Foldons, protein structural modules, and exons.
Foldons, which are kinetically competent, quasi-independently folding units of a protein, may be defined using energy landscape analysis. Foldons can be identified by maxima in a scan of the ratio of a contiguous segment's energetic stability gap to the energy variance of that segment's molten globule states, reflecting the requirement of minimal frustration. The predicted foldons are compared with the exons and structural modules for 16 of the 30 proteins studied. Statistical analysis indicates a strong correlation between the energetically determined foldons and Go's geometrically defined structural modules, but there are marked sequence-dependent effects. There is only a weak correlation of foldons to exons. For gammaII-crystallin, myoglobin, barnase, alpha-lactalbumin, and cytochrome c the foldons and some noncontiguous clusters of foldons compare well with intermediates observed in experiment.
Panchenko
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AR
School of Chemical Sciences, University of Illinois, Urbana 61801, USA.
Luthey-Schulten
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Z
Wolynes
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PG
D000465:Algorithms; D007611:Aprotinin / Q000737:chemistry; D001426:Bacterial Proteins; D055592:Biophysical Phenomena; D001703:Biophysics; D005091:Exons; D007700:Kinetics; D007874:Leghemoglobin / Q000737:chemistry; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D012260:Ribonucleases / Q000737:chemistry; D013329:Structure-Activity Relationship; D013816:Thermodynamics
D001426:Bacterial Proteins; D007874:Leghemoglobin; D011506:Proteins; D007611:Aprotinin; D012260:Ribonucleases; C019760:Bacillus amyloliquefaciens ribonuclease