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Design of proteins with hydrophobic and polar amino acids

✍ Scribed by Cristian Micheletti; Flavio Seno; Amos Maritan; Jayanth R. Banavar

Publisher: John Wiley and Sons
Year: 1998
Tongue: English
Weight: 279 KB
Volume: 32
Category: Article
ISSN: 0887-3585
DOI: 10.1002/(sici)1097-0134(19980701)32:1<80::aid-prot9>3.0.co;2-i

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✦ Synopsis

A two amino acid (hydrophobic and polar) scheme is used to perform the design on target conformations corresponding to the native states of 20 single chain proteins. Strikingly, the percentage of successful identification of the nature of the residues benchmarked against naturally occurring proteins and their homologues is around 75%, independent of the complexity of the design procedure. Typically, the lowest success rate occurs for residues such as alanine that have a high secondary structure functionality. Using a simple lattice model, we argue that one possible shortcoming of the model studied may involve the coarse-graining of the 20 kinds of amino acids into just two effective types. Pro-

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