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Enzymes

Enzymes

Inside living organisms, enzymes act as catalysts for many biochemical reactions involved in cellular metabolism. The role of enzymes is to reduce the activation energies of biochemical reactions by forming complexes with its substrates. The lowering of activation energies favor an increase in the rates of biochemical reactions.
Enzyme deficiencies can often translate into life-threatening diseases. For example, a genetic abnormality resulting in the deficiency of the enzyme G6PD...

Genome Annotation and Assembly

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.

Enzyme Kinetics

Enzyme Kinetics

Enzymes speed up reactions by lowering the activation energy of the reactants. The speed at which the enzyme turns reactants into products is called the rate of reaction. Several factors impact the rate of reaction, including the number of available reactants. Enzyme kinetics is the study of how an enzyme changes the rate of a reaction.
Scientists typically study enzyme kinetics with a fixed amount of enzyme in the controlled environment of a test tube. When more reactant, or substrate, is...

Enzyme-linked Receptors

Enzyme-linked Receptors

Enzyme-linked receptors are proteins that act as both receptor and enzyme, activating multiple intracellular signals. This is a large group of receptors that include the receptor tyrosine kinase (RTK) family. Many growth factors and hormones bind to and activate the RTKs.
Neurotrophin (NT) receptors are a family of RTKs, including trkA, trkB, and trkC (tropomyosin-related kinase) receptors. TrkA is specific for nerve growth factor (NGF), neurotrophin-6, and neurotrophin-7. TrkB binds...

Enzyme Inhibition

Enzyme Inhibition

Inhibitors are molecules that reduce enzyme activity by binding to the enzyme. In a normally functioning cell, enzymes are regulated by a variety of inhibitors. Drugs and other toxins can also inhibit enzymes. Some inhibitors bind to the enzyme’s active site, while others inhibit enzymatic activity by binding to other sites on the protein structure.

Introduction to Enzymes

Introduction to Enzymes

The use of enzymes by humans dates to 7000 BCE. Humans first used enzymes to ferment sugars and produce alcohol without knowing that this was an enzyme-catalyzed reaction. Wilhelm Kuhne coined the term 'enzyme' in 1877 from the Greek words ‘en’ meaning ‘in’ or ‘within’ and ‘zyme’ meaning ‘yeast.’
Most enzymes are proteins that speed up biochemical reactions without being consumed. Enzymes contain one or more active sites that...

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Antigen-Capture Enzyme-Linked Immunosorbent Assay for Specific Detection of Mycoplasma pneumoniae

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Improved enzyme annotation with EC-specific cutoffs using DETECT v2.

Nirvana Nursimulu^1,2, Leon L Xu¹, James D Wasmuth³

¹Program in Molecular Medicine, The Hospital for Sick Children, 21-9709 PGCRL, 686 Bay Street, Toronto, ON, Canada.

Bioinformatics (Oxford, England)

|May 4, 2018

Summary

DETECT v2 is an improved enzyme annotation tool that accurately assigns enzyme function (Enzyme Commission numbers) by considering protein sequence diversity. This version enhances enzyme class capture and provides specific cutoffs for greater precision and recall in functional assignments.

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Area of Science:

Bioinformatics
Enzymology
Computational Biology

Background:

Accurate enzyme annotation is crucial for understanding biological pathways and functions.
Existing tools may not fully capture the impact of sequence diversity on enzymatic function.
Enzyme Commission (EC) number assignment is a standard for classifying enzymes.

Purpose of the Study:

To introduce DETECT v2, an enhanced enzyme annotation tool.
To improve the assignment of enzymatic function (EC numbers) by incorporating sequence diversity.
To evaluate the performance of DETECT v2 in capturing enzyme classes and its application in pathway analysis.

Main Methods:

Development of DETECT v2, an algorithm considering protein sequence diversity for enzyme annotation.
Implementation of EC-specific cutoffs to refine assignment precision and recall.
Performance evaluation using established benchmarks and pathway contexts.

Main Results:

DETECT v2 captures a broader range of enzyme classes compared to its predecessor.
EC-specific cutoffs significantly enhance the precision and recall of enzyme function assignments.
The tool demonstrates robust performance in the context of biological pathways.

Conclusions:

DETECT v2 offers a more accurate and comprehensive approach to enzyme annotation.
The consideration of sequence diversity and EC-specific cutoffs improves functional assignment reliability.
This tool aids in the functional characterization of proteins and pathway elucidation.