Our recent work in PNAS ‘Photoinduced hole hopping through tryptophans in proteins‘ presents a thorough investigation of water dynamics and electrostatic field fluctuations on the electron (hole) hopping dynamics in two rhenium-modified azurins. The research was done in collaboration with our excellent colleagues at Caltech, Queen Mary University of London, and Heyrovsky Institute of Czech Academy of Sciences. We have employed QM/MM/MD TD-DFT dynamics on ps-timescales, which were complemented by advanced QM-analysis in the vicinity of electronic state crossing points. Accounting for explicit (MM) solvent we have described that the local hydration of key residues and ligands, which are involved in electron transport, fluctuates in time. Our results revealed that the electron hopping occurs, when the intrinsic hydration of TRP residue is not optimal for the initial electronic state, and instead resembles the hydration of the final state. Consequently, when the electron hop is attempted, the solvent environment is ready to stabilize it. In more generalized view, the electrostatic field fluctuations are good measures to judge if the system is approaching the electronic state crossing region.
Enjoy reading of our manuscript and if you are really interested check also our extensive SI.-)
We have employed extensive densimetry measurements of guanidinium chloride at UCT Prague, and performed MD simulations at UCT Prague, IOCB Prague, and at Ruđer Bošković Institute, Zagreb. We have collected data on temperature and pressure response of guanidinium chloride hydration, allowing us to determine volumetric properties at infinite dilution, i.e., at single ion limit. We have clearly demonstrated this response is anomalous, on the half way between ordinary ions (e.g. sodium) and hydrophobic molecules (e.g. benzene). Employing directional analysis and Kirkwood-Buff theory, MD simulations point to hydrophobe-like hydration of quasi-aromatic faces and ion-like hydration of in-plane NH2 moieties. Enjoy the reading of our paper in the ‘Battino and Wilhelm’ Special Issue of the Journal of Chemical Thermodynamics. link
We are happy that we have received within 21st OPEN call 1150k CPUhrs for computational support of our GACR (Insight in preferential interactions, bridging, and cononsolvency on PNIPAM). Me and my students, we are looking forward to using Barbora and other supercomputers. Thank you IT4I!
We researched the NIPAM/water solution by means of molecular dynamics, osmometry, densimetry and ITC-calorimetry. Employing Kirkwood-Buff inversion, we gathered improved force-field and provided consistent micro- and macroscopic insight. link
Within the collaboration with Darmstadt simulation group (prof. Nico van der Vegt) we have investigated the generic stabilizing effect of TMAO on pentaalanine and other uncharged peptides. TMAO effect at both ambient and deep-ocean conditions was studied and peptide-length and chain-termination challenges were resolved. link
Finally, we were happy to experimentally support our Santa Barbara and Darmstadt colleagues, in their review article on thermodynamic effect of TMAO and urea mixtures with implications on protein denaturation/protection. Complete Kirkwood-Buff description is available over very broad range of concentrations. link
New season of Teochem seminars is here. You can expect a high quality mixture of Czech and foreign speakers The seminars will take place on many Fridays and on few Mondays. We start on Friday, September 20 at 14.30. link
We have just published two works on combined experimental (time-resolved spectroscopy) and theory (ab-initio QM/MD) investigation of electron transfer over large distance (conjugated amino acid sequence) in Azurin.
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.
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
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. Such 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.