Physchem.cz

The main focus of this thesis is to develop coarse-grained force fields which enable quantitative prediction of the net charge of peptides and proteins at various pH. It builds on the previous work of our research group, where we have shown that very simple models can quantitatively predict net charge of model peptides [1] and their interactions with polyelectrolytes at various pH [2,3]. Simultaneously, we would like to develop a realistic coarse-grained representation of globular proteins, for modeling their solutions at high concentrations.[4] The goal is to augment the earlier models in order to more accurately describe hydrophobic and steric interactions and hydrogen bonding. The main tasks of the PhD candidate will include running coarse-grained simulations using Espresso or LAMMPS and all-atom simulations using Gromacs or LAMPPS.
Potential candidates are encouraged to contactpeter.kosovan@natur.cuni.czfor additional information.

References:

[1] Lunkad, R.; Murmiliuk, A.; Hebbeker, P.; Boublík, M.; Tošner, Z.; Štěpánek, M.; Košovan, P. Quantitative Prediction of Charge Regulation in Oligopeptides.Mol. Syst. Des. Eng.2021,6(2), 122–131.https://doi.org/10.1039/D0ME00147C.
[2] Pineda, S. P.; Staňo, R.; Murmiliuk, A.; Blanco, P. M.; Montes, P.; Tošner, Z.; Groborz, O.; Pánek, J.; Hrubý, M.; Štěpánek, M.; Košovan, P. Charge Regulation Triggers Condensation of Short Oligopeptides to Polyelectrolytes.JACS Au2024, jacsau.3c00668.https://doi.org/10.1021/jacsau.3c00668.
[3] Lunkad, R.; Barroso da Silva, F. L.; Košovan, P. Both Charge-Regulation and Charge-Patch Distribution Can Drive Adsorption on the Wrong Side of the Isoelectric Point.J. Am. Chem. Soc.2022,144(4), 1813–1825.https://doi.org/10.1021/jacs.1c11676.
[4] Pineda S, Blanco P, Staňo R, Košovan P. Patchy charge distribution affects the pH in protein solutions during dialysis. ChemRxiv. 2024; doi:10.26434/chemrxiv-2024-2fzdp