3D Complex: A Structural Classification of Protein Complexes
Author Information
Author(s): Levy Emmanuel D, Pereira-Leal Jose B, Chothia Cyrus, Teichmann Sarah A
Primary Institution: Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
Hypothesis
How many different protein complexes exist in the Protein Data Bank (PDB)?
Conclusion
The study presents a hierarchical classification of protein complexes, revealing a strong bias towards small, homomeric, and symmetrical complexes.
Supporting Evidence
- More than half of the structures in the Protein Data Bank are protein complexes.
- The classification reveals that between one-half and two-thirds of known structures are multimeric.
- Most complexes contain four subunits or less.
- Symmetry is a common feature in protein complexes.
- Errors in quaternary structure assignments were identified through comparison with the Protein Quaternary Structure database.
Takeaway
This study helps us understand how proteins work together by classifying them into groups based on their shapes and how they connect.
Methodology
The study uses a graph representation of protein complexes to classify them hierarchically based on their structural features.
Potential Biases
The study may be biased towards smaller, more easily crystallized proteins, potentially overlooking larger complexes.
Limitations
The classification may not account for all possible protein interactions and relies on existing data from the Protein Data Bank.
Digital Object Identifier (DOI)
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