prof. RNDr. Jiří Šponer, DrSc.

Tel: 58 563 4760, E-mail: jiri.sponer@upol.cz, Room: 3.006

Research interests Education Employment International experience

Publications

2017

  1. Cassone G, Šponer J, Saija F, Di Mauro E, Saitta AM, Šponer JE: Stability of 2’,3’ and 3’,5’ cyclic nucleotides in formamide and in water: a theoretical insight into the factors controlling accumulation of nucleic acid building blocks in the prebiotic pool. Phys. Chem. Chem. Phys., 19, 1817-1825, 2017. (DOI)
  2. Costanzo G, Giorgi A, Scipioni A, Timperio AM, Mancone C, Tripodi M, Kapralov M, Krasavin E, Kruse H, Šponer J, Šponer JE, Ranc Václav , Otyepka M, Pino S, Di Mauro E: Non-Enzymatic Oligomerization of 3',5' Cyclic CMP Induced by Proton- and UV-Irradiation Hints at a Non-Fastidious Origin of RNA. ChemiBioChem, 18(5), 1535–1543, 2017. (DOI)
  3. Diarra dit Konté N, Krepl M, Damberger FF, Duss O, Šponer J, Allain FH: Aromatic side-chain conformational switch on the surface of the RNA Recognition Motif enables RNA discrimination. Nat. Commun., 8(654), 2017. (DOI)
  4. Figiel M, Krepl M, Poznaňaski J, Golab A, Šponer J, Nowotny M: Coordination between the polymerase and RNase H activity of HIV-1 reverse transcriptase. Nucleic Acids Res., 45(6), 3341–3352, 2017. (DOI)
  5. Havrila M, Stadlbauer P, Islam B, Otyepka M, Šponer J: Effect of Monovalent Ion Parameters on Molecular Dynamics Simulations of G-Quadruplexes. J. Chem. Theory Comput., 13(8), 3911–3926, 2017. (DOI)
  6. Islam B, Stadlbauer P, Ley AG, Pérez-Hernández G, Haider S, Neidle S, Bussi G, Banáš P, Otyepka M, Šponer J: Exploring the Dynamics of Propeller Loops in Human Telomeric DNA Quadruplexes Using Atomistic Simulations. J. Chem. Theory Comput., 13(6), 2458–2480, 2017. (DOI)
  7. Krepl M, Blatter M, Cléry A, Damberger FF, Allain FH, Šponer J: Structural study of the Fox-1 RRM protein hydration reveals a role for key water molecules in RRM-RNA recognition. Nucleic Acids Res., 45(13), 8046–8063, 2017. (DOI)
  8. 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, ASAP, 2017. (DOI)
  9. Pokorná P, Krepl M, Kruse H, Šponer J: MD and QM/MM Study of the Quaternary HutP Homohexamer Complex with mRNA, L-histidine Ligand and Mg2+. J. Chem. Theory Comput., 13(11), 5658–5670, 2017. (DOI)
  10. Saladino R, Bizzarri BM, Botta L, Šponer J, Šponer JE, Georgelin T, Jaber M, Rigaud B, Kapralov M, Timoshenko GN, Rozanov A, Krasavin E, Timperio AM, Di Mauro E: Proton irradiation: a key to the challenge of N-glycosidic bond formation in a prebiotic context. Sci. Rep., 7, 14709, 2017. (DOI)
  11. 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)
  12. 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)
  13. Zgarbová M, Jurečka P, Banáš P, Havrila M, Šponer J, Otyepka M: Noncanonical α/γ Backbone Conformations in RNA and the Accuracy of Their Description by the AMBER Force Field. J. Phys. Chem. B, 121(11), 2420–2433, 2017. (DOI)
  14. Zgarbová M, Jurečka P, Lankaš F, Cheatham TE, Šponer J, Otyepka M: Influence of BII Backbone Substates on DNA Twist: A Unified View and Comparison of Simulation and Experiment for all 136 Distinct Tetranucleotide Sequences. J. Chem. Inf. Model., 57(2), 275–287, 2017. (DOI)

2016

  1. Bottaro S, Banáš P, Šponer J, Bussi G: Free Energy Landscape of GAGA and UUCG RNA Tetraloops. J. Phys. Chem. Lett., 7, 4032–4038, 2016. (DOI)
  2. Dršata T, Zgarbová M, Jurečka P, Šponer J, Lankaš F: On the Use of Molecular Dynamics Simulations for Probing Allostery through DNA. Biophys. J., 110(4), 874–876, 2016. (DOI)
  3. Galindo-Murillo R, Robertson JC, Zgarbová M, Šponer J, Otyepka M, Jurečka P, Cheatham TE: Assessing the current state of AMBER force field modifications for DNA. J. Chem. Theory Comput., 12(8), 4114–4127, 2016. (DOI)
  4. 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)
  5. Stadlbauer P, Mazzanti L, Cragnolini T, Wales DJ, Derreumaux P, Pasquali S, Šponer J: Coarse-Grained Simulations Complemented by Atomistic Molecular Dynamics Provide New Insights into Folding and Unfolding of Human Telomeric G-Quadruplexes. J. Chem. Theory Comput., 12(12), 6077–6097, 2016. (DOI)

2015

  1. Dubecký M, Walter NG, Šponer J, Otyepka M, Banáš P: Chemical Feasibility of the General Acid / Base Mechanism of glmS Ribozyme Self-Cleavage. Biopolymers, 103(10), 550–562, 2015. (DOI)
  2. Estarellas C, Otyepka M, Koča J, Banáš P, Krepl M, Šponer J: Molecular dynamic simulations of protein/RNA complexes: CRISPR/Csy4 endoribonuclease. Biochim. Biophys. Acta, Gen. Subj., 1850(5), 1072-1090, 2015. (DOI)
  3. 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)
  4. Havrila M, Zgarbová M, Jurečka P, Banáš P, Krepl M, Otyepka M, Šponer J: Microsecond-Scale MD Simulations of HIV-1 DIS Kissing-Loop Complexes Predict Bulged-In Conformation of the Bulged Bases and Reveal Interesting Differences Between Available Variants of the AMBER RNA Force Fields. J. Phys. Chem. B, 119, 15176−15190, 2015. (DOI)
  5. Krepl M, Havrila M, Stadlbauer P, Banáš P, Otyepka M, Pasulka J, Štefl R, Šponer J: Can We Execute Stable Microsecond-Scale Atomistic Simulations of Protein–RNA Complexes?. J. Chem Theory Comput., 11(3), 1220-1243, 2015. (DOI)
  6. 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)
  7. Mlýnský V, Walter NG, Šponer J, Otyepka M, Banáš P: The role of an active site Mg 2+ in HDV ribozyme self-cleavage: insights from QM/MM calculations. Phys. Chem. Chem. Phys., 17(1), 670-679, 2015. (DOI)
  8. Sripathi KN, Banáš P, Réblová K, Šponer J, Otyepka M, Walter NG: Wobble pairs of the HDV ribozyme play specific roles in stabilization of active site dynamics. Phys. Chem. Chem. Phys., 17(8), 5887-5900, 2015. (DOI)
  9. 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)
  10. Zgarbová M, Šponer J, Otyepka M, Cheatham TE, Galindo-Murillo R, Jurečka P: Refinement of the Sugar-Phosphate Backbone Torsion Beta for the AMBER Force Fields Improves the Description of Z-DNA and B-DNA. J. Chem. Theory Comput., 11(12), 5723–5736, 2015. (DOI)

2014

  1. Dršata T, Špačková N, Jurečka P, Zgarbová M, Šponer J, Lankaš F: Mechanical properties of symmetric and asymmetric DNA A-tracts: implications for looping and nucleosome positioning. Nucleic Acids Res., 42(11), 7383-7394, 2014. (DOI)
  2. Dršata T, Zgarbová M, Špačková N, Jurečka P, Šponer J, Lankaš F: Mechanical Model of DNA Allostery. J. Phys. Chem. Lett., 5(21), 3831-3835, 2014. (DOI)
  3. 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)
  4. Mládek A, Banáš P, Jurečka P, Otyepka M, Zgarbová M, Šponer J: Energies and 2′-Hydroxyl Group Orientations of RNA Backbone Conformations. Benchmark CCSD(T)/CBS Database, Electronic Analysis, and Assessment of DFT Methods and MD Simulations. J. Chem. Theory Comput., 10(1), 463-480, 2014. (DOI)
  5. Mlýnský V, Banáš P, Šponer J, van der Kamp MW, Mulholland AJ, Otyepka M: Comparison of ab Initio, DFT, and Semiempirical QM/MM Approaches for Description of Catalytic Mechanism of Hairpin Ribozyme. J. Chem. Theory Comput., 10(4), 1608-1622, 2014. (DOI)
  6. 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)
  7. Sripathi KN, Tay WW, Banáš P, Otyepka M, Šponer J, Walter NG: Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape. RNA, 20(7), 1112-1128, 2014. (DOI)
  8. Zgarbová M, Otyepka M, Šponer J, Lankaš F, Jurečka P: Base Pair Fraying in Molecular Dynamics Simulations of DNA and RNA. J. Chem. Theory Comput., 10(8), 3177-3189, 2014. (DOI)

2013

  1. Krepl M, Otyepka M, Banáš P, Šponer J: Effect of Guanine to Inosine Substitution on Stability of Canonical DNA and RNA Duplexes: Molecular Dynamics Thermodynamics Integration Study. J. Phys. Chem. B, 117(6), 1872-1879, 2013. (DOI)
  2. 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)
  3. Mládek A, Krepl M, Svozil D, Čech P, Otyepka M, Banáš P, Zgarbová M, Jurečka P, Šponer J: Benchmark quantum-chemical calculations on a complete set of rotameric families of the DNA sugar–phosphate backbone and their comparison with modern density functional theory. Phys. Chem. Chem. Phys., 15(19), 7295-7310, 2013. (DOI)
  4. Šponer J, Šponer JE, Mládek A, Banáš P, Jurečka P, Otyepka M: How to understand quantum chemical computations on DNA and RNA systems? A practical guide for non-specialists. Methods, 64(1), 3-11, 2013. (DOI)
  5. Šponer J, Šponer JE, Mládek A, Jurečka P, Banáš P, Otyepka M: Nature and magnitude of aromatic base stacking in DNA and RNA: Quantum chemistry, molecular mechanics and experiment. Biopolymers, 99(12), 978–988, 2013. (DOI)
  6. Zgarbová M, Luque FJ, Šponer J, Cheatham TE, Otyepka M, Jurečka P: Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters. J. Chem. Theory Comput., 9(5), 2339-2354, 2013. (DOI)

2012

  1. Banáš P, Mládek A, Otyepka M, Zgarbová M, Jurečka P, Svozil D, Lankaš F, Šponer J: Can We Accurately Describe the Structure of Adenine Tracts in B-DNA? Reference Quantum-Chemical Computations Reveal Overstabilization of Stacking by Molecular Mechanics. J. Chem. Theory Comput., 8(7), 2448-2460, 2012. (DOI)
  2. Banáš P, Sklenovský P, Wedekind JE, Šponer J, Otyepka M: Molecular Mechanism of preQ 1 Riboswitch Action: A Molecular Dynamics Study. J. Phys. Chem. B, 116(42), 12721-12734, 2012. (DOI)
  3. 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)
  4. Krepl M, Zgarbová M, Stadlbauer P, Otyepka M, Banáš P, Koča J, Cheatham TE, Jurečka P, Šponer J: Reference Simulations of Noncanonical Nucleic Acids with Different chi Variants of the AMBER Force Field: Quadruplex DNA, Quadruplex RNA, and Z-DNA. J. Chem. Theory Comput., 8(7), 2506-2520, 2012. (DOI)
  5. Šponer J, Mládek A, Šponer JE, Svozil D, Zgarbová M, Banáš P, Jurečka P, Otyepka M: The DNA and RNA sugar–phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies. Phys. Chem. Chem. Phys., 14(44), 15257-15277, 2012. (DOI)
  6. Šponer J, Otyepka M, Banáš P, Réblová K, Walter NG: Chapter 6. Molecular Dynamics Simulations of RNA Molecules. 129-155, 2012. (DOI)
  7. Zgarbová M, Luque FJ, Šponer J, Otyepka M, Jurečka P: A Novel Approach for Deriving Force Field Torsion Angle Parameters Accounting for Conformation-Dependent Solvation Effects. J. Chem. Theory Comput., 8(9), 3232-3242, 2012. (DOI)

2011

  1. Mlýnský V, Banáš P, Walter NG, Šponer J, Otyepka M: QM/MM Studies of Hairpin Ribozyme Self-Cleavage Suggest the Feasibility of Multiple Competing Reaction Mechanisms. J. Phys. Chem. B, 115(47), 13911-13924, 2011. (DOI)
  2. 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)
  3. Zgarbová M, Jurečka P, Banáš P, Otyepka M, Šponer JE, Leontis NB, Zirbel CL, Šponer J: Noncanonical Hydrogen Bonding in Nucleic Acids. Benchmark Evaluation of Key Base–Phosphate Interactions in Folded RNA Molecules Using Quantum-Chemical Calculations and Molecular Dynamics Simulations. J. Phys. Chem. A, 115(41), 11277-11292, 2011. (DOI)
  4. Zgarbová M, Otyepka M, Šponer J, Mládek A, Banáš P, Cheatham TE, Jurečka P: Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles. J. Chem. Theory Comput., 7(9), 2886-2902, 2011. (DOI)

2010

  1. Banáš P, Hollas D, Zgarbová M, Jurečka P, Orozco M, Cheatham TE, Šponer J, Otyepka M: Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins. J. Chem. Theory Comput., 6(12), 3836-3849, 2010. (DOI)
  2. Banáš P, Walter NG, Šponer J, Otyepka M: Protonation States of the Key Active Site Residues and Structural Dynamics of the glmS Riboswitch As Revealed by Molecular Dynamics. J. Phys. Chem. B, 114(26), 8701-8712, 2010. (DOI)
  3. Mládek A, Šponer JE, Jurečka P, Banáš P, Otyepka M, Svozil D, Šponer J: Conformational Energies of DNA Sugar−Phosphate Backbone: Reference QM Calculations and a Comparison with Density Functional Theory and Molecular Mechanics. J. Chem. Theory Comput., 6(12), 3817-3835, 2010. (DOI)
  4. Mlýnský V, Banáš P, Hollas D, Réblová K, Walter NG, Šponer J, Otyepka M: Extensive Molecular Dynamics Simulations Showing That Canonical G8 and Protonated A38H + Forms Are Most Consistent with Crystal Structures of Hairpin Ribozyme. J. Phys. Chem. B, 114(19), 6642-6652, 2010. (DOI)
  5. Morgado CA, Jurečka P, Svozil D, Hobza P, Šponer J: Reference MP2/CBS and CCSD(T) quantum-chemical calculations on stacked adenine dimers. Comparison with DFT-D, MP2.5, SCS(MI)-MP2, M06-2X, CBS(SCS-D) and force field descriptions. Phys. Chem. Chem. Phys., 12(14), 3522-3534, 2010. (DOI)
  6. Šponer JE, Vázquez-Mayagoitia Á, Sumpter BG, Leszczynski J, Šponer J, Otyepka M, Banáš P, Fuentes-Cabrera M: Theoretical Studies on the Intermolecular Interactions of Potentially Primordial Base-Pair Analogues. Chem. Eur. J., 16(10), 3057-3065, 2010. (DOI)
  7. Zgarbová M, Otyepka M, Šponer J, Hobza P, Jurečka P: Large-scale compensation of errors in pairwise-additive empirical force fields: comparison of AMBER intermolecular terms with rigorous DFT-SAPT calculations. Phys. Chem. Chem. Phys., 12(35), 10476-10493, 2010. (DOI)

2009

  1. Banáš P, Jurečka P, Walter NG, Šponer J, Otyepka M: Theoretical studies of RNA catalysis: Hybrid QM/MM methods and their comparison with MD and QM. Methods, 49(2), 202-216, 2009. (DOI)
  2. Beššeová I, Otyepka M, Réblová K, Šponer J: Dependence of A-RNA simulations on the choice of the force field and salt strength. Phys. Chem. Chem. Phys., 11(45), 10701-10711, 2009. (DOI)
  3. Morgado CA, Jurečka P, Svozil D, Hobza P, Šponer J: Balance of Attraction and Repulsion in Nucleic-Acid Base Stacking: CCSD(T)/Complete-Basis-Set-Limit Calculations on Uracil Dimer and a Comparison with the Force-Field Description. J. Chem. Theory Comput., 5(6), 1524-1544, 2009. (DOI)
  4. Šponer J, Zgarbová M, Jurečka P, Riley KE, Šponer JE, Hobza P: Reference Quantum Chemical Calculations on RNA Base Pairs Directly Involving the 2′-OH Group of Ribose. J. Chem. Theory Comput., 5(4), 1166-1179, 2009. (DOI)

2008

  1. Banáš P, Rulíšek L, Hánošová V, Svozil D, Walter NG, Šponer J, Otyepka M: General Base Catalysis for Cleavage by the Active-Site Cytosine of the Hepatitis Delta Virus Ribozyme: QM/MM Calculations Establish Chemical Feasibility.. J. Phys. Chem. B, 112(35), 11177-11187, 2008. (DOI)

2007

  1. Meneni SR, Shell SM, Gao L, Jurečka P, Lee W, Šponer J, Zou Y, Chiarelli MP, Cho BP: Spectroscopic and Theoretical Insights into Sequence Effects of Aminofluorene-Induced Conformational Heterogeneity and Nucleotide Excision Repair. Biochemistry, 46(40), 11263-11278, 2007. (DOI)