Original Paper

Journal of Molecular Modeling

, Volume 17, Issue 9, pp 2227-2235

First online:

Molecular dynamics of the “hydrophobic patch” that immobilizes hydrophobin protein HFBII on silicon

  • Clara MoldovanAffiliated withTheory Modelling and Design Centre, Tyndall National Institute, University College Cork
  • , Damien ThompsonAffiliated withTheory Modelling and Design Centre, Tyndall National Institute, University College Cork Email author 

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The experimentally-observed stable, electrically-conducting interface formed between hydrophobin protein HFBII and silicon provides a model system for the Bio/ICT interfaces required for bionanoelectronics. The present work used molecular dynamics (MD) computer simulations to investigate the atom-scale details of the assembly and structure of the HFBII/silicon interface, using models on the order of 40,000 atoms to compute energy profiles for the full protein interacting with a bare Si(111) substrate in aqueous solution. Five nanoseconds of free, equilibrated dynamics were performed for six models with initial protein:silicon separations ranging from 1.2 to 0.2 nanometers in steps of 0.2 nm. Three of the models formed extensive protein:silicon van der Waals’s interfacial contacts. The model with 0.2 nm starting separation serves as an illustrative example of the dynamic interface created, whereby hydrophobic patch residues cycle between flat and more protruding patch conformations that favor respectively close inter-patch and close patch-surface contacts, with protein:surface separations cycling between 0.2 and 0.4 nm over the 5 ns of dynamics. Analysis of residue-based binding energies at the interface reveal three leucines Leu19, Leu21 and Leu63, together with isoleucine Ile22 and alanine Ala61, as the primary drivers towards adhesion on bare silicon, providing the atom-scale details of HFBII’s hydrophobic patch which in turn provides leads for the engineering of more tightly-coupled interfaces.


Atom-scale computer simulations reveal the structure, dynamics and energetics of hydrophobin protein HFBII immobilisation on bare silicon, a prototype for ordered organic/inorganic interfaces in future bionanoelectronics devices.


Bio/ICT interfacing Computer simulation Hydrophobin Molecular dynamics Nanobiotechnology Protein engineering Self-assembly Silicon technology