Structure of a novel 13 nm dodecahedral nanocage assembled from a redesigned bacterial microcompartment shell protein

Jorda, J.; Leibly, D. J.; Thompson, M. C.; Yeates, T. O.

doi:10.1039/c6cc00851h

Title: Structure of a novel 13 nm dodecahedral nanocage assembled from a redesigned bacterial microcompartment shell protein

Journal Article · Wed Mar 09 00:00:00 EST 2016 · ChemComm

DOI:https://doi.org/10.1039/c6cc00851h· OSTI ID:1466773

Jorda, J. ^[1]; Leibly, D. J. ^[2]; Thompson, M. C. ^[3]; Yeates, T. O. ^[2]

Univ. of California, Los Angeles, CA (United States). UCLA-DOE Institute for Genomics and Proteomics
Univ. of California, Los Angeles, CA (United States). UCLA-DOE Institute for Genomics and Proteomics and Department of Chemistry and Biochemistry
Univ. of California, Los Angeles, CA (United States). Department of Chemistry and Biochemistry

In this paper, we report the crystal structure of a novel 60-subunit dodecahedral cage that results from self-assembly of a re-engineered version of a natural protein (PduA) from the Pdu microcompartment shell. Biophysical data illustrate the dependence of assembly on solution conditions, opening up new applications in microcompartment studies and nanotechnology.

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Research Organization:: Univ. of California, Los Angeles, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES)

Grant/Contract Number:: FC03-02ER63421

OSTI ID:: 1466773

Journal Information:: ChemComm, Vol. 52, Issue 28; ISSN 1359-7345

Publisher:: Royal Society of ChemistryCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 23 works

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References (23)

Accurate design of co-assembling multi-component protein nanomaterials King, Neil P.; Bale, Jacob B.; Sheffler, William Nature, Vol. 510, Issue 7503 https://doi.org/10.1038/nature13404	journal	May 2014
Nanohedra: Using symmetry to design self assembling protein cages, layers, crystals, and filaments Padilla, J. E.; Colovos, C.; Yeates, T. O. Proceedings of the National Academy of Sciences, Vol. 98, Issue 5 https://doi.org/10.1073/pnas.041614998	journal	February 2001
Computational Design of Self-Assembling Protein Nanomaterials with Atomic Level Accuracy King, N. P.; Sheffler, W.; Sawaya, M. R. Science, Vol. 336, Issue 6085 https://doi.org/10.1126/science.1219364	journal	May 2012
On the predictability of the orientation of protein domains joined by a spanning alpha-helical linker Lai, Yen-Ting; Jiang, Lin; Chen, Wuyang Protein Engineering Design and Selection, Vol. 28, Issue 11 https://doi.org/10.1093/protein/gzv035	journal	August 2015
Bacterial Microcompartment Organelles: Protein Shell Structure and Evolution Yeates, Todd O.; Crowley, Christopher S.; Tanaka, Shiho Annual Review of Biophysics, Vol. 39, Issue 1 https://doi.org/10.1146/annurev.biophys.093008.131418	journal	April 2010
Structure and Mechanisms of a Protein-Based Organelle in Escherichia coli Tanaka, S.; Sawaya, M. R.; Yeates, T. O. Science, Vol. 327, Issue 5961 https://doi.org/10.1126/science.1179513	journal	December 2009
Protein-based organelles in bacteria: carboxysomes and related microcompartments Yeates, Todd O.; Kerfeld, Cheryl A.; Heinhorst, Sabine Nature Reviews Microbiology, Vol. 6, Issue 9 https://doi.org/10.1038/nrmicro1913	journal	August 2008
PHENIX: a comprehensive Python-based system for macromolecular structure solution Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221 https://doi.org/10.1107/S0907444909052925	journal	January 2010
Structure of a designed protein cage that self-assembles into a highly porous cube Lai, Yen-Ting; Reading, Eamonn; Hura, Greg L. Nature Chemistry, Vol. 6, Issue 12 https://doi.org/10.1038/nchem.2107	journal	November 2014
Directed Evolution of a Protein Container Worsdorfer, B.; Woycechowsky, K. J.; Hilvert, D. Science, Vol. 331, Issue 6017 https://doi.org/10.1126/science.1199081	journal	February 2011
Quasi-equivalent viruses: a paradigm for protein assemblies 1 1Edited by T. Richmond Johnson, John E.; Speir, Jeffrey A. Journal of Molecular Biology, Vol. 269, Issue 5 https://doi.org/10.1006/jmbi.1997.1068	journal	July 1997
Re-engineering protein interfaces yields copper-inducible ferritin cage assembly Huard, Dustin J. E.; Kane, Kathleen M.; Tezcan, F. Akif Nature Chemical Biology, Vol. 9, Issue 3 https://doi.org/10.1038/nchembio.1163	journal	January 2013
Diverse Bacterial Microcompartment Organelles Chowdhury, C.; Sinha, S.; Chun, S. Microbiology and Molecular Biology Reviews, Vol. 78, Issue 3 https://doi.org/10.1128/MMBR.00009-14	journal	September 2014
Structure of a 16-nm Cage Designed by Using Protein Oligomers Lai, Y. -T.; Cascio, D.; Yeates, T. O. Science, Vol. 336, Issue 6085 https://doi.org/10.1126/science.1219351	journal	May 2012
Design of a single-chain polypeptide tetrahedron assembled from coiled-coil segments Gradišar, Helena; Božič, Sabina; Doles, Tibor Nature Chemical Biology, Vol. 9, Issue 6 https://doi.org/10.1038/nchembio.1248	journal	April 2013
Alanine Scanning Mutagenesis Identifies an Asparagine–Arginine–Lysine Triad Essential to Assembly of the Shell of the Pdu Microcompartment Sinha, Sharmistha; Cheng, Shouqiang; Sung, Yea Won Journal of Molecular Biology, Vol. 426, Issue 12 https://doi.org/10.1016/j.jmb.2014.04.012	journal	June 2014
Structural Symmetry and Protein Function Goodsell, David S.; Olson, Arthur J. Annual Review of Biophysics and Biomolecular Structure, Vol. 29, Issue 1 https://doi.org/10.1146/annurev.biophys.29.1.105	journal	June 2000
Minimalist Representations and the Importance of Nearest Neighbor Effects in Protein Folding Simulations Colubri, Andrés; Jha, Abhishek K.; Shen, Min-yi Journal of Molecular Biology, Vol. 363, Issue 4 https://doi.org/10.1016/j.jmb.2006.08.035	journal	November 2006
Enzymatic assembly of DNA molecules up to several hundred kilobases Gibson, Daniel G.; Young, Lei; Chuang, Ray-Yuan Nature Methods, Vol. 6, Issue 5, p. 343-345 https://doi.org/10.1038/nmeth.1318	journal	April 2009
Creating regular arrays of nanoparticles with self-assembling protein building blocks Howorka, Stefan Journal of Materials Chemistry, Vol. 17, Issue 20 https://doi.org/10.1039/b701221g	journal	January 2007
Structure of the PduU Shell Protein from the Pdu Microcompartment of Salmonella Crowley, Christopher S.; Sawaya, Michael R.; Bobik, Thomas A. Structure, Vol. 16, Issue 9 https://doi.org/10.1016/j.str.2008.05.013	journal	September 2008
Structural Insight into the Mechanisms of Transport across the Salmonella enterica Pdu Microcompartment Shell Crowley, Christopher S.; Cascio, Duilio; Sawaya, Michael R. Journal of Biological Chemistry, Vol. 285, Issue 48 https://doi.org/10.1074/jbc.M110.160580	journal	September 2010
Comparative Protein Structure Modeling Using MODELLER Webb, Benjamin; Sali, Andrej Current Protocols in Bioinformatics, Vol. 47, Issue 1 https://doi.org/10.1002/0471250953.bi0506s47	journal	September 2014

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Quantitative characterization of all single amino acid variants of a viral capsid-based drug delivery vehicle Hartman, Emily C.; Jakobson, Christopher M.; Favor, Andrew H. Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-03783-y	journal	April 2018
De novo targeting to the cytoplasmic and luminal side of bacterial microcompartments Lee, Matthew J.; Mantell, Judith; Brown, Ian R. Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-05922-x	journal	August 2018
Encapsulation mechanisms and structural studies of GRM2 bacterial microcompartment particles Kalnins, Gints; Cesle, Eva-Emilija; Jansons, Juris Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-019-14205-y	journal	January 2020
Tailoring lumazine synthase assemblies for bionanotechnology Azuma, Yusuke; Edwardson, Thomas G. W.; Hilvert, Donald Chemical Society Reviews, Vol. 47, Issue 10 https://doi.org/10.1039/c8cs00154e	journal	January 2018
Self-Assembly Stability and Variability of Bacterial Microcompartment Shell Proteins in Response to the Environmental Change Faulkner, Matthew; Zhao, Long-Sheng; Barrett, Steve Nanoscale Research Letters, Vol. 14, Issue 1 https://doi.org/10.1186/s11671-019-2884-3	journal	February 2019
Functionalization of Bacterial Microcompartment Shell Proteins With Covalently Attached Heme Huang, Jingcheng; Ferlez, Bryan H.; Young, Eric J. Frontiers in Bioengineering and Biotechnology, Vol. 7 https://doi.org/10.3389/fbioe.2019.00432	journal	January 2020
Engineering the Bacterial Microcompartment Domain for Molecular Scaffolding Applications Young, Eric J.; Burton, Rodney; Mahalik, Jyoti P. Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.01441	journal	July 2017
The Phenix software for automated determination of macromolecular structures Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Methods, Vol. 55, Issue 1 https://doi.org/10.1016/j.ymeth.2011.07.005	journal	September 2011
Facile methods for heterologous production of bacterial microcompartments in diverse host species Yeates, Todd O.; Bobik, Thomas A. Microbial Biotechnology, Vol. 11, Issue 1 https://doi.org/10.1111/1751-7915.12869	journal	December 2017

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