6KOS

Crystal structure of SUWA (Super WA20), a hyper-stable de novo protein with a dimeric bisecting topology

Summary for 6KOS

• Entry DOI: 10.2210/pdb6kos/pdb
• Related: 3VJF
• Descriptor: SUWA (Super WA20) (2 entities in total)
• Functional Keywords: thermostable protein design, de novo protein, binary patterned design, four helix bundle, 3d domain swapping, bisecting u topology
• Biological source: synthetic construct
• Total number of polymer chains: 4
• Total formula weight: 50169.04

Authors

Kimura, N.,Arai, R. (deposition date: 2019-08-13, release date: 2020-01-29, Last modification date: 2023-11-22)

Primary citation

Kimura, N.,Mochizuki, K.,Umezawa, K.,Hecht, M.H.,Arai, R.
HyperstableDe NovoProtein with a Dimeric Bisecting Topology.
Acs Synth Biol, 9:254-259, 2020

PubMed Abstract: Recently, we designed and assembled protein nanobuilding blocks (PN-Blocks) from an intermolecularly folded dimeric protein called WA20. Using this dimeric 4-helix bundle, we constructed a series of self-assembling supramolecular nanostructures including polyhedra and chain-type complexes. Here we describe the stabilization of WA20 by designing mutations that stabilize the helices and hydrophobic core. The redesigned proteins denature with substantially higher midpoints, with the most stable variant, called Super WA20 (SUWA), displaying an extremely high midpoint ( = 122 °C), much higher than the of WA20 (75 °C). The crystal structure of SUWA reveals an intermolecularly folded dimer with bisecting U topology, similar to the parental WA20 structure, with two long α-helices of a protomer intertwined with the helices of another protomer. Molecular dynamics simulations demonstrate that the redesigned hydrophobic core in the center of SUWA significantly suppresses the deformation of helices observed in the same region of WA20, suggesting this is a critical factor stabilizing the SUWA structure. This hyperstable protein is expected to be useful as nanoscale pillars of PN-Block components in new types of self-assembling nanoarchitectures.

PubMed: 31951376
DOI: 10.1021/acssynbio.9b00501

Experimental method

X-RAY DIFFRACTION (2 Å)