We are looking for an ambitious master student with interest in both analytical and computational chemistry for a 9 months MSc project.
Please send applications to Jocelyne Vreede (J.Vreede@uva.nl) or Alina Astefanei (A.Astefanei@uva.nl) before December 16. The applications should contain a short motivation letter and a CV.
The peptide EntF* is a metabolite of the EntF quorum sensing peptide, produced by Enterococcus species in the human intestinal microbiota, and is involved in the metastasis of colorectal cancer to liver and lungs. Pharmacokinetic and pharmacodynamic biological properties of EntF* may depend on the replacement of L-amino acids by their D-form. Initial liquid chromatography experiments combined with ion mobility mass spectrometry (LC-IMS-MS) showed that replacing the L amino acids in EntF* by the D-form leads to more or less extended forms of EntF*, depending on which L amino acid is replaced by the D enantiomer.
In this project, the student will perform LC-IMS-MS experiments using different diastereomeric forms of EntF* to obtain experimental collisional cross section (CCS) data of different peptides. In addition, the student will perform molecular dynamics simulations to provide a comprehensive understanding of the effect of incorporating D amino acids on the peptide conformation. The information obtained will be correlated for a deeper understanding of the studied systems, and on a larger scope, allow the interpretation of experimental data in terms of detailed molecular conformations.