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Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
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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.
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ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...
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The organelle-specific signaling sequences direct proteins synthesized in the cytosol to their final destination like ER, mitochondria, peroxisomes, etc. Some of the proteins directed to ER are then trafficked via vesicles to other organelles within the cell or the extracellular environment through the Golgi complex. For example, the rough ER synthesizes soluble proteins for transportation to the lysosomes or secretion out of the cell. It can also synthesize transmembrane proteins that can...
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The addition or removal of phosphate groups from proteins is the most common chemical modification that regulates cellular processes. These modifications can affect the structure, activity, stability, and localization of proteins within cells as well as their interactions with other proteins.
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A sizable fraction of proteins destined for ER are first synthesized in the cell cytosol and then transported across the ER membrane–a process called post-translational translocation. Similar to cotranslationally translocated proteins, these proteins also use the Sec translocon complex to enter the ER lumen.
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Post-translational modifications in the Protein Data Bank.

Lucy C Schofield1, Jordan S Dialpuri1, Garib N Murshudov2

  • 1York Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom.

Acta Crystallographica. Section D, Structural Biology
|August 29, 2024
PubMed
Summary
This summary is machine-generated.

Post-translational modifications (PTMs) are crucial for protein function but challenging to model. This review examines PTMs in protein structures and their prevalence in the Protein Data Bank for accurate modeling.

Keywords:
Protein Data Bankacetylationglycosylationphosphorylationpost-translational modifications

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Molecular Biology

Background:

  • Proteins undergo post-translational modifications (PTMs), the covalent attachment of chemical groups to amino acids.
  • PTMs include phosphorylation, glycosylation, ubiquitination, and pyroglutamic acid formation, altering protein properties.
  • These modifications are vital for cellular functions like enzymatic activity, localization, interactions, and stability.

Purpose of the Study:

  • To highlight the role of PTMs in protein structures.
  • To review the prevalence of PTMs within the Protein Data Bank (PDB).
  • To provide examples of accurately modeled PTMs for reference.

Main Methods:

  • Literature review focusing on PTMs in protein structures.
  • Analysis of PTM representation in the Protein Data Bank.
  • Identification and curation of PTM examples for structural modeling.

Main Results:

  • PTMs significantly impact protein structure and function.
  • The Protein Data Bank contains numerous examples of PTMs, but accurate depiction can be challenging.
  • Specific examples of well-modeled PTMs are identified for reference.

Conclusions:

  • Accurate representation of PTMs in structural studies is essential.
  • The Protein Data Bank serves as a valuable resource for understanding PTMs in protein structures.
  • This review offers guidance for researchers modeling proteins with PTMs.