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Restricted sidechain plasticity in the structures of native proteins and complexes
Author(s) -
Fleishman Sarel J.,
Khare Sagar D.,
Koga Nobuyasu,
Baker David
Publication year - 2011
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1002/pro.604
Subject(s) - native state , plasticity , selection (genetic algorithm) , chemical physics , range (aeronautics) , protein structure , energy landscape , chemistry , protein design , biophysics , crystallography , biological system , materials science , computer science , physics , biology , biochemistry , thermodynamics , artificial intelligence , composite material
Protein‐design methodology can now generate models of protein structures and interfaces with computed energies in the range of those of naturally occurring structures. Comparison of the properties of native structures and complexes to isoenergetic design models can provide insight into the properties of the former that reflect selection pressure for factors beyond the energy of the native state. We report here that sidechains in native structures and interfaces are significantly more constrained than designed interfaces and structures with equal computed binding energy or stability, which may reflect selection against potentially deleterious non‐native interactions.