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Folding minimal sequences: the lower bound for sequence complexity of globular proteins
P Romero1, Z Obradovic, A K Dunker
1School of Electrical Engineering and Computer Science, Washington State University, Pullman 99164-4660, USA.
FEBS Letters
|January 6, 2000
Summary
Sequence complexity measures, including alphabet size and informational entropy, reveal insights into protein folding. Specific complexity values appear necessary for globular proteins to fold correctly with biological function.
Area of Science:
- Computational Biology
- Biophysics
- Protein Science
Background:
- Minimal proteins present unique challenges for understanding protein folding.
- Sequence complexity is a key factor influencing protein structure and function.
Purpose of the Study:
- To apply formal measures of sequence complexity, alphabet size and informational entropy, to minimal protein folding studies.
- To determine if specific complexity thresholds are indicative of globular protein folding and function.
Main Methods:
- Analysis of two prior studies on minimal protein folding.
- Calculation of alphabet size and informational entropy for protein segments.
- Comparison of complexity measures between designed and natural protein structures.
Main Results:
- A designed four-helix bundle protein exhibited complexity measures more akin to a coiled-coil dimer than natural counterparts.
- Globular protein segments and a simplified sarc homology 3 domain share lower bounds for alphabet size (10) and entropy (approx. 2.9).
Conclusions:
- The determined complexity values (alphabet size ≥ 10, entropy ≈ 2.9) are proposed as necessary and sufficient for globular protein folding.
- These complexity thresholds correlate with the ability of proteins to achieve rigid side chain packing and biological function.
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