PDB_Amyloid: an extended live amyloid structure list from the PDB

Area of Science:

• Structural Biology
• Biophysics
• Computational Biology

Background:

• The Protein Data Bank (PDB) houses over 135,000 entries, but few amyloid structures are available due to insolubility.
• Amyloid structures in the PDB are primarily derived from solid-state Nuclear Magnetic Resonance (NMR) data.
• Identifying amyloid structures and similar motifs in large protein databases presents a significant challenge.

Purpose of the Study:

• To create an automatically updated web server for identifying deposited amyloid structures in the PDB.
• To discover globular proteins containing amyloid-like substructures using geometric criteria.
• To provide a regularly updated resource for researchers studying protein aggregation and amyloid formation.

Main Methods:

• Geometric analysis of deposited protein structures in the PDB.
• Development of an automated web server to apply geometric conditions for structure identification.
• Literature review to validate the amyloid-forming propensity of identified globular proteins.

Main Results:

• Successfully identified deposited amyloid structures and globular proteins with amyloid-like substructures based on geometric properties.
• Demonstrated that specific geometric conditions are sufficient for identifying these structures.
• Found evidence that many identified globular proteins are prone to forming amyloids.

Conclusions:

• The developed web server effectively identifies amyloid and partial amyloid structures within the PDB.
• Geometric analysis is a powerful method for detecting amyloidogenic regions in proteins.
• The findings contribute to a better understanding of protein aggregation and provide a valuable resource for further research.