Premium
Emergence of highly designable protein‐backbone conformations in an off‐lattice model
Author(s) -
Miller Jonathan,
Zeng Chen,
Wingreen Ned S.,
Tang Chao
Publication year - 2002
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.10107
Subject(s) - protein design , protein structure , lattice (music) , protein folding , amino acid , physics , crystallography , biological system , chemistry , computational biology , biology , genetics , nuclear magnetic resonance , acoustics
Despite the variety of protein sizes, shapes, and backbone configurations found in nature, the design of novel protein folds remains an open problem. Within simple lattice models it has been shown that all structures are not equally suitable for design. Rather, certain structures are distinguished by unusually high designability: the number of amino acid sequences for which they represent the unique lowest energy state; sequences associated with such structures possess both robustness to mutation and thermodynamic stability. Here we report that highly designable backbone conformations also emerge in a realistic off‐lattice model. The highly designable conformations of a chain of 23 amino acids are identified and found to be remarkably insensitive to model parameters. Although some of these conformations correspond closely to known natural protein folds, such as the zinc finger and the helix‐turn‐helix motifs, others do not resemble known folds and may be candidates for novel fold design. Proteins 2002;47:506–512. © 2002 Wiley‐Liss, Inc.