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Exploring protein sequence space using knowledge-based potentials.

A Babajide·R Farber·I L Hofacker·J Inman·A S Lapedes·P F Stadler
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Abstract

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 sequence-structure relations in protein space. In particular, we test the following two propositions which were found to be important for efficient 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 different potential functions, M. Sippl's PROSA pair potential and a neural network based potential, are used to verify these claims.

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Amino Acid SequenceAnimalsComputer SimulationEvolution, MolecularModels, ChemicalProtein ConformationProtein FoldingJournal ArticleResearch Support, Non-U.S. Gov'tResearch Support, U.S. Gov't, Non-P.H.S.

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A Babajide, R Farber, I L Hofacker, J Inman, A S Lapedes, P F Stadler. 2001-09-07. Exploring protein sequence space using knowledge-based potentials.. https://doi.org/10.1006/jtbi.2001.2343

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