Design of amino acid sequences to fold into C-alpha model proteins

Andrea Amatori, Guido Tiana, L. Sutto, Jesper Ferkinghoff-Borg, Antonio Trovato, Richardo A. Broglia

Research output: Contribution to journalJournal articleResearchpeer-review

Abstract

In order to extend the results obtained with minimal lattice models to more realistic systems, we study a model where proteins are described as a chain of 20 kinds of structureless amino acids moving in a continuum space and interacting through a contact potential controlled by a 2020 quenched random matrix. The goal of the present work is to design and characterize amino acid sequences folding to the SH3 conformation, a 60-residue recognition domain common to many regulatory proteins. We show that a number of sequences can fold, starting from a random conformation, to within a distance root-mean-square deviation between 2.6 and 4.0 Å from the native state. Good folders are those sequences displaying in the native conformation an energy lower than a sequence-independent threshold energy.
Original languageEnglish
JournalJournal of Chemical Physics
Issue number123
Pages (from-to)54904
ISSN0021-9606
Publication statusPublished - 2005
Externally publishedYes

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