8A3J

X-ray crystal structure of a de novo designed antiparallel coiled-coil heterotetramer with 3 heptad repeats, apCC-Tet*3-A2B2

Summary for 8A3J

• Entry DOI: 10.2210/pdb8a3j/pdb
• Descriptor: apCC-Tet*3-A, apCC-Tet*3-B (3 entities in total)
• Functional Keywords: coiled coil, 4-helix bundle, de novo protein design, peptide assembly, de novo protein
• Biological source: synthetic construct; More
• Total number of polymer chains: 8
• Total formula weight: 21116.90

Authors

Naudin, E.A.,Mylemans, B.,Albanese, K.I.,Woolfson, D.N. (deposition date: 2022-06-08, release date: 2022-10-05, Last modification date: 2022-11-23)

Primary citation

Naudin, E.A.,Albanese, K.I.,Smith, A.J.,Mylemans, B.,Baker, E.G.,Weiner, O.D.,Andrews, D.M.,Tigue, N.,Savery, N.J.,Woolfson, D.N.
From peptides to proteins: coiled-coil tetramers to single-chain 4-helix bundles.
Chem Sci, 13:11330-11340, 2022

PubMed Abstract: The design of completely synthetic proteins from first principles- protein design-is challenging. This is because, despite recent advances in computational protein-structure prediction and design, we do not understand fully the sequence-to-structure relationships for protein folding, assembly, and stabilization. Antiparallel 4-helix bundles are amongst the most studied scaffolds for protein design. We set out to re-examine this target, and to determine clear sequence-to-structure relationships, or design rules, for the structure. Our aim was to determine a common and robust sequence background for designing multiple 4-helix bundles. In turn, this could be used in chemical and synthetic biology to direct protein-protein interactions and as scaffolds for functional protein design. Our approach starts by analyzing known antiparallel 4-helix coiled-coil structures to deduce design rules. In terms of the heptad repeat, -, the sequence signature of many helical bundles-the key features that we identify are: = Leu, = Ile, = Ala, = Gln, and the use of complementary charged residues at b and c. Next, we implement these rules in the rational design of synthetic peptides to form antiparallel homo- and heterotetramers. Finally, we use the sequence of the homotetramer to derive in one step a single-chain 4-helix-bundle protein for recombinant production in . All of the assembled designs are confirmed in aqueous solution using biophysical methods, and ultimately by determining high-resolution X-ray crystal structures. Our route from peptides to proteins provides an understanding of the role of each residue in each design.

PubMed: 36320580
DOI: 10.1039/d2sc04479j

Experimental method

X-RAY DIFFRACTION (2.1 Å)