@article{Sahtoe2021,

title = {Transferrin receptor targeting by de novo sheet extension},

author = {Sahtoe, Danny D. and Coscia, Adrian and Mustafaoglu, Nur and Miller, Lauren M. and Olal, Daniel and Vulovic, Ivan and Yu, Ta-Yi and Goreshnik, Inna and Lin, Yu-Ru and Clark, Lars and Busch, Florian and Stewart, Lance and Wysocki, Vicki H. and Ingber, Donald E. and Abraham, Jonathan and Baker, David},

url = {https://www.pnas.org/content/118/17/e2021569118, PNAS

},

doi = {10.1073/pnas.2021569118},

year  = {2021},

date = {2021-04-27},

urldate = {2021-04-27},

journal = {Proceedings of the National Academy of Sciences},

abstract = {The de novo design of proteins that bind natural target proteins is useful for a variety of biomedical and biotechnological applications. We describe a design strategy to target proteins containing an exposed beta edge strand. We use the approach to design binders to the human transferrin receptor which shuttles back and forth across the blood{textendash}brain barrier. Such binders could be useful for the delivery of therapeutics into the brain.The de novo design of polar protein{textendash}protein interactions is challenging because of the thermodynamic cost of stripping water away from the polar groups. Here, we describe a general approach for designing proteins which complement exposed polar backbone groups at the edge of beta sheets with geometrically matched beta strands. We used this approach to computationally design small proteins that bind to an exposed beta sheet on the human transferrin receptor (hTfR), which shuttles interacting proteins across the blood{textendash}brain barrier (BBB), opening up avenues for drug delivery into the brain. We describe a design which binds hTfR with a 20 nM Kd, is hyperstable, and crosses an in vitro microfluidic organ-on-a-chip model of the human BBB. Our design approach provides a general strategy for creating binders to protein targets with exposed surface beta edge strands.Crystal structures have been deposited in the RCSB PDB with the accession nos. 6WRX, 6WRW, and 6WRV. Additional supporting data has been deposited in the online Zenodo repository (https://zenodo.org/record/4594115) (47). All other study data are included in the article and/or supporting information.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Butterfield2017,

title = {Evolution of a designed protein assembly encapsulating its own RNA genome},

author = {Butterfield, Gabriel L.*

and Lajoie, Marc J.*

and Gustafson, Heather H.

and Sellers, Drew L.

and Nattermann, Una

and Ellis, Daniel

and Bale, Jacob B.

and Ke, Sharon

and Lenz, Garreck H.

and Yehdego, Angelica

and Ravichandran, Rashmi

and Pun, Suzie H.

and King, Neil P.

and Baker, David},

url = {http://dx.doi.org/10.1038/nature25157

https://www.bakerlab.org/wp-content/uploads/2017/12/Nature_Butterfield_et_al_2017.pdf},

doi = {10.1038/nature25157},

issn = {1476-4687},

year  = {2017},

date = {2017-12-13},

journal = {Nature},

abstract = {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 the encapsulation of nucleic acids. In the simplest examples, viruses use capsids to surround their genomes. Although these naturally occurring systems have been modified to change their tropism and to display proteins or peptides, billions of years of evolution have favoured efficiency at the expense of modularity, making viral capsids difficult to engineer. Synthetic systems composed of non-viral proteins could provide a ‘blank slate’ to evolve desired properties for drug delivery and other biomedical applications, while avoiding the safety risks and engineering challenges associated with viruses. Here we create synthetic nucleocapsids, which are computationally designed icosahedral protein assemblies with positively charged inner surfaces that can package their own full-length mRNA genomes. We explore the ability of these nucleocapsids to evolve virus-like properties by generating diversified populations using Escherichia coli as an expression host. Several generations of evolution resulted in markedly improved genome packaging (more than 133-fold), stability in blood (from less than 3.7% to 71% of packaged RNA protected after 6hours of treatment), and in vivo circulation time (from less than 5minutes to approximately 4.5hours). The resulting synthetic nucleocapsids package one full length RNA genome for every 11 icosahedral assemblies, similar to the best recombinant adeno-associated virus vectors. Our results show that there are simple evolutionary paths through which protein assemblies can acquire virus-like genome packaging and protection. Considerable effort has been directed at ‘top-down’ modification of viruses to be safe and effective for drug delivery and vaccine applications; the ability to design synthetic nanomaterials computationally and to optimize them through evolution now enables a complementary ‘bottom-up’ approach with considerable advantages in programmability and control.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Hsia2016,

title = {Design of a hyperstable 60-subunit protein icosahedron},

author = { Yang Hsia* and Jacob B. Bale* and Shane Gonen and Dan Shi and William Sheffler and Kimberly K. Fong and Nattermann and Chunfu Xu and Po-Ssu Huang and Rashmi Ravichandran and Sue Yi and Trisha N. Davis and Tamir Gonen and Neil P. King and David Baker},

url = {https://www.bakerlab.org/wp-content/uploads/2016/06/Hsia_Nature_2016.pdf},

doi = {10.1038/nature18010},

year  = {2016},

date = {2016-06-15},

journal = {Nature},

abstract = {The icosahedron is the largest of the Platonic solids, and icosahedral protein structures are widely used in biological systems for packaging and transport. There has been considerable interest in repurposing such structures for applications ranging from targeted delivery to multivalent immunogen presentation. The ability to design proteins that self-assemble into precisely specified, highly ordered icosahedral structures would open the door to a new generation of protein containers with properties custom-tailored to specific applications. Here we describe the computational design of a 25-nanometre icosahedral nanocage that self-assembles from trimeric protein building blocks. The designed protein was produced in Escherichia coli, and found by electron microscopy to assemble into a homogenous population of icosahedral particles nearly identical to the design model. The particles are stable in 6.7 molar guanidine hydrochloride at up to 80 degrees Celsius, and undergo extremely abrupt, but reversible, disassembly between 2 molar and 2.25 molar guanidinium thiocyanate. The icosahedron is robust to genetic fusions: one or two copies of green fluorescent protein (GFP) can be fused to each of the 60 subunits to create highly fluorescent ‘standard candles’ for use in light microscopy, and a designed protein pentamer can be placed in the centre of each of the 20 pentameric faces to modulate the size of the entrance/ exit channels of the cage. Such robust and customizable nanocages should have considerable utility in targeted drug delivery, vaccine design and synthetic biology.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}