Skip to main content
SpringerLink
Log in

A Protocol for the Design of Protein and Peptide Nanostructure Self-Assemblies Exploiting Synthetic Amino Acids

  • Protocol
  • First Online:
Computational Protein Design

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1529))

Abstract

In recent years there has been increasing interest in nanostructure design based on the self-assembly properties of proteins and polymers. Nanodesign requires the ability to predictably manipulate the properties of the self-assembly of autonomous building blocks, which can fold or aggregate into preferred conformational states. The design includes functional synthetic materials and biological macromolecules. Autonomous biological building blocks with available 3D structures provide an extremely rich and useful resource. Structural databases contain large libraries of protein molecules and their building blocks with a range of sizes, shapes, surfaces, and chemical properties. The introduction of engineered synthetic residues or short peptides into these building blocks can greatly expand the available chemical space and enhance the desired properties. Herein, we summarize a protocol for designing nanostructures consisting of self-assembling building blocks, based on our recent works. We focus on the principles of nanostructure design with naturally occurring proteins and synthetic amino acids, as well as hybrid materials made of amyloids and synthetic polymers.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 99.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 129.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 179.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Ferrari M (2005) Cancer nanotechnology: opportunities and challenges. Nat Rev Cancer 5(3):161–171

    Article  CAS  PubMed  Google Scholar 

  2. Ferrari M (2005) Nanovector therapeutics. Curr Opin Chem Biol 9(4):343–346

    Article  CAS  PubMed  Google Scholar 

  3. Blanco E et al (2011) Nanomedicine in cancer therapy: innovative trends and prospects. Cancer Sci 102(7):1247–1252

    Article  CAS  PubMed  Google Scholar 

  4. Gradišar H, Jerala R (2014) Self-assembled bionanostructures: proteins following the lead of DNA nanostructures. J Nanobiotechnol 12:4

    Article  CAS  Google Scholar 

  5. Rubin DJ et al (2015) Structural, nanomechanical, and computational characterization of d,l-cyclic peptide assemblies. ACS Nano 9(3):3360–3368

    Article  CAS  PubMed  Google Scholar 

  6. Balzani V, Credi A, Venturi M (2009) Light powered molecular machines. Chem Soc Rev 38(6):1542–1550

    Article  CAS  PubMed  Google Scholar 

  7. King NP et al (2012) Computational design of self-assembling protein nanomaterials with atomic level accuracy. Science 336(6085):1171–1174

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Zhang Z-J et al (2013) A double-leg donor–acceptor molecular elevator: new insight into controlling the distance of two platforms. Org Lett 15(7):1698–1701

    Article  CAS  PubMed  Google Scholar 

  9. Pei H et al (2014) Functional DNA nanostructures for theranostic applications. Acc Chem Res 47(2):550–559

    Article  CAS  PubMed  Google Scholar 

  10. Rangnekar A, LaBean TH (2014) Building DNA nanostructures for molecular computation, templated assembly, and biological applications. Acc Chem Res 47(6):1778–1788

    Article  CAS  PubMed  Google Scholar 

  11. Bindewald E et al (2008) RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign. Nucleic Acids Res 36(database issue):D392–D397

    CAS  PubMed  Google Scholar 

  12. Mathur D, Henderson ER (2013) Complex DNA nanostructures from oligonucleotide ensembles. ACS Synth Biol 2(4):180–185

    Article  CAS  PubMed  Google Scholar 

  13. Li H, LaBean TH, Leong KW (2011) Nucleic acid-based nanoengineering: novel structures for biomedical applications. Interface Focus 1(5):702–724

    Article  PubMed  PubMed Central  Google Scholar 

  14. Grabow WW et al (2011) Self-assembling RNA nanorings based on RNAI/II inverse kissing complexes. Nano Lett 11(2):878–887

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Miller BG, Raines RT (2005) Reconstitution of a defunct glycolytic pathway via recruitment of ambiguous sugar kinases†. Biochemistry 44(32):10776–10783

    Article  CAS  PubMed  Google Scholar 

  16. Bang D, Kent SBH (2005) His(6) tag-assisted chemical protein synthesis. Proc Natl Acad Sci U S A 102(14):5014–5019

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Miller Y, Ma B, Nussinov R (2015) Polymorphism in self-assembly of peptide-based β-hairpin contributes to network morphology and hydrogel mechanical rigidity. J Phys Chem B 119(2):482–490

    Article  CAS  PubMed  Google Scholar 

  18. Tsai H-H et al (2004) In silico protein design by combinatorial assembly of protein building blocks. Protein Sci 13(10):2753–2765

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Main ERG et al (2005) A recurring theme in protein engineering: the design, stability and folding of repeat proteins. Curr Opin Struct Biol 15(4):464–471

    Article  CAS  PubMed  Google Scholar 

  20. Jenkins J, Mayans O, Pickersgill R (1998) Structure and evolution of parallel [beta]-helix proteins. J Struct Biol 122(1–2):236–246

    Article  CAS  PubMed  Google Scholar 

  21. Haspel N et al (2006) De novo tubular nanostructure design based on self-assembly of [beta]-helical protein motifs. Structure 14(7):1137–1148

    Article  CAS  PubMed  Google Scholar 

  22. Bernstein FC, The protein data bank et al (1977) Eur J Biochem 80(2):319–324

    Article  CAS  PubMed  Google Scholar 

  23. Haspel N et al (2007) Changing the charge distribution of {beta}-helical-based nanostructures can provide the conditions for charge transfer. Biophys J 93(1):245–253

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Schmitz K (2010) Amino acids, peptides and proteins in organic chemistry. Volume 1–Origins and synthesis of amino acids. Edited by Andrew B. Hughes. Angew Chem Int Ed 49(22):3717–3718

    Article  CAS  Google Scholar 

  25. Vadim AS, Kunisuke I (2009) Asymmetric synthesis and application of α-amino acids. In: ACS symposium series, vol 1009. American Chemical Society, p. 512.

    Google Scholar 

  26. Christophorou MA et al (2014) Citrullination regulates pluripotency and histone H1 binding to chromatin. Nature 507(7490):104–108

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Cativiela C, Ordonez M (2009) Recent progress on the stereoselective synthesis of cyclic quaternary alpha-amino acids. Tetrahedron Asymmetry 20(1):1–63

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Michaux J, Niel G, Campagne JM (2009) Stereocontrolled routes to beta, beta′-disubstituted alpha-amino acids. Chem Soc Rev 38(7):2093–2116

    Article  CAS  PubMed  Google Scholar 

  29. Degenkolb T, Bruckner H (2008) Peptaibiomics: towards a myriad of bioactive peptides containing C(alpha)-dialkylamino acids? Chem Biodivers 5(9):1817–1843

    Article  CAS  PubMed  Google Scholar 

  30. Schwarzer D, Finking R, Marahiel MA (2003) Nonribosomal peptides: from genes to products. Nat Prod Rep 20(3):275–287

    Article  CAS  PubMed  Google Scholar 

  31. Nestor JJ Jr (2009) The medicinal chemistry of peptides. Curr Med Chem 16(33):4399–4418

    Article  CAS  PubMed  Google Scholar 

  32. Horne WS, Gellman SH (2008) Foldamers with heterogeneous backbones. Acc Chem Res 41(10):1399–1408

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Ersmark K, Del Valle JR, Hanessian S (2008) Chemistry and biology of the aeruginosin family of serine protease inhibitors. Angew Chem Int Ed Engl 47(7):1202–1223

    Article  CAS  PubMed  Google Scholar 

  34. Voloshchuk N, Montclare JK (2010) Incorporation of unnatural amino acids for synthetic biology. Mol Biosyst 6(1):65–80

    Article  CAS  PubMed  Google Scholar 

  35. Wu X, Schultz PG (2009) Synthesis at the interface of chemistry and biology. J Am Chem Soc 131(35):12497–12515

    Article  CAS  PubMed  Google Scholar 

  36. Murakami H et al (2000) Site-directed incorporation of fluorescent nonnatural amino acids into streptavidin for highly sensitive detection of biotin. Biomacromolecules 1(1):118–125

    Article  CAS  PubMed  Google Scholar 

  37. Vazquez ME et al (2003) Fluorescent caged phosphoserine peptides as probes to investigate phosphorylation-dependent protein associations. J Am Chem Soc 125(34):10150–10151

    Article  CAS  PubMed  Google Scholar 

  38. Alfonta L et al (2003) Site-specific incorporation of a redox-active amino acid into proteins. J Am Chem Soc 125(48):14662–14663

    Article  CAS  PubMed  Google Scholar 

  39. Lemke EA et al (2007) Control of protein phosphorylation with a genetically encoded photocaged amino acid. Nat Chem Biol 3(12):769–772

    Article  CAS  PubMed  Google Scholar 

  40. Wang W et al (2007) Genetically encoding unnatural amino acids for cellular and neuronal studies. Nat Neurosci 10(8):1063–1072

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Cellitti SE et al (2008) In vivo incorporation of unnatural amino acids to probe structure, dynamics, and ligand binding in a large protein by nuclear magnetic resonance spectroscopy. J Am Chem Soc 130(29):9268–9281

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Summerer D et al (2006) A genetically encoded fluorescent amino acid. Proc Natl Acad Sci U S A 103(26):9785–9789

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Lee HS et al (2009) Genetic incorporation of a small, environmentally sensitive, fluorescent probe into proteins in Saccharomyces cerevisiae. J Am Chem Soc 131(36):12921–12923

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Zanuy D et al (2007) Use of constrained synthetic amino acids in beta-helix proteins for conformational control. J Phys Chem B 111(12):3236–3242

    Article  CAS  PubMed  Google Scholar 

  45. Zanuy D et al (2009) Protein segments with conformationally restricted amino acids can control supramolecular organization at the nanoscale. J Chem Inf Model 49(7):1623–1629

    Article  CAS  PubMed  Google Scholar 

  46. Tu RS, Tirrell M (2004) Bottom-up design of biomimetic assemblies. Adv Drug Deliv Rev 56(11):1537–1563

    Article  CAS  PubMed  Google Scholar 

  47. Lee MR et al (2009) Nylon-3 copolymers that generate cell-adhesive surfaces identified by library screening. J Am Chem Soc 131(46):16779–16789

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Revilla-Lopez G et al (2010) NCAD, a database integrating the intrinsic conformational preferences of non-coded amino acids. J Phys Chem B 114(21):7413–7422

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Aleman C (1997) Conformational properties of [alpha]-amino acids disubstituted at the [alpha]-carbon. J Phys Chem B 101(25):5046–5050

    Article  CAS  Google Scholar 

  50. Alemán C, Casanovas J, Galembeck SE (1998) PAPQMD parametrization of molecular systems with cyclopropyl rings: conformational study of homopeptides constituted by l-aminocyclopropane-l-carboxylic acid. J Computer-Aided Molecular Design 12(3):259–273

    Article  PubMed  Google Scholar 

  51. Gomez-Catalan J, Aleman C, Perez JJ (2000) Conformational profile of 1-aminocyclopropanecarboxylic acid. Theor Chem Acc 103(5):380–389

    Article  CAS  Google Scholar 

  52. Benedetti E et al (1989) Structural versatility of peptides containing C-alpha, alpha-dialkylated glycines. An X-ray diffraction study of 6 1-aminocyclopropane-1-carboxylic acid rich peptides. Int J Biol Macromol 11(6):353–360

    Article  CAS  PubMed  Google Scholar 

  53. Benedetti E et al (1989) Structural versatility of peptides from C[alpha, alpha] dialkylated glycines: linear Ac3c homo-oligopeptides. Biopolymers 28(1):175–184

    Article  CAS  Google Scholar 

  54. Fabiano N et al (1993) Conformational versatility of the N-alpha-acylated tripeptide amide tail of oxytocin - synthesis and crystallographic characterization of 3C-2-alpha-backbone modified, conformationally restricted analogs. Int J Pept Protein Res 42(5):459–465

    Article  CAS  PubMed  Google Scholar 

  55. Valle G et al (1989) Linear oligopeptides. 200. crystallographic characterization of conformation of 1-aminocyclopropane-1-carboxylic acid residue (Ac3c) in simple derivatives and peptides. Int J Pept Protein Res 34(1):56–65

    Article  CAS  PubMed  Google Scholar 

  56. Aleman C et al (2002) Influence of the phenyl side chain on the conformation of cyclopropane analogues of phenylalanine. J Phys Chem B 106(45):11849–11858

    Article  CAS  Google Scholar 

  57. Toniolo C et al (2001) Control of peptide conformation by the Thorpe-Ingold effect (C-alpha-tetrasubstitution). Biopolymers 60(6):396–419

    Article  CAS  PubMed  Google Scholar 

  58. Hruby VJ et al (1997) Design of peptides, proteins, and peptidomimetics in chi space. Biopolymers 43(3):219–266

    Article  CAS  PubMed  Google Scholar 

  59. Jimenez AI, Cativiela C, Marraud M (2000) A gamma-turn induced by a highly constrained cyclopropane analogue of phenylalanine (c(3)diPhe) in the solid state. Tetrahedron Lett 41(28):5353–5356

    Article  CAS  Google Scholar 

  60. Jimenez AI et al (1998) Beta-turn preferences induced by 2,3-methanophenylalanine chirality. J Am Chem Soc 120(37):9452–9459

    Article  CAS  Google Scholar 

  61. Jimenez AI et al (1997) Folding types of dipeptides containing the diastereoisomeric cyclopropanic analogues of phenylalanine. Tetrahedron Lett 38(43):7559–7562

    Article  CAS  Google Scholar 

  62. Casanovas J et al (2003) N-Acetyl-N′-methylamide derivative of (2S,3S)-1-amino-2,3-diphenylcyclopropanecarboxylic acid: theoretical analysis of the conformational impact produced by the incorporation of the second phenyl group to the cyclopropane analogue of phenylalanine. J Org Chem 68(18):7088–7091

    Article  CAS  PubMed  Google Scholar 

  63. Jiménez AI, Ballano G, Cativiela C (2005) First observation of two consecutive gamma turns in a crystalline linear dipeptide. Angew Chem Int Ed 44(3):396–399

    Article  CAS  Google Scholar 

  64. Casanovas J et al (2006) Conformational analysis of a cyclopropane analogue of phenylalanine with two geminal phenyl substituents. J Phys Chem B 110(11):5762–5766

    Article  CAS  PubMed  Google Scholar 

  65. Crisma M et al (2006) Preferred 3D-structure of peptides rich in a severely conformationally restricted cyclopropane analogue of phenylalanine. Chemistry 12(1):251–260

    Article  CAS  Google Scholar 

  66. Royo S et al (2005) Turn and helical peptide handedness governed exclusively by side-chain chiral centers. J Am Chem Soc 127(7):2036–2037

    Article  CAS  PubMed  Google Scholar 

  67. Kale L et al (1999) NAMD2: greater scalability for parallel molecular dynamics. J Comput Phys 151(1):283–312

    Article  CAS  Google Scholar 

  68. MacKerell AD et al (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 102(18):3586–3616

    Article  CAS  PubMed  Google Scholar 

  69. William LJ et al (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79(2):926–935

    Article  Google Scholar 

  70. Darden T et al (1999) New tricks for modelers from the crystallography toolkit: the particle mesh Ewald algorithm and its use in nucleic acid simulations. Structure 7(3):R55–R60

    Article  CAS  PubMed  Google Scholar 

  71. Haspel N et al (2004) A comparative study of amyloid fibril formation by residues 15–19 of the human calcitonin hormone: a single beta-sheet model with a small hydrophobic core. J Mol Biol 345(5):1213–1227

    Article  PubMed  CAS  Google Scholar 

  72. Ma B, Nussinov R (2002) Stabilities and conformations of Alzheimer’s beta-amyloid peptide oligomers (Abeta 16–22, Abeta 16–35, and Abeta 10–35): sequence effects. Proc Natl Acad Sci U S A 99(22):14126–14131

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Ma B, Nussinov R (2002) Molecular dynamics simulations of alanine rich {beta}-sheet oligomers: insight into amyloid formation. Protein Sci 11(10):2335–2350

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Ma B, Nussinov R (2003) Molecular dynamics simulations of the unfolding of {beta}2-microglobulin and its variants. Protein Eng 16(8):561–575

    Article  CAS  PubMed  Google Scholar 

  75. Zanuy D, Ma B, Nussinov R (2003) Short peptide amyloid organization: stabilities and conformations of the islet amyloid peptide NFGAIL. Biophys J 84(3):1884–1894

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  76. Zanuy D, Nussinov R (2003) The sequence dependence of fiber organization. A comparative molecular dynamics study of the islet amyloid polypeptide segments 22–27 and 22–29. J Mol Biol 329(3):565–584

    Article  CAS  PubMed  Google Scholar 

  77. Luhrs T et al (2005) 3D structure of Alzheimer’s amyloid-{beta}(1–42) fibrils. Proc Natl Acad Sci U S A 102(48):17342–17347

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Petkova AT et al (2002) A structural model for Alzheimer’s beta-amyloid fibrils based on experimental constraints from solid state NMR. Proc Natl Acad Sci U S A 99(26):16742–16747

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  79. Reches M, Porat Y, Gazit E (2002) Amyloid fibril formation by pentapeptide and tetrapeptide fragments of human calcitonin. J Biol Chem 277(38):35475–35480

    Article  CAS  PubMed  Google Scholar 

  80. Zanuy D et al (2004) Peptide sequence and amyloid formation: molecular simulations and experimental study of a human islet amyloid polypeptide fragment and its analogs. Structure 12(3):439–455

    Article  CAS  PubMed  Google Scholar 

  81. Thompson JD, Gibson TJ, Higgins DG (2002) Multiple sequence alignment using ClustalW and ClustalX. Curr Protoc Bioinformatics Chapter 2:Unit 2.3.

    Google Scholar 

  82. Zhang S (2003) Fabrication of novel biomaterials through molecular self-assembly. Nat Biotechnol 21(10):1171–1178

    Article  CAS  PubMed  Google Scholar 

  83. Liu TY et al (2013) Self-adjuvanting polymer-peptide conjugates as therapeutic vaccine candidates against cervical cancer. Biomacromolecules 14(8):2798–2806

    Article  CAS  PubMed  Google Scholar 

  84. Maji SK et al (2009) Functional amyloids as natural storage of peptide hormones in pituitary secretory granules. Science 325(5938):328–332

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  85. Vandermeulen GWM, Klok H-A (2004) Peptide/protein hybrid materials: enhanced control of structure and improved performance through conjugation of biological and synthetic polymers. Macromol Biosci 4(4):383–398

    Article  CAS  PubMed  Google Scholar 

  86. Haspel N et al (2012) Conformational exploration of two peptides and their hybrid polymer conjugates: potentialities as self-aggregating materials. J Phys Chem B 116(48):13941–13952

    Article  CAS  PubMed  Google Scholar 

  87. Murase SK et al (2014) Molecular characterization of l-phenylalanine terminated poly(l-lactide) conjugates. RSC Adv 4(44):23231–23241

    Article  CAS  Google Scholar 

  88. Fan Y et al (2005) l-Phe end-capped poly(l-lactide) as macroinitiator for the synthesis of poly(l-lactide)-b-poly(l-lysine) block copolymer. Biomacromolecules 6(6):3051–3056

    Article  CAS  PubMed  Google Scholar 

  89. Castelletto V, Hamley IW (2009) Self assembly of a model amphiphilic phenylalanine peptide/polyethylene glycol block copolymer in aqueous solution. Biophys Chem 141(2–3):169–174

    Article  CAS  PubMed  Google Scholar 

  90. Zanuy D, Hamley IW, Aleman C (2011) Modeling the tetraphenylalanine-PEG hybrid amphiphile: from DFT calculations on the peptide to molecular dynamics simulations on the conjugate. J Phys Chem B 115(28):8937–8946

    Article  CAS  PubMed  Google Scholar 

  91. Fabregat G et al (2013) An electroactive and biologically responsive hybrid conjugate based on chemical similarity. Polym Chem 4(5):1412–1424

    Article  CAS  Google Scholar 

  92. Fabregat G et al (2013) Design of hybrid conjugates based on chemical similarity. RSC Adv 3(43):21069–21083

    Article  CAS  Google Scholar 

  93. Groenendaal L et al (2003) Electrochemistry of poly(3,4-alkylenedioxythiophene) derivatives. Adv Mater 15(11):855–879

    Article  CAS  Google Scholar 

  94. Kirchmeyer S, Reuter K (2005) Scientific importance, properties and growing applications of poly(3,4-ethylenedioxythiophene). J Mater Chem 15(21):2077–2088

    Article  CAS  Google Scholar 

  95. Maione S et al (2014) Electro-biocompatibility of conjugates designed by chemical similarity. J Pept Sci 20(7):537–546

    Article  CAS  PubMed  Google Scholar 

  96. Maione S, Gil A, Fabregat G, Del Valle LJ, Triguero J, Laurent A, Jacquemin D, Estrany F, Zanuy D, Cativiela C, Alemán C (2015) Electroactive polymer-peptide conjugates for adhesive biointerfaces. Biomater. Sci. (3):1395–1405.

    Google Scholar 

  97. Gosal WS et al (2005) Competing pathways determine fibril morphology in the self-assembly of [beta]2-microglobulin into amyloid. J Mol Biol 351(4):850–864

    Article  CAS  PubMed  Google Scholar 

  98. Lashuel HA et al (2002) Amyloid pores from pathogenic mutations. Nature 418(6895):291

    Article  CAS  PubMed  Google Scholar 

  99. Lashuel HA et al (2002) Alpha-synuclein, especially the parkinson’s disease-associated mutants, forms pore-like annular and tubular Protofibrils. J Mol Biol 322(5):1089–1102

    Article  CAS  PubMed  Google Scholar 

  100. Dauer W, Przedborski S (2003) Parkinson’s disease: mechanisms and models. Neuron 39(6):889–909

    Article  CAS  PubMed  Google Scholar 

  101. Dobson CM (2005) Structural biology: prying into prions. Nature 435(7043):747–749

    Article  CAS  PubMed  Google Scholar 

  102. Meredith SC (2006) Protein denaturation and aggregation: cellular responses to denatured and aggregated proteins. Ann N Y Acad Sci 1066(1):181–221

    Article  CAS  Google Scholar 

  103. Selkoe DJ (2001) Alzheimer’s disease: genes, proteins, and therapy. Physiol Rev 81(2):741–766

    CAS  PubMed  Google Scholar 

  104. Tycko R (2004) Progress towards a molecular-level structural understanding of amyloid fibrils. Curr Opin Struct Biol 14(1):96–103

    Article  CAS  PubMed  Google Scholar 

  105. Si K et al (2010) Aplysia CPEB can form prion-like multimers in sensory neurons that contribute to long-term facilitation. Cell 140(3):421–435

    Article  CAS  PubMed  Google Scholar 

  106. Kagan BL, et al. (2011) Antimicrobial properties of amyloid peptides. Mol Pharm, Mol. Pharmaceutics, 2012, 9 (4):708–717

    Google Scholar 

  107. Zhang M, Zhao J, Zheng J (2014) Molecular understanding of a potential functional link between antimicrobial and amyloid peptides. Soft Matter 10(38):7425–7451

    Article  CAS  PubMed  Google Scholar 

  108. Slotta U et al (2007) Spider silk and amyloid fibrils: a structural comparison. Macromol Biosci 7(2):183–188

    Article  CAS  PubMed  Google Scholar 

  109. Sullan RMA et al (2009) Nanoscale structures and mechanics of barnacle cement. Biofouling 25(3):263–275

    Article  CAS  PubMed  Google Scholar 

  110. Ryu J, Park CB (2010) High stability of self-assembled peptide nanowires against thermal, chemical, and proteolytic attacks. Biotechnol Bioeng 105(2):221–230

    Article  CAS  PubMed  Google Scholar 

  111. Peralta MDR et al (2015) Engineering amyloid fibrils from β-solenoid proteins for biomaterials applications. ACS Nano 9(1):449–463

    Article  CAS  PubMed  Google Scholar 

  112. Arora A, Ha C, Park CB (2004) Insulin amyloid fibrillation at above 100°C: new insights into protein folding under extreme temperatures. Protein Sci 13(9):2429–2436

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  113. Kardos J et al (2011) Reversible heat-induced dissociation of β2-microglobulin amyloid fibrils. Biochemistry 50(15):3211–3220

    Article  CAS  PubMed  Google Scholar 

  114. Reches M, Gazit E (2003) Casting metal nanowires within discrete self-assembled peptide nanotubes. Science 300(5619):625–627

    Article  CAS  PubMed  Google Scholar 

  115. Sakai H et al (2013) Formation of functionalized nanowires by control of self-assembly using multiple modified amyloid peptides. Adv Funct Mater 23(39):4881–4887

    Article  CAS  Google Scholar 

  116. Scheibel T et al (2003) Conducting nanowires built by controlled self-assembly of amyloid fibers and selective metal deposition. Proc Natl Acad Sci U S A 100(8):4527–4532

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  117. Gras SL et al (2008) Functionalised amyloid fibrils for roles in cell adhesion. Biomaterials 29(11):1553–1562

    Article  CAS  PubMed  Google Scholar 

  118. Holmes TC et al (2000) Extensive neurite outgrowth and active synapse formation on self-assembling peptide scaffolds. Proc Natl Acad Sci U S A 97(12):6728–6733

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  119. Koutsopoulos S et al (2009) Controlled release of functional proteins through designer self-assembling peptide nanofiber hydrogel scaffold. Proc Natl Acad Sci U S A 106(12):4623–4628

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  120. Li D et al (2014) Structure-based design of functional amyloid materials. J Am Chem Soc 136(52):18044–18051

    Article  CAS  PubMed  Google Scholar 

  121. Chamberlain AK et al (2001) Characterization of the structure and dynamics of amyloidogenic variants of human lysozyme by NMR spectroscopy. Protein Sci 10(12):2525–2530

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  122. Tycko R (2000) Solid-state NMR as a probe of amyloid fibril structure. Curr Opin Chem Biol 4(5):500–506

    Article  CAS  PubMed  Google Scholar 

  123. Mousseau N, Derreumaux P (2005) Exploring the early steps of amyloid peptide aggregation by computers. Acc Chem Res 38(11):885–891

    Article  CAS  PubMed  Google Scholar 

  124. Makabe K et al (2006) Atomic structures of peptide self-assembly mimics. Proc Natl Acad Sci U S A 103(47):17753–17758

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  125. Benseny-Cases N, Cocera M, Cladera J (2007) Conversion of non-fibrillar [beta]-sheet oligomers into amyloid fibrils in Alzheimer’s disease amyloid peptide aggregation. Biochem Biophys Res Commun 361(4):916–921

    Article  CAS  PubMed  Google Scholar 

  126. Legleiter J et al (2004) Effect of different anti-A[beta] antibodies on a[beta] fibrillogenesis as assessed by atomic force microscopy. J Mol Biol 335(4):997–1006

    Article  CAS  PubMed  Google Scholar 

  127. Wang Z et al (2003) AFM and STM study of [beta]-amyloid aggregation on graphite. Ultramicroscopy 97(1–4):73–79

    Article  CAS  PubMed  Google Scholar 

  128. Morriss-Andrews A, Shea J-E (2014) Simulations of protein aggregation: insights from atomistic and coarse-grained models. J Phys Chem Lett 5(11):1899–1908

    Article  CAS  PubMed  Google Scholar 

  129. Tsai H-H et al (2005) Energy landscape of amyloidogenic peptide oligomerization by parallel-tempering molecular dynamics simulation: significant role of Asn ladder. Proc Natl Acad Sci U S A 102(23):8174–8179

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  130. Zheng J et al (2006) Structural stability and dynamics of an amyloid-forming peptide GNNQQNY from the yeast prion sup-35. Biophys J 91(3):824–833

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  131. Zheng J et al (2007) Nanostructure design using protein building blocks enhanced by conformationally constrained synthetic residues. Biochemistry 46(5):1205–1218

    Article  CAS  PubMed  Google Scholar 

  132. Nguyen HD, Hall CK (2006) Spontaneous fibril formation by polyalanines: discontinuous molecular dynamics simulations. J Am Chem Soc 128(6):1890–1901

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  133. Andrusier N et al (2008) Principles of flexible protein-protein docking. Proteins 73(2):271–289

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  134. Brooks BR et al (1983) CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 4(2):187–217

    Article  CAS  Google Scholar 

  135. Im W, Feig M, Brooks CL III (2003) An implicit membrane generalized born theory for the study of structure, stability, and interactions of membrane proteins. Biophys J 85(5):2900–2918

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  136. Wang Q et al (2011) Structural, morphological, and kinetic studies of beta-amyloid peptide aggregation on self-assembled monolayers. Phys Chem Chem Phys 13(33):15200–15210

    Article  CAS  PubMed  Google Scholar 

  137. Yu X et al (2010) Atomic-scale simulations confirm that soluble [beta]-sheet-rich peptide self-assemblies provide amyloid mimics presenting similar conformational properties. Biophys J 98(1):27–36

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  138. Yu X, Wang Q, Zheng J (2010) Structural determination of A[beta]25-35 micelles by molecular dynamics simulations. Biophys J 99(2):666–674

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  139. Zheng J et al (2010) Molecular modeling of two distinct triangular oligomers in amyloid beta-protein. J Phys Chem B 114(1):463–470

    Article  CAS  PubMed  Google Scholar 

  140. Li L, Zheng J (2010) Computational modeling of amyloid oligomeric structures. Inter J Liquid State Sci 1(1):1–13

    Google Scholar 

  141. Zheng J et al (2008) Annular structures as intermediates in fibril formation of alzheimer A[beta]17-42. J Phys Chem B 112(22):6856–6865

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  142. Yu X, Zheng J (2011) Polymorphic structures of Alzheimer’s β-amyloid globulomers. PLoS One 6(6):e20575

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  143. Zhao J et al (2011) Structural polymorphism of human islet amyloid polypeptide (hIAPP) oligomers highlights the importance of interfacial residue interactions. Biomacromolecules 12(1):210–220

    Article  CAS  PubMed  Google Scholar 

  144. Zhao J et al (2011) Heterogeneous triangular structures of human islet amyloid polypeptide (amylin) with internal hydrophobic cavity and external wrapping morphology reveal the polymorphic nature of amyloid fibrils. Biomacromolecules 12(5):1781–1794

    Article  CAS  PubMed  Google Scholar 

  145. Luo Y et al (2013) Molecular insights into the reversible formation of tau protein fibrils. Chem Commun 49(34):3582–3584

    Article  CAS  Google Scholar 

  146. Siddiqua A et al (2012) Conformational basis for asymmetric seeding barrier in filaments of three- and four-repeat tau. J Am Chem Soc 134(24):10271–10278

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  147. Yu X et al (2012) Cross-seeding and conformational selection between three- and four-repeat human Tau proteins. J Biol Chem 287(18):14950–14959

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  148. Im W, Lee MS, Brooks CL III (2003) Generalized born model with a simple smoothing function. J Comput Chem 24(14):1691–1702

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

J.Z. thanks for financial supports from the National Science Foundation (CAREER Award 0952624, 1510099, and 1607475) and Alzheimer Association—New Investigator Research Grant (2015-NIRG-341372), and National Natural Science Foundation of China (NSFC-21528601). The calculations were carried out in part on the UMass Boston research cluster. This work has been funded in whole or in part with Federal funds from the National Cancer Institute, National Institutes of Health, under contract number HHSN261200800001E. The content of this publication does not necessarily reflect the views or policies of the Department of Health and Human Services, nor does mention of trade names, commercial products, or organizations imply endorsement by the U.S. Government. This research was supported (in part) by the Intramural Research Program of the NIH, National Cancer Institute, Center for Cancer Research.

Author information

Authors and Affiliations

  1. Department of Computer Science, The University of Massachusetts Boston, 100 Morrissey Blvd., Boston, MA, 02125, USA

    Nurit Haspel

  2. Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH, 44325, USA

    Jie Zheng

  3. Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, 08028, Barcelona, Spain

    Carlos Aleman & David Zanuy

  4. Center for Research in Nano-Engineering, Universitat Politècnica de Catalunya, Campus Sud, Edifici C’, C/Pasqual i Vila s/n, E-08028, Barcelona, Spain

    Carlos Aleman

  5. Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Sackler Inst. of Molecular Medicine, Tel Aviv University, Tel Aviv, 69978, Israel

    Ruth Nussinov

  6. Basic Science Program, Leidos Biomedical Research, Inc., Frederick, MD, 21702, USA

    Ruth Nussinov

  7. Cancer and Inflammation Program, National Cancer Institute, Frederick, MD, 21702, USA

    Ruth Nussinov

Authors
  1. Nurit Haspel
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jie Zheng
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Carlos Aleman
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. David Zanuy
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Ruth Nussinov
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Nurit Haspel .

Editor information

Editors and Affiliations

  1. Department of Plants and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel

    Ilan Samish

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer Science+Business Media New York

About this protocol

Cite this protocol

Haspel, N., Zheng, J., Aleman, C., Zanuy, D., Nussinov, R. (2017). A Protocol for the Design of Protein and Peptide Nanostructure Self-Assemblies Exploiting Synthetic Amino Acids. In: Samish, I. (eds) Computational Protein Design. Methods in Molecular Biology, vol 1529. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6637-0_17

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-6637-0_17

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6635-6

  • Online ISBN: 978-1-4939-6637-0

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation