Generic ingredients in Hofmeister series

In our recent contribution with Berlin & Freiburg colleagues, we provide a generic evidence on sufficient interaction ingredients between biomolecules and salts (effective B2-interaction and mean field electrostatics) to manifest in the direct, or reverse Hofmeister series. More details can be found in the manuscript.

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Chudoba R.; Heyda J.; Dzubiella J. Tuning the collapse transition of weakly charged polymers by ion-specific screening and adsorption. Soft Matter, 2018, 14, 9631-9642

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Arginine ‘Magic’ Established in Accounts

We knew that guanidinium cation is an unique species, which desire our attention. Its ability to form cation-cation pairs is manifested in aqueous solutions of guanidinium salts as well as between arginine sidechains in proteins. Gdm-stackingSuch arginine magic was pointed out to lead to an unexpected attraction between polyarginine chains with consequences to the action of arginine-rich cell penetrating peptides.

For more, check our recent review in Accounts of Chemical Research.
doi: 10.1021/acs.accounts.8b00098

600k hours for collapse kinetics of PNIPAM

615 000 CPU hours were granted in 12th IT4I call for our project entitled: “Collapse kinetics of themoresponsive polymer chain and hydration dynamics”. Denis and Vladimir will be investigating how does the PNIPAM chain collapse, and how does the properties of interfacial water changes near the critical temperature.

More details about projects supported in this IT4I call in Ostrava – link.

Bottom-up and Top-down Coarse-Grained model for poly-ethylene-oxide polymers

We have developed a temperature T-dependent coarse-grained Hamiltonian of polyethylene glycol/oxide (PEG/PEO) in aqueous solution, which may be used in implicit-solvent material models in a wide temperature (i.e., solvent quality) range.

Our approach combined bottom-up approach, i.e., large scale atomistic MD simulations, and top-down closure, when explicitly targeting macroscopic experimental properties, such as scaling of polymer chain length and osmotic pressure equation of state.

Happy reading and employing!!! link

Positively charged poly-arginine chains are very special

Ilustrace-PNAS-Heyda

First publication in PNAS!
Very thorough joint experimental (NMR, SAXS) & theoretical (umbrella-sampling, MD, mean field modeling) work of a group around Mikael Lund and his collaborators provided strong support on unusual self-association of highly charged poly-arginine chains. Note that like-charged species normally repel each other. This behavior is unique for arginine, and diminishes upon mutation to lysine (another positively charged amino acid). On the other end, purely poly-lysine chains behave as standard polyelectrolytes.

Long poly-arginine segment are found in many cell penetrating peptides, also known as arginine-rich peptides (RRPs), which can spontaneously traverse biological membranes in so called direct mode. Therefore this unusual binding motif may have a potential biological role.

jp-2011-03519p_0013
Note that the rare like-charge attraction has its origin already on the level of guanidinium cations. link1, link2, research

The origin of this story goes back to 2012, to Pavel Jungwirth‘s group in Prague, when Mario Vazdar did first MD simulations of many deca-arginine and deca-lysine chains, and we have quantified the observed like-charged association. The motivation was the obsess by guanidinium and arginine systems, and a talk of Robin Curtis (University of Manchester) on his DLS experiments from around 2010.

Experiments in light in MD simulations and theory (seminar N403049)

In 2017, we will follow topics of bachelor thesis of the participating students.

  • Modeling of chromatography via MD simulation
  • Efficient sampling of rare events
  • Generic modeling of a salting out effect
  • Basics of the Lattice Boltzmann method

PS: In 2016 we investigated concepts of Kirkwood-Buff theory, and in 2015, we were dealing with special techniques of free energy calculation.