Skip to main content

Peptide Nanotubes: A Crystallographic Approach

  • Chapter
  • First Online:
Nanotechnology for Energy and Environmental Engineering

Part of the book series: Green Energy and Technology ((GREEN))

  • 824 Accesses

Abstract

Molecular self-assembly has led to a breakthrough in the field of nanomaterials. This has also resulted in a myriad of potential applications in biology and chemistry. Peptides have proven to be the most promising platforms owing to their biocompatibility and diversity. They are also most studied amongst the other classes of organic building blocks due to their uncanny resemblance to the proteins. There is a wide spectrum of literature available wherein the self-assembly of peptides has been constructed using several amino acids and sequences. The wide range of potential applications of such structures has been explored in drug delivery, surfactants, tissue engineering, etc. This chapter focuses on peptide self-assembly formed by non-coded amino acids, and formation of different nanostructures, using a crystallographic approach.

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

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
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

  • Abromovich LA, Reches M, Sedan VL, Allen S, Tendler SJB, Gazit E (2006) Thermal and chemical stability of diphenylalanine peptide nanotubes: implications for nanotechnological applications. Langmuir 22:1313–1320

    Article  CAS  Google Scholar 

  • Ajayan PM, Ebbesen TW (1997) Nanometer size tubes of carbon. Rep Prog Phys 60:1025–1062

    Article  CAS  Google Scholar 

  • Ajo D, Casarin M, Granozzi G (1982) On the conformational flexibility of model compounds of β-substituted α, β-unsaturated peptides. J Mol Struct 86:297–300

    Article  Google Scholar 

  • Akazome M, Ueno Y, Ooiso H, Ogura K (2000) Enantioselective inclusion of methyl phenyl sulfoxides and benzyl methyl sulfoxides by (R)-phenylglycyl-(R)-phenylglycine and the crystal structures of the inclusion cavities. J Org Chem 65:68–76

    Article  CAS  Google Scholar 

  • Allgaier H, Jung G, Wener RG, Scheider U, Zahner H (1986) Eidermin: sequencing of a heterodetic tertracyclic 21-peptide amide antibiotic. Eur J Biochem 160:9–22

    Article  CAS  Google Scholar 

  • Aubry A, Allier F, Boussard G, Marraud M (1985) Crystal structure of a dehydromonopeptide, (Z)-N-Ac-ΔPhe-NHMe. Biopolymers 24:639–646

    Article  CAS  Google Scholar 

  • Balaram P (1999) De novo design: backbone conformational constraints in nucleating helices and beta-hairpins. J Pept Res 54:195–199

    Article  CAS  Google Scholar 

  • Benedetti E (1977) Structure and conformation of peptides: a critical analysis of crystallographic data. In: Goodman M, Meienhofer J (eds) Peptides proceedings of fifth american peptide symposium. Wiley, pp. 257–273

    Google Scholar 

  • Brady SF, Cochran DW, Nutt RF, Holly FW, Bennett CD, Paleveda WJ, Curley PE, Arison BH, Saperstein R, Veber DF (1984) Synthesis and conformational study of a cyclic hexapeptide analog of somatostatin containing dehydrophenylalanine. Int J Peptide Protein Res 23:212–222

    Article  CAS  Google Scholar 

  • Brandl M, Weiss MS, Jabs A, Sühnel J, Hilgenfeld R (2001) C-h⋯π-interactions in proteins. J Mol Biol 307(1):357–377

    Google Scholar 

  • Brasun J, Makowski M, Oldziej S, Swiatek-Kozlowska J (2004) Coordination ability of pentapeptides with two dehydro-amino acid residues inserted into their sequences. J Inorg Biochem 98:1391–1398

    Article  CAS  Google Scholar 

  • Broda MA, Siodlak D, Rzeszotarska B (2005) Conformational investigation of alpha, beta-dehydropeptides. XV: N-acetyl-alpha, beta-dehydroamino acid N ‘N’ dimethylamides: conformational properties from infrared and theoretical studies. J Pept Sci 11:546–555

    Article  CAS  Google Scholar 

  • Bruker (1998) SMART, SAINT, XPREP and SHELXTL. Bruker AXS Inc., 5465 East Cheryl Parkway, Madison, WI, USA, pp 53711–5373

    Google Scholar 

  • Chopra NG, Luyken RJ, Cherrey K, Crespi VH, Cohen ML, Louie SG, Zettl A (1995) Boron nitride nanotubes. Science 269:966–967

    Article  CAS  Google Scholar 

  • DeGrado WF (1988) Design of peptides and proteins. Adv Protein Chem 39:51–124

    Article  CAS  Google Scholar 

  • Dessau RM, Schlenker JL, Higgins JB (1990) Framework topology of aluminophosphate AlPO4-8: the first 14-ring molecular sieve. Zeolites 10:522–524

    Article  CAS  Google Scholar 

  • Dossena A, Marchelli R, Pochini A (1974) New metabolites of Aspergillus amstelodami related to the biogenesis of neoechinulin. J Chem Soc Chem Commun 771–772

    Google Scholar 

  • Engels M, Bashford D, Ghadiri MR (1995) Structure and dynamics of self-assembling peptide nanotubes and the channel-mediated water organization and self-diffusion. a molecular dynamics study. J Am Chem Soc 117:9151–9158

    Article  CAS  Google Scholar 

  • English ML, Stammer CH (1978) D-Ala2, ΔzPhe4-methionine enkephalin amide, a dehydropeptide hormone. Biochem Biophys Res Commun 85(2):780–782

    Google Scholar 

  • Etter MC, MacDonald JC, Bernstein J (1990) Graph-set analysis of hydrogen-bond patterns in organic crystals. Acta Crystallogr B 46:256–262

    Article  Google Scholar 

  • Fei Z, Zhao D, Geldbach TJ, Scopelitti R, Dyson PJ (2005) A synthetic zwitterionic water channel: characterisation in the solid state by X-ray crystallography and NMR spectroscopy. Angew Chem Int Ed 44:5720–5725

    Article  CAS  Google Scholar 

  • Fisher GH, Berryer P, Ryan JW, Chauhan VS, Stammer CH (1981) Dehydrophenylalanyl analogs of bradykinin: synthesis and biological activities. Arch Biochem Biophys 211:269–275

    Article  CAS  Google Scholar 

  • Gazit E (2007) Self-assembled peptide nanostructures: the design of molecular building blocks and their technological utilization. Chem Soc Rev 36:1263–1269

    Article  CAS  Google Scholar 

  • Ghadiri MR, Granja JR, Milligan RA, McRee DE, Khazanovich N (1993) Self-assembling organic nanotubes based on a cyclic peptide architecture. Nature 366:324–327

    Article  CAS  Google Scholar 

  • Ghadiri MR, Granja JR, Buehler LK (1994) Artificial transmembrane ion channels from self-assembling peptide nanotubes. Nature 369:301–304

    Article  CAS  Google Scholar 

  • Gorbitz CH (2001) Nanotube formation by hydrophobic dipeptides. Chem Eur J 7:5153–5159

    Article  CAS  Google Scholar 

  • Gorbitz CH (2002a) An exceptionally stable peptide nanotube system with flexible pores. Acta Crystallogr Sect B 58:849–854

    Article  CAS  Google Scholar 

  • Gorbitz CH (2002b) Beta turns, water cage formation and hydrogen bonding in the structures of L-valyl-L-phenylalanine. Acta Crystallogr B 58:512–518

    Article  CAS  Google Scholar 

  • Gorbitz CH (2003) Nanotubes from hydrophobic dipeptides: pore size regulation through side chain substitution. New J Chem 27:1789–1793

    Article  Google Scholar 

  • Gorbitz CH (2006) The structure of nanotubes formed by diphenylalanine, the core recognition motif of Alzheimer’s beta-amyloid polypeptide. Chem Commun (Camb) 2332–2334

    Google Scholar 

  • Görbitz CH (1999) Acta Crystallogr C Cryst Struct Commun 55(12):2171–2177

    Google Scholar 

  • Gorbitz CH, Nilsen M, Szeto K, Tangen LW (2005) Microporous organic crystals: an unusual case for L-leucyl-L-serine. Chem Commun 14:4288–4290

    Article  CAS  Google Scholar 

  • Gross E, Morell JL (1967) The presence of dehydroalanine in the antibiotic nisin and its relationship to activity. J Am Chem Soc 89:2791–2792

    Article  CAS  Google Scholar 

  • Gupta M, Bagaria A, Mishra A, Mathur P, Basu A, Ramakumar S, Chauhan VS (2007) Self-assembly of a dipeptide-containing conformationally restricted dehydrophenylalanine residue to form ordered nanotubes. Adv Mater 19:858–861

    Article  CAS  Google Scholar 

  • Hallinan EA, Mazur RH (1979) In peptides: structure and biological function. Gross E, Meienhofer (eds) Pierce Chemical Co., Rochford, Illinois. pp. 475–477

    Google Scholar 

  • Harada A, Li J, Kamachi M (1993) Synthesis of a tubular polymer from threaded cyclodextrins. Nature 364:516–518

    Article  CAS  Google Scholar 

  • Hauser CAE, Zhang SG (2010) Designer self-assembling peptide nanofiber biological materials. Chem Soc Rev 39:2780–2790

    Article  CAS  Google Scholar 

  • Helle IH, Løkken CV, Görbitz CH, Dalhus B (2004) Acta Crystallogr C Cryst Struct Commun 60(10):o771–o772

    Google Scholar 

  • Horwich AL, Weber-Ban EU, Finley D (1999) Chaperone rings in protein folding and degradation. Proc Natl Acad Sci USA 96:11033–11040

    Article  CAS  Google Scholar 

  • Iijima S (1991) Helical microtubules of graphitic carbon. Nature 354:56–58

    Google Scholar 

  • Jain RM, Chauhan VS (1996) Conformational characteristics of peptides containing α, β-dehydroamino acid residues. Biopolymers (Peptide Science) 40:105–119

    Article  CAS  Google Scholar 

  • Johnson CK (1976) ORTEP. A Fortran thermal-ellipsoid plot program for crystal structure illustrations. ORNL Report 5138. Oak Ridge National Laboratory, Tennessee, USA

    Google Scholar 

  • Jung G (1991) Lantibiotics-Ribosomally synthesised biologically active polypeptides containing sulfide bridges and α, β-dehydroamino acids. Angew Chem Int Ed Engl 30:1051–1068

    Article  Google Scholar 

  • Karle IL (1992) Folding, aggregation and molecular recognition in peptides. Acta Crystallogr. B48:341–356

    Article  CAS  Google Scholar 

  • Kaur P, Patnaik GK, Raghubir R, Chauhan VS (1992) Synthesis and biological evaluation of dehydrophenylalanine containing substance P fragments. Bull Chem Soc Jpn 65:3412–3418

    Article  CAS  Google Scholar 

  • Kim HS, Hartgerink JD, Ghadiri MR (1998) Oriented self-assembly of cyclic peptide nanotubes in lipid membranes. J Am Chem Soc 120:4417–4424

    Article  CAS  Google Scholar 

  • Komatsubara S, Kisumi M, Chibata I, Gregorio MMV, Müller US, Crout DHG (1977) Stereochemistry of the conversions in vivo of L- and D-threonine into 2-oxobutanoic acid by the L-and D-threonine dehydratases of Serratia marcescens J Chem Soc Chem Commun 839–841

    Google Scholar 

  • Langer M, Pauling A, Retey J (1995) The role of dehydroalanine in catalysis by histidine ammonia lyase. Angew Chem Int Ed Engl 34:1464

    Article  CAS  Google Scholar 

  • Lehn JM (1993) Supramolecular chemistry. Science 260:1762–1763

    Article  CAS  Google Scholar 

  • Liu DR, Schultz PG (1999) Progress toward the evolution of an organism with an expanded genetic code. Proc Natl Acad Sci USA 96:4780–4785

    Article  CAS  Google Scholar 

  • Liu K, Kozono D, Kato Y, Agre P, Hazama A, Yasui M (2005) Conversion of aquaporin 6 from an anion channel to a water-selective channel by a single amino acid substitution. Proc Natl Acad Sci USA 102:2192–2197

    Article  CAS  Google Scholar 

  • Mahler A, Reches M, Rechter M, Cohen S, Gazit E (2006) Rigid, self‐assembled hydrogel composed of a modified aromatic dipeptide. Adv Mater 18(11):1365–1370

    Google Scholar 

  • Mandal D, Shirazi NA, Parang K (2014) Self-assembly of peptides to nanostructures. Org Biomol Chem 12(22):3544–3561

    Article  CAS  Google Scholar 

  • Mathur P, Ramakumar S, Chauhan VS (2004) Peptide design using alpha, beta-dehydro amino acids: from beta-turns to helical hairpins. Biopolymers 76:150–161

    Article  CAS  Google Scholar 

  • Meier WM, Olson DH (1988) Atlas of zeolite structure types, Butterworths, London: Mendel D, Cornish VW, Schultz PG (1995) Site-directed mutagenesis with an expanded genetic code. Annu Rev Biophys Biomol Struct 24:435–462

    Google Scholar 

  • Mendel D, Cornish VW, Schultz PG (1995) Site-directed mutagenesis with an expanded genetic code. Annu Rev Biophys Biomol Struct 24:435–462

    Article  CAS  Google Scholar 

  • Middleton DA, Madine J, Castelletto V, Hamley IW (2013) Insights into the molecular architecture of a peptide nanotube using FTIR and solid-state NMR spectroscopic measurements on an aligned sample. Angew Chem Int Ed 52:10537–10540

    Article  CAS  Google Scholar 

  • Morelli MAC, Saviano G, Temussi PA, Balboni G, Salvadori S, Tomatis R (1989) NMR studies of a series of dehydrodermorphins. Biopolymers 28:129–138

    Article  Google Scholar 

  • Narula P, Patel HC, Singh TP, Chauhan VS, Sharma AK (1988) Crystal structure and molecular conformation of N-boc-L-pro-dehydro-leu-OCH3. Biopolymers 27(10):1595–1606

    Google Scholar 

  • Nitz TJ, Shimohigashi Y, Costa T, Chen H, Stammer CH (1986) Synthesis and receptor binding affinity of both E-and Z-dehydrophenylalanine enkephalins. Int J Peptide Protein Res 27:522–529

    Article  CAS  Google Scholar 

  • Noda K, Shimohigashi Y, Izumiya N (1983) α, β-dehydroamino acids and peptides. In: Gross E, Meienhofer J (eds) The peptides 5. Academic Press, NewYork, pp 285–339

    Google Scholar 

  • Nonner W, Eisenberg B (1998) Ion permeation and glutamate residues linked by Poisson-Nernst-Planck theory in L-type calcium channels. Biophys J 75:1287–1305

    Article  CAS  Google Scholar 

  • Noren CJ, Anthony-Cahill SJ, Griffith MC, Schultz PG (1989) A general method for incorporation of unnatural amino acids into proteins. Science 244:182–188

    Article  CAS  Google Scholar 

  • Pauling L (1939) The nature of the chemical bond. Cornell University Press, Ithaka, NewYork

    Google Scholar 

  • Pieroni O, Fissi A, Salvadori S, Balboni G, Tomatis R (1986) Dehydro-demorphins. Int J Peptide Protein Res 28:91–100

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Salvadori S, Marastoni M, Balboni G, Marzola G, Tomatis R (1986a) Dehydro-demorphins. Int J Peptide Protein Res 28:254–261

    Article  CAS  Google Scholar 

  • Salvadori S, Marastoni M, Balboni G, Marzola G, Tomatis R (1986b) Dehydro-demorphins. Int J Peptide Protein Res 28:262–273

    Article  CAS  Google Scholar 

  • Sheldrick GM (1996) SADABS, Siemens area detector absorption software. Universitat Gottingen, Germany

    Google Scholar 

  • Sheldrick GM (1997) SHELX-97 A program for automatic solution and refinement of crystal structures. University of Gottingen, Gottingen, Germany

    Google Scholar 

  • Shimohigashi Y, Costa T, Stammer CH (1981) Dehydro-enkephalins: Receptor binding activity of unsaturated analogs of LeuS-Enkephalins. FEBS Lett 133:269–271

    Article  CAS  Google Scholar 

  • Shimohigashi Y, English ML, Stammer CH, Costa T (1982) Dehydro enkephalin. IV. Descriminative recognition of δ and μ opiate receptors by enkephalin analogs. Biochem Biophys Res Commun 104:583–590

    Article  CAS  Google Scholar 

  • Shimohigashi Y, Dunning JW, Kolar AJ Jr, Stammer CH (1983a) Dehydro-enkephalins. Int J Peptide Protein Res 21:202–208

    Article  CAS  Google Scholar 

  • Shimohigashi Y, Stammer CH, Costa T, Vonvoigtlander PF (1983b) Synthesis and biological activity of ΔPhe4-enkephalins. Int J Peptide Protein Res 22:489–494

    Article  CAS  Google Scholar 

  • Shimohigashi Y, Costa T, Nitz TJ, Chen H, Stammer CH (1984) Importance of the stereo-orientation of aromatic groups in enkephalins to opiate receptor recognition. Biochem Biophys Res Commun 121:966–972

    Article  CAS  Google Scholar 

  • Shimohigashi Y, Kodama H, Imazu S, Horimoto H, Sakaguchi K, Waki M, Uchida H, Kondo M, Kato T, Izumiya N (1987) [4,4′-(Z)-Dehydrophenylalanine]gramicidin S with stabilised bioactive conformation and strong antimicrobial activity. FEBS Lett 222:251–255

    Article  CAS  Google Scholar 

  • Sidhu PS, Udachin KA, Ripmeester JA (2004) Water and tris(5-acetyl-3-thienyl) methane (TATM) assemble into a one-dimensional channel compound. Chem Commun (Camb) 12:1358–1359

    Article  Google Scholar 

  • Singh TP, Kaur P (1996) Conformation and design of peptides with α, β-dehydro-amino acid residues. Prog Biophys Mol Biol 66:141–165

    Article  CAS  Google Scholar 

  • Singh TP, Narula P, Patel HC (1990) α,β-Dehydro residues in the design of peptide and protein structures. Acta Crystallogr B Struct Sci 46(4):539–545

    Google Scholar 

  • Videnova-Adrabiska Veneta (2002) Ring templated nanochannel architecture of imidazolium phosphonoacetate. J Mater Chem 12:2931–2935

    Article  Google Scholar 

  • Venkatraman J, Shankaramma SC, Balaram P (2001) Design of folded peptides. Chem Rev 101:3131–3152

    Article  CAS  Google Scholar 

  • Voges D, Zwickl P, Baumeister W (1999) The 26S proteasome: a molecular machine designed for controlled proteolysis. Annu Rev Biochem 68:1015–1068

    Article  CAS  Google Scholar 

  • Whitesides GM, Grzybowski B (2002) Self-assembly at all scales. Science 295:24182421

    Article  Google Scholar 

  • Wong TW, Goldberg AR (1984) Kinetics and mechanism of angiotensin phosphorylation by the transforming gene product of Rous sarcoma virus. J Biol Chem 259:3127–3131

    CAS  Google Scholar 

  • Xu Z, Sigler PB (1998) GroEL/GroES: structure and function of a two-stroke folding machine. J Struct Biol 124:129–141

    Google Scholar 

  • Zwickl P, Voges D, Baumeister W (1999) The proteasome: a macromolecular assembly designed for controlled proteolysis. Philos Trans R Soc Lond B Biol Sci 354:1501–1511

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Ashima Bagaria .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2020 Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Bagaria, A., Ramakumar, S. (2020). Peptide Nanotubes: A Crystallographic Approach. In: Ledwani, L., Sangwai, J. (eds) Nanotechnology for Energy and Environmental Engineering. Green Energy and Technology. Springer, Cham. https://doi.org/10.1007/978-3-030-33774-2_4

Download citation

  • DOI: https://doi.org/10.1007/978-3-030-33774-2_4

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-33773-5

  • Online ISBN: 978-3-030-33774-2

  • eBook Packages: EnergyEnergy (R0)

Publish with us

Policies and ethics