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 20 20 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.

Design of amino acid sequences to fold into C_alpha-model proteins / A. Amatori, G. Tiana, L. Sutto, J.Ferkinghoff-Borg, A. Trovato, R. A. Broglia. - In: THE JOURNAL OF CHEMICAL PHYSICS. - ISSN 0021-9606. - 123:5(2005), pp. 054904.54904-1-054904.54904-7.

Design of amino acid sequences to fold into C_alpha-model proteins

G. Tiana
Secondo
;
R. A. Broglia
Ultimo
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 20 20 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.
lattice theory; macromolecules; molecular biophysics; proteins.
Settore FIS/04 - Fisica Nucleare e Subnucleare
Settore FIS/03 - Fisica della Materia
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/2434/8357
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