Literature DB >> 24870237

Accurate design of co-assembling multi-component protein nanomaterials.

Neil P King1, Jacob B Bale2, William Sheffler3, Dan E McNamara4, Shane Gonen5, Tamir Gonen6, Todd O Yeates7, David Baker8.   

Abstract

The self-assembly of proteins into highly ordered nanoscale architectures is a hallmark of biological systems. The sophisticated functions of these molecular machines have inspired the development of methods to engineer self-assembling protein nanostructures; however, the design of multi-component protein nanomaterials with high accuracy remains an outstanding challenge. Here we report a computational method for designing protein nanomaterials in which multiple copies of two distinct subunits co-assemble into a specific architecture. We use the method to design five 24-subunit cage-like protein nanomaterials in two distinct symmetric architectures and experimentally demonstrate that their structures are in close agreement with the computational design models. The accuracy of the method and the number and variety of two-component materials that it makes accessible suggest a route to the construction of functional protein nanomaterials tailored to specific applications.

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Year:  2014        PMID: 24870237      PMCID: PMC4137318          DOI: 10.1038/nature13404

Source DB:  PubMed          Journal:  Nature        ISSN: 0028-0836            Impact factor:   49.962


  37 in total

1.  Computational design of a symmetric homodimer using β-strand assembly.

Authors:  P Benjamin Stranges; Mischa Machius; Michael J Miley; Ashutosh Tripathy; Brian Kuhlman
Journal:  Proc Natl Acad Sci U S A       Date:  2011-12-05       Impact factor: 11.205

2.  A de novo designed protein protein interface.

Authors:  Po-Ssu Huang; John J Love; Stephen L Mayo
Journal:  Protein Sci       Date:  2007-12       Impact factor: 6.725

3.  Folding DNA to create nanoscale shapes and patterns.

Authors:  Paul W K Rothemund
Journal:  Nature       Date:  2006-03-16       Impact factor: 49.962

4.  Directed evolution of a protein container.

Authors:  Bigna Wörsdörfer; Kenneth J Woycechowsky; Donald Hilvert
Journal:  Science       Date:  2011-02-04       Impact factor: 47.728

5.  Generation of protein lattices by fusing proteins with matching rotational symmetry.

Authors:  John C Sinclair; Karen M Davies; Catherine Vénien-Bryan; Martin E M Noble
Journal:  Nat Nanotechnol       Date:  2011-07-31       Impact factor: 39.213

Review 6.  Nanomaterials based on DNA.

Authors:  Nadrian C Seeman
Journal:  Annu Rev Biochem       Date:  2010       Impact factor: 23.643

7.  Metal-mediated affinity and orientation specificity in a computationally designed protein homodimer.

Authors:  Bryan S Der; Mischa Machius; Michael J Miley; Jeffrey L Mills; Thomas Szyperski; Brian Kuhlman
Journal:  J Am Chem Soc       Date:  2011-12-15       Impact factor: 15.419

8.  Three-dimensional structures self-assembled from DNA bricks.

Authors:  Yonggang Ke; Luvena L Ong; William M Shih; Peng Yin
Journal:  Science       Date:  2012-11-30       Impact factor: 47.728

9.  Modeling symmetric macromolecular structures in Rosetta3.

Authors:  Frank DiMaio; Andrew Leaver-Fay; Phil Bradley; David Baker; Ingemar André
Journal:  PLoS One       Date:  2011-06-22       Impact factor: 3.240

10.  Metal-directed, chemically tunable assembly of one-, two- and three-dimensional crystalline protein arrays.

Authors:  Jeffrey D Brodin; X I Ambroggio; Chunyan Tang; Kristin N Parent; Timothy S Baker; F Akif Tezcan
Journal:  Nat Chem       Date:  2012-03-04       Impact factor: 24.427

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  133 in total

1.  Computational design of co-assembling protein-DNA nanowires.

Authors:  Yun Mou; Jiun-Yann Yu; Timothy M Wannier; Chin-Lin Guo; Stephen L Mayo
Journal:  Nature       Date:  2015-09-02       Impact factor: 49.962

2.  Computational design and experimental verification of a symmetric protein homodimer.

Authors:  Yun Mou; Po-Ssu Huang; Fang-Ciao Hsu; Shing-Jong Huang; Stephen L Mayo
Journal:  Proc Natl Acad Sci U S A       Date:  2015-08-12       Impact factor: 11.205

3.  Shaping quaternary assemblies of water-soluble non-peptide helical foldamers by sequence manipulation.

Authors:  Gavin W Collie; Karolina Pulka-Ziach; Caterina M Lombardo; Juliette Fremaux; Frédéric Rosu; Marion Decossas; Laura Mauran; Olivier Lambert; Valérie Gabelica; Cameron D Mackereth; Gilles Guichard
Journal:  Nat Chem       Date:  2015-09-28       Impact factor: 24.427

4.  Introduction of a polar core into the de novo designed protein Top7.

Authors:  Benjamin Basanta; Kui K Chan; Patrick Barth; Tiffany King; Tobin R Sosnick; James R Hinshaw; Gaohua Liu; John K Everett; Rong Xiao; Gaetano T Montelione; David Baker
Journal:  Protein Sci       Date:  2016-03-07       Impact factor: 6.725

5.  Principles Governing the Self-Assembly of Coiled-Coil Protein Nanoparticles.

Authors:  Giuliana Indelicato; Newton Wahome; Philippe Ringler; Shirley A Müller; Mu-Ping Nieh; Peter Burkhard; Reidun Twarock
Journal:  Biophys J       Date:  2016-02-02       Impact factor: 4.033

Review 6.  Methods for the directed evolution of proteins.

Authors:  Michael S Packer; David R Liu
Journal:  Nat Rev Genet       Date:  2015-06-09       Impact factor: 53.242

7.  Change in structure and ligand binding properties of hyperstable cytochrome c555 from Aquifex aeolicus by domain swapping.

Authors:  Masaru Yamanaka; Satoshi Nagao; Hirofumi Komori; Yoshiki Higuchi; Shun Hirota
Journal:  Protein Sci       Date:  2015-01-14       Impact factor: 6.725

8.  Multifarious assembly mixtures: systems allowing retrieval of diverse stored structures.

Authors:  Arvind Murugan; Zorana Zeravcic; Michael P Brenner; Stanislas Leibler
Journal:  Proc Natl Acad Sci U S A       Date:  2014-12-22       Impact factor: 11.205

9.  Structure of a designed tetrahedral protein assembly variant engineered to have improved soluble expression.

Authors:  Jacob B Bale; Rachel U Park; Yuxi Liu; Shane Gonen; Tamir Gonen; Duilio Cascio; Neil P King; Todd O Yeates; David Baker
Journal:  Protein Sci       Date:  2015-08-06       Impact factor: 6.725

10.  DNA-mediated engineering of multicomponent enzyme crystals.

Authors:  Jeffrey D Brodin; Evelyn Auyeung; Chad A Mirkin
Journal:  Proc Natl Acad Sci U S A       Date:  2015-03-23       Impact factor: 11.205

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