A Basis Set of de Novo Coiled-Coil Peptide Oligomers for Rational Protein Design and Synthetic Biology

• DOI: 10.1021/sb300028q
• Publication Date: 2012-05-04T18:18:42Z
• Authors: Jordan M. Fletcher; Aimee L. Boyle; Marc Bruning; Gail J. Bartlett; Thomas L. Vincent; Nathan R. Zaccai; Craig T. Armstrong; Elizabeth H. C. B...; Paula J. Booth; R. Leo Brady; Andrew R. Thomson; Derek N. Woolfson
• Keywords: Synthetic Biology; Coiled coil; Rational design; Protein design; Protein Engineering; Basis (linear algebra)

Protein engineering, chemical biology, and synthetic biology would benefit from toolkits of peptide protein components that could be exchanged reliably between systems while maintaining their structural functional integrity. Ideally, such should highly defined predictable in all respects sequence, structure, stability, interactions, function. To establish one toolkit, here we present a basis set de novo designed α-helical coiled-coil peptides adopt well-characterized parallel dimeric, trimeric, tetrameric states. The designs are based on sequence-to-structure relationships both the literature analysis database known X-ray crystal structures. These give foreground sequences to specify targeted oligomer state. A key feature design process is sequence positions outside these sites considered non-essential for specificity; as such, they referred background, kept non-descript, available mutation required later. Synthetic were characterized solution by circular-dichroism spectroscopy analytical ultracentrifugation, structures determined crystallography. Intriguingly, hitherto widely used empirical rule-of-thumb dimer specification does not hold system. However, desired oligomeric state achieved database-informed redesign particular confirmed experimentally. We envisage will use directing controlling assembly, with potential applications biology. help endeavors, introduce Pcomp, an on-line registry protein-design synthetic-biology applications.