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Related Concept Videos

Proteomics01:33

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
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,...
Protein Modifications in the RER01:26

Protein Modifications in the RER

Modification of secretory and transmembrane proteins entering the rough ER begins in the ER lumen. These modifications aid in protein folding and stabilize the acquired tertiary structure. Protein modifications in the rough ER co-occur at different stages of protein folding.
Broadly, these modifications can be categorized into four main categories — glycosylation, formation of disulfide bonds, assembly of protein subunits, and specific proteolytic cleavages like removal of signal sequences.
Biosynthesis of Lipids01:29

Biosynthesis of Lipids

Microbial membranes exhibit remarkable diversity in lipid composition, reflecting evolutionary adaptations to various environmental conditions. The three domains of life—Bacteria, Archaea, and Eukarya—synthesize membrane lipids through distinct biosynthetic pathways, leading to fundamental structural differences that impact membrane stability, function, and adaptability.Fatty Acid-Based Lipids in Bacteria and EukaryaBacteria and eukaryotes share a common fatty acid biosynthesis pathway, which...
Tail-anchoring of Proteins in the ER Membrane01:45

Tail-anchoring of Proteins in the ER Membrane

Tail-anchored, or TA, proteins are estimated to make up to 3-5% of membrane proteins found in the eukaryotic cell. Such proteins have a single transmembrane domain located approximately 30 amino acid residues upstream from the C-terminal end. As a result, the signal recognition particle (SRP) cannot guide a TA protein to the ER membrane for cotranslational insertion. Hence, they are integrated into the ER membrane post-translationally using their C-terminal end as the anchor. TA proteins...

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A Protocol for the Identification of Protein-protein Interactions Based on 15N Metabolic Labeling, Immunoprecipitation, Quantitative Mass Spectrometry and Affinity Modulation
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Published on: September 24, 2012

Chemoisosterism in the proteome.

Xavier Jalencas1, Jordi Mestres

  • 1Chemogenomics Laboratory, Research Programme on Biomedical Informatics (GRIB), IMIM Hospital del Mar Research Institute and University Pompeu Fabra, Doctor Aiguader 88, 08003 Barcelona, Catalonia, Spain.

Journal of Chemical Information and Modeling
|January 15, 2013
PubMed
Summary
This summary is machine-generated.

Chemoisosterism describes protein environments that bind the same chemical fragments, complementing bioisosterism. This concept aids fragment-based drug discovery by identifying similar protein binding sites across different enzymes.

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Published on: December 18, 2013

Area of Science:

  • Computational chemistry
  • Structural biology
  • Drug discovery

Background:

  • Bioisosterism relates chemical fragments with similar biological activity.
  • Protein environments interacting with ligands are crucial for drug design.
  • Advances in structural biology provide extensive data on protein-ligand complexes.

Purpose of the Study:

  • Introduce chemoisosterism as a concept complementary to bioisosterism.
  • Define chemoisosterism for protein environments.
  • Explore the application of chemoisosterism in drug discovery.

Main Methods:

  • Leveraging the growing database of protein-ligand complex crystal structures.
  • Identifying chemoisosteric relationships between protein environments.
  • Utilizing chemoisosteric environments to predict ligand fragment positioning.

Main Results:

  • Defined chemoisosterism as the ability of protein environments to interact with the same chemical fragment.
  • Demonstrated that chemoisosteric environments from enzymes can accurately predict ligand fragment location in nuclear receptors.
  • Provided examples of chemoisosterism's utility in fragment-based drug discovery.

Conclusions:

  • Chemoisosterism offers a novel perspective on protein-ligand interactions.
  • This concept can enhance fragment-based drug discovery strategies.
  • Identifying chemoisosteric protein environments facilitates the design of new therapeutics.