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 …
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 …
electron diffraction (MicroED). Since that time, data collection and analysis schemes have …
Hallucinating symmetric protein assemblies
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 …
structure space beyond the sequences and structures of natural proteins. Here, we use deep …
Accurate design of megadalton-scale two-component icosahedral protein complexes
Nature provides many examples of self-and co-assembling protein-based molecular
machines, including icosahedral protein cages that serve as scaffolds, enzymes, and …
machines, including icosahedral protein cages that serve as scaffolds, enzymes, and …
Computational design of mechanically coupled axle-rotor protein assemblies
Natural molecular machines contain protein components that undergo motion relative to
each other. Designing such mechanically constrained nanoscale protein architectures with …
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 …
phenotype and protecting the genetic material, are solved elegantly in biological systems by …
High thermodynamic stability of parametrically designed helical bundles
We describe a procedure for designing proteins with backbones produced by varying the
parameters in the Crick coiled coil–generating equations. Combinatorial design calculations …
parameters in the Crick coiled coil–generating equations. Combinatorial design calculations …
Reconfigurable asymmetric protein assemblies through implicit negative design
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 …
biology but present a challenge for design because the components must not only contain …
De novo design of self-assembling helical protein filaments
We describe a general computational approach to designing self-assembling helical
filaments from monomeric proteins and use this approach to design proteins that assemble …
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 …
crucial bottleneck to the structural understanding of many important biological systems. To …