Evaluation of Steric Entanglement in Coiled-coil and Domain-swapped
Protein Interfaces using 3D Printed Models
Oligomeric protein interfaces involve non-covalent attractive forces
plus potential steric entanglement. 70 years ago, Crick proposed a
“Knobs in Holes” model for coiled-coil protein interfaces.
Subsequently, modifications to this model have been proposed, describing
either a “leucine zipper”, “jigsaw puzzle”, or a “peptide Velcro”
interface. These principally describe forms of steric entanglement that
may enhance oligomer stability; however, such entanglement has not been
rigorously evaluated since it is not possible to experimentally
eliminate intrinsic noncovalent attractive forces. 3D printing provides
a novel means to evaluate steric entanglement of protein interfaces in
the absence of attractive forces. Surprisingly, quantitation of the
energy required to dissociate various coiled-coil protein interfaces of
3D printed protein models suggests minimal steric entanglement.
Conversely, evaluation of domain swapped interfaces of symmetric protein
oligomers, differing by circular permutation, identifies extensive
potential steric entanglement. Combined with available experimental
data, the results suggest that steric entanglement of a protein
interface can contribute to kinetic trapping of both folding and
unfolding pathways. Steric entanglement of protein interfaces is
therefore postulated to be an undesirable property for naturally evolved
and designed protein oligomers.