Computational design of symmetrical eight-bladed β-propeller proteins

Two artificial β-propeller proteins with eight identical blades were designed, purified and crystallized. X-ray crystallography confirmed the perfectly symmetrical structures of these highly stable proteins.

[1]  David T. Jones,et al.  Protein superfamilles and domain superfolds , 1994, Nature.

[2]  K. Hirata,et al.  Crystal Engineering of Self-Assembled Porous Protein Materials in Living Cells. , 2017, ACS nano.

[3]  David Baker,et al.  A general computational approach for repeat protein design. , 2015, Journal of molecular biology.

[4]  C. Pace,et al.  Solvent denaturation of proteins and interpretations of the m value. , 2009, Methods in enzymology.

[5]  A. Broom,et al.  Designed protein reveals structural determinants of extreme kinetic stability , 2015, Proceedings of the National Academy of Sciences.

[6]  Randy J. Read,et al.  Phaser crystallographic software , 2007, Journal of applied crystallography.

[7]  M Wilmanns,et al.  Structural evidence for evolution of the beta/alpha barrel scaffold by gene duplication and fusion. , 2000, Science.

[8]  J. Söding,et al.  More than the sum of their parts: On the evolution of proteins from peptides , 2003, BioEssays : news and reviews in molecular, cellular and developmental biology.

[9]  M. Paoli,et al.  Engineering of beta-propeller protein scaffolds by multiple gene duplication and fusion of an idealized WD repeat. , 2006, Biomolecular engineering.

[10]  David Baker,et al.  Prediction of the structure of symmetrical protein assemblies , 2007, Proceedings of the National Academy of Sciences.

[11]  Thomas Wieland,et al.  Alignment-Annotator web server: rendering and annotating sequence alignments , 2014, Nucleic Acids Res..

[12]  E. Dalcanale,et al.  Cucurbit[7]uril-Dimethyllysine Recognition in a Model Protein. , 2018, Angewandte Chemie.

[13]  David Baker,et al.  Rational design of alpha-helical tandem repeat proteins with closed architectures , 2015, Nature.

[14]  Gert Vriend,et al.  A series of PDB related databases for everyday needs , 2010, Nucleic Acids Res..

[15]  W. Kabsch,et al.  Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features , 1983, Biopolymers.

[16]  Vincent B. Chen,et al.  Correspondence e-mail: , 2000 .

[17]  Nicholas P. Power,et al.  Protein camouflage in cytochrome c–calixarene complexes , 2012, Nature Chemistry.

[18]  Jiahui Chen,et al.  Improvements to the APBS biomolecular solvation software suite , 2017, Protein science : a publication of the Protein Society.

[19]  Kam Y. J. Zhang,et al.  Computational design of a symmetrical β-trefoil lectin with cancer cell binding activity , 2017, Scientific Reports.

[20]  Hiroki Noguchi,et al.  Computational design of a self-assembling symmetrical β-propeller protein , 2014, Proceedings of the National Academy of Sciences.

[21]  P. Emsley,et al.  Features and development of Coot , 2010, Acta crystallographica. Section D, Biological crystallography.

[22]  C. Ponting,et al.  On the evolution of protein folds: are similar motifs in different protein folds the result of convergence, insertion, or relics of an ancient peptide world? , 2001, Journal of structural biology.

[23]  Andreas Plückthun,et al.  Designing repeat proteins: modular leucine-rich repeat protein libraries based on the mammalian ribonuclease inhibitor family. , 2003, Journal of molecular biology.

[24]  Yong Xiong,et al.  Design of stable alpha-helical arrays from an idealized TPR motif. , 2003, Structure.

[25]  Hiroki Noguchi,et al.  Biomineralization of a Cadmium Chloride Nanocrystal by a Designed Symmetrical Protein. , 2015, Angewandte Chemie.

[26]  L. Longo,et al.  Evolution of a protein folding nucleus , 2016, Protein science : a publication of the Protein Society.

[27]  J Wade Harper,et al.  Structure of a Fbw7-Skp1-cyclin E complex: multisite-phosphorylated substrate recognition by SCF ubiquitin ligases. , 2007, Molecular cell.

[28]  Philip R. Evans,et al.  How good are my data and what is the resolution? , 2013, Acta crystallographica. Section D, Biological crystallography.

[29]  Yi Lu,et al.  Time-dependent, protein-directed growth of gold nanoparticles within a single crystal of lysozyme. , 2011, Nature nanotechnology.

[30]  Andrei N. Lupas,et al.  β-Propeller Blades as Ancestral Peptides in Protein Evolution , 2013, PloS one.

[31]  Michael Blaber,et al.  Experimental support for the evolution of symmetric protein architecture from a simple peptide motif , 2010, Proceedings of the National Academy of Sciences.

[32]  Randy J. Read,et al.  Acta Crystallographica Section D Biological , 2003 .

[33]  W. Qi,et al.  Synthesis of silver nanoparticles within cross-linked lysozyme crystals as recyclable catalysts for 4-nitrophenol reduction , 2013 .

[34]  Martin C. Cooper,et al.  Soft arc consistency revisited , 2010, Artif. Intell..

[35]  Orly Dym,et al.  De Novo Evolutionary Emergence of a Symmetrical Protein Is Shaped by Folding Constraints , 2016, Cell.

[36]  Marc S. Lewis,et al.  Modern analytical ultracentrifugation in protein science: A tutorial review , 2002, Protein science : a publication of the Protein Society.

[37]  Andreas Plückthun,et al.  Designed armadillo repeat proteins as general peptide-binding scaffolds: consensus design and computational optimization of the hydrophobic core. , 2008, Journal of molecular biology.

[38]  D. Baker,et al.  De novo design of a four-fold symmetric TIM-barrel protein with atomic-level accuracy , 2015, Nature chemical biology.

[39]  F. Tezcan,et al.  A Metal Organic Framework with Spherical Protein Nodes: Rational Chemical Design of 3D Protein Crystals. , 2015, Journal of the American Chemical Society.

[40]  M. Paoli,et al.  Protein folds propelled by diversity. , 2001, Progress in biophysics and molecular biology.

[41]  I. Yamashita,et al.  Rounding up: Engineering 12-membered rings from the cyclic 11-mer TRAP. , 2006, Structure.

[42]  Peter Schuck,et al.  Size-distribution analysis of proteins by analytical ultracentrifugation: strategies and application to model systems. , 2002, Biophysical journal.

[43]  Barry O'Sullivan,et al.  Multi-language evaluation of exact solvers in graphical model discrete optimization , 2016, Constraints.

[44]  Mike Tyers,et al.  WD40 repeat domain proteins: a novel target class? , 2017, Nature Reviews Drug Discovery.

[45]  Thomas Schiex,et al.  Guaranteed Discrete Energy Optimization on Large Protein Design Problems. , 2015, Journal of chemical theory and computation.

[46]  Birte Höcker,et al.  High-resolution crystal structure of an artificial (betaalpha)(8)-barrel protein designed from identical half-barrels. , 2009, Biochemistry.

[47]  Andreas Plückthun,et al.  Designed ankyrin repeat proteins (DARPins): binding proteins for research, diagnostics, and therapy. , 2015, Annual review of pharmacology and toxicology.

[48]  A. Valencia,et al.  Beta-propellers: associated functions and their role in human diseases. , 2003, Current medicinal chemistry.

[49]  Simon de Givry,et al.  Computational protein design as an optimization problem , 2014, Artif. Intell..

[50]  Dominique Durand,et al.  Design, production and molecular structure of a new family of artificial alpha-helicoidal repeat proteins (αRep) based on thermostable HEAT-like repeats. , 2010, Journal of molecular biology.

[51]  Matthew J. O’Meara,et al.  Combined covalent-electrostatic model of hydrogen bonding improves structure prediction with Rosetta. , 2015, Journal of chemical theory and computation.

[52]  Kam Y. J. Zhang,et al.  Evolution-Inspired Computational Design of Symmetric Proteins. , 2017, Methods in molecular biology.

[53]  M. Landon.  Protein structure: A Practical Approach : Edited by T.E. Creighton; IRL Press; Oxford University Press; Oxford, 1989; xviii + 355 pages; £30.00 , 1990 .