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Related Concept Videos

Enzymes02:34

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...
Introduction to Mechanisms of Enzyme Catalysis01:13

Introduction to Mechanisms of Enzyme Catalysis

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 a mild...
Structural Protein Function01:56

Structural Protein Function

Structural proteins are a category of proteins responsible for functions ranging from cell shape and movement to providing support to major structures such as bones, cartilage, hair, and muscles. This group includes proteins such as collagen, actin, myosin, and keratin.
Collagen, the most abundant protein in mammals, is found throughout the body. In connective tissue, such as skin, ligaments, and tendons, it provides tensile strength and elasticity.  In bones and teeth, it mineralizes to form...
Structural Protein Function01:56

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Protein Organization01:24

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.
Protein Organization01:13

Protein Organization

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Updated: May 19, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Relationship between global structural parameters and Enzyme Commission hierarchy: implications for function

Marcelo Boareto1, Michel E B Yamagishi, Nestor Caticha

  • 1Departamento de Física Geral, Instituto de Física, Universidade de São Paulo, SP, Brazil.

Computational Biology and Chemistry
|August 29, 2012
PubMed
Summary
This summary is machine-generated.

Global protein structure parameters are insufficient for predicting enzyme function based on the Enzyme Commission (EC) classification. Enzyme function prediction requires focusing on local features, like specific amino acids, rather than global attributes.

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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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Last Updated: May 19, 2026

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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Area of Science:

  • Biochemistry
  • Bioinformatics
  • Structural Biology

Background:

  • A significant number of proteins lack functional annotations despite structural determination.
  • Understanding the structure-function relationship is crucial for large-scale functional prediction.

Purpose of the Study:

  • To investigate if global physicochemical parameters of enzymes correlate with their classification within the Enzyme Commission (EC) hierarchy.
  • To assess the efficacy of global structural features for predicting enzyme function.

Main Methods:

  • Analysis of global physicochemical parameters for 1025 enzymes across EC hierarchical levels.
  • Introduction of a protein distance metric in physicochemical space using relevance theory and a cost function.
  • Application of unsupervised clustering and comparison of distance distributions (physicochemical and sequence-based) between EC groups.

Main Results:

  • Unsupervised clustering did not yield groupings consistent with the EC classification.
  • Histograms showed overlapping distance distributions between enzymes within and across EC groups, for both physicochemical and sequence-based distances.
  • Global structure parameters alone are insufficient to accurately segregate enzymes according to EC hierarchy.

Conclusions:

  • Enzyme function is primarily determined by local features, such as specific amino acids in active sites, rather than global structural properties.
  • Predictive models for enzyme function should prioritize identifying critical local features (e.g., active site residues) over relying solely on global attributes.
  • Protein function evolution likely involves recruitment, where conserved structural motifs can be repurposed for diverse enzymatic activities.