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Exploring Protein Sequence Space Using Knowledge-based Potentials

✍ Scribed by ADERONKE BABAJIDE; ROBERT FARBER; IVO L. HOFACKER; JEFF INMAN; ALAN S. LAPEDES; PETER F. STADLER

Publisher: Elsevier Science
Year: 2001
Tongue: English
Weight: 506 KB
Volume: 212
Category: Article
ISSN: 0022-5193
DOI: 10.1006/jtbi.2001.2343

No coin nor oath required. For personal study only.

✦ Synopsis

Knowledge-based potentials can be used to decide whether an amino acid sequence is likely to fold into a prescribed native protein structure. We use this idea to survey the se-quence}structure relations in protein space. In particular, we test the following two propositions which were found to be important for e$cient evolution: the sequences folding into a particular native fold form extensive neutral networks that percolate through sequence space. The neutral networks of any two native folds approach each other to within a few point mutations. Computer simulations using two very di!erent potential functions, M. Sippl's PROSA pair potential and a neural network based potential, are used to verify these claims.

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