skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Exploring the repeat protein universe through computational protein design

Abstract

A central question in protein evolution is the extent to which naturally occurring proteins sample the space of folded structures accessible to the polypeptide chain. Repeat proteins composed of multiple tandem copies of a modular structure unit are widespread in nature and have critical roles in molecular recognition, signalling, and other essential biological processes. Naturally occurring repeat proteins have been re-engineered for molecular recognition and modular scaffolding applications. In this paper, we use computational protein design to investigate the space of folded structures that can be generated by tandem repeating a simple helix–loop–helix–loop structural motif. Eighty-three designs with sequences unrelated to known repeat proteins were experimentally characterized. Of these, 53 are monomeric and stable at 95 °C, and 43 have solution X-ray scattering spectra consistent with the design models. Crystal structures of 15 designs spanning a broad range of curvatures are in close agreement with the design models with root mean square deviations ranging from 0.7 to 2.5 Å. Finally, our results show that existing repeat proteins occupy only a small fraction of the possible repeat protein sequence and structure space and that it is possible to design novel repeat proteins with precisely specified geometries, opening up a wide arraymore » of new possibilities for biomolecular engineering.« less

Authors:
 [1];  [1];  [1];  [2];  [3];  [4];  [5];  [6];  [7]
  1. Univ. of Washington, Seattle, WA (United States). Dept. of Biochemistry. Inst. for Protein Design
  2. Univ. of California, San Francisco, CA (United States). Dept. of Cellular and Molecular Pharmacology
  3. Univ. of California, San Francisco, CA (United States). Dept. of Microbiology and Immunology
  4. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Molecular Biophysics and Integrated Bioimaging
  5. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Molecular Biophysics and Integrated Bioimaging; Univ. of California, Santa Cruz, CA (United States). Dept. of Chemistry and Biochemistry
  6. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Molecular Biophysics and Integrated Bioimaging; Univ. of Texas M. D. Anderson Cancer Center, Houston, TX (United States). Dept. of Molecular and Cellular Oncology
  7. Univ. of Washington, Seattle, WA (United States). Dept. of Biochemistry. Inst. for Protein Design. Howard Hughes Medical Inst.
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22); National Science Foundation (NSF); Defense Threat Reduction Agency (DTRA) (United States); US Air Force Office of Scientific Research (AFOSR); Howard Hughes Medical Inst. (HHMI) (United States); National Inst. of Health (NIH) (United States); Damon Runyon Cancer Research Foundation (United States); Swiss National Science Foundation (SNSF); Human Frontier Science Program (HFSP) (France)
Contributing Org.:
Univ. of California, Santa Cruz, CA (United States); Univ. of Texas M. D. Anderson Cancer Center, Houston, TX (United States)
OSTI Identifier:
1378707
Grant/Contract Number:  
AC02-05CH11231; MCB-1445201; CHE-1332907; FA950-12-10112; HHMI-027779; GM105404; K99GM112982; DRG-2140-12; DRG-2136-12; PBZHP3-125470; LT000070/2009-L
Resource Type:
Accepted Manuscript
Journal Name:
Nature (London)
Additional Journal Information:
Journal Name: Nature (London); Journal Volume: 528; Journal Issue: 7583; Journal ID: ISSN 0028-0836
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; protein design; protein structure predictions

Citation Formats

Brunette, TJ, Parmeggiani, Fabio, Huang, Po-Ssu, Bhabha, Gira, Ekiert, Damian C., Tsutakawa, Susan E., Hura, Greg L., Tainer, John A., and Baker, David. Exploring the repeat protein universe through computational protein design. United States: N. p., 2015. Web. doi:10.1038/nature16162.
Brunette, TJ, Parmeggiani, Fabio, Huang, Po-Ssu, Bhabha, Gira, Ekiert, Damian C., Tsutakawa, Susan E., Hura, Greg L., Tainer, John A., & Baker, David. Exploring the repeat protein universe through computational protein design. United States. doi:10.1038/nature16162.
Brunette, TJ, Parmeggiani, Fabio, Huang, Po-Ssu, Bhabha, Gira, Ekiert, Damian C., Tsutakawa, Susan E., Hura, Greg L., Tainer, John A., and Baker, David. Wed . "Exploring the repeat protein universe through computational protein design". United States. doi:10.1038/nature16162. https://www.osti.gov/servlets/purl/1378707.
@article{osti_1378707,
title = {Exploring the repeat protein universe through computational protein design},
author = {Brunette, TJ and Parmeggiani, Fabio and Huang, Po-Ssu and Bhabha, Gira and Ekiert, Damian C. and Tsutakawa, Susan E. and Hura, Greg L. and Tainer, John A. and Baker, David},
abstractNote = {A central question in protein evolution is the extent to which naturally occurring proteins sample the space of folded structures accessible to the polypeptide chain. Repeat proteins composed of multiple tandem copies of a modular structure unit are widespread in nature and have critical roles in molecular recognition, signalling, and other essential biological processes. Naturally occurring repeat proteins have been re-engineered for molecular recognition and modular scaffolding applications. In this paper, we use computational protein design to investigate the space of folded structures that can be generated by tandem repeating a simple helix–loop–helix–loop structural motif. Eighty-three designs with sequences unrelated to known repeat proteins were experimentally characterized. Of these, 53 are monomeric and stable at 95 °C, and 43 have solution X-ray scattering spectra consistent with the design models. Crystal structures of 15 designs spanning a broad range of curvatures are in close agreement with the design models with root mean square deviations ranging from 0.7 to 2.5 Å. Finally, our results show that existing repeat proteins occupy only a small fraction of the possible repeat protein sequence and structure space and that it is possible to design novel repeat proteins with precisely specified geometries, opening up a wide array of new possibilities for biomolecular engineering.},
doi = {10.1038/nature16162},
journal = {Nature (London)},
number = 7583,
volume = 528,
place = {United States},
year = {2015},
month = {12}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Citation Metrics:
Cited by: 68 works
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

TM-align: a protein structure alignment algorithm based on the TM-score
journal, April 2005


CRYSOL – a Program to Evaluate X-ray Solution Scattering of Biological Macromolecules from Atomic Coordinates
journal, December 1995

  • Svergun, D.; Barberato, C.; Koch, M. H. J.
  • Journal of Applied Crystallography, Vol. 28, Issue 6
  • DOI: 10.1107/S0021889895007047

De novo design of a four-fold symmetric TIM-barrel protein with atomic-level accuracy
journal, November 2015

  • Huang, Po-Ssu; Feldmeier, Kaspar; Parmeggiani, Fabio
  • Nature Chemical Biology, Vol. 12, Issue 1
  • DOI: 10.1038/nchembio.1966

High thermodynamic stability of parametrically designed helical bundles
journal, October 2014


Tandem repeats in proteins: From sequence to structure
journal, September 2012


Design of Stable α-Helical Arrays from an Idealized TPR Motif
journal, May 2003


Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
journal, September 1997

  • Altschul, Stephen F.; Madden, Thomas L.; Schäffer, Alejandro A.
  • Nucleic Acids Research, Vol. 25, Issue 17, p. 3389-3402
  • DOI: 10.1093/nar/25.17.3389

PHENIX : building new software for automated crystallographic structure determination
journal, October 2002

  • Adams, Paul D.; Grosse-Kunstleve, Ralf W.; Hung, Li-Wei
  • Acta Crystallographica Section D Biological Crystallography, Vol. 58, Issue 11
  • DOI: 10.1107/S0907444902016657

Experimental support for the evolution of symmetric protein architecture from a simple peptide motif
journal, December 2010

  • Lee, Jihun; Blaber, Michael
  • Proceedings of the National Academy of Sciences, Vol. 108, Issue 1
  • DOI: 10.1073/pnas.1015032108

Toward High-Resolution de Novo Structure Prediction for Small Proteins
journal, September 2005


Accurate SAXS Profile Computation and its Assessment by Contrast Variation Experiments
journal, August 2013

  • Schneidman-Duhovny, Dina; Hammel, Michal; Tainer, John A.
  • Biophysical Journal, Vol. 105, Issue 4
  • DOI: 10.1016/j.bpj.2013.07.020

Design of a binding scaffold based on variable lymphocyte receptors of jawless vertebrates by module engineering
journal, February 2012

  • Lee, S. -C.; Park, K.; Han, J.
  • Proceedings of the National Academy of Sciences, Vol. 109, Issue 9
  • DOI: 10.1073/pnas.1113193109

Super-Resolution in Solution X-Ray Scattering and Its Applications to Structural Systems Biology
journal, May 2013


Designing Repeat Proteins: Well-expressed, Soluble and Stable Proteins from Combinatorial Libraries of Consensus Ankyrin Repeat Proteins
journal, September 2003


Computational design of a self-assembling symmetrical β-propeller protein
journal, October 2014

  • Voet, Arnout R. D.; Noguchi, Hiroki; Addy, Christine
  • Proceedings of the National Academy of Sciences, Vol. 111, Issue 42
  • DOI: 10.1073/pnas.1412768111

Design, Production and Molecular Structure of a New Family of Artificial Alpha-helicoidal Repeat Proteins (αRep) Based on Thermostable HEAT-like Repeats
journal, November 2010

  • Urvoas, Agathe; Guellouz, Asma; Valerio-Lepiniec, Marie
  • Journal of Molecular Biology, Vol. 404, Issue 2
  • DOI: 10.1016/j.jmb.2010.09.048

Control of repeat-protein curvature by computational protein design
journal, January 2015

  • Park, Keunwan; Shen, Betty W.; Parmeggiani, Fabio
  • Nature Structural & Molecular Biology, Vol. 22, Issue 2
  • DOI: 10.1038/nsmb.2938

XDS
journal, January 2010

  • Kabsch, Wolfgang
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2
  • DOI: 10.1107/S0907444909047337

RosettaRemodel: A Generalized Framework for Flexible Backbone Protein Design
journal, August 2011


Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS)
journal, July 2009

  • Hura, Greg L.; Menon, Angeli L.; Hammel, Michal
  • Nature Methods, Vol. 6, Issue 8
  • DOI: 10.1038/nmeth.1353

Designed Armadillo Repeat Proteins as General Peptide-Binding Scaffolds: Consensus Design and Computational Optimization of the Hydrophobic Core
journal, March 2008

  • Parmeggiani, Fabio; Pellarin, Riccardo; Larsen, Anders Peter
  • Journal of Molecular Biology, Vol. 376, Issue 5
  • DOI: 10.1016/j.jmb.2007.12.014

Designed Proteins To Modulate Cellular Networks
journal, June 2010

  • Cortajarena, Aitziber L.; Liu, Tina Y.; Hochstrasser, Mark
  • ACS Chemical Biology, Vol. 5, Issue 6
  • DOI: 10.1021/cb9002464

Implementation and performance of SIBYLS: a dual endstation small-angle X-ray scattering and macromolecular crystallography beamline at the Advanced Light Source
journal, January 2013

  • Classen, Scott; Hura, Greg L.; Holton, James M.
  • Journal of Applied Crystallography, Vol. 46, Issue 1
  • DOI: 10.1107/S0021889812048698

Calorimetric study of a series of designed repeat proteins: Modular structure and modular folding
journal, January 2011

  • Cortajarena, Aitziber L.; Regan, Lynne
  • Protein Science, Vol. 20, Issue 2
  • DOI: 10.1002/pro.564

An artificial PPR scaffold for programmable RNA recognition
journal, December 2014

  • Coquille, Sandrine; Filipovska, Aleksandra; Chia, Tiongsun
  • Nature Communications, Vol. 5, Issue 1
  • DOI: 10.1038/ncomms6729

MolProbity : all-atom structure validation for macromolecular crystallography
journal, December 2009

  • Chen, Vincent B.; Arendall, W. Bryan; Headd, Jeffrey J.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1
  • DOI: 10.1107/S0907444909042073

Coot model-building tools for molecular graphics
journal, November 2004

  • Emsley, Paul; Cowtan, Kevin
  • Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132
  • DOI: 10.1107/S0907444904019158

FoXS: a web server for rapid computation and fitting of SAXS profiles
journal, May 2010

  • Schneidman-Duhovny, D.; Hammel, M.; Sali, A.
  • Nucleic Acids Research, Vol. 38, Issue Web Server
  • DOI: 10.1093/nar/gkq461

When protein folding is simplified to protein coiling: the continuum of solenoid protein structures
journal, October 2000


RepeatsDB: a database of tandem repeat protein structures
journal, December 2013

  • Di Domenico, Tomás; Potenza, Emilio; Walsh, Ian
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt1175

Comprehensive macromolecular conformations mapped by quantitative SAXS analyses
journal, April 2013

  • Hura, Greg L.; Budworth, Helen; Dyer, Kevin N.
  • Nature Methods, Vol. 10, Issue 6
  • DOI: 10.1038/nmeth.2453

New developments in the ATSAS program package for small-angle scattering data analysis
journal, March 2012

  • Petoukhov, Maxim V.; Franke, Daniel; Shkumatov, Alexander V.
  • Journal of Applied Crystallography, Vol. 45, Issue 2
  • DOI: 10.1107/S0021889812007662

Computational design of a leucine-rich repeat protein with a predefined geometry
journal, November 2014

  • Rämisch, Sebastian; Weininger, Ulrich; Martinsson, Jonas
  • Proceedings of the National Academy of Sciences, Vol. 111, Issue 50
  • DOI: 10.1073/pnas.1413638111

BLAST+: architecture and applications
journal, January 2009

  • Camacho, Christiam; Coulouris, George; Avagyan, Vahram
  • BMC Bioinformatics, Vol. 10, Issue 1
  • DOI: 10.1186/1471-2105-10-421

Reconstruction of Functional β-Propeller Lectins via Homo-oligomeric Assembly of Shorter Fragments
journal, January 2007


HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment
journal, December 2011

  • Remmert, Michael; Biegert, Andreas; Hauser, Andreas
  • Nature Methods, Vol. 9, Issue 2
  • DOI: 10.1038/nmeth.1818

A General Computational Approach for Repeat Protein Design
journal, January 2015

  • Parmeggiani, Fabio; Huang, Po-Ssu; Vorobiev, Sergey
  • Journal of Molecular Biology, Vol. 427, Issue 2
  • DOI: 10.1016/j.jmb.2014.11.005

A census of protein repeats
journal, October 1999

  • Marcotte, Edward M.; Pellegrini, Matteo; Yeates, Todd O.
  • Journal of Molecular Biology, Vol. 293, Issue 1
  • DOI: 10.1006/jmbi.1999.3136

Enhancing the Stability and Folding Rate of a Repeat Protein through the Addition of Consensus Repeats
journal, January 2007


The Pfam protein families database
journal, November 2011

  • Punta, M.; Coggill, P. C.; Eberhardt, R. Y.
  • Nucleic Acids Research, Vol. 40, Issue D1
  • DOI: 10.1093/nar/gkr1065

Designed Armadillo Repeat Proteins: Library Generation, Characterization and Selection of Peptide Binders with High Specificity
journal, November 2012

  • Varadamsetty, Gautham; Tremmel, Dirk; Hansen, Simon
  • Journal of Molecular Biology, Vol. 424, Issue 1-2
  • DOI: 10.1016/j.jmb.2012.08.029

Consensus-derived structural determinants of the ankyrin repeat motif
journal, December 2002

  • Mosavi, L. K.; Minor, D. L.; Peng, Z. -y.
  • Proceedings of the National Academy of Sciences, Vol. 99, Issue 25
  • DOI: 10.1073/pnas.252537899

High-affinity binders selected from designed ankyrin repeat protein libraries
journal, April 2004

  • Binz, H. Kaspar; Amstutz, Patrick; Kohl, Andreas
  • Nature Biotechnology, Vol. 22, Issue 5, p. 575-582
  • DOI: 10.1038/nbt962

Accurate assessment of mass, models and resolution by small-angle scattering
journal, April 2013


Jalview Version 2--a multiple sequence alignment editor and analysis workbench
journal, January 2009


Software for the high-throughput collection of SAXS data using an enhanced Blu-Ice / DCS control system
journal, September 2010

  • Classen, Scott; Rodic, Ivan; Holton, James
  • Journal of Synchrotron Radiation, Vol. 17, Issue 6
  • DOI: 10.1107/S0909049510028566

    Works referencing / citing this record:

    Rigid helical-like assemblies from a self-aggregating tripeptide
    journal, April 2019


    Sibe: a computation tool to apply protein sequence statistics to predict folding and design in silico
    journal, September 2019


    Ambidextrous helical nanotubes from self-assembly of designed helical hairpin motifs
    journal, July 2019

    • Hughes, Spencer A.; Wang, Fengbin; Wang, Shengyuan
    • Proceedings of the National Academy of Sciences, Vol. 116, Issue 29
    • DOI: 10.1073/pnas.1903910116