scholarly journals EHreact: Extended Hasse Diagrams for the Extraction and Scoring of Enzymatic Reaction Templates

2021 ◽  
Author(s):  
Esther Heid ◽  
Samuel Goldman ◽  
Karthik Sankaranarayanan ◽  
Connor W. Coley ◽  
Christoph Flamm ◽  
...  
Keyword(s):  
Enzymatic Reaction ◽  
Hasse Diagrams

scholarly journals EHreact: Extended Hasse Diagrams for the Extraction and Scoring of Enzymatic Reaction Templates

2021 ◽  
Author(s):  
Esther Heid ◽  
Samuel Goldman ◽  
Karthik Sankaranarayanan ◽  
Connor W. Coley ◽  
Christoph Flamm ◽  
...  
Keyword(s):  
Expert Knowledge ◽  
Enzymatic Reaction ◽  
Software Tool ◽  
Optimal Number ◽  
Data Driven ◽  
Enzymatic Reactions ◽  
Hasse Diagrams ◽  
Large Databases ◽  
Rule Sets ◽  
The Given

Data-driven computer-aided synthesis planning utilizing organic or biocatalyzed reactions from large databases has gained increasing interest in the last decade, sparking the development of numerous tools to extract, apply and score general reaction templates. The generation of reaction rules for enzymatic reactions is especially challenging, since substrate promiscuity varies between enzymes, causing the optimal levels of rule specificity and optimal number of included atoms to differ between enzymes. This complicates an automated extraction from databases and has promoted the creation of manually curated reaction rule sets. Here we present EHreact, a purely data-driven open-source software tool to extract and score reaction rules from sets of reactions known to be catalyzed by an enzyme at appropriate levels of specificity without expert knowledge. EHreact extracts and groups reaction rules into tree-like structures, Hasse diagrams, based on common substructures in the imaginary transition structures. Each diagram can be utilized to output a single or a set of reaction rules, as well as calculate the probability of a new substrate to be processed by the given enzyme by inferring information about the reactive site of the enzyme from the known reactions and their grouping in the template tree. EHreact heuristically predicts the activity of a given enzyme on a new substrate, outperforming current approaches in accuracy and functionality.

scholarly journals EHreact: Extended Hasse Diagrams for the Extraction and Scoring of Enzymatic Reaction Templates

2021 ◽  
Author(s):  
Esther Heid ◽  
Samuel Goldman ◽  
Karthik Sankaranarayanan ◽  
Connor W. Coley ◽  
Christoph Flamm ◽  
...  
Keyword(s):  
Expert Knowledge ◽  
Enzymatic Reaction ◽  
Software Tool ◽  
Optimal Number ◽  
Data Driven ◽  
Enzymatic Reactions ◽  
Hasse Diagrams ◽  
Large Databases ◽  
Rule Sets ◽  
The Given

Data-driven computer-aided synthesis planning utilizing organic or biocatalyzed reactions from large databases has gained increasing interest in the last decade, sparking the development of numerous tools to extract, apply and score general reaction templates. The generation of reaction rules for enzymatic reactions is especially challenging, since substrate promiscuity varies between enzymes, causing the optimal levels of rule specificity and optimal number of included atoms to differ between enzymes. This complicates an automated extraction from databases and has promoted the creation of manually curated reaction rule sets. Here we present EHreact, a purely data-driven open-source software tool to extract and score reaction rules from sets of reactions known to be catalyzed by an enzyme at appropriate levels of specificity without expert knowledge. EHreact extracts and groups reaction rules into tree-like structures, Hasse diagrams, based on common substructures in the imaginary transition structures. Each diagram can be utilized to output a single or a set of reaction rules, as well as calculate the probability of a new substrate to be processed by the given enzyme by inferring information about the reactive site of the enzyme from the known reactions and their grouping in the template tree. EHreact heuristically predicts the activity of a given enzyme on a new substrate, outperforming current approaches in accuracy and functionality.

scholarly journals EHreact: Extended Hasse Diagrams for the Extraction and Scoring of Enzymatic Reaction Templates

2021 ◽  
Author(s):  
Esther Heid ◽  
Samuel Goldman ◽  
Karthik Sankaranarayanan ◽  
Connor W. Coley ◽  
Christoph Flamm ◽  
...  
Keyword(s):  
Expert Knowledge ◽  
Enzymatic Reaction ◽  
Software Tool ◽  
Optimal Number ◽  
Data Driven ◽  
Enzymatic Reactions ◽  
Hasse Diagrams ◽  
Large Databases ◽  
Rule Sets ◽  
The Given

Data-driven computer-aided synthesis planning utilizing organic or biocatalyzed reactions from large databases has gained increasing interest in the last decade, sparking the development of numerous tools to extract, apply and score general reaction templates. The generation of reaction rules for enzymatic reactions is especially challenging, since substrate promiscuity varies between enzymes, causing the optimal levels of rule specificity and optimal number of included atoms to differ between enzymes. This complicates an automated extraction from databases and has promoted the creation of manually curated reaction rule sets. Here we present EHreact, a purely data-driven open-source software tool to extract and score reaction rules from sets of reactions known to be catalyzed by an enzyme at appropriate levels of specificity without expert knowledge. EHreact extracts and groups reaction rules into tree-like structures, Hasse diagrams, based on common substructures in the imaginary transition structures. Each diagram can be utilized to output a single or a set of reaction rules, as well as calculate the probability of a new substrate to be processed by the given enzyme by inferring information about the reactive site of the enzyme from the known reactions and their grouping in the template tree. EHreact heuristically predicts the activity of a given enzyme on a new substrate, outperforming current approaches in accuracy and functionality.

Computer Simulation of Amperometric Biosensor Response to Mixtures of Compounds

2002 ◽  
Vol 7 (2) ◽  
pp. 3-14 ◽  
Author(s):  
R. Baronas ◽  
J. Christensen ◽  
F. Ivanauskas ◽  
J. Kulys
Keyword(s):  
Computer Simulation ◽  
Enzymatic Reaction ◽  
Diffusion Equations ◽  
Response Data ◽  
Finite Difference Technique ◽  
Stationary Diffusion ◽  
Biosensor Array ◽  
Menten Kinetic ◽  
Biosensor Response

A mathematical model of amperometric biosensors has been developed. The model bases on non-stationary diffusion equations containing a non-linear term related to Michaelis-Menten kinetic of the enzymatic reaction. The model describes the biosensor response to mixtures of multiple compounds in two regimes of analysis: batch and flow injection. Using computer simulation, large amount of biosensor response data were synthesised for calibration of a biosensor array to be used for characterization of wastewater. The computer simulation was carried out using the finite difference technique.

Bacterial Peptidoglycan Stapling with Functionalized D-Amino Acids

2019 ◽  
Author(s):  
Sylvia L. Rivera ◽  
Akbar Espaillat ◽  
Arjun K. Aditham ◽  
Peyton Shieh ◽  
Chris Muriel-Mundo ◽  
...  
Keyword(s):  
Cell Wall ◽  
Clinical Success ◽  
Bacterial Species ◽  
Enzymatic Reaction ◽  
Amino Acid Derivative ◽  
Wall Structure ◽  
Live Bacteria ◽  
Cross Links ◽  
Osmotic Lysis ◽  
Bacterial Peptidoglycan

Transpeptidation reinforces the structure of cell wall peptidoglycan, an extracellular heteropolymer that protects bacteria from osmotic lysis. The clinical success of transpeptidase-inhibiting β-lactam antibiotics illustrates the essentiality of these cross-linkages for cell wall integrity, but the presence of multiple, seemingly redundant transpeptidases in many bacterial species makes it challenging to determine cross-link function precisely. Here we present a technique to covalently link peptide strands by chemical rather than enzymatic reaction. We employ bio-compatible click chemistry to induce triazole formation between azido- and alkynyl-D-alanine residues that are metabolically installed in the cell walls of Gram-positive and Gram-negative bacteria. Synthetic triazole cross-links can be visualized by substituting azido-D-alanine with azidocoumarin-D-alanine, an amino acid derivative that undergoes fluorescent enhancement upon reaction with terminal alkynes. Cell wall stapling protects the model bacterium Escherichia coli from β-lactam treatment. Chemical control of cell wall structure in live bacteria can provide functional insights that are orthogonal to those obtained by genetics.<br>

The Role of Glyoxalase in Glycation and Carbonyl Stress Induced Metabolic Disorders

2020 ◽  
Vol 21 (9) ◽  
pp. 846-859
Author(s):  
Mohd Saeed ◽  
Mohd Adnan Kausar ◽  
Rajeev Singh ◽  
Arif J. Siddiqui ◽  
Asma Akhter
Keyword(s):  
Protein Misfolding ◽  
Covalent Binding ◽  
Critical Role ◽  
Enzymatic Reaction ◽  
Treatment Strategies ◽  
Bioactive Molecules ◽  
Carbonyl Stress ◽  
Defense System ◽  
Pathological Conditions ◽  
Age Related

Glycation refers to the covalent binding of sugar molecules to macromolecules, such as DNA, proteins, and lipids in a non-enzymatic reaction, resulting in the formation of irreversibly bound products known as advanced glycation end products (AGEs). AGEs are synthesized in high amounts both in pathological conditions, such as diabetes and under physiological conditions resulting in aging. The body’s anti-glycation defense mechanisms play a critical role in removing glycated products. However, if this defense system fails, AGEs start accumulating, which results in pathological conditions. Studies have been shown that increased accumulation of AGEs acts as key mediators in multiple diseases, such as diabetes, obesity, arthritis, cancer, atherosclerosis, decreased skin elasticity, male erectile dysfunction, pulmonary fibrosis, aging, and Alzheimer’s disease. Furthermore, glycation of nucleotides, proteins, and phospholipids by α-oxoaldehyde metabolites, such as glyoxal (GO) and methylglyoxal (MGO), causes potential damage to the genome, proteome, and lipidome. Glyoxalase-1 (GLO-1) acts as a part of the anti-glycation defense system by carrying out detoxification of GO and MGO. It has been demonstrated that GLO-1 protects dicarbonyl modifications of the proteome and lipidome, thereby impeding the cell signaling and affecting age-related diseases. Its relationship with detoxification and anti-glycation defense is well established. Glycation of proteins by MGO and GO results in protein misfolding, thereby affecting their structure and function. These findings provide evidence for the rationale that the functional modulation of the GLO pathway could be used as a potential therapeutic target. In the present review, we summarized the newly emerged literature on the GLO pathway, including enzymes regulating the process. In addition, we described small bioactive molecules with the potential to modulate the GLO pathway, thereby providing a basis for the development of new treatment strategies against age-related complications.

Mass transfer in heterogeneous system enzyme-substrate; Approximate analytical model for the case of liquid substrate-immobilized enzyme

1982 ◽  
Vol 47 (11) ◽  
pp. 3013-3018
Author(s):  
František Kaštánek ◽  
Jindřich Zahradník ◽  
Germanico Ocampo
Keyword(s):  
Mass Transfer ◽  
Heterogeneous System ◽  
Immobilized Enzyme ◽  
Enzymatic Reaction ◽  
Analytical Form ◽  
Approximate Model ◽  
Basic Type ◽  
Reaction Interface ◽  
Enzyme Substrate ◽  
Flow Intensity

Calculation procedure is suggested for flow intensity of substrate toward reaction interface of immobilized enzyme at simultaneous effect of enzymatic reaction and internal diffusion. The approximate model is presented in an analytical form for the basic type of Michaelis-Menten kinetics and for the case of inhibition in excess of substrate.

Enzymatic colorimetry of lecithin and sphingomyelin in aqueous solution.

1983 ◽  
Vol 29 (8) ◽  
pp. 1513-1517 ◽  
Author(s):  
M W McGowan ◽  
J D Artiss ◽  
B Zak
Keyword(s):  
Aqueous Solution ◽  
Hydrogen Peroxide ◽  
Amniotic Fluid ◽  
Enzymatic Reaction ◽  
Detergent Solution ◽  
Enzymatic Determination ◽  
Red Color ◽  
Hydrolysis Of ◽  
Zwitterionic Detergent

Abstract A procedure for the enzymatic determination of lecithin and sphingomyelin in aqueous solution is described. The phospholipids are first dissolved in chloroform:methanol (2:1 by vol), the solvent is evaporated, and the residue is redissolved in an aqueous zwitterionic detergent solution. The enzymatic reaction sequences of both assays involve hydrolysis of the phospholipids to produce choline, which is then oxidized to betaine, thus generating hydrogen peroxide. The hydrogen peroxide is subsequently utilized in the enzymatic coupling of 4-aminoantipyrine and sodium 2-hydroxy-3,5-dichlorobenzenesulfonate, an intensely red color being formed. The presence of a non-reacting phospholipid enhances the hydrolysis of the reacting phospholipid. Thus we added lecithin to the sphingomyelin standards and sphingomyelin to the lecithin standards. This precise procedure may be applicable to determination of lecithin and sphingomyelin in amniotic fluid.

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