Computer Simulations of Cell-Penetrating Peptides

Abstract

Cell penetrating peptides (CPPs) are short amino acid sequences that are able to translocate across cell membranes and pull large cargo molecules into the cytoplasm, affording them ideal properties for development into intracellular drug delivery vectors. Extensive experimental research has been documented in the literature with the aim of characterising the properties and cellular uptake mechanisms of CPPs, however detailed investigations into their interactions with the membrane that govern the translocation process remains a difficult challenge. To validate experimental observations, molecular modelling and simulations are frequently employed to probe CPP- membrane interactions at the atomistic level; however simulations of peptide-bilayer systems come with their own set of challenges, including sampling the peptide con- formational landscape and translocation pathway, and choosing a suitable force field to model the system. The aim of this project was to develop and validate simulation protocols for the accurate sampling of the CPP translocation process, paying specific attention to the peptide conformational changes that occur during translocation.
The peptide chosen as the subject for this study was TP2, a spontaneous membrane-translocating peptide (SMTP) that has been experimentally determined to penetrate across artificial and cellular membranes in a monomer-dependent manner. Although experimental data suggests that the peptide is mainly disordered in aqueous environments and adopts more structure in the membrane, the exact structure and membrane- translocation pathway of TP2 is unknown, so atomistic insight using molecular simulation would benefit the scientific community by adding more detail to the available knowledge of the peptide. The first endeavour for this project, therefore, was to predict the aqueous and membrane-associated structures of TP2 and to compare them against the negative control peptide ONEG, which has a similar primary structure but does not exhibit cell-penetrating activity. The predicted peptide structures were then used to initiate simulations of the peptides with POPC bilayers to study the interactions and free energy pathways that enable TP2 translocation.

The project resulted in the validation of a simulation protocol for the prediction of environment-specific peptide conformations, which could have scope in a vast range of peptide studies, and the identification of a possible membrane-translocating structure and pathway for TP2.

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Identifiers

ORCID for Jonathan Essex: orcid.org/0000-0003-2639-2746

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