Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Conserved Binding Sites01:49

Conserved Binding Sites

5.1K
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
5.1K
Conserved Binding Sites01:49

Conserved Binding Sites

1.9K
1.9K
Ligand Binding Sites02:40

Ligand Binding Sites

14.9K
Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
14.9K
Ligand Binding Sites02:40

Ligand Binding Sites

8.7K
8.7K
Structural Protein Function01:56

Structural Protein Function

29.9K
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...
29.9K
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

5.5K
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...
5.5K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Data Management and Analysis of Metal-Organic Framework Synthesis Using Data Models.

Journal of chemical information and modeling·2026
Same author

Enzymes for Synthesis and Degradation of Bio-Based Polyesters: Automatic In Silico Screening and Experimental Validation.

ChemSusChem·2026
Same author

Metabolic thermodynamics: pertinent reference state and energy potentials.

The FEBS journal·2026
Same author

Best Practices for Machine Learning-Assisted Protein Engineering.

Journal of chemical information and modeling·2025
Same author

Of Revolutions and Roadblocks: The Emerging Role of Machine Learning in Biocatalysis.

ACS central science·2025
Same author

Quantifying anthropogenic microparticle contamination in cave sediments: spatial heterogeneity matters.

Environmental pollution (Barking, Essex : 1987)·2025

Related Experiment Video

Updated: Jan 25, 2026

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
11:34

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Published on: August 9, 2019

7.1K

Navigating within thiamine diphosphate-dependent decarboxylases: Sequences, structures, functional positions, and

Patrick C F Buchholz1, Valerio Ferrario1,2, Martina Pohl3

  • 1Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany.

Proteins
|May 10, 2019
PubMed
Summary

Global sequence identity is insufficient for distinguishing enzyme function. Local sequence similarity and structural information are crucial for accurately classifying thiamine diphosphate-dependent decarboxylases and other enzyme families.

Keywords:
BioGPSbiocatalysisenzyme functionmolecular descriptorprincipal coordinate analysisprinciple component analysisprotein familysequence-structure-function relationship

More Related Videos

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

7.7K
PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins
12:24

PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins

Published on: July 2, 2010

54.2K

Related Experiment Videos

Last Updated: Jan 25, 2026

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
11:34

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Published on: August 9, 2019

7.1K
Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

7.7K
PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins
12:24

PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins

Published on: July 2, 2010

54.2K

Area of Science:

  • Biochemistry
  • Structural Biology
  • Bioinformatics

Background:

  • Thiamine diphosphate-dependent decarboxylases are enzymes catalyzing C-C bond reactions.
  • These enzymes are often grouped into distinct homologous sequence families.
  • Understanding enzyme family assignments is critical for predicting function.

Purpose of the Study:

  • To compare sequence and structural data of 53 ThDP-dependent decarboxylases.
  • To evaluate the effectiveness of global vs. local sequence similarity for enzyme classification.
  • To develop methods for improved homologous enzyme family assignment.

Main Methods:

  • Synergistic analysis of sequence and structural information.
  • Statistical approaches including Principal Component Analysis (PCA) and Principal Coordinate Analysis (PCoA).
  • Comparison of global and local sequence/structural properties, including active site analysis.

Main Results:

  • Global sequence identity alone is inadequate for distinguishing enzyme function.
  • Local sequence similarity, focusing on structurally equivalent positions, improves enzyme classification.
  • Integrating structural data, like active site properties and superimpositions, further enhances differentiation.

Conclusions:

  • Accurate enzyme family assignment requires more than global sequence identity.
  • Local sequence similarity and structural context are key for navigating homologous enzyme groups.
  • The applied methods can aid in classifying other enzyme families and identifying functionally relevant positions.