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Related Concept Videos

Conserved Binding Sites01:49

Conserved Binding Sites

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 analyses the...
Conserved Binding Sites01:49

Conserved Binding Sites

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 analyses the...
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

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 the...
Ligand Binding Sites02:40

Ligand Binding Sites

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...
Ligand Binding Sites02:40

Ligand Binding Sites

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...
Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...

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Related Experiment Video

Updated: Jun 15, 2026

Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

Modular architecture of nucleotide-binding pockets.

Pier Federico Gherardini1, Gabriele Ausiello, Robert B Russell

  • 1Centre for Molecular Bioinformatics, Department of Biology, University of Tor Vergata, Via della Ricerca Scientifica snc, 00133 Rome, Italy.

Nucleic Acids Research
|February 27, 2010
PubMed
Summary
This summary is machine-generated.

Biological ligands, like nucleotides, exhibit modularity. This study reveals that nucleotide-binding sites in proteins also show modular organization, reflecting ligand structure and suggesting evolutionary links.

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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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Last Updated: Jun 15, 2026

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09:51

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

Published on: July 16, 2017

Area of Science:

  • Biochemistry
  • Structural Biology
  • Evolutionary Biology

Background:

  • Complex biological systems often display modularity, facilitating optimization through evolution.
  • Biological ligands, such as nucleotides, are chemically modular, composed of recurring fragments.
  • Ligands can be promiscuous, binding to diverse protein structures.

Purpose of the Study:

  • To investigate if the chemical modularity of ligands is mirrored by modularity in protein binding sites.
  • To explore the relationship between nucleotide structure and the protein structural motifs that bind them.

Main Methods:

  • Analysis of nucleotide structure and composition into well-defined fragments (nucleobase, ribose, phosphates).
  • Examination of protein structure databases to identify and characterize nucleotide-binding sites.
  • Mapping of fragment-specific protein structural motifs within binding sites across various proteins and folds.

Main Results:

  • Nucleotide-binding sites demonstrate a clear modular organization.
  • These sites are composed of protein structural motifs specific to nucleotide fragments, paralleling ligand modularity.
  • The distribution of these motifs suggests evolutionary origins through divergence or convergence.

Conclusions:

  • Ligand chemical modularity is reflected in the modular structure of protein binding sites.
  • The observed modularity in binding sites can evolve through both common ancestry and convergent evolution.
  • This finding provides insights into the evolution of molecular recognition in biological systems.