Nanotubes, Plates, and Needles: Pathway-Dependent Self-Assembly of Computationally Designed Peptides.

Computationally designed peptides form desired antiparallel, tetrameric coiled-coil bundles that hierarchically assemble into a variety of well-controlled nanostructures depending on aqueous solution conditions. The bundles selectively self-assemble into different structures: nanotubes, platelets, or needle-like structures at solution pH values of 4.5, 7, and 10, respectively. The self-assembly produces hollow tubes or elongated needle-like structures at pH conditions associated with charged bundles (pH 4.5 or 10); at neutral pH, near the pI of the bundle, a plate-like self-assembled structure forms. Transmission electron microscopy and small-angle X-ray scattering show the nanotubes to be uniform with a tube diameter of ∼13 nm and lengths of up to several μm, yielding aspect ratios >1000. Combining the measured nanostructure geometry with the apparent charged states of the constituent amino acids, a tilted-bundle packing model is proposed for the formation of the homogeneous nanotubes. This work demonstrates the successful use of assembly pathway control for the construction of nanostructures with diverse, well-structured morphologies associated with the folding and self-association of a single type of molecule.

[1]  J. Saven,et al.  Transition from disordered aggregates to ordered lattices: kinetic control of the assembly of a computationally designed peptide. , 2017, Organic & biomolecular chemistry.

[2]  Andrew R Thomson,et al.  A monodisperse transmembrane α-helical peptide barrel. , 2017, Nature chemistry.

[3]  Xiang Ma,et al.  Tuning crystallization pathways through sequence engineering of biomimetic polymers. , 2017, Nature materials.

[4]  Nadrian C. Seeman,et al.  A device that operates within a self-assembled 3D DNA crystal. , 2017, Nature chemistry.

[5]  J. D. De Yoreo,et al.  Self‐Repair and Patterning of 2D Membrane‐Like Peptoid Materials , 2016 .

[6]  Martin Rother,et al.  Protein cages and synthetic polymers: a fruitful symbiosis for drug delivery applications, bionanotechnology and materials science. , 2016, Chemical Society reviews.

[7]  N. Sommerdijk,et al.  Studying Polymer Self-Assembly by Combined Cryogenic and Liquid Phase Transmission Electron Microscopy , 2016, Microscopy and Microanalysis.

[8]  Peijun Zhang,et al.  Peptide-Directed Assembly of Single-Helical Gold Nanoparticle Superstructures Exhibiting Intense Chiroptical Activity. , 2016, Journal of the American Chemical Society.

[9]  Hao Yan,et al.  3D Framework DNA Origami with Layered Crossovers. , 2016, Angewandte Chemie.

[10]  Jeffery G. Saven,et al.  Computationally designed peptides for self-assembly of nanostructured lattices , 2016, Science Advances.

[11]  David Baker,et al.  Accurate design of megadalton-scale two-component icosahedral protein complexes , 2016, Science.

[12]  Jing Sun,et al.  Extremely Stable Supramolecular Hydrogels Assembled from Nonionic Peptide Amphiphiles. , 2016, Langmuir : the ACS journal of surfaces and colloids.

[13]  G. Skiniotis,et al.  Flexible, symmetry-directed approach to assembling protein cages , 2016, Proceedings of the National Academy of Sciences.

[14]  Stephen Z. D. Cheng,et al.  Rational controlled morphological transitions in the self-assembled multi-headed giant surfactants in solution. , 2016, Chemical communications.

[15]  Quan Luo,et al.  Protein self-assembly via supramolecular strategies. , 2016, Chemical Society Reviews.

[16]  David Baker,et al.  Design of a hyperstable 60-subunit protein icosahedron , 2016, Nature.

[17]  S. Webb,et al.  Uniform patchy and hollow rectangular platelet micelles from crystallizable polymer blends , 2016, Science.

[18]  W. Chiu,et al.  Designer nanoscale DNA assemblies programmed from the top down , 2016, Science.

[19]  D. Danino,et al.  From Discs to Ribbons Networks: The Second Critical Micelle Concentration in Nonionic Sterol Solutions. , 2016, The journal of physical chemistry letters.

[20]  K. Downing,et al.  Self-assembly of crystalline nanotubes from monodisperse amphiphilic diblock copolypeptoid tiles , 2016, Proceedings of the National Academy of Sciences.

[21]  R. Zuckermann,et al.  Improved chemical and mechanical stability of peptoid nanosheets by photo-crosslinking the hydrophobic core. , 2016, Chemical communications.

[22]  P. Zavattieri,et al.  Self-Assembly of Coherently Dynamic, Auxetic Two-Dimensional Protein Crystals , 2016, Nature.

[23]  William M. Jacobs,et al.  Self-Assembly of Structures with Addressable Complexity. , 2016, Journal of the American Chemical Society.

[24]  G. Schatz,et al.  Simultaneous covalent and noncovalent hybrid polymerizations , 2016, Science.

[25]  R. Nolte,et al.  Natural supramolecular protein assemblies. , 2016, Chemical Society reviews.

[26]  D. Woolfson,et al.  Controlling the Assembly of Coiled–Coil Peptide Nanotubes , 2015, Angewandte Chemie.

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

[28]  Ranjan V. Mannige,et al.  Peptoid nanosheets exhibit a new secondary-structure motif , 2015, Nature.

[29]  R. Zuckermann,et al.  Sequence Programmable Peptoid Polymers for Diverse Materials Applications , 2015, Advanced materials.

[30]  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.

[31]  H. Sugiyama,et al.  Lipid-bilayer-assisted two-dimensional self-assembly of DNA origami nanostructures , 2015, Nature Communications.

[32]  Jiahua Zhu,et al.  Multigeometry Nanoparticles: Hybrid Vesicle/Cylinder Nanoparticles Constructed with Block Copolymer Solution Assembly and Kinetic Control , 2015 .

[33]  L. Serpell,et al.  Modular Design of Self-Assembling Peptide-Based Nanotubes. , 2015, Journal of the American Chemical Society.

[34]  D. Baker,et al.  Design of ordered two-dimensional arrays mediated by noncovalent protein-protein interfaces , 2015, Science.

[35]  D. Woolfson,et al.  Functionalized α-Helical Peptide Hydrogels for Neural Tissue Engineering , 2015, ACS biomaterials science & engineering.

[36]  Chih-Hao Hsu,et al.  Selective assemblies of giant tetrahedra via precisely controlled positional interactions , 2015, Science.

[37]  H. Dietz,et al.  Dynamic DNA devices and assemblies formed by shape-complementary, non–base pairing 3D components , 2015, Science.

[38]  Mitchell A. Winnik,et al.  Multidimensional hierarchical self-assembly of amphiphilic cylindrical block comicelles , 2015, Science.

[39]  D Baker,et al.  Structural plasticity of helical nanotubes based on coiled-coil assemblies. , 2015, Structure.

[40]  Chris Leighton,et al.  Sphericity and symmetry breaking in the formation of Frank–Kasper phases from one component materials , 2014, Proceedings of the National Academy of Sciences.

[41]  Richard B. Sessions,et al.  Computational design of water-soluble α-helical barrels , 2014, Science.

[42]  Ian Manners,et al.  Tailored hierarchical micelle architectures using living crystallization-driven self-assembly in two dimensions. , 2014, Nature chemistry.

[43]  R. Zuckermann,et al.  Assembly and molecular order of two-dimensional peptoid nanosheets through the oil–water interface , 2014, Proceedings of the National Academy of Sciences.

[44]  Honggang Cui,et al.  Amino Acid Sequence in Constitutionally Isomeric Tetrapeptide Amphiphiles Dictates Architecture of One-Dimensional Nanostructures , 2014, Journal of the American Chemical Society.

[45]  David Baker,et al.  Accurate design of co-assembling multi-component protein nanomaterials , 2014, Nature.

[46]  Jonathan E. Seppala,et al.  Size evolution of highly amphiphilic macromolecular solution assemblies via a distinct bimodal pathway , 2014, Nature Communications.

[47]  Maarten J. M. Wirix,et al.  Three-dimensional structure of P3HT assemblies in organic solvents revealed by cryo-TEM. , 2014, Nano letters.

[48]  J. Brodin,et al.  Exceptionally stable, redox-active supramolecular protein assemblies with emergent properties , 2014, Proceedings of the National Academy of Sciences.

[49]  Chunfu Xu,et al.  Rational design of helical nanotubes from self-assembly of coiled-coil lock washers. , 2013, Journal of the American Chemical Society.

[50]  R. L. Penn,et al.  Cryogenic Transmission Electron Microscopy: Aqueous Suspensions of Nanoscale Objects , 2013, Microscopy and Microanalysis.

[51]  Stephen Z. D. Cheng,et al.  Giant surfactants provide a versatile platform for sub-10-nm nanostructure engineering , 2013, Proceedings of the National Academy of Sciences.

[52]  N. Linden,et al.  Self-Assembling Cages from Coiled-Coil Peptide Modules , 2013, Science.

[53]  Jiahua Zhu,et al.  Hierarchical Assembly of Complex Block Copolymer Nanoparticles into Multicompartment Superstructures through Tunable Interparticle Associations , 2013 .

[54]  Brian H. Toby,et al.  GSAS‐II: the genesis of a modern open‐source all purpose crystallography software package , 2013 .

[55]  I. Hamley,et al.  Self-assembled arginine-coated peptide nanosheets in water. , 2013, Chemical communications.

[56]  Kyle L. Morris,et al.  The Structure of Cross‐β Tapes and Tubes Formed by an Octapeptide, αSβ1† , 2013, Angewandte Chemie.

[57]  T. Yeates,et al.  Principles for designing ordered protein assemblies. , 2012, Trends in cell biology.

[58]  Duilio Cascio,et al.  Structure of a 16-nm Cage Designed by Using Protein Oligomers , 2012, Science.

[59]  D. Baker,et al.  Computational Design of Self-Assembling Protein Nanomaterials with Atomic Level Accuracy , 2012, Science.

[60]  Christopher M. MacDermaid,et al.  Computational design of a protein crystal , 2012, Proceedings of the National Academy of Sciences.

[61]  A. Boyle,et al.  Rational Design of Peptide-Based Biosupramolecular Systems , 2012 .

[62]  Todd O Yeates,et al.  Nanobiotechnology: protein arrays made to order. , 2011, Nature nanotechnology.

[63]  A. Heeger,et al.  A Porphyrin–Fullerene Dyad with a Supramolecular “Double‐Cable” Structure as a Novel Electron Acceptor for Bulk Heterojunction Polymer Solar Cells , 2011, Advanced materials.

[64]  Floris P. J. T. Rutjes,et al.  Polymeric vesicles in biomedical applications , 2011 .

[65]  R. Mezzenga,et al.  Direct observation of time-resolved polymorphic states in the self-assembly of end-capped heptapeptides. , 2011, Angewandte Chemie.

[66]  A. Gulino,et al.  Pathway-dependent self-assembly of perylene diimide/peptide conjugates in aqueous medium. , 2011, Chemistry.

[67]  I. Manners,et al.  Pointed-oval-shaped micelles from crystalline-coil block copolymers by crystallization-driven living self-assembly. , 2010, Angewandte Chemie.

[68]  Heiner Friedrich,et al.  Imaging of self-assembled structures: interpretation of TEM and cryo-TEM images. , 2010, Angewandte Chemie.

[69]  D. Pochan,et al.  Cryogenic Transmission Electron Microscopy for Direct Observation of Polymer and Small-Molecule Materials and Structures in Solution , 2010 .

[70]  S. Stupp,et al.  Direct observation of morphological transformation from twisted ribbons into helical ribbons. , 2010, Journal of the American Chemical Society.

[71]  R. Levine,et al.  DNA computing circuits using libraries of DNAzyme subunits. , 2010, Nature nanotechnology.

[72]  R. Tycko,et al.  Measurement of amyloid fibril mass-per-length by tilted-beam transmission electron microscopy , 2009, Proceedings of the National Academy of Sciences.

[73]  H. Börner,et al.  Biotransformation on polymer-peptide conjugates: a versatile tool to trigger microstructure formation. , 2009, Angewandte Chemie.

[74]  Pamela E. Constantinou,et al.  From Molecular to Macroscopic via the Rational Design of a Self-Assembled 3D DNA Crystal , 2009, Nature.

[75]  D. Woolfson,et al.  A periodic table of coiled-coil protein structures. , 2009, Journal of molecular biology.

[76]  G. Fields,et al.  Solid phase peptide synthesis utilizing 9-fluorenylmethoxycarbonyl amino acids. , 2009, International journal of peptide and protein research.

[77]  Qiang He,et al.  Reversible transitions between peptide nanotubes and vesicle-like structures including theoretical modeling studies. , 2008, Chemistry.

[78]  V. Conticello,et al.  Design of a selective metal ion switch for self-assembly of peptide-based fibrils. , 2008, Journal of the American Chemical Society.

[79]  K. Nagayama,et al.  Growth process and molecular packing of a self-assembled lipid nanotube: phase-contrast transmission electron microscopy and XRD analyses. , 2008, Langmuir : the ACS journal of surfaces and colloids.

[80]  D. Pochan,et al.  Helix self-assembly through the coiling of cylindrical micelles. , 2007, Soft matter.

[81]  Sheng Zhong,et al.  Block Copolymer Assembly via Kinetic Control , 2007, Science.

[82]  Michael L Klein,et al.  Emerging Applications of Polymersomes in Delivery: from Molecular Dynamics to Shrinkage of Tumors. , 2007, Progress in polymer science.

[83]  Honggang Cui,et al.  Elucidating the assembled structure of amphiphiles in solution via cryogenic transmission electron microscopy. , 2007, Soft matter.

[84]  G. Seelig,et al.  Enzyme-Free Nucleic Acid Logic Circuits , 2022 .

[85]  Steven R. Kline,et al.  Reduction and analysis of SANS and USANS data using IGOR Pro , 2006 .

[86]  E. W. Meijer,et al.  Probing the Solvent-Assisted Nucleation Pathway in Chemical Self-Assembly , 2006, Science.

[87]  F. Würthner,et al.  Supramolecular stereomutation in kinetic and thermodynamic self-assembly of helical merocyanine dye nanorods. , 2005, Angewandte Chemie.

[88]  E. W. Meijer,et al.  About Supramolecular Assemblies of π-Conjugated Systems , 2005 .

[89]  D. Pochan,et al.  Toroidal Triblock Copolymer Assemblies , 2004, Science.

[90]  Shuguang Zhang,et al.  Molecular self-assembly of surfactant-like peptides to form nanotubes and nanovesicles , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[91]  H. Klok,et al.  Advanced drug delivery devices via self-assembly of amphiphilic block copolymers. , 2001, Advanced drug delivery reviews.

[92]  A. N. Semenov,et al.  Hierarchical self-assembly of chiral rod-like molecules as a model for peptide β-sheet tapes, ribbons, fibrils, and fibers , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[93]  Sébastien Lecommandoux,et al.  Supramolecular Materials via Block Copolymer Self-Assembly , 2001 .

[94]  Jennifer E. Padilla,et al.  Nanohedra: Using symmetry to design self assembling protein cages, layers, crystals, and filaments , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[95]  D. Raleigh,et al.  De novo design of helical bundles as models for understanding protein folding and function. , 2000, Accounts of chemical research.

[96]  D N Woolfson,et al.  Sticky-end assembly of a designed peptide fiber provides insight into protein fibrillogenesis. , 2000, Biochemistry.

[97]  R. Hodges,et al.  Effect of chain length on the formation and stability of synthetic alpha-helical coiled coils. , 1994, Biochemistry.

[98]  I. Chaiken,et al.  Controlled formation of model homo- and heterodimer coiled coil polypeptides. , 1993, Biochemistry.

[99]  L. Scriven,et al.  Direct imaging of surfactant micelles, vesicles, discs, and ripple phase structures by cryo-transmission electron microscopy , 1991 .

[100]  Francis Crick,et al.  The Fourier transform of a coiled-coil , 1953 .

[101]  Ludovico Cademartiri,et al.  Programmable self-assembly. , 2015, Nature materials.

[102]  I. Hamley Peptide nanotubes. , 2014, Angewandte Chemie.

[103]  K. Polizzi What is synthetic biology? , 2013, Methods in molecular biology.

[104]  Andrei N. Lupas,et al.  The structure of α-helical coiled coils , 2005 .

[105]  Qingmin Ji,et al.  Direct Sol−Gel Replication without Catalyst in an Aqueous Gel System: From a Lipid Nanotube with a Single Bilayer Wall to a Uniform Silica Hollow Cylinder with an Ultrathin Wall , 2004 .

[106]  E. Shapiro,et al.  Programmable and autonomous computing machine made of biomolecules , 2001, Nature.

[107]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[108]  R. Woody,et al.  The effect of conformation on the CD of interacting helices: A theoretical study of tropomyosin , 1990, Biopolymers.

[109]  J F Hainfeld,et al.  Mass mapping with the scanning transmission electron microscope. , 1986, Annual review of biophysics and biophysical chemistry.