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Coevolution of function and the folding landscape: correlation with density of native contacts
Ronald D Hills1, Charles L Brooks
1Department of Molecular Biology and Kellogg School of Science and Technology, Scripps Research Institute, La Jolla, California, USA.
Biophysical Journal
|August 19, 2008
Summary
Protein folding landscapes are finely tuned for specific biological functions. Differences in protein packing and dynamics, like in Spo0F, can create folding frustration, impacting protein function.
Area of Science:
- Proteomics
- Computational Biology
- Biophysics
Background:
- Proteins with identical topology can have unrelated functions.
- The folding landscape influences protein function.
Purpose of the Study:
- To explore the relationship between protein folding landscapes and function.
- To compare folding mechanisms of flavodoxin fold proteins (CheY, Spo0F, NtrC).
Main Methods:
- Coarse-grained simulations.
- Comparison of folding landscapes for CheY, Spo0F, and NtrC.
- Correlation of simulation and experimental results with native contact density.
Main Results:
- Folding landscapes are uniquely tuned to biological functions.
- Enhanced packing in Spo0F leads to folding landscape frustration.
- Protein regions with low native contact density structure late in folding and are functionally important.
Conclusions:
- Protein folding landscapes are optimized for function.
- Local protein density influences folding dynamics.
- Gō-like models effectively reproduce protein dynamics.
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