Prof. Jiří ​Šponer

B6: Department of Structure and Dynamics of Nucleic Acids (CEITEC), Masaryk University, Czech Republic


Computational studies of nucleic acids and their complexes with ligands and proteins, including atomistic classical simulations, advanced quantum-chemical calculations, bioinformatics and hybrid QM/MM methods. Structural molecular biology and biophysics. Physical chemistry of molecular interactions. Current main research topics: 1) RNA structural dynamics, folding and catalysis. 2) Protein-RNA complexes. 3) DNA, with focus on G-quadruplexes. 4) Diverse types of quantum-chemical studies on nucleic acids systems. 5) Origin of life (prebiotic chemistry). 6) Development of DNA and RNA simulation force fields.

Role in LightDyNAmics

Supervisor of ESR5

Selected Publications

  1. J. Šponer, G. Bussi, M. Krepl, P. Banáš, S. Bottaro, R. A. Cunha, A. Gil-Ley, G. Pinamonti, S. Poblete, P. Jurečka et al. “RNA Structural Dynamics as Captured by Molecular Simulations: A Comprehensive Overview.” Chemical Reviews, 2017, in press, DOI:10.1021/acs.chemrev.1027b00427.
  2. J. Šponer, G. Bussi, P. Stadlbauer, P. Kührová, P. Banáš, B. Islam, S, Haider, S. Neidle, M. Otyepka. “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.
  3. N. D. d. Konté, M. Krepl, F, F. Damberger, N. Ripin, O. Duss, J. Sponer, F. H-T. Allain. “Aromatic Side-chain Conformational Switch on the Surface of the RNA Recognition Motif Enables RNA Discrimination.” Nature Communications 2017, 8, e654.
  4. M. Zgarbová, J. Šponer, M. Otyepka, T. E. Cheatham, R. Galindo-Murillo, P. Jurečka. “Refinement of the Sugar–Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA.E Journal of Chemical Theory and Computation 2015, 11, 5723-5736
  5. J. Sponer, A. Mladek, N. Spackova, X. H. Cang, T. E. Cheatham III, S. Grimme. “Relative stability of different DNA guanine quadruplex stem topologies derived using large-scale quantum-chemical computations.” Journal of the American Chemical Society, 2012, 135, 9785-9796.