1. The role of the intracellular environment in modulation of biomolecular structure, dynamics and interactions.

Supervisor: Lukáš Trantírek, Ph.D.


The physical-chemical parameters of the intracellular space are actively contributing to regulation of biomolecular functions via influencing protein and nucleic acids structure and dynamics. While the coordinated and tightly controlled changes in the non-specific parameters of the intracellular space are permissive for broad range of fundamental physiological process including cellular division and differentiation, their deregulation leads to a number of human pathologies including cancer. The aim of this project is to explore a role of cellular environment in physiologically distinct cellular states on protein dynamics, structure and interactions with drug-like molecules.

The student will acquire advance knowledge and skills in human cell culture manipulations (cultivation, transfection, genome editing), DNA cloning, protein expression and purification, flow cytometry, confocal microscopy, and, in particular, with state-of-the-art in-cell NMR spectroscopy. The student will have the opportunity to present the results of his/her work at prestigious international conferences. Moreover, this project will involve collaboration with other leading researches in European institutes.

Prospective student should ideally have done masters in molecular/cellular biology, biochemistry, biomolecular chemistry, or biophysics. The experience with biomolecular NMR spectroscopy is advantage.  The most highly valued feature will however be excitement for science and strong drive in tackling important biochemical/biological, and biophysical questions.

Recommended literature:

  1. Broft P, Dzatko S, Krafcikova M, Wacker A, Hänsel-Hertsch R, Dötsch V, Trantirek L, Schwalbe H. In-Cell NMR Spectroscopy of Functional Riboswitch Aptamers in Eukaryotic Cells. Angew Chem Int Ed Engl. 2021;60(2):865-872.
  2. Krafcikova M, Dzatko S, Caron C, Granzhan A, Fiala R, Loja T, Teulade-Fichou MP, Fessl T, Hänsel-Hertsch R, Mergny JL, Foldynova-Trantirkova S, Trantirek L. Monitoring DNA-Ligand Interactions in Living Human Cells Using NMR Spectroscopy. J Am Chem Soc. 2019;141(34):13281-13285.
  3. Dzatko S, Krafcikova M, Hänsel-Hertsch R, Fessl T, Fiala R, Loja T, Krafcik D, Mergny JL, Foldynova-Trantirkova S, Trantirek L. Evaluation of the Stability of DNA i-Motifs in the Nuclei of Living Mammalian Cells. Angew Chem Int Ed Engl. 2018;57(8):2165-2169.
  4. Luchinat E, Barbieri L, Campbell TF, Banci L. Real-Time Quantitative In-Cell NMR: Ligand Binding and Protein Oxidation Monitored in Human Cells Using Multivariate Curve Resolution. Anal Chem. 2020 ;92(14):9997-10006.

Keywords: protein/DNA; structure; dynamics; protein/DNA-drug interactions; (in-cell) NMR spectroscopy.


2. Basic principles of DNA quadruplex folding landscape studied by advanced simulations.

Supervisor: Lukáš Trantírek, Ph.D.  & Prof. Dr. Jiří Šponer, D.Sc.


DNA guanine quadruplexes (G4) belong to the most important noncanonical nucleic acid structures. They regulate gene expression, are potential pharmacological targets, and are often used as a basis for DNA supramolecular assemblies and nanostructures. G4 molecules have intriguing folding mechanisms, which appear to be unique in the biomolecular world. Understanding of the basic principles of folding of biomolecules is an important scientific question per se.

The aim of the project is to study folding mechanisms of G4s and some other types of noncanonical nucleic acids using state of the art atomistic molecular dynamics (MD) simulations. The computational research will be conducted in one of the world-leading laboratories in the field of nucleic acids simulations, in a close collaboration with experimental laboratories, leading to clear interrelation between theory and experiment. The main techniques will be standard and diverse enhanced-sampling MD simulations; part of the research may be even development of cutting-edge methods (force fields and enhanced sampling protocols) for studies of biomolecular folding.

Perspective student should have done masters in physical chemistry, biochemistry, or related fields and have proven experience with computational chemistry applied to biomolecules. We expect dedication to solve intriguing scientific questions.

Recommended literature:

  1. Šponer, J.; Bussi, G.; Krepl, M.; Banáš, P.; Bottaro, S.; Cunha, R. A.; Gil-Ley, A.; Pinamonti, G.; Poblete, S.; Jurečka, P., et al., RNA Structural Dynamics as Captured by Molecular Simulations: A Comprehensive Overview. Chemical Reviews, 2018, 118, 4177–4338, DOI: 10.1021/acs.chemrev.7b00427
  2. Šponer, J.; Bussi, G.; Stadlbauer, P.; Kührová, P.; Banáš, P.; Islam, B.; Haider, S.; Neidle, S.; Otyepka, M., Folding of Guanine Quadruplex Molecules–funnel-like Mechanism or Kinetic Partitioning? An Overview from MD Simulation Studies. Biochimica et Biophysica Acta (BBA) - General Subjects, 2017, 1861, 1246–1263, DOI: 10.1016/j.bbagen.2016.12.008
  3. Živković, M. L.; Gajarský, M.; Beková, K.; Stadlbauer, P.; Vicherek, L.; Petrová, M.; Fiala, R.; Rosenberg, I.; Šponer, J.; Plavec, J.; Trantírek, L., Insight into Formation Propensity of Pseudocircular DNA G-hairpins. Nucleic Acids Research, 2021, 49, 2317–2332, DOI: 10.1093/nar/gkab029
  4. Stadlbauer, P.; Kührová, P.; Vicherek, L.; Banáš, P.; Otyepka, M.; Trantírek, L.; Šponer, J., Parallel G-triplexes and G-hairpins as Potential Transitory Ensembles in the Folding of Parallel-stranded DNA G-Quadruplexes. Nucleic Acids Research, 2019, 47, 7276–7293, DOI: 10.1093/nar/gkz610

Keywords: G quadruplex, Molecular dynamics, DNA folding


Lukáš Trantírek, Ph.D.
Lukáš Trantírek, Ph.D.
Research Group Leader Senior
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Silvie Trantírková, Ph.D.
Silvie Trantírková, Ph.D.
Senior Staff Scientist
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