Gradual development of protein-like global structures through functional selection.
This work focuses on streamlining the exploration of all possible sequences in an attempt to find polypeptides capable of folding into unique structures. Using a computer simulation, we have demonstrated the efficacy of constraining an 'active site' toward the correct configuration, in this case a particular conformation of a four-residue sequence, to bring about protein-like structure from a significant fraction of random sequences. The successive selections for a correct local configuration lead also to the gradual development of overall folding ability, helicity and compactness within 200 generations. The selection thus imposed alleviates an exhaustive search in sequence space.
Yomo
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T
Department of Biotechnology, Graduate School of Engineering, Osaka University, Osaka, 565-0871, Japan. yomo@mail.bio.eng.osakau.ac.jp
Saito
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S
Sasai
M
M
D003198:Computer Simulation; D008958:Models, Molecular; D011487:Protein Conformation