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 20x20 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 angstrom from the native state. Good folders are those sequences displaying in the native conformation an energy lower than a sequence-independent threshold energy. (C) 2005 American Institute of Physics.

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

TROVATO, ANTONIO;
2005

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 20x20 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 angstrom from the native state. Good folders are those sequences displaying in the native conformation an energy lower than a sequence-independent threshold energy. (C) 2005 American Institute of Physics.
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11577/1428386
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