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Title: Structure of a designed protein cage that self-assembles into a highly porous cube

Journal Article · · Nature Chemistry
DOI:https://doi.org/10.1038/nchem.2107· OSTI ID:1164570
 [1];  [2];  [3];  [4];  [2];  [4];  [5];  [2];  [6]
  1. Univ. of California, Los Angeles, CA (United States). UCLA-DOE Institute for Genomics and Proteomics
  2. Univ. of Oxford (United Kingdom). Dept of Chemistry
  3. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Santa Cruz, CA (United States)
  4. Scripps Research Inst., La Jolla, FL (United States)
  5. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Scripps Research Inst., La Jolla, FL (United States)
  6. Univ. of California, Los Angeles, CA (United States). UCLA-DOE Institute for Genomics and Proteomics; Univ. of California, Los Angeles, CA (United States). Dept. of Chemistry and Biochemistry; Univ. of California, Los Angeles, CA (United States). California Nanosystems Institute

Natural proteins can be versatile building blocks for multimeric, self-assembling structures. Yet, creating protein-based assemblies with specific geometries and chemical properties remains challenging. Highly porous materials represent particularly interesting targets for designed assembly. Here we utilize a strategy of fusing two natural protein oligomers using a continuous alpha-helical linker to design a novel protein that self assembles into a 750 kDa, 225 Å diameter, cube-shaped cage with large openings into a 130 Å diameter inner cavity. A crystal structure of the cage showed atomic level agreement with the designed model, while electron microscopy, native mass spectrometry, and small angle x-ray scattering revealed alternate assembly forms in solution. These studies show that accurate design of large porous assemblies with specific shapes is feasible, while further specificity improvements will likely require limiting flexibility to select against alternative forms. Finally, these results provide a foundation for the design of advanced materials with applications in bionanotechnology, nanomedicine and material sciences.

Research Organization:
Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
Grant/Contract Number:
AC02-05CH11231; CHE-1332907; R01GM067167
OSTI ID:
1164570
Journal Information:
Nature Chemistry, Vol. 6, Issue 12; ISSN 1755-4330
Publisher:
Nature Publishing GroupCopyright Statement
Country of Publication:
United States
Language:
ENGLISH
Citation Metrics:
Cited by: 206 works
Citation information provided by
Web of Science

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A Hollow Foldecture with Truncated Trigonal Bipyramid Shape from the Self‐Assembly of an 11‐Helical Foldamer journal August 2015
Protein Dimerization on a Phosphonated Calix[6]arene Disc journal April 2017
Auto‐regulated Protein Assembly on a Supramolecular Scaffold journal September 2018
Host–Guest Recognition and Fluorescence of a Tetraphenylethene‐Based Octacationic Cage journal January 2020
Design of Hollow Protein Nanoparticles with Modifiable Interior and Exterior Surfaces journal August 2018
Auto‐regulated Protein Assembly on a Supramolecular Scaffold journal October 2018
Host–Guest Recognition and Fluorescence of a Tetraphenylethene‐Based Octacationic Cage journal January 2020
Construction of a Triangle-Shaped Trimer and a Tetrahedron Using an α-Helix-Inserted Circular Permutant of Cytochrome c 555 journal March 2018
Multi‐Component Self‐Assembly of Proteins and Inorganic Particles: From Discrete Structures to Biomimetic Materials journal April 2019
Self‐Assembly in Protein‐Based Bionanomaterials journal October 2019
Elaborating a coiled-coil-assembled octahedral protein cage with additional protein domains: A Coiled-Coil-Assembled Octahedral Protein Cage journal October 2018
Metal‐dependent assembly of a protein nano‐cage journal August 2019
Design and structure of two new protein cages illustrate successes and ongoing challenges in protein engineering journal December 2019
Small angle X‐ray scattering‐assisted protein structure prediction in CASP13 and emergence of solution structure differences journal August 2019
Recent advances in protein-based nanoparticles journal July 2018
Hierarchical design of artificial proteins and complexes toward synthetic structural biology journal December 2017
Protein assembles into Archimedean geometry journal May 2019
Design of a hyperstable 60-subunit protein icosahedron journal June 2016
Designed proteins induce the formation of nanocage-containing extracellular vesicles journal November 2016
Gigadalton-scale shape-programmable DNA assemblies journal December 2017
Shaping quaternary assemblies of water-soluble non-peptide helical foldamers by sequence manipulation journal September 2015
Geometrical assembly of ultrastable protein templates for nanomaterials journal June 2016
Ultra-large supramolecular coordination cages composed of endohedral Archimedean and Platonic bodies journal May 2017
Quantitative characterization of all single amino acid variants of a viral capsid-based drug delivery vehicle journal April 2018
Lattice engineering enables definition of molecular features allowing for potent small-molecule inhibition of HIV-1 entry journal January 2019
Diverse protein assembly driven by metal and chelating amino acids with selectivity and tunability journal December 2019
Comparing proteins and nucleic acids for next-generation biomolecular engineering journal July 2018
Modular assembly of a protein nanotriangle using orthogonally interacting coiled coils journal September 2017
Protein cages and synthetic polymers: a fruitful symbiosis for drug delivery applications, bionanotechnology and materials science journal January 2016
Self-limited self-assembly of nanoparticles into supraparticles: towards supramolecular colloidal materials by design journal January 2016
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Coiled coil protein origami: from modular design principles towards biotechnological applications journal January 2018
Synthetic approaches to construct viral capsid-like spherical nanomaterials journal January 2018
The dynamical interplay between a megadalton peptide nanocage and solutes probed by microsecond atomistic MD; implications for design journal January 2019
The design and biomedical applications of self-assembled two-dimensional organic biomaterials journal January 2019
Self-assembly of engineered protein nanocages into reversible ordered 3D superlattices mediated by zinc ions journal January 2019
Crystallizing protein assemblies via free and grafted linkers journal January 2019
Flexible, symmetry-directed approach to assembling protein cages journal July 2016
Confirmation of intersubunit connectivity and topology of designed protein complexes by native MS journal January 2018
A roadmap for biocatalysis - functional and spatial orchestration of enzyme cascades journal July 2016
Computationally designed peptides for self-assembly of nanostructured lattices journal September 2016
Oriented assembly of anisotropic nanoparticles into frame-like superstructures journal August 2017
Accurate design of megadalton-scale two-component icosahedral protein complexes journal July 2016
Cucumber Necrosis Virus Recruits Cellular Heat Shock Protein 70 Homologs at Several Stages of Infection journal December 2015
Biomimetic Layer-by-Layer Self-Assembly of Nanofilms, Nanocoatings, and 3D Scaffolds for Tissue Engineering journal June 2018
Protein Dimerization on a Phosphonated Calix[6]arene Disc journal April 2017
Design of Hollow Protein Nanoparticles with Modifiable Interior and Exterior Surfaces journal August 2018
Protein Calligraphy: A New Concept Begins To Take Shape journal June 2016
Connecting two proteins using a fusion alpha helix stabilized by a chemical cross linker journal March 2016
Crystal structures of mono- and bi-specific diabodies and reduction of their structural flexibility by introduction of disulfide bridges at the Fv interface journal September 2016
Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry journal October 2018