as pH, temperature and aeration have a direct impact on the enzymatic demethylation of lignin. Considering the operational variables that allowed better demethylation values, the amount of methanol released increased to 363 mg/L, which means an improvement of 239 %. These results were also supported by the increase in molecular weight observed in the SEC analysis and the reduction of the intensity of the FT-IR bands related to the methyl/methoxyl groups.

Chemistry of difluoromethylene phosphonates: history, state of the art, and prospects

Difluoromethylene phosphonates are non-hydrolyzable bioisosteres of phosphates. They have proven their efficiency as inhibitors of the enzymes that specialize in utilizing these essential biogenic molecules. Difluoromethylene phosphonates show a broad spectrum of biological activity and are used as molecular tools to study enzymes and enzyme-substrate interactions. In this review, we briefly summarize the importance of difluoromethylene phosphonates as a distinct class of synthetic phosphonates resulting from multidisciplinary efforts of the organophosphorus, organofluorine, and bioorganic research communities. We outline the development of the synthetic chemistry of difluoromethylene phosphonates from the historical perspective, discuss the most recent trends in the field, and highlight the existing challenges and unsolved questions

A Piroxicam Inclusion Complexation for Solubility Enhancement: Design and Development

Published on:June 2022 Journal of Young Pharmacists, 2022; 14(2):192-197 Original Article | doi:10.5530/jyp.2022.14.36 Authors: Saravanakumar Kasimbedu1,*, Shilpaja Chella1, Bharathi T1, Nagaveni Pommala2, Durga Srinivasa Rao Mannepalli3 1Department of Pharmaceutics, Sree Vidyanikethan College of Pharmacy, Sree Sainath Nagar, Tirupati, Andhra Pradesh, INDIA. 2Department of Pharmaceutics, S.V.U. College of Pharmaceutical Sciences, S.V. University, Tirupati, Andhra Pradesh, INDIA.3Department of Pharmaceutics, Jagan’s Institute of Pharmaceutical Sciences, Muthukur, SPSR Nellore, Andhra Pradesh, INDIA. Abstract: Background: Over last few years, the physical and chemical characteristics of inclusion complexes have generated a lot of attention. One of the most important reasons for this is the significance of enzyme-substrate and drug-receptor interactions in inclusion complexes. Materials and Methods:The aim of the study was to design Piroxicam’s inclusion complexation, to improve its solubility by the reduction of particle size which leads to improve the particle surface area thereby increases the wettability of the mixture. Physical mixture, co-grinded mixture, kneading and solvent evaporation method were used to prepare the inclusion complexation of Piroxicam with β-cyclodextrin at 1:0.5, 1:1, and 1:2 w/w (Piroxicam/β-cyclodextrin) ratios. Results: Differential scanning calorimetry, Fourier-transform infrared and X-ray diffraction and scanning electron microscopy studies were used to investigate the interaction of Piroxicam with β-cyclodextrin. From scanning electron microscopic studies, it was observed that crystalline were formed as spherical in shape with rough surface, small piece and Pure Piroxicam in crystalline form with rough surfaces. From Scanning electron microscopic studies, it was observed that amorphous were formed as spherical in shape with smooth surface, wide piece and β-Cyclodextrine in amorphous form with rough surfaces. Conclusion: The inclusion complexations of Piroxicam with β-cyclodextrin exhibited higher saturation solubility and dissolution rate than that of the pure drug of Piroxicam. Formulation K2 showed more drug release rate by reducing the particle size with complexation technique like kneading technique.Keywords: Co-grinded mixture, Inclusion Complexation, Kneading, Wetting Property, Particle Shap

A Computational Alanine Scanning of Heptapeptide RRRSAGM Targeting Dengue NS2B/NS3 Protease

The pathogenic dengue virus (DV) transmitted mainly by the Aedes aegypti mosquito has been the most rapidly spreading mosquito-borne viral disease and became a serious threat to global health issue in tropical and sub-tropical countries. The clinical symptoms ranging from mild to a fatal dengue hemorrhagic fever and dengue shock syndrome, characterized by failure of the circulation system that may lead to death. There are still no drugs or vaccines available in the market to prevent or treat dengue infections. Hence, the development of successful drugs that are safe and offer a long-lasting protection against dengue viruses is needed. Recently, the discovery of peptides with high specificity, selectivity, and efficacy; and relatively safer than small-molecule drugs have become a promising agent for a new drug. Previously, a molecular dynamic simulation reported that peptide NRRRRSAGMI from the capsid’s cleavage region had the most hydrogen bonds with NS2B/NS3 protease, thus it leads into a starting linear heptapeptide R(P3)-R(P2)-R(P1)-S(P1’)-A(P2’)-G(P3’)-M(P4’). This study aimed to investigate the importance and specificity of individual amino acid residue of the heptapeptide substrate on the binding affinity and interaction to NS2B/NS3 dengue protease through computational alanine scanning. It showed that the changing of P1 and P2 arginine to alanine resulted to higher values of binding affinity. Thus, the arginine is an important residue at the P1 and P2 positions for the binding of the substrate peptide to DENV NS2B/NS3 protease, hence the amino acid residues which are essential for the enzyme-substrate interactions can be predicted through computational alanine scanning.
 HIGHLIGHTS
 
 Dengue is a mosquito-transmitted virus cause of arthropod-borne viral disease
 The discovery of peptides became a potential agent for dengue virus and previously peptide NRRRRSAGMI has been reported as starting linear heptapeptide RRRSAGM
 A computational alanine scanning based on the peptide RRRSAGM has been performed
 S1 and S2 pockets show strong preferences for basic amino acids, whereas the S3 pocket is less selective for basic residue
 The arginine at P1 and P2 positions of the heptapeptide substrate contribute significantly to the substrate binding affinity
 
 GRAPHICAL ABSTRACT

Ionic liquids as a tunable solvent and modifier for biocatalysis

ABSTRACT The use of biocompatible ionic liquids (bio-ILs) as a “green” solvent with uniquely tunable cations and anions, specific selectivity, and many other desirable physicochemical properties in biocatalysis has shown great promises to address many challenges. A plethora of studies have demonstrated ILs possess a range of exceptional capabilities in coordinating biocatalysis such as stabilizing enzyme structure, enhancing enzyme-substrate interaction, increasing substrate solubility and product separation/removal, and improving enzyme immobilization/recycling. Therefore, bio-ILs have been explored for biocatalysis in a wide range of homogenous as well as multiphasic systems including biphasic, multiphasic, microemulsion, and whole-cell systems. This review provides an overview of IL-enabled biocatalysis including enzymatic and whole-cell reactions in homogeneous and multiphasic systems. First, the properties of IL concentration, specific ion effect, pH, viscosity, alkyl chain length, hydrophobicity, and polarity on the structures and activities of enzymes are discussed together with characterization techniques to elucidate the mechanisms of IL-enzyme interactions. Second, while homogenous biocatalysis systems containing ILs are briefly introduced and summarized, particular attention is given to multiphasic systems. Furthermore, recent progress in using bio-ILs to modify emerging new enzyme carrier materials including carbonaceous and magnetic nanomaterials, gel microspheres, and membranes as well as their effect on increasing enzyme stability and recycling are highlighted. Finally, we provide our expert opinion for more innovative research in the field and future outlook for the industrial application of ILs in biocatalysis.

An internal docking site stabilizes substrate binding to γ-secretase: Analysis by molecular dynamics simulations

Amyloid precursor protein (APP) is cleaved and processed sequentially by γ-secretase yielding amyloid β (Aβ) peptides of different lengths. Longer Aβ peptides are associated with the formation of neurotoxic plaques related to Alzheimer’s disease. Based on the APP substrate-bound structure of γ-secretase, we investigated the enzyme-substrate interaction using molecular dynamics simulations and generated model structures that represent the sequentially cleaved intermediates during the processing reaction. The simulations indicated an internal docking site providing strong enzyme-substrate packing interaction. In the enzyme-substrate complex, it is located close to the region where the helical conformation of the substrate is interrupted and continues toward the active site in an extended conformation. The internal docking site consists of two non-polar pockets that are preferentially filled by large hydrophobic or aromatic substrate side chains to stabilize binding. Placement of smaller residues such as glycine can trigger a shift in the cleavage pattern during the simulations or results in destabilization of substrate binding. The reduced packing by smaller residues also influences the hydration of the active site and the formation of a catalytically active state. The simulations on processed substrate intermediates and a substrate G33I mutation offer an explanation of the experimentally observed relative increase of short Aβ fragment production for this mutation. In addition, studies on a substrate K28A mutation indicate that the internal docking site opposes the tendency of substrate dissociation due to a hydrophobic mismatch at the membrane boundary caused by K28 during processing and substrate movement toward the enzyme active site. The proposed internal docking site could also be useful for the specific design of new γ-secretase modulators.

Stereoselectivity of Interaction of Nonsteroidal Anti-Inflammatory Drug S-Ketoprofen with L/D-Tryptophan in Phospholipid Membranes.

The mechanisms of stereoselectivity of the interaction of chiral drugs with active sites of enzymes and cell receptors attract significant attention. The first reason is the difference in therapeutic activity of the enantiomers of the common drugs. Another reason is the interest in the role of chiral inversion of amino acids involved in various peptides in the development of many diseases including Alzheimer’s, Parkinson’s, type II diabetes, and a number of other pathological conditions. In our study we use elementary chemical process—electron transfer (ET) to simulate individual stages of ligand–receptor and enzyme–substrate interactions. In particular, previous studies of photoinduced ET in chiral donor-acceptor dyads consisting of the nonsteroidal anti-inflammatory drug (R/S)-ketoprofen and (L)-tryptophan show the stereo and spin selectivity of ET in diastereomers. The present study is devoted to the interaction of (S)-ketoprofen with L- and D-enantiomers of tryptophan in homogeneous aqueous solution and in phospholipid membranes. The study was done using the NMR technique and molecular modeling. These approaches confirm efficient penetration of ketoprofen into the lipid bilayer and binding with tryptophan molecule. The short-lived paramagnetic intermediates formed during the photoinduced ET from electron donor tryptophan to ketoprofen have been detected using the chemically induced dynamic nuclear polarization (CIDNP) technique. It was found that S-ketoprofen interacts stereoselectively with tryptophan enantiomers in the lipid membrane. The formation of the ketyl radical of ketoprofen under irradiation leads to the oxidation of membrane lipids and may be the cause of ketoprofen phototoxicity. However, in contrast to a homogeneous solution in phosphate buffer saline, where the amino acid tryptophan accelerates the photodecomposition of KP due to intramolecular hydrogen transfer, tryptophan in a lipid membrane significantly reduces the rate of photodegradation due to a reversible electron (or hydrogen) transfer reaction. The stereoselectivity in the rate of KP and lipids decomposition under UV irradiation of S-ketoprofen in the presence of tryptophan enantiomers in lipid bilayer has been detected.

Boost-RS: boosted embeddings for recommender systems and its application to enzyme-substrate interaction prediction.

MotivationDespite experimental and curation efforts, the extent of enzyme promiscuity on substrates continues to be largely unexplored and under documented. Providing computational tools for the exploration of the enzyme–substrate interaction space can expedite experimentation and benefit applications such as constructing synthesis pathways for novel biomolecules, identifying products of metabolism on ingested compounds, and elucidating xenobiotic metabolism. Recommender systems (RS), which are currently unexplored for the enzyme–substrate interaction prediction problem, can be utilized to provide enzyme recommendations for substrates, and vice versa. The performance of Collaborative-Filtering (CF) RSs; however, hinges on the quality of embedding vectors of users and items (enzymes and substrates in our case). Importantly, enhancing CF embeddings with heterogeneous auxiliary data, specially relational data (e.g. hierarchical, pairwise or groupings), remains a challenge.ResultsWe propose an innovative general RS framework, termed Boost-RS that enhances RS performance by ‘boosting’ embedding vectors through auxiliary data. Specifically, Boost-RS is trained and dynamically tuned on multiple relevant auxiliary learning tasks Boost-RS utilizes contrastive learning tasks to exploit relational data. To show the efficacy of Boost-RS for the enzyme–substrate prediction interaction problem, we apply the Boost-RS framework to several baseline CF models. We show that each of our auxiliary tasks boosts learning of the embedding vectors, and that contrastive learning using Boost-RS outperforms attribute concatenation and multi-label learning. We also show that Boost-RS outperforms similarity-based models. Ablation studies and visualization of learned representations highlight the importance of using contrastive learning on some of the auxiliary data in boosting the embedding vectors.Availability and implementationA Python implementation for Boost-RS is provided at https://github.com/HassounLab/Boost-RS. The enzyme-substrate interaction data is available from the KEGG database (https://www.genome.jp/kegg/).

Comparison of Acetaminophen Degradation by Laccases Immobilized by Two Different Methods via a Continuous Flow Microreactor Process Scheme.

The presence of micropollutants in wastewater is one of the most significant environmental challenges. Particularly, pollutants such as pharmaceutical residues present high stability and resistance to conventional physicochemical and biological degradation processes. Thus, we aimed at immobilizing a laccase enzyme by two different methods: the first one was based on producing alginate-laccase microcapsules through a droplet-based microfluidic system; the second one was based on covalent binding of the laccase molecules on aluminum oxide (Al2O3) pellets. Immobilization efficiencies approached 92.18% and 98.22%, respectively. Laccase immobilized by the two different methods were packed into continuous flow microreactors to evaluate the degradation efficiency of acetaminophen present in artificial wastewater. After cyclic operation, enzyme losses were found to be up to 75 µg/mL and 66 µg/mL per operation cycle, with a maximum acetaminophen removal of 72% and 15% and a retention time of 30 min, for the laccase-alginate microcapsules and laccase-Al2O3 pellets, respectively. The superior catalytic performance of laccase-alginate microcapsules was attributed to their higher porosity, which enhances retention and, consequently, increased the chances for more substrate–enzyme interactions. Finally, phytotoxicity of the treated water was lower than that of the untreated wastewater, especially when using laccase immobilized in alginate microcapsules. Future work will be dedicated to elucidating the routes for scaling-up and optimizing the process to assure profitability.

Mechanism-Based Design of Efficient PET Hydrolases.

Polyethylene terephthalate (PET) is the most widespread synthetic polyester, having been utilized in textile fibers and packaging materials for beverages and food, contributing considerably to the global solid waste stream and environmental plastic pollution. While enzymatic PET recycling and upcycling have recently emerged as viable disposal methods for a circular plastic economy, only a handful of benchmark enzymes have been thoroughly described and subjected to protein engineering for improved properties over the last 16 years. By analyzing the specific material properties of PET and the reaction mechanisms in the context of interfacial biocatalysis, this Perspective identifies several limitations in current enzymatic PET degradation approaches. Unbalanced enzyme-substrate interactions, limited thermostability, and low catalytic efficiency at elevated reaction temperatures, and inhibition caused by oligomeric degradation intermediates still hamper industrial applications that require high catalytic efficiency. To overcome these limitations, successful protein engineering studies using innovative experimental and computational approaches have been published extensively in recent years in this thriving research field and are summarized and discussed in detail here. The acquired knowledge and experience will be applied in the near future to address plastic waste contributed by other mass-produced polymer types (e.g., polyamides and polyurethanes) that should also be properly disposed by biotechnological approaches.

Factors determining the enzyme catalytic power caused by noncovalent interactions: Charge alterations in enzyme active sites

Understanding the origin of the enormous catalytic power of enzymes is very important. Electrostatic interactions and desolvation are the phenomena that are most proposed to explain the catalysis of enzymes; however, they also decelerate enzymatic reactions. How enzymes catalyze reactions through noncovalent interactions is still not well-understood. In this study, we explored how enzyme-substrate noncovalent interactions affect the free energy barriers (ΔG‡s) of reactions by using a theoretical derivation approach. We found that enzymes reduce ΔG‡s of reactions by decreasing positive charges and/or increasing negative charges in the electron-donating centers and by decreasing negative charges and/or increasing positive charges in the electron-accepting centers of reactions. Enzyme-substrate noncovalent interactions are essential approaches through which the charge alterations lead to ΔG‡ reductions. Validations with reported experimental data demonstrated that this charge alteration mechanism can explain the catalyses caused by diverse types of noncovalent interactions. Electrostatic interactions and desolvation are the most observed noncovalent interactions essential for ΔG‡ reductions. This mechanism does not contradict any specific enzymatic catalysis and overcomes the shortages of the electrostatic interaction and desolvation mechanisms. This study can provide useful guidance in exploring enzymatic catalysis and designing catalyst.