Doctoral Studies

Biomolecular Chemistry - Field

Topic name: Calculation of binding affinities of phosphopeptides towards 14-3-3 that are important in neurobiochemistry of the brain.


Předběžné zadání:
14-3-3 proteins play key role in the neurobiochemistry of brain and are also associated with neurodegenerative amyloid diseases such as Alzheimer and Parkinson disease. 14-3-3 proteins bind more than 850 diverse target phosphoproteins, thereby forcing conformational changes or/and stabilizing active conformations in their target proteins. However, the preparation of high quantities of phosphorylated samples in high concentrations, needed for experimental measurement of binding affinities, is usually very difficult. Therefore, this task will be addressed by the accurate free energy calculations that represent an attractive alternative to the highly demanding experimental determination of the binding affinities. The aim of this PhD thesis is the calculation of binding affinities of phosphorylated peptides in the complex with 14-3-3. Different schemes of Hamiltonian replica exchange molecular dynamics (H-REMD) where enhanced sampling results from the application of distance restraints at distances of increasing lengths will be applied. The main advantage of applying H-REMD over sequential umbrella sampling simulations comes from the fact that the replicas exchange in a controlled manner exploiting natural movements rather than trying to overcome high temporary energy barriers (e.g. a temporary steric obstacle on the ligand pathway due to protein dynamics). Moreover, multiple binding paths can be sampled reversibly, where the application of distance-field restraints will ensure that the peptide finds the proper position in the 14-3-3 binding groove. We will apply this approach to a set of phosphopeptides bound to 14-3-3 and calculate their absolute binding affinities. The binding affinities obtained from the potential of mean force of small peptides binding to 14-3-3 will be compared to experimental binding affinities measured by ITC and NMR titration experiments. PhD student will be applying techniques of molecular dynamics, H-REMD methodology, free energy calculations and their analysis leading to the determination of the binding affinities by using software GROMOS.
RNDr. Mgr. Jozef Hritz, Ph.D. (BNMRS CSB CEITEC MU), učo 107254 vedoucí práce

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