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An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
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All meta-directing substituents are deactivating groups. These substituents withdraw electrons from the aromatic ring, making the ring less reactive toward electrophilic substitution. For example, the nitration of nitrobenzene is 100,000 times slower than that of benzene because of the deactivating effect of the nitro group. The first step in an electrophilic aromatic substitution is the addition of an electrophile to form a resonance-stabilized carbocation. The energy diagrams for...
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Secondary amines react with nitrous acid to form N-nitrosamines, as depicted in Figure 1. Nitrous acid, a weak and unstable acid, is formed in situ from an aqueous solution of sodium nitrite and strong acids, such as hydrochloric acid or sulfuric acid, in cold conditions. In the presence of an acid, the nitrous acid gets protonated. The subsequent loss of water results in the formation of the electrophile known as nitrosonium ion.
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Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
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Kinetic Studies and Significance
In a chemical reaction, a relationship exists between the concentration of reactants and the rate at which the reaction proceeds. The study to measure this relationship is known as the kinetics of a chemical reaction. Kinetic studies are used to deduce the rate law of a chemical reaction, which provides information about the species involved during the transition state of the rate-determining step. Thus, kinetic studies help to derive the mechanism of a...
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Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
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SwissPalm 2: Protein S-Palmitoylation Database.

Mathieu Blanc1, Fabrice P A David2, F Gisou van der Goot3

  • 1Global Health Institute, School of Life Sciences, EPFL, Lausanne, Switzerland.

Methods in Molecular Biology (Clifton, N.J.)
|June 2, 2019
PubMed
Summary

Protein S-palmitoylation, a key protein modification, is vital for biological processes. The SwissPalm database now offers an updated version, SwissPalm 2, consolidating extensive palmitoyl-proteome data and aiding comparative analysis across species.

Keywords:
ConfidenceDHHCDatabasePalmitoyl-proteomesPalmitoylationPosttranslational modificationProteomicsS-acylation

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Proteomics

Background:

  • Protein S-palmitoylation is a crucial post-translational modification found in eukaryotes.
  • It plays a significant role in regulating diverse biological processes.
  • The growing volume of palmitoyl-proteome data necessitates centralized resources for analysis.

Purpose of the Study:

  • To update and enhance the SwissPalm database with new palmitoyl-proteome datasets.
  • To provide improved tools for comparing and analyzing palmitoylated protein data.
  • To facilitate research on protein S-palmitoylation across different species.

Main Methods:

  • Centralization of published palmitoyl-proteome datasets.
  • Inclusion of curated data from scientific literature.
  • Development of comparative analysis tools.
  • Integration of ortholog information.

Main Results:

  • SwissPalm 2 now includes 38 palmitoyl-proteomes from 17 species.
  • The database offers enhanced features for data comparison.
  • Ortholog data has been incorporated for cross-species analysis.

Conclusions:

  • SwissPalm 2 serves as a comprehensive resource for studying protein S-palmitoylation.
  • The updated database supports comparative proteomics and evolutionary studies.
  • It aids researchers in understanding the biological roles of palmitoylated proteins.