Scientific Internship: Simulation of multiplexing in immune cell receptors using eGFRD

Date posted June 23, 2020
Type Scientific Internships

When your body gets infected, the immune system rapidly spreads the message using small signaling molecules, so called interleukines. These interleukines bind to immune cell surface receptors, which transduce the external signal to internal signaling pathways by recruiting other membrane proteins. The interaction of these membrane proteins leads to a series of molecular switches on the intracellular side, which initiates a physiological response specific to the ligand present on the outside. Interestingly, the receptor for interleukin 2 (IL-2) can also recognize IL-15. The receptor conformation is identical, yet the interleukins induce different phenotypes. How does the cell differentiate between these two ligands? A possible answer lies in the receptor binding dynamics.

Goal of the project
The goal of your project is to test this hypothesis by performing eGFRD simulations of the receptor binding and assembly dynamics. eGFRD is a highly efficient and exact scheme to simulate reaction-diffusion systems at the particle level. For more information, see www.GFRD.org.

About the group

The Biochemical Networks Group combines analytical theory with innovative computational techniques to elucidate general design principles of cell signaling. To this end, it uses ideas from statistical physics and measures from information theory.

This is a collaboration with the Physics of Cellular Interactions Group headed by Dr. Kristina Ganzinger, which conducts single-molecule experiments on the diffusion and interactions of interleukin membrane receptors in in-vitro systems using multi-color microscopy. These experiments will be used to develop the model, while the simulations will be used to propose new experiments.

Qualifications

You have a Bachelors degree in physics, chemistry or biology and participate in a Master study in one of these areas. You have a nationality of an EU-member state and/or you are a student at a Netherlands University. You must be available for at least 6 months. We are looking for an enthusiastic student with a strong background in statistical physics and an affinity with molecular simulations or modelling more broadly.

Terms of employment

At the start of the traineeship your trainee plan will be set out, in consultation with your AMOLF supervisor.

Contact info

Prof. dr. Pieter Rein ten Wolde
Group leader Biochemical Networks Group
E-mail: tenwolde@amolf.nl
Phone: +31 (0)20-754 7100

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–  Resume;
–  List of followed courses plus grades.

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