Research Interests of Department of Biophysical Chemistry

The Biophysical Chemistry department implements two basic research lines employing fluorescence spectroscopy and microscopy (“Biospectroscopy”), and electrochemical methods (“Bioelectrochemistry”). Supported by computational approaches, both directions aim at a common goal: to understand the structure, functionality and dynamics of biologically relevant systems at a molecular and atomistic level. The systems of interest lay within the context of current topics related to neurodegenerative diseases, cell signaling, immune response, gene therapy and enzymology. Specifically, we are focused on: 

Biospectroscopy

  • Monitoring structure, functionality and dynamics of biomembranes. Namely by studying formation of lipid nanoheterogeneities, impact of ions and oxidized lipids on membrane organization, and role of ganglioside organization in ganglioside-protein interactions related to disease (e.g. neurodegenerative diseases). (Cebecauer et al., 2018)
     
  • Studying aggregation phenomena of peptides and proteins leading to gain/loss of function or toxicity, and elucidating the role of the biomembranes in these aggregation processes. (Koukalová et al., 2018)
     
  • Studying nanoscopic organization of proteins at the plasma membrane of cells of relevance to disease, immune response and signaling, through super-resolution microscopy. (Lukeš et al., 2017)
     
  • Deepening the understanding of the relationship between the function and hydration/dynamics of enzymes. (Kokkonen et al., 2018)
     
  • Studying and characterizing DNA condensation processes by advanced in vivo fluorescence microscopy for better understanding and design of lipoplexes for gene therapy. (Pruchnik, Kral, and Hof, 2018)
     
  • Developing novel fluorescence methods and their implementation to the research of biological systems. For instance, the first calibration-free Fluorescence Correlation Spectroscopy technique (z-scan FCS), fluorescence lifetime correlation spectroscopy (FLCS), fluorescence spectral correlation spectroscopy (FSCS), fluorescence leakage assays, dynamic saturation optical Microscopy (DSOM), Förster resonance energy transfer combined with Monte-Carlo simulations (MC-FRET) and super resolution optical fluctuation microscopy (SOFI) were developed or significantly improved within the department. (Benda et al., 2014; Humpolíčková et al., 2010; Kapusta et al., 2012; Štefl et al., 2014)

 

Bioelectrochemistry

  • Studying electrochemical processes of biomimetic ions and molecules at the polarized interfaces between two immiscible electrolyte solutions (ITIES). (Langmaier, Záliš, and Samec, 2018)
     
  • Investigating the nature and effects of interfacial instabilities in two-phase liquid systems. (Trojánek, Mareček, and Samec, 2018)
     
  • Spectroscopic, kinetics, and theoretical investigations of excited-state dynamics and photoinduced electron transfer in transition-metal containing (bio)molecules relevant to solar energy conversion and photocatalysis. (Takematsu et al., 2019)
     
  • Theoretical characterization of systems containing several redox centers: interpretation of their spectroscopic and electrochemical properties in relation to electron transfer between individual redox sites. (Darnton et al., 2016)

 

Presentation of the Department of Biophysical Chemistry 

Biophysical Chemistry department

Biophysical Chemistry department

Biophysical Chemistry department

Biophysical Chemistry department

Biophysical Chemistry department

Biophysical Chemistry department

Biophysical Chemistry department

Biophysical Chemistry department

Biophysical Chemistry department

Highlighted publications

Benda, A., Kapusta, P., Hof, M., and Gaus, K. (2014). Fluorescence spectral correlation spectroscopy (FSCS) for probes with highly overlapping emission spectra. Opt. Express 22(3), 2973-2988.

Cebecauer, M., Amaro, M., Jurkiewicz, P., Sarmento, M. J., Šachl, R., Cwiklik, L., and Hof, M. (2018). Membrane Lipid Nanodomains. Chem. Rev. 118(23), 11259-11297.

Darnton, T. V., Hunter, B. M., Hill, M. G., Záliš, S., Vlček, A., and Gray, H. B. (2016). Reduced and Superreduced Diplatinum Complexes. J. Am. Chem. Soc. 138(17), 5699-5705.

Humpolíčková, J., Benda, A., Machan, R., Enderlein, J., and Hof, M. (2010). Dynamic saturation optical microscopy: employing dark-state formation kinetics for resolution enhancement. Phys. Chem. Chem. Phys. 12(39), 12457-12465.

Kapusta, P., Macháň, R., Benda, A., and Hof, M. (2012). Fluorescence Lifetime Correlation Spectroscopy (FLCS): Concepts, Applications and Outlook. International Journal of Molecular Sciences 13(10), 12890-12910.

Kokkonen, P., Sýkora, J., Prokop, Z., Ghose, A., Bednář, D., Amaro, M., Beerens, K., Bidmanová, S., Slánská, M., Brezovský, J., Damborský, J., and Hof, M. (2018). Molecular Gating of an Engineered Enzyme Captured in Real Time. J. Am. Chem. Soc. 140(51), 17999-18008.

Koukalová, A., Pokorná, S., Boyle, A. L., Mora, N., Kros, A., Hof, M., and Šachl, R. (2018). Distinct roles of SNARE-mimicking lipopeptides during initial steps of membrane fusion. Nanoscale 10(40), 19064-19073.

Langmaier, J., Záliš, S., and Samec, Z. (2018). Lipophilicity of acetylcholine and related ions examined by ion transfer voltammetry at a polarized room-temperature ionic liquid membrane. J. Electroanal. Chem. 815, 183-188.

Lukeš, T., Glatzová, D., Kvíčalová, Z., Levet, F., Benda, A., Letschert, S., Sauer, M., Brdička, T., Lasser, T., and Cebecauer, M. (2017). Quantifying protein densities on cell membranes using super-resolution optical fluctuation imaging. Nat. Commun. 8.

Pruchnik, H., Kral, T., and Hof, M. (2018). Lipid and DNA interaction with the triorganotin dimethylaminophenylazobenzoates studied by DSC and spectroscopy methods. Journal of Thermal Analysis and Calorimetry 134(1), 691-700.

Štefl, M., Benda, A., Gregor, I., and Hof, M. (2014). The fast polarization modulation based dualfocus fluorescence correlation spectroscopy. Opt. Express 22(1), 885-899.

Takematsu, K., Williamson, H. R., Nikolovski, P., Kaiser, J. T., Sheng, Y. L., Pospíšil, P., Towrie, M., Heyda, J., Hollas, D., Záliš, S., Gray, H. B., Vlček, A., and Winkler, J. R. (2019). Two Tryptophans Are Better Than One in Accelerating Electron Flow through a Protein. Acs Central Science 5(1), 192-200.

Trojánek, A., Mareček, V., and Samec, Z. (2018). Open circuit potential transients associated with single emulsion droplet collisions at an interface between two immiscible electrolyte solutions. Electrochem. Commun. 86, 113-116.

Department of Biophysical Chemistry

Head
doc. RNDr. Šachl Radek Ph.D.
Deputy Head
doc. Ing. Petráková Vladimíra Ph.D.