Computational and experimental identification of an exceptionally efficient ethyl ester synthetase with broad substrate specificity and high product yield, suggests potential for industrial biocatalysis.

Transesterification plays a crucial role in the synthesis of diverse esters in organic synthesis but is barely reported in biocatalysis. Here, we computationally identify the salicylic acid-binding protease 2 (SABP2) as an efficient ethyl ester bond synthetase by QM/MM MD and free energy simulations and present the practical and effective utilization of SABP2 as an eco-friendly biocatalyst for transesterification reactions by a series of experiments. Our findings demonstrate that SABP2 efficiently catalyzes the transesterification reaction between the carboxyl acid group of promiscuous aromatic substrates and ethanol to produce the corresponding ethyl esters.

Discovery of a novel homocysteine thiolactone hydrolase and the catalytic activity of its natural variants.

Homocysteine thiolactone (HTL), a toxic metabolite of homocysteine (Hcy) in hyperhomocysteinemia (HHcy), is known to modify protein structure and function, leading to protein damage through formation of N-Hcy-protein. HTL has been highly linked to HHcy-associated cardiovascular and neurodegenerative diseases. The protective role of HTL hydrolases against HTL-associated vascular toxicity and neurotoxicity have been reported.

Attack Site Density of a Highly-efficient PET Hydrolases.

Introduction: Poly (ethylene terephthalate) (PET) is one of the most abundant polyester materials used in daily life and it is also one of the main culprits of environmental pollution. ICCG (F243I/D238C/S283C/Y127G) is an enzyme that performs four modifications on the leaf branch compost keratase (LCC). It shows excellent performance in the hydrolysis of PET and has a great potential in further applications.

Ellman's method-based determination of acibenzolar-S-methyl in tobacco by transesterification with methanol and SABP2-catalyzed hydrolysis.

Acibenzolar-S-methyl (ASM) is the most commercially successful biological antibacterial agent used for crop through systemic acquired resistance (SAR). In this study, a reproducible and accurate procedure, based on the spectrophotometric/microplate reader analysis, has been developed to detect ASM in tobacco leaves. This method involves oxidation of methyl mercaptan by the Ellman's reagent 5,5'-dithio-bis (2-nitrobenzoic acid) (DTNB) to form the yellow derivative 5'-thio-2-nitrobenzoic acid (TNB), measurable at 412 nm.

Computational Design and Crystal Structure of a Highly Efficient Benzoylecgonine Hydrolase.

Benzoylecgonine (BZE) is the major toxic metabolite of cocaine and is responsible for the long-term cocaine-induced toxicity owing to its long residence time in humans. BZE is also the main contaminant following cocaine consumption. Here, we identified the bacterial cocaine esterase (CocE) as a BZE-metabolizing enzyme (BZEase), which can degrade BZE into biological inactive metabolites (ecgonine and benzoic acid).

One- and Two-Proton Transfer Mechanisms Coexist in One Active Site.

Acibenzolar--methyl (ASM) is one of the most successfully commercialized plant activators of the systemic acquired resistance (SAR). However, its activation (hydrolysis) mechanism catalyzed by the salicylic acid binding protein 2 (SABP2) remains elusive. The fundamental catalytic mechanism of the SABP2-catalyzed hydrolysis of the ASM had been investigated by extensive computational and experimental studies, including QM/MM simulations, charge transfer analysis, small-molecule synthesis, and biochemical assays.

Human Acetyl-CoA Carboxylase 1 Is an Isomerase: Carboxyl Transfer Is Activated by Catalytic Effect of Isomerization.

Obesity and its related diseases such as cancer and diabetes are leading life-threatening issues in the modern world. Thus, new drugs toward obesity and obesity-caused diseases are highly desired. Human acetyl-CoA carboxylase 1 (hACC1) in charge of the rate-limiting step of the human fatty acid synthesis was recognized as an attractive target for rational drug design.

The catalytic mechanism of S-acyltransferases: acylation is triggered on by a loose transition state and deacylation is turned off by a tight transition state.

Dynamic protein S-palmitoylation catalyzed by S-acyltransferases is one of the fundamental post-translational modifications involved not only in a wide range of vital cellular processes but also in a series of human health and diseases-related issues (such as brain development and behavior, immune response regulation, tumor suppressor, and cancer). Interestingly, human S-acyltransferase has been recognized as a promising drug-target for cancer treatment. Despite the prominent importance, the fundamental catalytic mechanism of S-acyltransferases remains elusive.

Catalytic Reaction Mechanism for Drug Metabolism in Human Carboxylesterase-1: Cocaine Hydrolysis Pathway.

Carboxylesterase-1 (CE-1) is a crucial enzyme responsible for metabolism/activation/inactivation of xenobiotics (therapeutic agents, prodrugs, abused drugs, and organophosphorus nerve agents etc.) and also involved in many other biological processes. In this study, we performed extensive computational modeling and simulations to understand the fundamental reaction mechanism of cocaine hydrolysis catalyzed by CE-1, revealing that CE-1-catalyzed cocaine hydrolysis follows a novel reaction pathway with only two reaction steps: a single-step acylation process and a single-step deacylation process.

Kinetic characterization of cholinesterases and a therapeutically valuable cocaine hydrolase for their catalytic activities against heroin and its metabolite 6-monoacetylmorphine.

As the most popularly abused one of opioids, heroin is actually a prodrug. In the body, heroin is hydrolyzed/activated to 6-monoacetylmorphine (6-MAM) first and then to morphine to produce its toxic and physiological effects. It has been known that heroin hydrolysis to 6-MAM and morphine is accelerated by cholinesterases, including acetylcholinesterase (AChE) and/or butyrylcholinesterase (BChE).

QM/MM free energy Simulations of an efficient Gluten Hydrolase (Kuma030) Implicate for a Reactant-State Based Protein-Design Strategy for General Acid/Base Catalysis.

It is a grand attraction for contemporary biochemists to computationally design enzymes for novel chemical transformation or improved catalytic efficiency. Rosetta by Baker et al. is no doubt the leading software in the protein design society.

Circular exponential amplification of photoinduced electron transfer using hairpin probes, G-quadruplex DNAzyme and silver nanocluster-labeled DNA for ultrasensitive fluorometric determination of pathogenic bacteria.

The authors describe a fluorometric strategy for the detection of pathogenic bacteria with ultrasensitivity and high specificity. This strategy relies on the combination of target-modulated photoinduced electron transfer (PET) between G-quadruplex DNAzyme and DNA (labeled with silver nanoclusters) along with hairpin probe-based circular exponential amplification. The reaction system involves three hairpin probes (H1, H2 and H3).

Understanding the Catalytic Mechanism and the Nature of the Transition State of an Attractive Drug-Target Enzyme (Shikimate Kinase) by Quantum Mechanical/Molecular Mechanical (QM/MM) Studies.

Shikimate kinase (SK) is the fifth bacterial enzyme involved in the shikimate pathway for biosynthesis of life-indispensable components, such as aromatic amino acids. The absence of the shikimate pathway in humans makes SK an attractive target for the rational design of drugs aimed at pathogenesis bacteria, such as Mycobacterium tuberculosis and Helicobacter pylori. However, an effective inhibitor of SK (e.

Understanding the Catalytic Mechanism and the Substrate Specificity of an Engineered Gluten Hydrolase by QM/MM Molecular Dynamics and Free Energy Simulations.

Celiac sprue, also known as gluten-sensitive enteropathy, is a chronic disease suffered by approximately 1% of the world's population. Engineered enzymes have been emerging to treat celiac disease by hydrolyzing the pathogenic peptides of gluten. For example, Kuma010 has been studied experimentally and proved to be a promising gluten hydrolase under gastric conditions.

Role of Histidine 547 of Human Dopamine Transporter in Molecular Interaction with HIV-1 Tat and Dopamine Uptake.

HIV-1 Tat plays an important role in HIV-associated neurocognitive disorders (HAND) by disrupting neurotransmission including dopamine uptake by human dopamine transporter (hDAT). Previous studies have demonstrated that HIV-1 Tat directly binds to hDAT and some amino-acid mutations that attenuate the hDAT-Tat binding also significantly decreased dopamine uptake activity of hDAT. This combined computational-experimental study demonstrates that histidine-547 (H547) of hDAT plays a crucial role in the hDAT-Tat binding and dopamine uptake by hDAT, and that the H547A mutation can not only considerably attenuate Tat-induced inhibition of dopamine uptake, but also significantly increase the Vmax of hDAT for dopamine uptake.

Potential anti-obesity effects of a long-acting cocaine hydrolase.

A long-acting cocaine hydrolase, known as CocH3-Fc(M3), engineered from human butyrylcholinesterase (BChE) was tested, in this study, for its potential anti-obesity effects. Mice on a high-fat diet gained significantly less body weight when treated weekly with 1 mg/kg CocH3-Fc(M3) compared to control mice, though their food intake was similar. There is no correlation between the average body weight and the average food intake, which is consistent with the previously reported observation in BChE knockout mice.

Unexpected Reaction Pathway for butyrylcholinesterase-catalyzed inactivation of "hunger hormone" ghrelin.

Extensive computational modeling and simulations have been carried out, in the present study, to uncover the fundamental reaction pathway for butyrylcholinesterase (BChE)-catalyzed hydrolysis of ghrelin, demonstrating that the acylation process of BChE-catalyzed hydrolysis of ghrelin follows an unprecedented single-step reaction pathway and the single-step acylation process is rate-determining. The free energy barrier (18.8 kcal/mol) calculated for the rate-determining step is reasonably close to the experimentally-derived free energy barrier (~19.

PPCM: Combing Multiple Classifiers to Improve Protein-Protein Interaction Prediction.

Determining protein-protein interaction (PPI) in biological systems is of considerable importance, and prediction of PPI has become a popular research area. Although different classifiers have been developed for PPI prediction, no single classifier seems to be able to predict PPI with high confidence. We postulated that by combining individual classifiers the accuracy of PPI prediction could be improved.

Substrate-Assisted Catalysis in the Reaction Catalyzed by Salicylic Acid Binding Protein 2 (SABP2), a Potential Mechanism of Substrate Discrimination for Some Promiscuous Enzymes.

Although one of an enzyme's hallmarks is the high specificity for their natural substrates, substrate promiscuity has been reported more frequently. It is known that promiscuous enzymes generally show different catalytic efficiencies to different substrates, but our understanding of the origin of such differences is still lacking. Here we report the results of quantum mechanical/molecular mechanical simulations and an experimental study of salicylic acid binding protein 2 (SABP2).

Molecular and biochemical characterization of the jasmonic acid methyltransferase gene from black cottonwood (Populus trichocarpa).

Methyl jasmonate is a metabolite known to be produced by many plants and has roles in diverse biological processes. It is biosynthesized by the action of S-adenosyl-l-methionine:jasmonic acid carboxyl methyltransferase (JMT), which belongs to the SABATH family of methyltransferases. Herein is reported the isolation and biochemical characterization of a JMT gene from black cottonwood (Populus trichocarpa).

QM/MM MD and free energy simulations of G9a-like protein (GLP) and its mutants: understanding the factors that determine the product specificity.

Certain lysine residues on histone tails could be methylated by protein lysine methyltransferases (PKMTs) using S-adenosyl-L-methionine (AdoMet) as the methyl donor. Since the methylation states of the target lysines play a fundamental role in the regulation of chromatin structure and gene expression, it is important to study the property of PKMTs that allows a specific number of methyl groups (one, two or three) to be added (termed as product specificity). It has been shown that the product specificity of PKMTs may be controlled in part by the existence of specific residues at the active site.

Understanding product specificity of protein lysine methyltransferases from QM/MM molecular dynamics and free energy simulations: the effects of mutation on SET7/9 beyond the Tyr/Phe switch.

The results of hybrid quantum mechanical/molecular mechanical (QM/MM) free energy (potential of mean force) simulations for methyl-transfer processes in SET7/9 and its Y245A mutant are compared to address the question concerning the change of the product specificity as well as catalytic efficiency due to the mutation. One of the key questions is whether or not the free energy profiles of methyl transfers may be used to predict the change of the product specificity as a result of the mutations for the residues that are not located at the Tyr/Phe switch position. The simulations show that while the wild-type SET7/9 is a monomethylase, the Y245→A mutation increases the ability of the enzyme to add more methyl groups on the target lysine (i.

Stability and sugar recognition ability of ricin-like carbohydrate binding domains.

Lectins are a class of proteins known for their novel binding to saccharides. Understanding this sugar recognition process can be crucial in creating structure-based designs of proteins with various biological roles. We focus on the sugar binding of a particular lectin, ricin, which has two β-trefoil carbohydrate-binding domains (CRDs) found in several plant protein toxins.