Probing peptide-nanomaterial interfaces by means of molecular dynamics

  • Federica De Leo

    Student thesis: Doc typesDoctor of Sciences


    Modified graphitic nanomaterials (GNMs), such as fullerene, carbon nanotubes (CNTs) and graphene, have recently emerged as new multifunctional platforms for application in nanomedicine and biology. Particularly, the idea of merging nanotechnology and biology represents nowadays a fascinating avenue to confer a new functional essence to GNMs through chemical modification with biomolecules, i.e. peptides, proteins or enzymes. Additionally, this approach allows overcoming one of the main barrier to exploit GNMs potentialities, that is their insolubility and the difficulties in separating them. Effectively, the biomolecular modification of GNMs increases their (poor) solubility and biocompatibility, leading to a resulting biohybrid compound which, thanks to the new functional property, is exploitable for several applications ranging from imaging and bio-sensing, nanomedicine and cancer therapy, gene therapy, drug delivery and tissue engineering. Consequently, the deep knowledge of the free and spontaneous tendency of GNMs to interact with proteins, interpreted as non-covalent interaction driven by their chemical nature, results of pivotal importance for the achievement of a contrived and conscious human manipulation towards tailored applications. In Chapter 1 of this thesis we illustrate how the study of the non-covalent GNMs/proteins interactions ultimately leads to the control and engineering of new materials for biomedical applications and represent a guide to predict parasite adsorbing processes that would bring at toxicological implications.
    Deeply involved in this research field, we herein present three projects developed during my doctoral studies concerning the probing of protein/nanomaterials interfaces through Molecular Dynamics (MD) simulations. By applying chiefly classical computational techniques (thoroughly described in Chapter 2), we have been able to contribute to the comprehension of the chemico-physical and dynamical aspects ruling the spontaneous tendency of large proteins, such as antibodies, or small peptides to interact with GNMs or inorganic surfaces. Interestingly, in a transversal and interdisciplinary manner, the three projects are developed in collaboration with the experimental team of our group, which contributed with precious experimental evidences. Therefore, the theoretical studies presented herein worked as a powerful complement to either validate, rationalize, predict and guide the experimental findings.
    Specifically, Chapter 3 describes all-atom explicit solvent MD simulations investigating the structural and dynamical properties of a non-covalent bioconjugate in which the monoclonal Cetuximab antibody (Ctx) is adsorbed on a CNT surface. Upon selection of the three most representative adsorption modes as obtained by docking studies, force-field MD and DFT simulations unambiguously showed that hydrophobic interactions mainly govern the adsorption of the Ctx protein on the graphitic surface. Moreover, the conjugation with the nanomaterial does not affect the secondary structure of Ctx. The predicted structural models are consistent with the experimental data, thus rationalizing the intact structural stability and recognition properties of the Ctx immobilized on CNT. MD simulations clearly support the reliability of the used bioconjugation strategy for engineering stable and responsive hybrid nanomaterials for therapeutic applications. Moreover, a remarkable structural similarity of Ctx with antibodies of different isotypes suggests that in principle the CNT framework can interact in the same manner with most of antibodies currently used in clinical applications.
    Additionally, we have been able to design a new Janus-type proteinic β-sheet able to directionally functionalize graphene in the view of biological applications. In particular, we provide computational evidences that a 13-mer polypeptide can fold stably in an antiparallel β-sheet exposing a hydrophobic side, prone to the anchoring to graphene, and a hydrophilic face devoted to functionalization purposes. Additionally, pyrenyl functionalities have been inserted in the hydrophobic side and their presence was demonstrated to be fundamental to improve the β-sheet adsorption on graphene. The theoretical design is here guiding the production of the β-sheet protein that, in collaboration with Dr. Riccardo Marega and Laure-Elie Carloni of our group, is now under experimental validation.
    Finally, in Chapter 4 we investigate the self-assembly of Ile-Gly-Asp (IGD)-containing peptide on Au as new motogenic surface studying the migratory response of cancer cells and human dermal fibroblast. IGDQK-SH pentapeptide was used to produce one full and two mixed self assembled monolayers (SAMs), the latter prepared by backfilling the peptide SAM with two molecular fillers with different hydrophobicity. Both structural (AFM and WCA analysis) and functional (biological tests) characterizations reveal that different morphologies can drastically affect the motogenic response as very different behaviors are observed for the three produced SAMs. Therefore, classical MD simulations have been performed to model the three produced systems both in the assembling (MeOH) and in the biological test conditions (water). By means of a thorough trajectory analysis we have been able to demonstrate that the efficient motogenic activity is correlated to the proper organization and correct sequence orientation. The systems in which pronounced peptide affinity to the Au surface and interpeptide interactions were observed correspond to poorly organized materials where the sequence exposition was drastically affected and the surface response was compromised. The simulated outcomes are in excellent agreement with the experimental results furthermore clarifying the motogenic activity with structural insights. By this way, we have been able to complement and validate the experimental outcomes explaining with atomistic detailed information the structural-activity relationship of the prepared peptide-based motogenic Au surface.
    Date of Award20 Jan 2015
    Original languageEnglish
    Awarding Institution
    • University of Namur
    SupervisorDavide BONIFAZI (Supervisor), Johan Wouters (Jury), Benoit CHAMPAGNE (Jury), Alessandra Magistrato (Jury), Iris ANTES (Jury) & Alessandro De Vita (Jury)


    • Molecular Dynamics
    • Bionanotechnology
    • Supramolecular Interactions

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