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Simple electrostatic model improves designed protein sequences
Author(s) -
Zollars Eric S.,
Marshall Shan A.,
Mayo Stephen L.
Publication year - 2006
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 - 10.1110/ps.062105506
Subject(s) - electrostatics , parameterized complexity , simple (philosophy) , physics , poisson–boltzmann equation , static electricity , stability (learning theory) , engrailed , function (biology) , chemical physics , chemistry , statistical physics , biological system , computer science , homeobox , biology , algorithm , quantum mechanics , ion , microbiology and biotechnology , biochemistry , philosophy , gene expression , epistemology , machine learning , gene
Electrostatic interactions are important for both protein stability and function, including binding and catalysis. As protein design moves into these areas, an accurate description of electrostatic energy becomes necessary. Here, we show that a simple distance‐dependent Coulombic function parameterized by a comparison to Poisson‐Boltzmann calculations is able to capture some of these electrostatic interactions. Specifically, all three helix N‐capping interactions in the engrailed homeodomain fold are recovered using the newly parameterized model. The stability of this designed protein is similar to a protein forced by sequence restriction to have beneficial electrostatic interactions.