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 »
- Authors:
-
- Univ. of Washington, Seattle, WA (United States). Dept. of Biochemistry. Inst. for Protein Design
- Univ. of California, San Francisco, CA (United States). Dept. of Cellular and Molecular Pharmacology
- Univ. of California, San Francisco, CA (United States). Dept. of Microbiology and Immunology
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Molecular Biophysics and Integrated Bioimaging
- 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
- 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
- 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 Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Basic Energy Sciences (BES); 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. https://doi.org/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. https://doi.org/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 = {Wed Dec 16 00:00:00 EST 2015},
month = {Wed Dec 16 00:00:00 EST 2015}
}
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Works referenced in this record:
TM-align: a protein structure alignment algorithm based on the TM-score
journal, April 2005
- Zhang, Y.
- Nucleic Acids Research, Vol. 33, Issue 7
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
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
High thermodynamic stability of parametrically designed helical bundles
journal, October 2014
- Huang, Po-Ssu; Oberdorfer, Gustav; Xu, Chunfu
- Science, Vol. 346, Issue 6208
Tandem repeats in proteins: From sequence to structure
journal, September 2012
- Kajava, Andrey V.
- Journal of Structural Biology, Vol. 179, Issue 3
Design of Stable α-Helical Arrays from an Idealized TPR Motif
journal, May 2003
- Main, Ewan R. G.; Xiong, Yong; Cocco, Melanie J.
- Structure, Vol. 11, Issue 5
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
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
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
Toward High-Resolution de Novo Structure Prediction for Small Proteins
journal, September 2005
- Bradley, P.
- Science, Vol. 309, Issue 5742
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
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
Super-Resolution in Solution X-Ray Scattering and Its Applications to Structural Systems Biology
journal, May 2013
- Rambo, Robert P.; Tainer, John A.
- Annual Review of Biophysics, Vol. 42, Issue 1
Designing Repeat Proteins: Well-expressed, Soluble and Stable Proteins from Combinatorial Libraries of Consensus Ankyrin Repeat Proteins
journal, September 2003
- Binz, H. Kaspar; Stumpp, Michael T.; Forrer, Patrik
- Journal of Molecular Biology, Vol. 332, Issue 2
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
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
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
XDS
journal, January 2010
- Kabsch, Wolfgang
- Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2
RosettaRemodel: A Generalized Framework for Flexible Backbone Protein Design
journal, August 2011
- Huang, Po-Ssu; Ban, Yih-En Andrew; Richter, Florian
- PLoS ONE, Vol. 6, Issue 8
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
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
Designed Proteins To Modulate Cellular Networks
journal, June 2010
- Cortajarena, Aitziber L.; Liu, Tina Y.; Hochstrasser, Mark
- ACS Chemical Biology, Vol. 5, Issue 6
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
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
An artificial PPR scaffold for programmable RNA recognition
journal, December 2014
- Coquille, Sandrine; Filipovska, Aleksandra; Chia, Tiongsun
- Nature Communications, Vol. 5, Issue 1
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
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
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
When protein folding is simplified to protein coiling: the continuum of solenoid protein structures
journal, October 2000
- Kobe, Bostjan; Kajava, Andrey V.
- Trends in Biochemical Sciences, Vol. 25, Issue 10
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
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
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
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
BLAST+: architecture and applications
journal, January 2009
- Camacho, Christiam; Coulouris, George; Avagyan, Vahram
- BMC Bioinformatics, Vol. 10, Issue 1
Reconstruction of Functional β-Propeller Lectins via Homo-oligomeric Assembly of Shorter Fragments
journal, January 2007
- Yadid, Itamar; Tawfik, Dan S.
- Journal of Molecular Biology, Vol. 365, Issue 1
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
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
A census of protein repeats
journal, October 1999
- Marcotte, Edward M.; Pellegrini, Matteo; Yeates, Todd O.
- Journal of Molecular Biology, Vol. 293, Issue 1
Enhancing the Stability and Folding Rate of a Repeat Protein through the Addition of Consensus Repeats
journal, January 2007
- Tripp, Katherine W.; Barrick, Doug
- Journal of Molecular Biology, Vol. 365, Issue 4
The Pfam protein families database
journal, November 2011
- Punta, M.; Coggill, P. C.; Eberhardt, R. Y.
- Nucleic Acids Research, Vol. 40, Issue D1
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
Rosetta3: An Object-Oriented Software Suite for the Simulation and Design of Macromolecules
book, January 2011
- Leaver-Fay, Andrew; Tyka, Michael; Lewis, Steven M.
- Computer Methods, Part C
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
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
Accurate assessment of mass, models and resolution by small-angle scattering
journal, April 2013
- Rambo, Robert P.; Tainer, John A.
- Nature, Vol. 496, Issue 7446
Jalview Version 2--a multiple sequence alignment editor and analysis workbench
journal, January 2009
- Waterhouse, A. M.; Procter, J. B.; Martin, D. M. A.
- Bioinformatics, Vol. 25, Issue 9
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
Exploring the gas access routes in a [NiFeSe] hydrogenase using crystals pressurized with krypton and oxygen
journal, August 2020
- Zacarias, Sónia; Temporão, Adriana; Carpentier, Philippe
- JBIC Journal of Biological Inorganic Chemistry, Vol. 25, Issue 6
Coriander Genomics Database: a genomic, transcriptomic, and metabolic database for coriander
journal, April 2020
- Song, Xiaoming; Nie, Fulei; Chen, Wei
- Horticulture Research, Vol. 7, Issue 1
Why does the Aβ peptide of Alzheimer share structural similarity with antimicrobial peptides?
journal, March 2020
- Pastore, Annalisa; Raimondi, Francesco; Rajendran, Lawrence
- Communications Biology, Vol. 3, Issue 1
Designed armadillo repeat proteins as general peptide-binding scaffolds: consensus design and computational optimization of the hydrophobic core
text, January 2008
- Parmeggiani, F.; Pellarin, R.; Larsen, A. P.
- Elsevier
An artificial PPR scaffold for programmable RNA recognition
text, January 2014
- Coquille, Sandrine; Filipovska, Aleksandra; Chia, Tiong Sun
- Unpublished
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, A.
- Journal of Molecular Biology, Vol. 404, Issue 2, p. 307-327
Designed armadillo repeat proteins: library generation, characterization and selection of Peptide binders with high specificity
text, January 2012
- Varadamsetty, Gautham; Tremmel, Dirk; Hansen, Simon
- Elsevier
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
Reconstruction of Functional β-Propeller Lectins via Homo-oligomeric Assembly of Shorter Fragments
journal, January 2007
- Yadid, Itamar; Tawfik, Dan S.
- Journal of Molecular Biology, Vol. 365, Issue 1
Tandem repeats in proteins: From sequence to structure
journal, September 2012
- Kajava, Andrey V.
- Journal of Structural Biology, Vol. 179, Issue 3
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
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
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
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
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
Jalview Version 2--a multiple sequence alignment editor and analysis workbench
journal, January 2009
- Waterhouse, A. M.; Procter, J. B.; Martin, D. M. A.
- Bioinformatics, Vol. 25, Issue 9
TM-align: a protein structure alignment algorithm based on the TM-score
journal, April 2005
- Zhang, Y.
- Nucleic Acids Research, Vol. 33, Issue 7
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
Toward High-Resolution de Novo Structure Prediction for Small Proteins
journal, September 2005
- Bradley, P.
- Science, Vol. 309, Issue 5742
An artificial PPR scaffold for programmable RNA recognition
text, January 2014
- Coquille, Sandrine; Filipovska, Aleksandra; Chia, Tiong Sun
- Unpublished
Folding and unfolding mechanism of highly stable full-consensus ankyrin repeat proteins
text, January 2008
- K., Wetzel, S.; G., Settanni,; M., Kenig,
- Elsevier
Design of armadillo repeat protein scaffolds
dissertation, January 2008
- F., Parmeggiani,
- University of Zurich
Works referencing / citing this record:
Functional Proteins from Short Peptides: Dayhoff's Hypothesis Turns 50
journal, November 2016
- Romero Romero, M. Luisa; Rabin, Avigayel; Tawfik, Dan S.
- Angewandte Chemie International Edition, Vol. 55, Issue 52
Essentials of de novo protein design: Methods and applications
journal, July 2018
- Marcos, Enrique; Silva, Daniel-Adriano
- Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 8, Issue 6
Hierarchical design of artificial proteins and complexes toward synthetic structural biology
journal, December 2017
- Arai, Ryoichi
- Biophysical Reviews, Vol. 10, Issue 2
Accurate de novo design of hyperstable constrained peptides
journal, September 2016
- Bhardwaj, Gaurav; Mulligan, Vikram Khipple; Bahl, Christopher D.
- Nature, Vol. 538, Issue 7625
The coming of age of de novo protein design
journal, September 2016
- Huang, Po-Ssu; Boyken, Scott E.; Baker, David
- Nature, Vol. 537, Issue 7620
Design of coiled-coil protein-origami cages that self-assemble in vitro and in vivo
journal, October 2017
- Ljubetič, Ajasja; Lapenta, Fabio; Gradišar, Helena
- Nature Biotechnology, Vol. 35, Issue 11
Computational design of self-assembling cyclic protein homo-oligomers
journal, December 2016
- Fallas, Jorge A.; Ueda, George; Sheffler, William
- Nature Chemistry, Vol. 9, Issue 4
De novo design of a hyperstable non-natural protein–ligand complex with sub-Å accuracy
journal, August 2017
- Polizzi, Nicholas F.; Wu, Yibing; Lemmin, Thomas
- Nature Chemistry, Vol. 9, Issue 12
Rigid helical-like assemblies from a self-aggregating tripeptide
journal, April 2019
- Bera, Santu; Mondal, Sudipta; Xue, Bin
- Nature Materials, Vol. 18, Issue 5
Advances in protein structure prediction and design
journal, August 2019
- Kuhlman, Brian; Bradley, Philip
- Nature Reviews Molecular Cell Biology, Vol. 20, Issue 11
Controlling protein assembly on inorganic crystals through designed protein interfaces
journal, July 2019
- Pyles, Harley; Zhang, Shuai; De Yoreo, James J.
- Nature, Vol. 571, Issue 7764
De novo design of bioactive protein switches
journal, July 2019
- Langan, Robert A.; Boyken, Scott E.; Ng, Andrew H.
- Nature, Vol. 572, Issue 7768
Multi-input chemical control of protein dimerization for programming graded cellular responses
journal, September 2019
- Foight, Glenna Wink; Wang, Zhizhi; Wei, Cindy T.
- Nature Biotechnology, Vol. 37, Issue 10
Designed peptides that assemble into cross-α amyloid-like structures
journal, July 2018
- Zhang, Shao-Qing; Huang, Hai; Yang, Junjiao
- Nature Chemical Biology, Vol. 14, Issue 9
An in silico argument for mitochondrial microRNA as a determinant of primary non function in liver transplantation
journal, February 2018
- Khorsandi, Shirin Elizabeth; Salehi, Siamak; Cortes, Miriam
- Scientific Reports, Vol. 8, Issue 1
Extreme stability in de novo-designed repeat arrays is determined by unusually stable short-range interactions
journal, June 2018
- Geiger-Schuller, Kathryn; Sforza, Kevin; Yuhas, Max
- Proceedings of the National Academy of Sciences, Vol. 115, Issue 29
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
Multi-scale structural analysis of proteins by deep semantic segmentation
journal, August 2019
- Eguchi, Raphael R.; Huang, Po-Ssu
- Bioinformatics, Vol. 36, Issue 6
RepeatsDB 2.0: improved annotation, classification, search and visualization of repeat protein structures
journal, November 2016
- Paladin, Lisanna; Hirsh, Layla; Piovesan, Damiano
- Nucleic Acids Research, Vol. 45, Issue D1
The topology of evolutionary novelty and innovation in macroevolution
journal, October 2017
- Erwin, Douglas H.
- Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 372, Issue 1735
Tailored Design of Protein Nanoparticle Scaffolds for Multivalent Presentation of Viral Glycoprotein Antigens
posted_content, January 2020
- Ueda, George; Antanasijevic, Aleksandar; Fallas, Jorge A.
Design of structurally distinct proteins using strategies inspired by evolution
journal, May 2016
- Jacobs, T. M.; Williams, B.; Williams, T.
- Science, Vol. 352, Issue 6286
The cytotoxic Staphylococcus aureus PSMα3 reveals a cross-α amyloid-like fibril
journal, February 2017
- Tayeb-Fligelman, Einav; Tabachnikov, Orly; Moshe, Asher
- Science, Vol. 355, Issue 6327
Principles for designing proteins with cavities formed by curved β sheets
journal, January 2017
- Marcos, Enrique; Basanta, Benjamin; Chidyausiku, Tamuka M.
- Science, Vol. 355, Issue 6321
Self-assembly of genetically encoded DNA-protein hybrid nanoscale shapes
journal, March 2017
- Praetorius, Florian; Dietz, Hendrik
- Science, Vol. 355, Issue 6331
De novo design of self-assembling helical protein filaments
journal, November 2018
- Shen, Hao; Fallas, Jorge A.; Lynch, Eric
- Science, Vol. 362, Issue 6415
Sibe: a computation tool to apply protein sequence statistics to predict folding and design in silico
journal, September 2019
- Cheung, Ngaam J.; Yu, Wookyung
- BMC Bioinformatics, Vol. 20, Issue 1
PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta
journal, January 2010
- Chaudhury, S.; Lyskov, S.; Gray, J. J.
- Bioinformatics, Vol. 26, Issue 5, p. 689-691
RepeatsDB 2.0: improved annotation, classification, search and visualization of repeat protein structures
journal, December 2016
- Paladin, Lisanna; Hirsh, Layla; Piovesan, Damiano
- Nucleic Acids Research, Vol. 45, Issue 6
Design of structurally distinct proteins using strategies inspired by evolution
text, January 2016
- ,
- The University of North Carolina at Chapel Hill University Libraries
Sibe: a computation tool to apply protein sequence statistics to predict folding and design in silico
text, January 2019
- Cheung, Ngaam J.; Yu, Wookyung
- Apollo - University of Cambridge Repository
Charging of Proteins in Native Mass Spectrometry
journal, October 2016
- Susa, Anna C.; Xia, Zijie; Tang, Henry Y. H.
- Journal of the American Society for Mass Spectrometry, Vol. 28, Issue 2
Curvature of designed armadillo repeat proteins allows modular peptide binding
journal, February 2018
- Hansen, Simon; Ernst, Patrick; König, Sebastian L. B.
- Journal of Structural Biology, Vol. 201, Issue 2
Computational design of protein self-assembly
journal, August 2016
- Norn, Christoffer H.; André, Ingemar
- Current Opinion in Structural Biology, Vol. 39
Computational design of self-assembling cyclic protein homo-oligomers
journal, December 2016
- Fallas, Jorge A.; Ueda, George; Sheffler, William
- Nature Chemistry, Vol. 9, Issue 4
Structural basis for specific single-stranded RNA recognition by designer pentatricopeptide repeat proteins
journal, April 2016
- Shen, Cuicui; Zhang, Delin; Guan, Zeyuan
- Nature Communications, Vol. 7, Issue 1
Structural and functional insight into the effect of AFF4 dimerization on activation of HIV-1 proviral transcription
journal, February 2020
- Tang, Dan; Chen, Chunjing; Liao, Ga
- Cell Discovery, Vol. 6, Issue 1
Controlling protein assembly on inorganic crystals through designed protein interfaces
journal, July 2019
- Pyles, Harley; Zhang, Shuai; De Yoreo, James J.
- Nature, Vol. 571, Issue 7764
De novo design of bioactive protein switches
journal, July 2019
- Langan, Robert A.; Boyken, Scott E.; Ng, Andrew H.
- Nature, Vol. 572, Issue 7768
Designed peptides that assemble into cross-α amyloid-like structures
journal, July 2018
- Zhang, Shao-Qing; Huang, Hai; Yang, Junjiao
- Nature Chemical Biology, Vol. 14, Issue 9
An in silico argument for mitochondrial microRNA as a determinant of primary non function in liver transplantation
journal, February 2018
- Khorsandi, Shirin Elizabeth; Salehi, Siamak; Cortes, Miriam
- Scientific Reports, Vol. 8, Issue 1
Folding and Stabilization of Native-Sequence-Reversed Proteins
journal, April 2016
- Zhang, Yuanzhao; Weber, Jeffrey K.; Zhou, Ruhong
- Scientific Reports, Vol. 6, Issue 1
Protein knotting through concatenation significantly reduces folding stability
journal, December 2016
- Hsu, Shang-Te Danny
- Scientific Reports, Vol. 6, Issue 1
ISAMBARD: an open-source computational environment for biomolecular analysis, modelling and design
journal, June 2017
- Wood, Christopher W.; Heal, Jack W.; Thomson, Andrew R.
- Bioinformatics, Vol. 33, Issue 19
Multi-scale structural analysis of proteins by deep semantic segmentation
journal, August 2019
- Eguchi, Raphael R.; Huang, Po-Ssu
- Bioinformatics, Vol. 36, Issue 6
RepeatsDB 2.0: improved annotation, classification, search and visualization of repeat protein structures
journal, December 2016
- Paladin, Lisanna; Hirsh, Layla; Piovesan, Damiano
- Nucleic Acids Research, Vol. 45, Issue 6
The topology of evolutionary novelty and innovation in macroevolution
journal, October 2017
- Erwin, Douglas H.
- Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 372, Issue 1735
Design: An assay based on single-polypeptide-chain heterodimeric A2AR/D2R and non-oligomerized fusions for in vivo analysis of their allosteric receptor-receptor interactions
journal, July 2016
- Kamiya, Toshio; Masuko, Takashi; Oscar, Dasiel
- BioRxiv
The solvent-excluded surfaces of water-soluble proteins
posted_content, April 2018
- Wang, Lincong
- BioRxiv
Sibe: a computation tool to apply protein sequence statistics to folding and design
journal, April 2019
- Cheung, Ngaam J.; Yu, Wookyung
- BMC Bioinformatics
Pathway dissection, regulation, engineering and application: lessons learned from biobutanol production by solventogenic clostridia
journal, March 2020
- Li, Shubo; Huang, Li; Ke, Chengzhu
- Biotechnology for Biofuels, Vol. 13, Issue 1
Inferring repeat-protein energetics from evolutionary information
journal, June 2017
- Espada, Rocío; Parra, R. Gonzalo; Mora, Thierry
- PLOS Computational Biology, Vol. 13, Issue 6
Long-range correlation in protein dynamics: Confirmation by structural data and normal mode analysis
journal, February 2020
- Tang, Qian-Yuan; Kaneko, Kunihiko
- PLOS Computational Biology, Vol. 16, Issue 2
Consistency Principle for Protein Design
journal, January 2020
- Koga, Rie; Koga, Nobuyasu
- Seibutsu Butsuri, Vol. 60, Issue 6
The Folding of de Novo Designed Protein DS119 via Molecular Dynamics Simulations
journal, April 2016
- Wang, Moye; Hu, Jie; Zhang, Zhuqing
- International Journal of Molecular Sciences, Vol. 17, Issue 5