<br/>Many fields of engineering have exploited the use of modular parts to streamline the generation of novel circuits, machines and apparatus. Protein engineers are beginning to follow this trend by generating modular protein-protein interaction units that can be used to facilitate the generation of novel protein structures, assemblies and pathways. However, a limited number of well-characterized parts are available for use. In this work, we sought to design a set of orthogonal antiparallel homodimeric coiled coils to expand the number of available parts. Very few antiparallel homodimeric coiled coils have been reported in the literature, and none have been measured for orthogonality. To properly consider all of the states important in this design problem, a computational methodology was employed that used the distance-dependent statistical potential DFIRE integrated with the CLASSY multistate protein design framework. Biophysical characterization of five designed antiparallel coiled coils confirmed the successful design of three peptides that preferentially formed orthogonal antiparallel homodimers. Experiments further established that the designed antiparallel coiled coils from this work are orthogonal to a previously reported antiparallel homodimer. Two designed sequences that formed higher-order structures highlight shortcomings of the current computational methodology. The successful designs represent a significant contribution to the existing toolbox of protein-protein interactions, and help to further validate the CLASSY multistate design framework.

Computational design of orthogonal antiparallel homodimers

251st National Meeting (2016)

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