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Title: Controlling protein assembly on inorganic crystals through designed protein interfaces

Abstract

The ability of proteins and other macromolecules to interact with inorganic surfaces is essential to biological function. The proteins involved in these interactions are highly charged and often rich in carboxylic acid side chains, but the structures of most protein–inorganic interfaces are unknown. We explored the possibility of systematically designing structured protein–mineral interfaces, guided by the example of ice-binding proteins, which present arrays of threonine residues (matched to the ice lattice) that order clathrate waters into an ice-like structure. Here we design proteins displaying arrays of up to 54 carboxylate residues geometrically matched to the potassium ion (K+) sublattice on muscovite mica (001). At low K+ concentration, individual molecules bind independently to mica in the designed orientations, whereas at high K+ concentration, the designs form two-dimensional liquid-crystal phases, which accentuate the inherent structural bias in the muscovite lattice to produce protein arrays ordered over tens of millimetres. Incorporation of designed protein–protein interactions preserving the match between the proteins and the K+ lattice led to extended self-assembled structures on mica: designed end-to-end interactions produced micrometre-long single-protein-diameter wires and a designed trimeric interface yielded extensive honeycomb arrays. The nearest-neighbour distances in these hexagonal arrays could be set digitally between 7.5 and 15.9more » nanometres with 2.1-nanometre selectivity by changing the number of repeat units in the monomer. In conclusion, these results demonstrate that protein–inorganic lattice interactions can be systematically programmed and set the stage for designing protein–inorganic hybrid materials.« less

Authors:
 [1];  [2];  [2]; ORCiD logo [3]
  1. Univ. of Washington, Seattle, WA (United States). Inst. for Protein Design
  2. Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Univ. of Washington, Seattle, WA (United States)
  3. Univ. of Washington, Seattle, WA (United States). Inst. for Protein Design, and Howard Hughes Medical Inst.
Publication Date:
Research Org.:
Energy Frontier Research Centers (EFRC) (United States). The Center for the Science of Synthesis Across Scales (CSSAS); Univ. of Washington, Seattle, WA (United States); Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES); National Institutes of Health (NIH); USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1595483
Grant/Contract Number:  
SC0019288; SC0018940; AC02-05CH11231; AC05-76RL01830
Resource Type:
Accepted Manuscript
Journal Name:
Nature (London)
Additional Journal Information:
Journal Name: Nature (London); Journal Volume: 571; Journal Issue: 7764; Journal ID: ISSN 0028-0836
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; 59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Pyles, Harley, Zhang, Shuai, De Yoreo, James J., and Baker, David. Controlling protein assembly on inorganic crystals through designed protein interfaces. United States: N. p., 2019. Web. doi:10.1038/s41586-019-1361-6.
Pyles, Harley, Zhang, Shuai, De Yoreo, James J., & Baker, David. Controlling protein assembly on inorganic crystals through designed protein interfaces. United States. https://doi.org/10.1038/s41586-019-1361-6
Pyles, Harley, Zhang, Shuai, De Yoreo, James J., and Baker, David. Wed . "Controlling protein assembly on inorganic crystals through designed protein interfaces". United States. https://doi.org/10.1038/s41586-019-1361-6. https://www.osti.gov/servlets/purl/1595483.
@article{osti_1595483,
title = {Controlling protein assembly on inorganic crystals through designed protein interfaces},
author = {Pyles, Harley and Zhang, Shuai and De Yoreo, James J. and Baker, David},
abstractNote = {The ability of proteins and other macromolecules to interact with inorganic surfaces is essential to biological function. The proteins involved in these interactions are highly charged and often rich in carboxylic acid side chains, but the structures of most protein–inorganic interfaces are unknown. We explored the possibility of systematically designing structured protein–mineral interfaces, guided by the example of ice-binding proteins, which present arrays of threonine residues (matched to the ice lattice) that order clathrate waters into an ice-like structure. Here we design proteins displaying arrays of up to 54 carboxylate residues geometrically matched to the potassium ion (K+) sublattice on muscovite mica (001). At low K+ concentration, individual molecules bind independently to mica in the designed orientations, whereas at high K+ concentration, the designs form two-dimensional liquid-crystal phases, which accentuate the inherent structural bias in the muscovite lattice to produce protein arrays ordered over tens of millimetres. Incorporation of designed protein–protein interactions preserving the match between the proteins and the K+ lattice led to extended self-assembled structures on mica: designed end-to-end interactions produced micrometre-long single-protein-diameter wires and a designed trimeric interface yielded extensive honeycomb arrays. The nearest-neighbour distances in these hexagonal arrays could be set digitally between 7.5 and 15.9 nanometres with 2.1-nanometre selectivity by changing the number of repeat units in the monomer. In conclusion, these results demonstrate that protein–inorganic lattice interactions can be systematically programmed and set the stage for designing protein–inorganic hybrid materials.},
doi = {10.1038/s41586-019-1361-6},
journal = {Nature (London)},
number = 7764,
volume = 571,
place = {United States},
year = {2019},
month = {7}
}

Journal Article:
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Figures / Tables:

Figure 1 Figure 1: Design and characterization of lattice-matched protein monomers. a, Model of DHR10-mica18 protein lattice-matched to mica (001) surface through the K+ sublattice. One eighteen-repeat DHR10-mica18 molecule is shown from side and top views. Repeats 1-3 illustrate the lattice-matched glutamate (glu) side chains. Repeats 4-6 show the α-helical secondary structuresmore » that contain the matched glutamates. Repeats 7-9 show the full designedhelical repeat protein backbone. Repeats 10-12 show the full backbone and all amino acid side chains. Repeats 13-15 show all atoms as spheres. Repeats 16-18 show the external surface of the protein. The arrows indicate the orientations of the mica lattice. b, Projection view looking along the Y-direction. Lattice-matched glutamates are shown as sticks and other side chains as thinner lines. c, DHR10-mica18 bound to K+ superlattice in the six symmetry equivalent orientations predicted by the protein-mica interface design model. d, AFM image of DHR10-mica18 adsorbed on mica, showing two of the three predominate orientations that are distinguishable by AFM (anti-parallel orientations look similar). Protein is at 0.1 uM and buffer is 10 mM KCl and 20 mM Tris. The arrows in the right-up corner indicate the orientations of K+ sublattice and mica lattice. The scale bar is 5 nm. e, AFM of mica (001) beneath the proteins in panel D, showing the mica lattice directions. The scale bar is 5 nm.« less

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Works referenced in this record:

Crystallizing the function of the magnetosome membrane mineralization protein Mms6
journal, June 2016

  • Staniland, Sarah S.; Rawlings, Andrea E.
  • Biochemical Society Transactions, Vol. 44, Issue 3
  • DOI: 10.1042/BST20160057

Solid-state NMR studies of proteins immobilized on inorganic surfaces
journal, September 2015


Ice-binding proteins: a remarkable diversity of structures for stopping and starting ice growth
journal, November 2014


Combinatorial codon scrambling enables scalable gene synthesis and amplification of repetitive proteins
journal, January 2016

  • Tang, Nicholas C.; Chilkoti, Ashutosh
  • Nature Materials, Vol. 15, Issue 4
  • DOI: 10.1038/nmat4521

Exploring the repeat protein universe through computational protein design
journal, December 2015

  • Brunette, Tj; Parmeggiani, Fabio; Huang, Po-Ssu
  • Nature, Vol. 528, Issue 7583
  • DOI: 10.1038/nature16162

Structural analysis of intrinsically disordered proteins by small-angle X-ray scattering
journal, January 2012

  • Bernadó, Pau; Svergun, Dmitri I.
  • Mol. BioSyst., Vol. 8, Issue 1
  • DOI: 10.1039/C1MB05275F

Recursive Directional Ligation by Plasmid Reconstruction Allows Rapid and Seamless Cloning of Oligomeric Genes
journal, April 2010

  • McDaniel, Jonathan R.; MacKay, J. Andrew; Quiroz, Felipe García
  • Biomacromolecules, Vol. 11, Issue 4
  • DOI: 10.1021/bm901387t

Differential Modulating Effect of MoS 2 on Amyloid Peptide Assemblies
journal, February 2018

  • Wang, Jie; Liu, Lei; Ge, Daohan
  • Chemistry - A European Journal, Vol. 24, Issue 14
  • DOI: 10.1002/chem.201704593

Expression and characterization of 15N-labeled human C-reactive protein in Escherichia coli and Pichia pastoris for use in isotope-dilution mass spectrometry
journal, September 2012

  • Kilpatrick, Eric L.; Liao, Wei-Li; Camara, Johanna E.
  • Protein Expression and Purification, Vol. 85, Issue 1
  • DOI: 10.1016/j.pep.2012.06.019

Automated in-line gel filtration for native state mass spectrometry
journal, February 2008

  • Waitt, Greg M.; Xu, Robert; Wisely, G. Bruce
  • Journal of the American Society for Mass Spectrometry, Vol. 19, Issue 2
  • DOI: 10.1016/j.jasms.2007.05.008

De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity
journal, May 2016


Tuning crystallization pathways through sequence engineering of biomimetic polymers
journal, April 2017

  • Ma, Xiang; Zhang, Shuai; Jiao, Fang
  • Nature Materials, Vol. 16, Issue 7
  • DOI: 10.1038/nmat4891

Surface-Induced Dissociation of Noncovalent Protein Complexes in an Extended Mass Range Orbitrap Mass Spectrometer
journal, January 2019


Soluble expression of proteins correlates with a lack of positively-charged surface
journal, November 2013

  • Chan, Pedro; Curtis, Robin A.; Warwicker, Jim
  • Scientific Reports, Vol. 3, Issue 1
  • DOI: 10.1038/srep03333

Potassium Ion Mediated Collagen Microfibril Assembly on Mica
journal, December 2008

  • Loo, Richard W.; Goh, M. Cynthia
  • Langmuir, Vol. 24, Issue 23
  • DOI: 10.1021/la803041v

Foldit Standalone: a video game-derived protein structure manipulation interface using Rosetta
journal, May 2017


Osteopontin
journal, July 2000


Evidence for algebraic orientational order in a two-dimensional hard-core nematic
journal, March 1985


Formation of oriented molecular nanowires on mica surface
journal, April 2002

  • Akutagawa, T.; Ohta, T.; Hasegawa, T.
  • Proceedings of the National Academy of Sciences, Vol. 99, Issue 8
  • DOI: 10.1073/pnas.082644299

Developing a molecular picture of soil organic matter–mineral interactions by quantifying organo–mineral binding
journal, August 2017


Control of Calcite Crystal Morphology by a Peptide Designed To Bind to a Specific Surface
journal, November 1997

  • DeOliveira, Daniel B.; Laursen, Richard A.
  • Journal of the American Chemical Society, Vol. 119, Issue 44
  • DOI: 10.1021/ja972270w

Energetic basis for the molecular-scale organization of bone
journal, December 2014

  • Tao, Jinhui; Battle, Keith C.; Pan, Haihua
  • Proceedings of the National Academy of Sciences, Vol. 112, Issue 2
  • DOI: 10.1073/pnas.1404481112

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

All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins
journal, April 1998

  • MacKerell, A. D.; Bashford, D.; Bellott, M.
  • The Journal of Physical Chemistry B, Vol. 102, Issue 18
  • DOI: 10.1021/jp973084f

Direct observation of kinetic traps associated with structural transformations leading to multiple pathways of S-layer assembly
journal, July 2012

  • Shin, S. -H.; Chung, S.; Sanii, B.
  • Proceedings of the National Academy of Sciences, Vol. 109, Issue 32
  • DOI: 10.1073/pnas.1201504109

Confirmation of intersubunit connectivity and topology of designed protein complexes by native MS
journal, January 2018

  • Sahasrabuddhe, Aniruddha; Hsia, Yang; Busch, Florian
  • Proceedings of the National Academy of Sciences, Vol. 115, Issue 6
  • DOI: 10.1073/pnas.1713646115

Atomically resolved three-dimensional structures of electrolyte aqueous solutions near a solid surface
journal, July 2016

  • Martin-Jimenez, Daniel; Chacon, Enrique; Tarazona, Pedro
  • Nature Communications, Vol. 7, Issue 1
  • DOI: 10.1038/ncomms12164

Characterizing flexible and intrinsically unstructured biological macromolecules by SAS using the Porod-Debye law
journal, April 2011

  • Rambo, Robert P.; Tainer, John A.
  • Biopolymers, Vol. 95, Issue 8
  • DOI: 10.1002/bip.21638

Surface-Assisted Large-Scale Ordering of DNA Origami Tiles
journal, June 2014

  • Aghebat Rafat, Ali; Pirzer, Tobias; Scheible, Max B.
  • Angewandte Chemie International Edition, Vol. 53, Issue 29
  • DOI: 10.1002/anie.201403965

Computational Design of Virus-Like Protein Assemblies on Carbon Nanotube Surfaces
journal, May 2011


PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta
journal, January 2010


Aspects of native proteins are retained in vacuum
journal, October 2006


RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite
journal, June 2011


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
  • DOI: 10.1038/nchem.2673

The Molecular Basis for Binding of an Electron Transfer Protein to a Metal Oxide Surface
journal, August 2017

  • Fukushima, Tatsuya; Gupta, Sayan; Rad, Behzad
  • Journal of the American Chemical Society, Vol. 139, Issue 36
  • DOI: 10.1021/jacs.7b06560

De Novo Design of Peptide−Calcite Biomineralization Systems
journal, September 2010

  • Masica, David L.; Schrier, Sarah B.; Specht, Elizabeth A.
  • Journal of the American Chemical Society, Vol. 132, Issue 35
  • DOI: 10.1021/ja1001086

Additive controlled crystallization
journal, January 2011


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


Comparison of the surface structure of the tetrahedral sheets of muscovite and phlogopite by AFM
journal, February 2001


Epitaxially Guided Assembly of Collagen Layers on Mica Surfaces
journal, September 2011


Graphene Symmetry Amplified by Designed Peptide Self-Assembly
journal, June 2016


Self-Assembly of Colloidal Nanocrystals: From Intricate Structures to Functional Materials
journal, August 2016


Mollusk Shell Formation: A Source of New Concepts for Understanding Biomineralization Processes
journal, January 2006

  • Addadi, Lia; Joester, Derk; Nudelman, Fabio
  • Chemistry - A European Journal, Vol. 12, Issue 4
  • DOI: 10.1002/chem.200500980

Bayesian Deconvolution of Mass and Ion Mobility Spectra: From Binary Interactions to Polydisperse Ensembles
journal, April 2015


Template-Directed Assembly of a de Novo Designed Protein
journal, June 2002

  • Brown, Christina L.; Aksay, Ilhan A.; Saville, Dudley A.
  • Journal of the American Chemical Society, Vol. 124, Issue 24
  • DOI: 10.1021/ja0261271

Mollusk Shell Formation: A Source of New Concepts for Understanding Biomineralization Processes
journal, April 2006


Mechanism of pore opening in the calcium-activated chloride channel TMEM16A
journal, February 2021


Ice-nucleating proteins are activated by low temperatures to control the structure of interfacial water
journal, February 2021

  • Roeters, Steven J.; Golbek, Thaddeus W.; Bregnhøj, Mikkel
  • Nature Communications, Vol. 12, Issue 1
  • DOI: 10.1038/s41467-021-21349-3

RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite
text, January 2011

  • Paul, Murphy,; David, Baker,; Nobuyasu, Koga,
  • The University of North Carolina at Chapel Hill University Libraries
  • DOI: 10.17615/qh1b-9733

Foldit Standalone: a video game-derived protein structure manipulation interface using Rosetta
text, January 2017

  • B., Siegel, Justin; David, Baker,; Firas, Khatib,
  • The University of North Carolina at Chapel Hill University Libraries
  • DOI: 10.17615/mvrr-v077

Works referencing / citing this record:

Direct investigation of current transport in cells by conductive atomic force microscopy
journal, December 2019

  • Zhao, W.; Cheong, L. ‐Z.; Xu, S.
  • Journal of Microscopy, Vol. 277, Issue 1
  • DOI: 10.1111/jmi.12861

Residue-centric modeling and design of saccharide and glycoconjugate structures
journal, November 2016

  • Labonte, Jason W.; Adolf-Bryfogle, Jared; Schief, William R.
  • Journal of Computational Chemistry, Vol. 38, Issue 5
  • DOI: 10.1002/jcc.24679

Yoink: An interaction-based partitioning API : An Interaction-Based Partitioning API
journal, January 2018

  • Zheng, Min; Waller, Mark P.
  • Journal of Computational Chemistry, Vol. 39, Issue 13
  • DOI: 10.1002/jcc.25146

Integration of the Rosetta suite with the python software stack via reproducible packaging and core programming interfaces for distributed simulation
journal, November 2019

  • Ford, Alexander S.; Weitzner, Brian D.; Bahl, Christopher D.
  • Protein Science, Vol. 29, Issue 1
  • DOI: 10.1002/pro.3721

Rapid and accurate structure-based therapeutic peptide design using GPU accelerated thermodynamic integration
journal, January 2019

  • Garton, Michael; Corbi-Verge, Carles; Hu, Yuan
  • Proteins: Structure, Function, and Bioinformatics, Vol. 87, Issue 3
  • DOI: 10.1002/prot.25644

Using PyMOL as a platform for computational drug design
journal, January 2017

  • Yuan, Shuguang; Chan, H. C. Stephen; Hu, Zhenquan
  • WIREs Computational Molecular Science, Vol. 7, Issue 2
  • DOI: 10.1002/wcms.1298

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
  • DOI: 10.1002/wcms.1374

GPT2 mutations in autosomal recessive developmental disability: extending the clinical phenotype and population prevalence estimates
journal, August 2019


Validation of protein backbone structures calculated from NMR angular restraints using Rosetta
journal, May 2019


A Unified De Novo Approach for Predicting the Structures of Ordered and Disordered Proteins
journal, June 2020

  • Ferrie, John J.; Petersson, E. James
  • The Journal of Physical Chemistry B, Vol. 124, Issue 27
  • DOI: 10.1021/acs.jpcb.0c02924

Biocontainment of genetically modified organisms by synthetic protein design
journal, January 2015

  • Mandell, Daniel J.; Lajoie, Marc J.; Mee, Michael T.
  • Nature, Vol. 518, Issue 7537
  • DOI: 10.1038/nature14121

Structure of promoter-bound TFIID and model of human pre-initiation complex assembly
journal, March 2016

  • Louder, Robert K.; He, Yuan; López-Blanco, José Ramón
  • Nature, Vol. 531, Issue 7596
  • DOI: 10.1038/nature17394

Computational design of a symmetrical β-trefoil lectin with cancer cell binding activity
journal, July 2017


Conformational sampling of the intrinsically disordered dsRBD-1 domain from Arabidopsis thaliana DCL1
journal, January 2018

  • Suárez, Irina P.; Gauto, Diego F.; Hails, Guillermo
  • Physical Chemistry Chemical Physics, Vol. 20, Issue 16
  • DOI: 10.1039/c7cp07908g

Structures of the prefusion form of measles virus fusion protein in complex with inhibitors
journal, February 2018

  • Hashiguchi, Takao; Fukuda, Yoshinari; Matsuoka, Rei
  • Proceedings of the National Academy of Sciences, Vol. 115, Issue 10
  • DOI: 10.1073/pnas.1718957115

Improved protein structure prediction using predicted interresidue orientations
journal, January 2020

  • Yang, Jianyi; Anishchenko, Ivan; Park, Hahnbeom
  • Proceedings of the National Academy of Sciences, Vol. 117, Issue 3
  • DOI: 10.1073/pnas.1914677117

Structural Diversity in the Type IV Pili of Multidrug-resistant Acinetobacter
journal, September 2016

  • Piepenbrink, Kurt H.; Lillehoj, Erik; Harding, Christian M.
  • Journal of Biological Chemistry, Vol. 291, Issue 44
  • DOI: 10.1074/jbc.M116.751099

Structure-based prediction of Wnt binding affinities for Frizzled-type cysteine-rich domains
journal, July 2017

  • Agostino, Mark; Pohl, Sebastian Öther-Gee; Dharmarajan, Arun
  • Journal of Biological Chemistry, Vol. 292, Issue 27
  • DOI: 10.1074/jbc.m117.786269

Plasmodium falciparum Hsp70-x: a heat shock protein at the host–parasite interface
journal, September 2013

  • Hatherley, Rowan; Blatch, Gregory L.; Bishop, Özlem Tastan
  • Journal of Biomolecular Structure and Dynamics, Vol. 32, Issue 11
  • DOI: 10.1080/07391102.2013.834849

NGLview–interactive molecular graphics for Jupyter notebooks
journal, December 2017


refineD: improved protein structure refinement using machine learning based restrained relaxation
journal, February 2019


A Comprehensive, High-Resolution Map of a Gene’s Fitness Landscape
journal, February 2014

  • Firnberg, Elad; Labonte, Jason W.; Gray, Jeffrey J.
  • Molecular Biology and Evolution, Vol. 31, Issue 6
  • DOI: 10.1093/molbev/msu081

RCD+: Fast loop modeling server
journal, May 2016

  • López-Blanco, José Ramón; Canosa-Valls, Alejandro Jesús; Li, Yaohang
  • Nucleic Acids Research, Vol. 44, Issue W1
  • DOI: 10.1093/nar/gkw395

Contribution of an unusual CDR2 element of a single domain antibody in ricin toxin binding affinity and neutralizing activity
journal, July 2018

  • Rudolph, Michael J.; Vance, David J.; Kelow, Simon
  • Protein Engineering, Design and Selection, Vol. 31, Issue 7-8
  • DOI: 10.1093/protein/gzy022

Accelerated simulation of evolutionary trajectories in origin-fixation models
journal, February 2017

  • Teufel, Ashley I.; Wilke, Claus O.
  • Journal of The Royal Society Interface, Vol. 14, Issue 127
  • DOI: 10.1098/rsif.2016.0906

Structural basis for distinct roles of SMAD2 and SMAD3 in FOXH1 pioneer-directed TGF-β signaling
journal, October 2019

  • Aragón, Eric; Wang, Qiong; Zou, Yilong
  • Genes & Development, Vol. 33, Issue 21-22
  • DOI: 10.1101/gad.330837.119

WebLogo: A Sequence Logo Generator
journal, May 2004

  • Crooks, Gavin E.; Hon, Gary; Chandonia, John-Marc
  • Genome Research, Vol. 14, Issue 6, p. 1188-1190
  • DOI: 10.1101/gr.849004

Development of a script-based versatile three-dimensional body measurement system
journal, September 2018

  • Kim, Minsuk; Kim, Sungmin
  • International Journal of Clothing Science and Technology, Vol. 30, Issue 5
  • DOI: 10.1108/ijcst-10-2017-0159

Molecular properties of gp100‐reactive T‐cell receptors drive the cytokine profile and antitumor efficacy of transgenic host T cells
journal, August 2018

  • Eby, Jonathan M.; Smith, Angela R.; Riley, Timothy P.
  • Pigment Cell & Melanoma Research, Vol. 32, Issue 1
  • DOI: 10.1111/pcmr.12724

Chiral switching in biomineral suprastructures induced by homochiral l-amino acid
journal, August 2018

  • Jiang, Wenge; Pacella, Michael S.; Vali, Hojatollah
  • Science Advances, Vol. 4, Issue 8
  • DOI: 10.1126/sciadv.aas9819

Computational design of water-soluble α-helical barrels
journal, October 2014

  • Thomson, Andrew R.; Wood, Christopher W.; Burton, Antony J.
  • Science, Vol. 346, Issue 6208
  • DOI: 10.1126/science.1257452

Rv2744c Is a PspA Ortholog That Regulates Lipid Droplet Homeostasis and Nonreplicating Persistence in Mycobacterium tuberculosis
journal, June 2016

  • Armstrong, Richard M.; Adams, Katherine L.; Zilisch, Joseph E.
  • Journal of Bacteriology, Vol. 198, Issue 11
  • DOI: 10.1128/jb.01001-15

Mass spectrometry–driven exploration reveals nuances of neoepitope-driven tumor rejection
journal, July 2019


The scoring of poses in protein-protein docking: current capabilities and future directions
journal, January 2013

  • Moal, Iain H.; Torchala, Mieczyslaw; Bates, Paul A.
  • BMC Bioinformatics, Vol. 14, Issue 1
  • DOI: 10.1186/1471-2105-14-286

An Integrated Framework Advancing Membrane Protein Modeling and Design
journal, September 2015

  • Alford, Rebecca F.; Koehler Leman, Julia; Weitzner, Brian D.
  • PLOS Computational Biology, Vol. 11, Issue 9
  • DOI: 10.1371/journal.pcbi.1004398

Benchmarking and Analysis of Protein Docking Performance in Rosetta v3.2
journal, August 2011


Beyond Thermodynamic Constraints: Evolutionary Sampling Generates Realistic Protein Sequence Variation
journal, April 2018


Serverification of Molecular Modeling Applications: The Rosetta Online Server That Includes Everyone (ROSIE)
text, January 2013

  • Brian, Kuhlman,; Tanja, Kortemme,; Benjamin, Borgo,
  • The University of North Carolina at Chapel Hill University Libraries
  • DOI: 10.17615/7c93-y342

RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite
text, January 2011

  • Paul, Murphy,; David, Baker,; Nobuyasu, Koga,
  • The University of North Carolina at Chapel Hill University Libraries
  • DOI: 10.17615/qh1b-9733

Structure Based Prediction of Neoantigen Immunogenicity
journal, August 2019

  • Riley, Timothy P.; Keller, Grant L. J.; Smith, Angela R.
  • Frontiers in Immunology, Vol. 10
  • DOI: 10.3389/fimmu.2019.02047

Wnt Binding Affinity Prediction for Putative Frizzled-Type Cysteine-Rich Domains
journal, August 2019

  • Agostino, Mark; Pohl, Sebastian Öther-Gee
  • International Journal of Molecular Sciences, Vol. 20, Issue 17
  • DOI: 10.3390/ijms20174168

Structural modeling of human cardiac sodium channel pore domain
text, January 2017


Contacts-based prediction of binding affinity in protein–protein complexes
journal, July 2015


Acidic C-terminal domains autoregulate the RNA chaperone Hfq
journal, August 2017

  • Santiago-Frangos, Andrew; Jeliazkov, Jeliazko R.; Gray, Jeffrey J.
  • eLife, Vol. 6
  • DOI: 10.7554/elife.27049

Interplay of disordered and ordered regions of a human small heat shock protein yields an ensemble of ‘quasi-ordered’ states
journal, October 2019

  • Clouser, Amanda F.; Baughman, Hannah ER; Basanta, Benjamin
  • eLife, Vol. 8
  • DOI: 10.7554/eLife.50259

Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.