Doktorské studium

Studijní obor Strukturní biologie

Název práce: Vliv membránových vlastností na konformace peptidu

Školitel: doc. RNDr. Robert Vácha, PhD.

Oficiální zadání:
Peptide and protein conformations are influenced by composition of phospholipid membrane, which they are interacting with. This is particularly important for antimicrobial and neurodegenerative peptides (such as Abeta peptide related to Alzheimer’s disease), which can disrupt cellular membrane by formation of toxic membrane pores. The lipid composition of the membrane can enhance or prevent the peptide aggregation and/or pore formation and thus determine the fate of the cell. Despite the importance, we do not understand the relation except few recent examples (e.g. DOI: 10.1002/anie.201603178). The aim of this project is to unravel the relationship between the membrane composition and peptide conformations. This information could lead to a new diet preventing the Alzheimer’s disease or to a rational design of new antimicrobial peptides. Student will master tools of computer simulations, in particular molecular dynamics technique, and methods to calculate free energies. Moreover, he/she will learn advantages and disadvantages of various protein and membrane parameterizations including all-atom and coarse-grained models.

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