From structure to sequence and back again.
With a simple lattice model and sequence design algorithm, we can design sequences to fit arbitrary compact globular structures. We judged the success of the design algorithm by performing exhaustive conformational searches to determine if a designed sequence's lowest energy conformation matched the target for which it was designed. Designed sequences tend to be much better optimized for their targets than a natural sequence is optimized for its lowest energy model conformation. We examined the effect of varying the number of available amino acid types on the success of the design method. It was more difficult but not impossible to successfully design discriminating sequences using fewer amino acid types.
Hinds
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Department of Structural Biology, Stanford University School of Medicine, CA 94305, USA.
Levitt
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D000465:Algorithms; D000595:Amino Acid Sequence; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D017510:Protein Folding; D012269:Ribosomal Proteins / Q000737:chemistry; D013816:Thermodynamics
D012269:Ribosomal Proteins