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Title: Designing and defining dynamic protein cage nanoassemblies in solution

Abstract

Central challenges in the design of large and dynamic macromolecular assemblies for synthetic biology lie in developing effective methods for testing design strategies and their outcomes, including comprehensive assessments of solution behavior. Here, we created and validated an advanced design of a 600-kDa protein homododecamer that self-assembles into a symmetric tetrahedral cage. The monomeric unit is composed of a trimerizing apex-forming domain genetically linked to an edge-forming dimerizing domain. Enhancing the crystallographic results, high-throughput small-angle x-ray scattering (SAXS) comprehensively contrasted our modifications under diverse solution conditions. To generate a phase diagram associating structure and assembly, we developed force plots that measure dissimilarity among multiple SAXS data sets. These new tools, which provided effective feedback on experimental constructs relative to design, have general applicability in analyzing the solution behavior of heterogeneous nanosystems and have been made available as a web-based application. Specifically, our results probed the influence of solution conditions and symmetry on stability and structural adaptability, identifying the dimeric interface as the weak point in the assembly. Force plots comparing SAXS data sets further reveal more complex and controllable behavior in solution than captured by our crystal structures. Lastly, these methods for objectively and comprehensively comparing SAXS profiles for systemsmore » critically affected by solvent conditions and structural heterogeneity provide an enabling technology for advancing the design and bioengineering of nanoscale biological materials.« less

Authors:
 [1];  [2];  [3];  [3];  [4];  [5]
  1. Univ. of California, Los Angeles, CA (United States). UCLA-DOE Inst. for Genomics and Proteomics
  2. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Santa Cruz, CA (United States). Dept. of Chemistry and Biochemistry
  3. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  4. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of Texas, Houston, TX (United States). MD Anderson Cancer Center, Dept. of Molecular and Cellular Oncology
  5. Univ. of California, Los Angeles, CA (United States). UCLA-DOE Inst. 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 Inst.
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1409425
Grant/Contract Number:  
AC02-05CH11231; AC02-06CH11357; CHE-1332907; FC02-02ER63421
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Science Advances
Additional Journal Information:
Journal Volume: 2; Journal Issue: 12; Journal ID: ISSN 2375-2548
Publisher:
AAAS
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Protein Design; Self-assembly; symmetry; protein dynamics; conformational change; SAXS; macromolecular crystallography

Citation Formats

Lai, Y. -T., Hura, G. L., Dyer, K. N., Tang, H. Y. H., Tainer, J. A., and Yeates, T. O. Designing and defining dynamic protein cage nanoassemblies in solution. United States: N. p., 2016. Web. doi:10.1126/sciadv.1501855.
Lai, Y. -T., Hura, G. L., Dyer, K. N., Tang, H. Y. H., Tainer, J. A., & Yeates, T. O. Designing and defining dynamic protein cage nanoassemblies in solution. United States. https://doi.org/10.1126/sciadv.1501855
Lai, Y. -T., Hura, G. L., Dyer, K. N., Tang, H. Y. H., Tainer, J. A., and Yeates, T. O. 2016. "Designing and defining dynamic protein cage nanoassemblies in solution". United States. https://doi.org/10.1126/sciadv.1501855. https://www.osti.gov/servlets/purl/1409425.
@article{osti_1409425,
title = {Designing and defining dynamic protein cage nanoassemblies in solution},
author = {Lai, Y. -T. and Hura, G. L. and Dyer, K. N. and Tang, H. Y. H. and Tainer, J. A. and Yeates, T. O.},
abstractNote = {Central challenges in the design of large and dynamic macromolecular assemblies for synthetic biology lie in developing effective methods for testing design strategies and their outcomes, including comprehensive assessments of solution behavior. Here, we created and validated an advanced design of a 600-kDa protein homododecamer that self-assembles into a symmetric tetrahedral cage. The monomeric unit is composed of a trimerizing apex-forming domain genetically linked to an edge-forming dimerizing domain. Enhancing the crystallographic results, high-throughput small-angle x-ray scattering (SAXS) comprehensively contrasted our modifications under diverse solution conditions. To generate a phase diagram associating structure and assembly, we developed force plots that measure dissimilarity among multiple SAXS data sets. These new tools, which provided effective feedback on experimental constructs relative to design, have general applicability in analyzing the solution behavior of heterogeneous nanosystems and have been made available as a web-based application. Specifically, our results probed the influence of solution conditions and symmetry on stability and structural adaptability, identifying the dimeric interface as the weak point in the assembly. Force plots comparing SAXS data sets further reveal more complex and controllable behavior in solution than captured by our crystal structures. Lastly, these methods for objectively and comprehensively comparing SAXS profiles for systems critically affected by solvent conditions and structural heterogeneity provide an enabling technology for advancing the design and bioengineering of nanoscale biological materials.},
doi = {10.1126/sciadv.1501855},
url = {https://www.osti.gov/biblio/1409425}, journal = {Science Advances},
issn = {2375-2548},
number = 12,
volume = 2,
place = {United States},
year = {Wed Dec 14 00:00:00 EST 2016},
month = {Wed Dec 14 00:00:00 EST 2016}
}

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Cited by: 37 works
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New designed protein assemblies
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Monitoring Structural Transitions in Icosahedral Virus Protein Cages by Site-Directed Spin Labeling
journal, March 2011


Structure and Flexibility of Nanoscale Protein Cages Designed by Symmetric Self-Assembly
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Self-Assembling Nano-Architectures Created from a Protein Nano-Building Block Using an Intermolecularly Folded Dimeric de Novo Protein
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Accurate assessment of mass, models and resolution by small-angle scattering
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Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS)
journal, July 2009


Correlation Map, a goodness-of-fit test for one-dimensional X-ray scattering spectra
journal, April 2015


Reprogramming an ATP-driven protein machine into a light-gated nanocage
journal, November 2013


Structure of a bifunctional membrane-RNA binding protein, influenza virus matrix protein M1
journal, March 1997


Nanohedra: Using symmetry to design self assembling protein cages, layers, crystals, and filaments
journal, February 2001


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journal, January 2007


On the predictability of the orientation of protein domains joined by a spanning alpha-helical linker
journal, August 2015


High-throughput biological small-angle X-ray scattering with a robotically loaded capillary cell
journal, February 2012


Structure of a 16-nm Cage Designed by Using Protein Oligomers
journal, May 2012


Computational Design of Self-Assembling Protein Nanomaterials with Atomic Level Accuracy
journal, May 2012


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journal, February 2013


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journal, April 2010


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journal, June 2000


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Structure and flexibility within proteins as identified through small angle X-ray scattering
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Works referencing / citing this record:

Rational Design of Supramolecular Dynamic Protein Assemblies by Using a Micelle-Assisted Activity-Based Protein-Labeling Technology
journal, October 2018


Small angle X-ray scattering and cross-linking for data assisted protein structure prediction in CASP 12 with prospects for improved accuracy
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A review on virus protein self-assembly
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Design of coiled-coil protein-origami cages that self-assemble in vitro and in vivo
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Engineering protein assemblies with allosteric control via monomer fold-switching
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Bioengineering Strategies for Protein-Based Nanoparticles
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Modeling Symmetric Macromolecular Structures in Rosetta3
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Engineering protein assemblies with allosteric control via monomer fold-switching
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Bioengineering Strategies for Protein-Based Nanoparticles
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