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Related Concept Videos

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 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...
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...

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Related Experiment Video

Updated: May 26, 2026

Specificity Analysis of Protein Lysine Methyltransferases Using SPOT Peptide Arrays
08:48

Specificity Analysis of Protein Lysine Methyltransferases Using SPOT Peptide Arrays

Published on: November 29, 2014

Druggability of methyl-lysine binding sites.

C Santiago1, K Nguyen, M Schapira

  • 1Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada.

Journal of Computer-Aided Molecular Design
|December 8, 2011
PubMed
Summary

Researchers analyzed methyl-lysine binding modules, crucial for epigenetic regulation. While generally less druggable than bromodomains, some methyl-lysine readers present exceptions for therapeutic development.

Area of Science:

  • Epigenetics and chromatin biology
  • Structural biology
  • Drug discovery

Background:

  • Methylated and acetylated lysine residues on histone peptides are recognized by specific structural modules.
  • These readers are key to chromatin-mediated signaling and epigenetic gene regulation.
  • Dysregulation of epigenetic mechanisms is linked to various diseases.

Purpose of the Study:

  • To systematically analyze the structure of methyl-lysine binding modules.
  • To predict the druggability landscape of these epigenetic readers.
  • To compare their druggability with acetyl-lysine binding bromodomains.

Main Methods:

  • Systematic structural analysis of methyl-lysine binding proteins.
  • Development of a predictive druggability landscape.

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Methods to Identify the NMR Resonances of the 13C-Dimethyl N-terminal Amine on Reductively Methylated Proteins
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Methods to Identify the NMR Resonances of the 13C-Dimethyl N-terminal Amine on Reductively Methylated Proteins

Published on: December 12, 2013

Application of MassSQUIRM for Quantitative Measurements of Lysine Demethylase Activity
07:02

Application of MassSQUIRM for Quantitative Measurements of Lysine Demethylase Activity

Published on: March 11, 2012

Related Experiment Videos

Last Updated: May 26, 2026

Specificity Analysis of Protein Lysine Methyltransferases Using SPOT Peptide Arrays
08:48

Specificity Analysis of Protein Lysine Methyltransferases Using SPOT Peptide Arrays

Published on: November 29, 2014

Methods to Identify the NMR Resonances of the 13C-Dimethyl N-terminal Amine on Reductively Methylated Proteins
13:59

Methods to Identify the NMR Resonances of the 13C-Dimethyl N-terminal Amine on Reductively Methylated Proteins

Published on: December 12, 2013

Application of MassSQUIRM for Quantitative Measurements of Lysine Demethylase Activity
07:02

Application of MassSQUIRM for Quantitative Measurements of Lysine Demethylase Activity

Published on: March 11, 2012

  • Comparative analysis with known druggable targets like bromodomains.

    • Main Results:

    • Methyl-lysine binding modules are generally less druggable than bromodomains.
    • A predictive landscape highlights varying druggability across different methyl-lysine readers.
    • Specific methyl-lysine binding proteins were identified as notable exceptions with potential for drug development.

    Conclusions:

    • While challenging, targeting methyl-lysine readers is feasible for certain proteins.
    • This study provides a framework for identifying druggable epigenetic targets.
    • Findings may guide the development of novel therapeutics for epigenetic-dysregulated diseases.