A set of computationally designed orthogonal antiparallel homodimers that expands the synthetic coiled-coil toolkit.

TitleA set of computationally designed orthogonal antiparallel homodimers that expands the synthetic coiled-coil toolkit.
Publication TypeJournal Article
Year of Publication2014
AuthorsNegron C, Keating AE
JournalJ Am Chem Soc
Volume136
Issue47
Pagination16544-56
Date Published2014 Nov 26
ISSN1520-5126
KeywordsComputational Biology, Peptides, Protein Engineering
Abstract

Molecular engineering of protein assemblies, including the fabrication of nanostructures and synthetic signaling pathways, relies on the availability of modular parts that can be combined to give different structures and functions. Currently, a limited number of well-characterized protein interaction components are available. Coiled-coil interaction modules have been demonstrated to be useful for biomolecular design, and many parallel homodimers and heterodimers are available in the coiled-coil toolkit. In this work, we sought to design a set of orthogonal antiparallel homodimeric coiled coils using a computational approach. There are very few antiparallel homodimers described in the literature, and none have been measured for cross-reactivity. We tested the ability of the distance-dependent statistical potential DFIRE to predict orientation preferences for coiled-coil dimers of known structure. The DFIRE model was then combined with the CLASSY multistate protein design framework to engineer sets of three orthogonal antiparallel homodimeric coiled coils. Experimental measurements confirmed the successful design of three peptides that preferentially formed antiparallel homodimers that, furthermore, did not interact with one additional previously reported antiparallel homodimer. Two designed peptides that formed higher-order structures suggest how future design protocols could be improved. The successful designs represent a significant expansion of the existing protein-interaction toolbox for molecular engineers.

DOI10.1021/ja507847t
Alternate JournalJ. Am. Chem. Soc.
PubMed ID25337788
PubMed Central IDPMC4277747
Grant ListGM67681 / GM / NIGMS NIH HHS / United States