Protein assembly by design

J Zhu, N Avakyan, A Kakkis, AM Hoffnagle… - Chemical …, 2021 - ACS Publications
Proteins are nature's primary building blocks for the construction of sophisticated molecular
machines and dynamic materials, ranging from protein complexes such as photosystem II …

The cryo-EM method microcrystal electron diffraction (MicroED)

BL Nannenga, T Gonen - Nature methods, 2019 - nature.com
In 2013 we established a cryo-electron microscopy (cryo-EM) technique called microcrystal
electron diffraction (MicroED). Since that time, data collection and analysis schemes have …

Hallucinating symmetric protein assemblies

BIM Wicky, LF Milles, A Courbet, RJ Ragotte… - Science, 2022 - science.org
Deep learning generative approaches provide an opportunity to broadly explore protein
structure space beyond the sequences and structures of natural proteins. Here, we use deep …

Accurate design of megadalton-scale two-component icosahedral protein complexes

JB Bale, S Gonen, Y Liu, W Sheffler, D Ellis, C Thomas… - Science, 2016 - science.org
Nature provides many examples of self-and co-assembling protein-based molecular
machines, including icosahedral protein cages that serve as scaffolds, enzymes, and …

Computational design of mechanically coupled axle-rotor protein assemblies

A Courbet, J Hansen, Y Hsia, N Bethel, YJ Park, C Xu… - Science, 2022 - science.org
Natural molecular machines contain protein components that undergo motion relative to
each other. Designing such mechanically constrained nanoscale protein architectures with …

Evolution of a designed protein assembly encapsulating its own RNA genome

GL Butterfield, MJ Lajoie, HH Gustafson, DL Sellers… - Nature, 2017 - nature.com
The challenges of evolution in a complex biochemical environment, coupling genotype to
phenotype and protecting the genetic material, are solved elegantly in biological systems by …

High thermodynamic stability of parametrically designed helical bundles

PS Huang, G Oberdorfer, C Xu, XY Pei, BL Nannenga… - science, 2014 - science.org
We describe a procedure for designing proteins with backbones produced by varying the
parameters in the Crick coiled coil–generating equations. Combinatorial design calculations …

Reconfigurable asymmetric protein assemblies through implicit negative design

DD Sahtoe, F Praetorius, A Courbet, Y Hsia, BIM Wicky… - Science, 2022 - science.org
Asymmetric multiprotein complexes that undergo subunit exchange play central roles in
biology but present a challenge for design because the components must not only contain …

De novo design of self-assembling helical protein filaments

H Shen, JA Fallas, E Lynch, W Sheffler, B Parry… - Science, 2018 - science.org
We describe a general computational approach to designing self-assembling helical
filaments from monomeric proteins and use this approach to design proteins that assemble …

The collection of MicroED data for macromolecular crystallography

D Shi, BL Nannenga, MJ De La Cruz, J Liu… - Nature …, 2016 - nature.com
The formation of large, well-ordered crystals for crystallographic experiments remains a
crucial bottleneck to the structural understanding of many important biological systems. To …