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How many protein folding motifs are there?
1College of Pharmacy, University of Michigan, Ann Arbor 48109, USA.
Journal of Molecular Biology
|September 8, 1995
Summary
Researchers explored the number of protein folding motifs using a quantitative similarity measure. They found approximately 128 distinct motifs exist, with 28 potentially undiscovered novel folds.
Area of Science:
- Structural biology
- Computational biology
- Biophysics
Background:
- Determining 3D protein structures is advancing rapidly.
- Discovering novel protein folding motifs is becoming increasingly rare.
- Quantifying the total number of possible protein folds is a key question.
Purpose of the Study:
- To estimate the total number of distinct protein folding motifs.
- To determine how many known motifs have been experimentally observed.
- To identify potential novel protein folds.
Main Methods:
- Utilized a quantitative measure of conformational similarity, rho (based on optimal rigid body superposition).
- Employed the discrete cosine transform to generate all possible 3D chain conformations.
- Analyzed single-chain proteins (≤170 residues, excluding beta-barrels).
Main Results:
- Identified approximately 128 distinct folding motifs with a similarity cutoff of rho > 1.0.
- Found that 100 of these motifs have been observed experimentally.
- Calculated that 28 potential motifs remain undiscovered or unobserved.
Conclusions:
- The number of protein folding motifs is finite and quantifiable.
- A significant number of potential protein folds may yet to be discovered.
- The remaining motifs could represent novel folds or challenge current protein folding principles.