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(Probably) all possible protein folds at low resolution
1College of Pharmacy, University of Michigan, Ann Arbor 48109, USA.
Summary
Researchers explored protein structure diversity by analyzing C alpha coordinates. They found 128 distinct artificial protein structures, with 28 not matching existing Protein Data Bank entries, suggesting many protein folds remain undiscovered.
Area of Science:
- Structural bioinformatics
- Computational biology
- Protein structure analysis
Background:
- Extensive databases of experimentally determined protein structures exist.
- The question of whether all distinct protein folds have been identified remains open.
Purpose of the Study:
- To determine the extent of diversity in protein folds.
- To estimate the number of undiscovered protein folds.
Main Methods:
- Analysis focused on C alpha atomic coordinates, excluding gapped alignments for different chain lengths.
- A similarity measure based on rigid body superposition was used, prioritizing overall geometric resemblance.
- The discrete cosine transform constructed exhaustive sets of dissimilar C alpha traces.
Main Results:
- For protein chains of 170 residues or less (excluding beta-barrels), 128 artificial structures were generated.
- Of these, 28 artificial structures did not resemble any known structures in the Protein Data Bank.
Conclusions:
- The findings suggest that a significant number of protein folds may still be undiscovered.
- This computational approach provides a framework for exploring the space of possible protein structures.