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Protein Design pp 53–70Cite as

Combination of Theoretical and Experimental Approaches for the Design and Study of Fibril-Forming Peptides

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1216))

Abstract

Self-assembling peptides that can form supramolecular structures such as fibrils, ribbons, and nanotubes are of particular interest to modern bionanotechnology and materials science. Their ability to form biocompatible nanostructures under mild conditions through non-covalent interactions offers a big biofabrication advantage. Structural motifs extracted from natural proteins are an important source of inspiration for the rational design of such peptides. Examples include designer self-assembling peptides that correspond to natural coiled-coil motifs, amyloid-forming proteins, and natural fibrous proteins. In this chapter, we focus on the exploitation of structural information from beta-structured natural fibers. We review a case study of short peptides that correspond to sequences from the adenovirus fiber shaft. We describe both theoretical methods for the study of their self-assembly potential and basic experimental protocols for the assessment of fibril-forming assembly.

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Acknowledgments

GA and PhT acknowledge financial support from the University of Cyprus program “Computational Investigation of Peptide Sequences from the Adenovirus and Reovirus Fiber Shaft: Insights on the Self-assembly of Peptide-based Nanostructures and the Stability of the Triple-beta Spiral Fold,” and the program UPGRADE/0609/11, “Self-Assembly and Folding of Biologically-inspired Peptide Sequences From Natural Fibrous Proteins: Insights From Highly-Intensive Computational Studies” that is co-funded by Desmi 2009–2010 of the Cyprus Research Promotion Foundation, the Republic of Cyprus, and the European Regional Development Fund. Simulations were conducted in Linux clusters of the Biophysics group, partly financed through program UPGRADE/0609/11. E.K. and A.M. acknowledge funding form the European Union (STREP NMP-CT-2006-033256, “BeNatural”).

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Authors and Affiliations

  1. Department of Physics, University of Cyprus, 20537, CY1678, Nicosia, Cyprus

    Phanourios Tamamis & Georgios Archontis

  2. Department of Materials Science and Technology, University of Crete, Biology Building, Γ.224δ, 710 03, Heraklion, Crete, Greece

    Emmanouil Kasotakis & Anna Mitraki

  3. Institute for Electronic Structure and Laser, Foundation for Research and Technology-Hellas (IESL-FORTH), Vassilika Vouton, 710 03, Heraklion, Crete, Greece

    Anna Mitraki

Authors
  1. Phanourios Tamamis
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  2. Emmanouil Kasotakis
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  3. Georgios Archontis
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  4. Anna Mitraki
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Corresponding author

Correspondence to Anna Mitraki .

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  1. Department of Chemistry, University of Basel, Switzerland

    Valentin Köhler

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Tamamis, P., Kasotakis, E., Archontis, G., Mitraki, A. (2014). Combination of Theoretical and Experimental Approaches for the Design and Study of Fibril-Forming Peptides. In: Köhler, V. (eds) Protein Design. Methods in Molecular Biology, vol 1216. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-1486-9_3

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  • DOI: https://doi.org/10.1007/978-1-4939-1486-9_3

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