Related Experiment Video
Updated: Aug 11, 2025
14:37
Modeling an Enzyme Active Site using Molecular Visualization Freeware
Published on: December 25, 2021
10.0K
EnzymeML: seamless data flow and modeling of enzymatic data.
Simone Lauterbach1, Hannah Dienhart1, Jan Range1
1Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany.
Nature Methods
|February 9, 2023
Summary
Reproducibility in enzyme kinetics is difficult due to complex data. EnzymeML, an XML-based language, standardizes enzymatic data storage and exchange, enhancing data findability, accessibility, interoperability, and reusability (FAIR).
Area of Science:
- Biochemistry
- Computational Biology
- Data Science
Background:
- Enzyme kinetics research faces challenges in data reproducibility and reusability.
- Kinetic parameter estimation is complex, depending on enzyme, reaction conditions, and modeling methods.
Purpose of the Study:
- To develop a standardized method for storing and exchanging enzymatic data.
- To improve the findability, accessibility, interoperability, and reusability (FAIR) of enzyme kinetic data.
Main Methods:
- Development of EnzymeML, an XML-based markup language for enzymatic data.
- Demonstration of EnzymeML feasibility through six diverse experimental scenarios.
Main Results:
- EnzymeML enables comprehensive data and metadata storage, including reaction conditions, time courses, kinetic parameters, and models.
- The EnzymeML toolbox facilitates seamless data communication across experimental and computational platforms.
Conclusions:
- EnzymeML addresses the complexity of biocatalytic reaction system design by standardizing data.
- EnzymeML promotes FAIR data principles, enhancing collaboration and advancing enzyme kinetics research.
Related Concept Videos
01:19Enzyme Kinetics
97.6K
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...
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...
97.6K
01:19Introduction to Enzyme Kinetics
20.3K
Enzyme kinetics studies the rates of biochemical reactions. Scientists monitor the reaction rates for a particular enzymatic reaction at various substrate concentrations. Additional trials with inhibitors or other molecules that affect the reaction rate may also be performed.
The experimenter can then plot the initial reaction rate or velocity (Vo) of a given trial against the substrate concentration ([S]) to obtain a graph of the reaction properties. For many enzymatic reactions involving a...
The experimenter can then plot the initial reaction rate or velocity (Vo) of a given trial against the substrate concentration ([S]) to obtain a graph of the reaction properties. For many enzymatic reactions involving a...
20.3K
01:07Catalytically Perfect Enzymes
4.1K
The theory of catalytically perfect enzymes was first proposed by W.J. Albery and J. R. Knowles in 1976. These enzymes catalyze biochemical reactions at high-speed. Their catalytic efficiency values range from 108-109 M-1s-1. These enzymes are also called 'diffusion-controlled' as the only rate-limiting step in the catalysis is that of the substrate diffusion into the active site. Examples include triose phosphate isomerase, fumarase, and superoxide dismutase.
Most enzymes...
Most enzymes...
4.1K
01:00Enzyme-linked Receptors
79.2K
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...
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...
79.2K
01:22Introduction to Enzymes
18.9K
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...
Most enzymes are proteins that speed up biochemical reactions without being consumed. Enzymes contain one or more active sites that...
18.9K
02:34Enzymes
82.1K
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...
Enzyme deficiencies can often translate into life-threatening diseases. For example, a genetic abnormality resulting in the deficiency of the enzyme G6PD...
82.1K