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 language | English |
---|---|
Journal | Journal of Chemical Physics |
Issue number | 123 |
Pages (from-to) | 54904 |
ISSN | 0021-9606 |
Publication status | Published - 2005 |
Externally published | Yes |