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Related Concept Videos

Caspases01:24

Caspases

Caspase, a family of cysteine proteases, serve as effectors in apoptosis. The ced3 gene in C.elegans was first identified to be involved in apoptosis. This gene encodes the ced-3 caspase that is similar to the interleukin-1-beta converting enzyme or ICE in mammals. In addition to apoptosis, caspases also function in the inflammatory response. Inflammatory caspases are essential in activating pro-inflammatory cytokines that recruit immune cells and block the replication of pathogens inside cells.
Allosteric Proteins-ATCase01:19

Allosteric Proteins-ATCase

Binding sites linkages can regulate a protein's function.  For example, enzyme activity is often regulated through a feedback mechanism where the end product of the biochemical process serves as an inhibitor.
Aspartate transcarbamoylase (ATCase) is a cytosolic enzyme that catalyzes the condensation of L-aspartate and carbamoyl phosphate to  N-carbamoyl-L-aspartate. This reaction is the first step in pyrimidine biosynthesis. UTP and CTP, the end products of the pyrimidine synthesis pathway,...
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.
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Protein Kinases and Phosphatases02:54

Protein Kinases and Phosphatases

Proteins undergo chemical modifications that trigger changes in the charge, structure, and conformation of the proteins. Phosphorylation, acetylation, glycosylation, nitrosylation, ubiquitination, lipidation, methylation, and proteolysis are various protein modifications that regulate protein activity. Such modifications are usually enzyme-driven.
Protein kinases
Many proteins in the cell are regulated by phosphorylation, the addition of a phosphate group. A family of enzymes called kinases...
Protein Kinases and Phosphatases02:54

Protein Kinases and Phosphatases

Proteins undergo chemical modifications that trigger changes in the charge, structure, and conformation of the proteins. Phosphorylation, acetylation, glycosylation, nitrosylation, ubiquitination, lipidation, methylation, and proteolysis are various protein modifications that regulate protein activity. Such modifications are usually enzyme-driven.
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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...

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Measuring Caspase Activity Using a Fluorometric Assay or Flow Cytometry
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Functional classification of protein kinase binding sites using Cavbase.

Daniel Kuhn1, Nils Weskamp, Eyke Hüllermeier

  • 1Department of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany.

Chemmedchem
|August 19, 2007
PubMed
Summary

We developed Cavbase, a novel method for classifying protein kinase families by analyzing active site binding pockets. This approach reveals functional relationships missed by sequence analysis, aiding drug discovery and inhibitor optimization.

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Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Drug discovery

Background:

  • Drug discovery increasingly targets entire gene families, necessitating tools to analyze protein family similarities and differences.
  • Understanding key functional features of proteins requires effective methods for comparing protein families.

Purpose of the Study:

  • To present a novel method, Cavbase, for classifying protein families based on active site properties.
  • To apply Cavbase to functionally classify the binding pockets of protein kinases.
  • To provide a new perspective on functional properties across protein space using binding pocket analysis.

Main Methods:

  • Developed Cavbase for describing and comparing protein binding pockets.
  • Applied Cavbase to a diverse set of kinase cavities, analyzing recurring functional recognition patterns in active sites.
  • Utilized small-molecule inhibition data to rationalize cross-reactivities.

Main Results:

  • Proposed a functional classification of protein kinases based on active site binding motifs.
  • Demonstrated clear separation of MAP and c-Abl kinase subfamilies, revealing cross-relations missed by sequence-based methods.
  • Highlighted features crucial for optimizing protein kinase inhibitors and rationalized cross-reactivities.

Conclusions:

  • Cavbase offers a novel classification of protein kinases based on binding pocket structure, providing insights beyond sequence analysis.
  • This classification aids in identifying potential kinase targets and optimizing inhibitor design.
  • The method reveals functional similarities and cross-reactivities among kinases, valuable for drug discovery efforts.