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Related Concept Videos

Introduction to Enzyme Kinetics01:19

Introduction to Enzyme Kinetics

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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...
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Enzyme Kinetics01:19

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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...
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Introduction to Mechanisms of Enzyme Catalysis01:13

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For many years, scientists thought that enzyme-substrate binding took place in a simple "lock-and-key" fashion. This model stated that the enzyme and substrate fit together perfectly in one instantaneous step. However, current research supports a more refined view scientists call induced fit. The induced-fit model expands upon the lock-and-key model by describing a more dynamic interaction between enzyme and substrate. As the enzyme and substrate come together, their interaction causes...
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Enzymes02:34

Enzymes

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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.
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Most chemical reactions in cells require enzymes—biological catalysts that speed up the reaction without being consumed or permanently changed. They reduce the activation energy needed to convert the reactants into products. Enzymes are proteins, that usually work by binding to a substrate—a reactant molecule that they act upon.
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Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...
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Identification of Kinase-substrate Pairs Using High Throughput Screening
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A structure-oriented kinetics dataset of enzyme-substrate interactions.

Sowmya Ramaswamy Krishnan1, Nishtha Pandey1, Rajgopal Srinivasan1

  • 1TCS Research (Life Sciences division), Tata Consultancy Services, Hyderabad, 500081, India.

Scientific Data
|August 26, 2025
PubMed
Summary
This summary is machine-generated.

This study introduces SKiD, a dataset linking enzyme kinetic parameters (kcat and Km) with 3D structures. This resource enhances understanding of enzyme function and aids in enzyme design and synthetic biology applications.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Bioinformatics

Background:

  • Enzymes are crucial biological catalysts governing biochemical reactions.
  • Enzyme kinetics, defined by kcat and Km, quantifies efficiency and specificity.
  • A gap exists in linking kinetic parameters with enzyme-substrate complex 3D structures.

Purpose of the Study:

  • To create SKiD, a dataset integrating enzyme kinetic parameters (kcat, Km) with 3D structural data.
  • To bridge the gap between enzyme kinetics and structural biology.
  • To support advancements in enzyme design, synthetic biology, and metabolic engineering.

Main Methods:

  • Integrated data from existing bioinformatics resources.
  • Utilized automated programs for data processing and computational predictions.
  • Manually resolved erroneous data and preserved metadata like assay conditions.
  • Provided 3D coordinates of enzyme-substrate complexes with UniProtKB identifiers.

Main Results:

  • Developed SKiD, a comprehensive dataset linking kinetic parameters with 3D structures.
  • Successfully integrated and curated kinetic and structural data for enzymes.
  • Included metadata and 3D coordinates for enzyme-substrate complexes.

Conclusions:

  • SKiD provides a valuable resource for understanding the structural basis of enzyme function.
  • The dataset facilitates research in enzyme design, synthetic biology, and metabolic engineering.
  • Mapping kinetics to structure offers deeper insights into enzymatic mechanisms.