Mgr. Petra Kührová, Ph.D.

Tel: 58 563 4766, E-mail: petra.kuhrova@upol.cz, Room: 3.007

Research interests

2002 – 07 Mgr. – Education of Mathematic and Chemistry, Palacký University, Olomouc
2007 – 11 Ph.D. – Department of Physical chemistry, Palacký University, Olomouc

2009 – 2011 Junior Researcher, Department of Physical chemistry, Palacký University, Olomouc
2012 – Junior Researcher, Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacký University, Olomouc
2013 – Assistant Professor, Department of Physical chemistry, Palacký University, Olomouc

2010, 2011, 2012, 2013 – Department of Chemistry, University of Cambridge, UK; group of Dr. Robert Best
2014, 2015 – NIH, Washington DC, USA; group of Dr. Robert Best

Dr. Robert Best, NIH, Washington DC, USA – folding of biomelcules, coarse-grained model of protein/DNA complexes

Mlýnský V, Kührová P, Kühr T, Otyepka M, Bussi G, Banáš P, Šponer J: Fine-Tuning of the AMBER RNA Force Field with a New Term Adjusting Interactions of Terminal Nucleotides. J. Chem. Theory Comput., 16(6), 3936-3946, 2020. (DOI)

Kührová P, Mlýnský V, Zgarbová M, Krepl M, Bussi G, Best RB, Otyepka M, Šponer J, Banáš P: Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions. J. Chem. Theory Comput., 15(5), 3288-3305, 2019. (DOI)
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 Res., 47(14), 7276–7293, 2019. (DOI)
Suddala KC, Price IR, Dandpat SS, Janeček M, Kührová P, Šponer J, Banáš P, Ke A, Walter NG: Local-to-global signal transduction at the core of a Mn2+ sensing riboswitch. Nat. Commun., 10, 4304, 2019. (DOI)

Havrila M, Stadlbauer P, Kührová P, Banáš P, Mergny J, Otyepka M, Šponer J: Structural dynamics of propeller loop: towards folding of RNA G-quadruplex. Nucleic Acids Res., 46(17), 8754–8771, 2018. (DOI)

Mlýnský V, Kührová P, Jurečka P, Šponer J, Otyepka M, Banáš P: Mapping the Chemical Space of the RNA Cleavage and its Implications for Ribozyme Catalysis. J. Phys. Chem. B, 121(48), 10828–10840, 2017. (DOI)
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. Biochim. Biophys. Acta, Gen. Subj., 1861(5), 1246–1263, 2017. (DOI)
Šponer J, Krepl M, Banáš P, Kührová P, Zgarbová M, Jurečka P, Havrila M, Otyepka M: How to understand atomistic molecular dynamics simulations of RNA and protein– RNA complexes? WIREs RNA, 8(3), e1405, 2017. (DOI)

Kührová P, Best RB, Bottaro S, Bussi G, Šponer J, Otyepka M, Banáš P: Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies. J. Chem. Theory Comput., 12(9), 4534–4548, 2016. (DOI)

Haldar S, Kührová P, Banáš P, Spiwok V, Šponer J, Hobza P, Otyepka M: Insights into Stability and Folding of GNRA and UNCG Tetraloops Revealed by Microsecond Molecular Dynamics and Well-Tempered Metadynamics. J. Chem. Theory Comput., 11(8), 3866-3877, 2015. (DOI)
Mlýnský V, Kührová P, Zgarbová M, Jurečka P, Walter NG, Otyepka M, Šponer J, Banáš P: Reactive Conformation of the Active Site in the Hairpin Ribozyme Achieved by Molecular Dynamics Simulations with $epsilon$/$zeta$ Force Field Reparametrizations. J. Phys. Chem. B., 119(11), 4220-4229, 2015. (DOI)
Stadlbauer P, Kührová P, Banáš P, Koča J, Bussi G, Trantírek L, Otyepka M, Šponer J: Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations. Nucleic. Acids Res., 43(20), 9626-9644, 2015. (DOI)

Kührová P, Otyepka M, Šponer J, Banáš P: Are Waters around RNA More than Just a Solvent? – An Insight from Molecular Dynamics Simulations. J. Chem. Theory Comput., 10(1), 401-411, 2014. (DOI)
Šponer J, Banáš P, Jurečka P, Zgarbová M, Kührová P, Havrila M, Krepl M, Stadlbauer P, Otyepka M: Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome. J. Phys. Chem. Lett., 5(10), 1771-1782, 2014. (DOI)

Kührová P, Banáš P, Best RB, Šponer J, Otyepka M: Computer Folding of RNA Tetraloops? Are We There Yet?. J. Chem. Theory Comput., 9(4), 2115-2125, 2013. (DOI)

Beššeová I, Banáš P, Kührová P, Košinová P, Otyepka M, Šponer J: Simulations of A-RNA Duplexes. The Effect of Sequence, Solute Force Field, Water Model, and Salt Concentration. J. Phys. Chem. B, 116(33), 9899-9916, 2012. (DOI)
Kührová P, De Simone A, Otyepka M, Best RB: Force-Field Dependence of Chignolin Folding and Misfolding: Comparison with Experiment and Redesign. Biophys. J., 102(8), 1897-1906, 2012. (DOI)

Sklenovský P, Florová P, Banáš P, Réblová K, Lankaš F, Otyepka M, Šponer J: Understanding RNA Flexibility Using Explicit Solvent Simulations: The Ribosomal and Group I Intron Reverse Kink-Turn Motifs. J. Chem. Theory Comput., 7(9), 2963-2980, 2011. (DOI)

Florová P, Sklenovský P, Banáš P, Otyepka M: Explicit Water Models Affect the Specific Solvation and Dynamics of Unfolded Peptides While the Conformational Behavior and Flexibility of Folded Peptides Remain Intact. J. Chem. Theory Comput., 6(11), 3569-3579, 2010. (DOI)