Design of three-dimensional domain-swapped dimers and fibrous oligomers

Design of three-dimensional domain-swapped dimers and fibrous oligomers

^*UCLA-DOE Laboratory of Structural Biology and the Department of Chemistry and Biochemistry, P.O. Box 951570, University of California, Los Angeles, CA 90095-1570; ^§The Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6059; and ^†Molecular Biology Institute, Box 951570, University of California, Los Angeles, CA 90095-1570

Contributed by William F. DeGrado

Abstract

Three-dimensional (3D) domain-swapped proteins are intermolecularly folded analogs of monomeric proteins; both are stabilized by the identical interactions, but the individual domains interact intramolecularly in monomeric proteins, whereas they form intermolecular interactions in 3D domain-swapped structures. The structures and conditions of formation of several domain-swapped dimers and trimers are known, but the formation of higher order 3D domain-swapped oligomers has been less thoroughly studied. Here we contrast the structural consequences of domain swapping from two designed three-helix bundles: one with an up-down-up topology, and the other with an up-down-down topology. The up-down-up topology gives rise to a domain-swapped dimer whose structure has been determined to 1.5 Å resolution by x-ray crystallography. In contrast, the domain-swapped protein with an up-down-down topology forms fibrils as shown by electron microscopy and dynamic light scattering. This demonstrates that design principles can predict the oligomeric state of 3D domain-swapped molecules, which should aid in the design of domain-swapped proteins and biomaterials.

Footnotes

↵ ‡ Present address: Molecular Simulations, 9685 Scranton Road, San Diego, CA 92121.
↵ ¶ Present address: Bristol-Myers Squibb Company, Mail Stop H13-05, P.O. Box 4000, Princeton, NJ 08543-4000.
↵ ‖ To whom reprint requests should be addressed. E-mail: david{at}mbi.ucla.edu.
Data deposition: The atomic coordinates have been deposited in the Protein Data Bank, www.rcsb.org (PDB ID code 1g6u).
Abbreviations:

CD,

circular dichroism;

DSD,

domain-swapped dimer;

DSAg,

domain-swapped aggregate;

Gdn⋅HCl,

guanidine hydrochloride;

3D,

three-dimensional