The EntF peptide is involved in communication between intestinal bacteria, but also serves as a model system for a plethora of analytical techniques. Chromatography in combination with ion-mobility mass spectrometry indicates that ncorporating D amino acids at various positions in EntF results in different results in size, shape and hydrophobicity of the peptide. At this point molecular understanding is lacking.
In this project, we aim to provide molecular understanding by performing long molecular dynamics simulations of EntF under various conditions. With these simulations, we will map out the conformational space of the peptide, and thus explain the experimental observations.
This project is in collaboration with dr. Rob Haselberg in the BioAnalytical Chemistry group at the VU.