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FOR THE RECORD

Simple electrostatic model improves designed protein sequences

¹ Biochemistry and Molecular Biophysics, California Institute of Technology, Pasadena, California 91125, USA
² Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
³ Howard Hughes Medical Institute, California Institute of Technology, Pasadena, California 91125, USA

(RECEIVED January 24, 2006; FINAL REVISION May 12, 2006; ACCEPTED May 15, 2006)

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.

Keywords: protein design; electrostatics; engrailed; N-capping

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