Supervisor:  Robert Vácha

Annotation: Antimicrobial peptides (AMPs) can disrupt the membrane barrier function and kill bacteria, including resistant bacteria recognized by the UN and WHO as one of the biggest threats to global health. AMPs are part of the host-defense system of many organisms and promising candidates to become a new class of therapeutics. Particularly advantageous are peptides that kill bacteria by the formation of leaky pores in their membranes because bacteria have difficulties to develop resistance against such peptides. However, the peptide sequence motives responsible for pore formation remain elusive. This project is focused on evaluation and design of sequence motives able to stabilize pores by reducing the membrane line tension associated with the pore. The main tool will be Molecular dynamics simulations with free energy calculations using Gromacs program package and coarse-grained force field. This project will be complemented by experiments providing verification and feedback of membrane disruption. The findings are expected to lead to the design of new antimicrobial peptides.

Requirements on candidates:

Experience with Molecular dynamics simulations on membranes and/or proteins, the previous use of free energy calculation methods is advantageous

More information on CEITEC PhD School website: https://ls-phd.ceitec.cz/ and Research Group website: https://vacha.ceitec.cz/

In case you are interested. ​Please, submit your CV and motivation letter via Registration Form.

Listen to the experiences of our PhD students:

·         Cosimo Lobello – Medical Genomics Group

·         Abigail Rubiato Cuyacot – Functional Genomics and Proteomics of Plants Group

·         Karel Škubník – Structural Virology Group