Design of amino acid sequences to fold into C(alpha)-model proteins.
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 A from the native state. Good folders are those sequences displaying in the native conformation an energy lower than a sequence-independent threshold energy.
Amatori
A
A
Department of Physics, University of Milano, Via Festa del Perdono 7, 20122 Milano, Italy.
Tiana
G
G
Sutto
L
L
Ferkinghoff-Borg
J
J
Trovato
A
A
Broglia
R A
RA
D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry*; D002627:Chemistry, Physical / Q000379:methods*; D018360:Crystallography, X-Ray; D006801:Humans; D008958:Models, Molecular; D015233:Models, Statistical; D008968:Molecular Conformation; D008969:Molecular Sequence Data; D011487:Protein Conformation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D018909:src Homology Domains; D019061:src-Family Kinases / Q000737:chemistry
D000596:Amino Acids; D011506:Proteins; D019061:src-Family Kinases