Elucidating self-assembly and antimicrobial strategies of synthetic peptides
: an in silico investigation

Student thesis: Doctoral ThesisDoctor of Philosophy


The modern insurgence of antimicrobial resistance prompted the research of new drug alternatives. In parallel, the problem of their delivery has stimulated the research of novel biomimietic vehicles. Synthetic materials can be designed to perform both functions effectively. Recently engineered nanocapsules were shown to promote bacterial membrane poration and gene delivery into mammalian cells. Their constitutive molecule, capzip, is a three branched peptide, which contains sequences inspired from a naturally occurring antimicrobial peptide (AMP). AMPs act on bacteria disrupting their membrane, a mechanism which does not strongly promote resistance. As the atomistic details of the capzip nanocapsule assembly are still unknown, this project studied its structure in water and its interaction with model membranes, by means of multiscale Molecular Dynamics simulations. The in silico investigation clarified the preferred structure that capzip adopts in order to form robust capsules. In particular, the original formulation of capzip included an amphiphilic pattern to promote antimicrobial activity, but simulations proved that this has a key role in granting structural stability as well. This provides insight for the development of the next generation of multi-branched antimicrobial molecules. The multiscale investigation performed prompted also a comparison between coarse-grained force fields, which will contribute to inform the choice of the most adapt one for future simulations of large peptidic assemblies. The structures found to be stable in solution were selected for further simulations at the interface with a model bacterial and mammalian membrane. The insertion of charged residues in the membrane ester region produced a local decrease in lipid mobility and, under the effect of an externally applied electric field in the physiological range, pore formation with subsequent membrane disruption. Coarse-grained simulations confirmed these findings, clarifying the attraction mechanism between the capsule and the model bacterial membrane. Moreover, they suggested a lower affinity with the model mammalian membrane. The exploration of the peptide-membrane interactions prompted an investigation of the currently used lipid parameters in the GROMOS atomistic force field. Given the inconsistency between the parametrisation of proteins and lipids found in the latest versions of the force field, we proposed a new parametrisation that reconcile these. The new parameters showed a peptide-membrane interaction which is less biased by the simulation's initial conditions.
Date of Award1 Apr 2020
Original languageEnglish
Awarding Institution
  • King's College London
SupervisorFranca Fraternali (Supervisor) & Chris Lorenz (Supervisor)

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