Modelling and analysis of early aggregation events of BMHP1-derived self-assembling peptides

Abstract

Despite the increasing use and development of peptide-based scaffolds in different fields including that of regenerative medicine, the understanding of the factors governing the self-assembly process and the relationship between sequence and properties have not yet been fully understood. BMHP1-derived self-assembling peptides (SAPs) have been developed and characterized showing that biotinylation at the N-terminal cap corresponds to better performing assembly and scaffold biomechanics. In this study, the effects of biotinylation on the self-assembly dynamics of seven BMHP1-derived SAPs have been investigated by molecular dynamics simulations. We confirmed that these SAPs self-assemble into β-structures and that proline acts as a β-breaker of the assembled aggregates. In biotinylated peptides, the formation of ordered β-structured aggregates is triggered by both the establishment of a dense and dynamic H-bonds network and the formation of a ‘hydrophobic wall’ available to interact with other peptides. Such conditions result from the peculiar chemical composition of the biotinyl-cap, given by the synergic cooperation of the uracil function of the ureido ring with the high hydrophobic portion consisting of the thiophenyl ring and valeryl chain. The inbuilt propensity of biotinylated peptides towards the formation of ordered small aggregates makes them ideal precursors of higher hierarchically organized self-assembled nanostructures as experimentally observed.

Keywords:

• self-assembly
• biotinylated peptides
• nematic order parameter
• hydrophobic wall

Acknowledgements

This work was supported by Fondazione Cariplo, grant no. 2011-0352, by the ‘Ricerca Corrente 2011’ funding granted by the Italian Ministry of Health and by the ‘5 × 1000’ voluntary contributions. The work was also funded by an educational grant from Amazon Web Services. We gratefully thank Roberto Cespa, Andrea Spitaleri, Ugo Cosentino and Giorgio Moro for their helpful suggestions, discussions and criticism.