Změnit instituci
Pokročilé nano a mikrotechnologie Pokročilé materiály Strukturní biologie Gen. a prot. rostlin. systémů Molekulární medicína Výzkum mozku a lidské mysli Molekulární vet. medicína

Výzkumná skupina Jiřího Šponera

Vedoucí výzkumné skupiny
Researcher ID
Telefon: +420 541 517 133
E-mail: ,
Kancelář:
Masarykova univerzita - CEITEC MU
Zástupce vedoucího výzkumné skupiny
Researcher ID
Telefon: +420 541 517 246
E-mail:
Kancelář:
Masarykova univerzita - CEITEC MU

Research areas

  • Studies of structure, dynamics and molecular interactions of nucleic acids and their complexes with proteins using explicit solvent molecular dynamics simulations; main attention is paid to functional RNAs, such as ribosomal RNAs and catalytic RNAs
  • Studies of canonical and noncanonical DNA molecules
  • Quantum chemical modelling of processes relevant to the prebiotic synthesis of nucleic acid components
  • Structural bioinformatics of RNA (classification of molecular interactions in nucleic acids based on structural and sequence data)
  • Testing and refinement of force fields for atomistic simulations of nucleic acids
  • Reference quantum-chemical calculations of molecular interactions and conformational substates in nucleic acids

Main objectives

  • Investigation of the role of RNA and DNA in development and human diseases.
  • Development of new methodologies for investigating the structure, interactions, and dynamics of biomolecules.

Content of research

Computational studies, combining a full range of leading computational methods (explicit solvent molecular dynamics simulations, quantum-chemical calculations, hybrid quantum-classical calculations and bioinformatics), will be used to unravel the key features of the RNA structure and the role of RNA in protein biosynthesis. The work will be initially devoted to ribosome and ribozymes where atomic resolution information is available. The research will be gradually extended to other RNA systems where enough experimental structural data is available.

Modern computational techniques can fill several major gaps in the present knowledge of the RNA function. We will classify RNA building blocks and their molecular interactions, to unravel the link between their physical-chemical properties and evolutionary patterns. We will analyse chemical reactions at the atomistic level of electronic structure description to capture catalytic strategies of ribozymes and to model prebiotic chemical reactions.

Extended studies will be carried out on selected DNA systems, mainly to understand the role of sequence-dependency of B-DNA structure and the principles of folding of quadruplex DNA.

Prebiotic chemical reactions will be studied using advanced electronic structure computations.

Free energy calculations, or molecular dynamics simulations, often critically depend on the adequacy of the molecular mechanical force fields and other methods describing the relationships between molecular structures and energies. Therefore, much effort will be devoted to the development and verification of these methods. This will mainly be done in the field of nucleic acids, where the main focus will be put on noncanonical architectures such as hairpin loops, which are notoriously difficult to describe by the force fields.

seznam / vizitky

Jméno a pozice

E-mail

Telefon

prof. RNDr. Jiří Šponer, DrSc.
Vedoucí výzkumné skupiny
+420 541 517 133
Judit Šponerová, PhD
Vedoucí výzkumný pracovník
+420 541 517 246
Mgr. Marek Havrila, Ph.D.
PhD student
Konstantinos Gkionis, Ph.D., M. Sc.
Výzkumný pracovník - postdoc
Barira Islam, Ph.D.

VYBRANÉ PUBLIKACE

2017

  • XU, JF; TSANAKOPOULOU, M; MAGNANI, CJ; SZABLA, R; SPONER, JE; SPONER, J; GORA, RW; SUTHERLAND, JD, 2017:A prebiotically plausible synthesis of pyrimidine beta-ribonucleosides and their phosphate derivatives involving photoanomerization. NATURE CHEMISTRY 9 (4), p. 303 - 309.

2016

  • CIVIS, S; SZABLA, R; SZYJA, BM; SMYKOWSKI, D; IVANEK, O; KNIZEK, A; KUBELIK, P; SPONER, J; FERUS, M; SPONER, JE, 2016:TiO2-catalyzed synthesis of sugars from formaldehyde in extraterrestrial impacts on the early Earth. SCIENTIFIC REPORTS 6
  • DRSATA, T; ZGARBOVA, M; JURECKA, P; SPONER, J; LANKAS, F, 2016:On the Use of Molecular Dynamics Simulations for Probing Allostery through DNA. BIOPHYSICAL JOURNAL 110 (4), p. 874 - 876.
  • GKIONIS, K; KRUSE, H; SPONER, J, 2016:Derivation of Reliable Geometries in QM Calculations of DNA Structures: Explicit Solvent QM/MM and Restrained Implicit Solvent QM Optimizations of G-Quadruplexes. JOURNAL OF CHEMICAL THEORY AND COMPUTATION 12 (4), p. 2000 - 2016.
  • KREPL, M; CLERY, A; BLATTER, M; ALLAIN, FHT; SPONER, J, 2016:Synergy between NMR measurements and MD simulations of protein/RNA complexes: application to the RRMs, the most common RNA recognition motifs. NUCLEIC ACIDS RESEARCH 44 (13), p. 6452 - 6470.
  • SPONER, JE; SPONER, J; NOVAKOVA, O; BRABEC, V; SEDO, O; ZDRAHAL, Z; COSTANZO, G; PINO, S; SALADINO, R; DI MAURO, E, 2016:Emergence of the First Catalytic Oligonucleotides in a Formamide-Based Origin Scenario. CHEMISTRY-A EUROPEAN JOURNAL 22 (11), p. 3572 - 3586.
  • SPONER, JE; SZABLA, R; GORA, RW; SAITTA, AM; PIETRUCCI, F; SAIJA, F; DI MAURO, E; SALADINO, R; FERUS, M; CIVIS, S; SPONER, J, 2016:Prebiotic synthesis of nucleic acids and their building blocks at the atomic level - merging models and mechanisms from advanced computations and experiments. PHYSICAL CHEMISTRY CHEMICAL PHYSICS 18 (30), p. 20047 - 20066.
  • SZABLA, R; GORA, RW; SPONER, J, 2016:Ultrafast excited-state dynamics of isocytosine. PHYSICAL CHEMISTRY CHEMICAL PHYSICS 18 (30), p. 20208 - 20218.

2015

  • FERUS, M; NESVORNY, D; SPONER, J; KUBELIK, P; MICHALCIKOVA, R; SHESTIVSKA, V; SPONER, JE; CIVIS, S, 2015:High-energy chemistry of formamide: A unified mechanism of nucleobase formation. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 112 (3), p. 657 - 662.
  • ISLAM, B; STADLBAUER, P; KREPL, M; KOCA, J; NEIDLE, S; HAIDER, S; SPONER, J, 2015:Extended molecular dynamics of a c-kit promoter quadruplex. NUCLEIC ACIDS RESEARCH 43 (18), p. 8673 - 8693.
  • OHNMACHT, SA; MARCHETTI, C; GUNARATNAM, M; BESSER, RJ; HAIDER, SM; DI VITA, G; LOWE, HL; MELLINAS-GOMEZ, M; DIOCOU, S; ROBSON, M; SPONER, J; ISLAM, B; PEDLEY, RB; HARTLEY, JA; NEIDLE, S, 2015:A G-quadruplex-binding compound showing anti-tumour activity in an in vivo model for pancreatic cancer. SCIENTIFIC REPORTS 5
  • STADLBAUER, P; KUHROVA, P; BANAS, P; KOCA, J; BUSSI, G; TRANTIREK, L; OTYEPKA, M; SPONER, J, 2015:Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations. NUCLEIC ACIDS RESEARCH 43 (20), p. 9626 - 9644.
  • SZABLA, R; CAMPOS, J; SPONER, JE; SPONER, J; GORA, RW; SUTHERLAND, JD, 2015:Excited-state hydrogen atom abstraction initiates the photochemistry of beta-2 '-deoxycytidine. CHEMICAL SCIENCE 6 (3), p. 2035 - 2043.
  • SZABLA, R; SPONER, J; GORA, RW, 2015:Electron-Driven Proton Transfer Along H2O Wires Enables Photorelaxation of pi sigma* States in Chromophore-Water Clusters. Journal of Physical Chemistry Letters 6 (8), p. 1467 - 1471.

2014

  • CIVIS, S; FERUS, M; SPONER, JE; SPONER, J; KAVAN, L; ZUKALOVA, M, 2014:Room temperature spontaneous conversion of OCS to CO2 on the anatase TiO2 surface. CHEMICAL COMMUNICATIONS 50 (57), p. 7712 - 7715.
  • DRSATA, T; SPACKOVA, N; JURECKA, P; ZGARBOVA, M; SPONER, J; LANKAS, F, 2014:Mechanical properties of symmetric and asymmetric DNA A-tracts: implications for looping and nucleosome positioning. NUCLEIC ACIDS RESEARCH 42 (11), p. 7383 - 7394.
  • GKIONIS, K; KRUSE, H; PLATTS, JA; MLADEK, A; KOCA, J; SPONER, J, 2014:Ion Binding to Quadruplex DNA Stems. Comparison of MM and QM Descriptions Reveals Sizable Polarization Effects Not Included in Contemporary Simulations. JOURNAL OF CHEMICAL THEORY AND COMPUTATION 10 (3), p. 1326 - 1340.
  • KUEHROVA, P; OTYEPKA, M; SPONER, J; BANAS, P, 2014:Are Waters around RNA More than Just a Solvent? - An Insight from Molecular Dynamics Simulations. JOURNAL OF CHEMICAL THEORY AND COMPUTATION 10 (1), p. 401 - 411.
  • MLADEK, A; BANAS, P; JURECKA, P; OTYEPKA, M; ZGARBOVA, M; SPONER, J, 2014: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. JOURNAL OF CHEMICAL THEORY AND COMPUTATION 10 (1), p. 463 - 480.
  • MLYNSKY, V; BANAS, P; SPONER, J; VAN DER KAMP, MW; MULHOLLAND, AJ; OTYEPKA, M, 2014:Comparison of ab Initio, DFT, and Semiempirical QM/MM Approaches for Description of Catalytic Mechanism of Hairpin Ribozyme. JOURNAL OF CHEMICAL THEORY AND COMPUTATION 10 (4), p. 1608 - 1622.
  • SZABLA, R; GORA, RW; SPONER, J; SPONER, JE, 2014:Molecular Mechanism of Diaminomaleonitrile to Diaminofumaronitrile Photoisomerization: An Intermediate Step in the Prebiotic Formation of Purine Nucleobases. CHEMISTRY-A EUROPEAN JOURNAL 20 (9), p. 2515 - 2521.
  • SZABLA, R; SPONER, JE; SPONER, J; SOBOLEWSKI, AL; GORA, RW, 2014:Solvent effects on the photochemistry of 4-aminoimidazole-5-carbonitrile, a prebiotically plausible precursor of purines. PHYSICAL CHEMISTRY CHEMICAL PHYSICS 16 (33), p. 17617 - 17626.

2013

  • HAVRILA, M; REBLOVA, K; ZIRBEL, CL; LEONTIS, NB; SPONER, J, 2013:lsosteric and Nonisosteric Base Pairs in RNA Motifs: Molecular Dynamics and Bioinformatics Study of the Sarcin Ricin Internal Loop. JOURNAL OF PHYSICAL CHEMISTRY B 117 (46), p. 14302 - 14319.
  • PINO, S; COSTANZO, G; GIORGI, A; SPONER, J; SPONER, JE; DI MAURO, E, 2013:Ribozyme Activity of RNA Nonenzymatically Polymerized from 3 ',5 '-Cyclic GMP. ENTROPY 15 (12), p. 5362 - 5383.
  • SPONER, J; MLADEK, A; SPACKOVA, N; CANG, XH; CHEATHAM, TE; GRIMME, S, 2013:Relative Stability of Different DNA Guanine Quadruplex Stem Topologies Derived Using Large-Scale Quantum-Chemical Computations. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 135 (26), p. 9785 - 9796.
  • SPONER, J; SPONER, JE; MLADEK, A; BANAS, P; JURECKA, P; OTYEPKA, M, 2013:How to understand quantum chemical computations on DNA and RNA systems? A practical guide for non-specialists. METHODS 64 (1), p. 3 - 11.
  • SPONER, J; SPONER, JE; MLADEK, A; JURECKA, P; BANAS, P; OTYEPKA, M, 2013:Nature and Magnitude of Aromatic Base Stacking in DNA and RNA: Quantum Chemistry, Molecular Mechanics, and Experiment. BIOPOLYMERS 99 (12), p. 978 - 988.
  • STADLBAUER, P; KREPL, M; CHEATHAM, TE; KOCA, J; SPONER, J, 2013:Structural dynamics of possible late-stage intermediates in folding of quadruplex DNA studied by molecular simulations. NUCLEIC ACIDS RESEARCH 41 (14), p. 7128 - 7143.
  • SZABLA, R; TUNA, D; GORA, RW; SPONER, J; SOBOLEWSKI, AL; DOMCKE, W, 2013:Photochemistry of 2-Aminooxazole, a Hypothetical Prebiotic Precursor of RNA Nucleotides. JOURNAL OF PHYSICAL CHEMISTRY LETTERS 4 (16), p. 2785 - 2788.

2012

  • BANAS, P; MLADEK, A; OTYEPKA, M; ZGARBOVA, M; JURECKA, P; SVOZIL, D; LANKAS, F; SPONER, J, 2012:Can We Accurately Describe the Structure of Adenine Tracts in B-DNA? Reference Quantum-Chemical Computations Reveal Overstabilization of Stacking by Molecular Mechanics. JOURNAL OF CHEMICAL THEORY AND COMPUTATION 8 (7), p. 2448 - 2460.
  • FERUS, M; CIVIS, S; MLADEK, A; SPONER, J; JUHA, L; SPONER, JE, 2012:On the Road from Formamide Ices to Nucleobases: IR-Spectroscopic Observation of a Direct Reaction between Cyano Radicals and Formamide in a High-Energy Impact Event. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 134 (51), p. 20788 - 20796.
  • SPONER, J; CANG, XH; CHEATHAM, TE, 2012:Molecular dynamics simulations of G-DNA and perspectives on the simulation of nucleic acid structures. METHODS 57 (1), p. 25 - 39.
  • SPONER, J; MLADEK, A; SPONER, JE; SVOZIL, D; ZGARBOVA, M; BANAS, P; JURECKA, P; OTYEPKA, M, 2012:The DNA and RNA sugar-phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies. PHYSICAL CHEMISTRY CHEMICAL PHYSICS 14 (44), p. 15257 - 15277.
  • SPONER, JE; SPONER, J, 2012:Is formamide nature's choice to create life? Comment on the paper "Formamide and the origin of life" by Raffaele Saladino et al.. PHYSICS OF LIFE REVIEWS 9 (1), p. 109 - 110.

2010

  • DITZLER, MA; OTYEPKA, M; SPONER, J; WALTER, NG, 2010:Molecular Dynamics and Quantum Mechanics of RNA: Conformational and Chemical Change We Can Believe In. ACCOUNTS OF CHEMICAL RESEARCH 43 (1), p. 40 - 47.
  • REBLOVA, K; RAZGA, F; LI, W; GAO, HX; FRANK, J; SPONER, J, 2010:Dynamics of the base of ribosomal A-site finger revealed by molecular dynamics simulations and Cryo-EM. NUCLEIC ACIDS RESEARCH 38 (4), p. 1325 - 1340.

GRANTY

  • Structural dynamics, molecular interactions and function of key RNA motifs (GA203/09/1476), Czech Science Foundation - Standard Grants, 2009 - 2013
  • Structure and dynamics of DNA. Advanced computational studies (GAP208/11/1822), Czech Science Foundation - Standard Grants, 2011 - 2016
  • Structure, dynamics, and reaction mechanism of catalytic RNA (IAA400040802), Academy of Sciences of the Czech Republic - Grants of distinctly investigative character focused on the sphere of research pursued at present particularly in the Academy of Sciences of the Czech Rep., 2008 - 2011
  • Centrum biologie RNA (P305/12/G034), Czech Science Foundation - Projects of Excellence, 2012 - 2018
  • Theoretical and experimental studies related to the prebiotic chemistry of nucleid acids (GAP208/10/2302), Czech Science Foundation - Standard Grants, 2010 - 2014

CURRENT RESEARCH INFRASTRUCTURE

The laboratory is presently equipped with several computer clusters of different architectures. The newest computer cluster cloud consists of four separate units. The first cluster is composed of 36 nodes with total number of 432 1.9 GHz E5-2420 Xeon cores with 0.8 TB of memory. Second unit dedicated for memory-demanding jobs comprises 12 nodes with 144 1.9 GHz E5-2420 Xeon CPU cores, each one having 96 GB of RAM memory. The third one is a GPU cluster composed of 8 clients with more than 8,000 GPU cores and 48 GB of GDDR5 memory. The last cluster consists of 12 separate nodes each one having 48 AMD Opteron 6238 2.6 GHz CPU cores with more than 60 TB of storage capacity in total. All computing units are interconnected and communicate via a fast Gigabit network operated by a Cisco SG500-52 switch. There are three additional older clusters. The first cluster contains 15 nodes with a total number of 30 CPUs (Intel Xeon 3.0 GHz), the second contains 30 nodes with a total number of 120 primitive (core) CPUs (AMD Opteron 285 and AMD Opteron 2220 DualCore), and the last one contains 43 nodes with a total number of 344 core CPUs (Intel Xeon E5430 QuadCore).

 

1. Multiscale Modeling of Nucleic Acids

Supervisor: prof. RNDr. Jiří Šponer, DrSc.
Consultants:prof. RNDr. Michal Otyepka, Ph.D., Judit Šponerová, PhD.

Annotation:

Nucleic acids (RNA and DNA) belong to the most important biomacromolecules. Studies of structure and dynamics of nucleic acids represent an important task of modern life sciences. Due to fast development of hardware and software, computational and theoretical approaches are frequently used in nucleic acids studies and represent a respected counterpart of experimental techniques. This PhD project will be based on integrated interdisciplinary utilization of a broad spectrum of computational methods (multi-scale modelling) ranging from state-of-the-art quantum-chemical (QM) approaches through modern explicit solvent molecular dynamics (MD) simulation methods up to bioinformatics. Cooperation with established experimental laboratories will provide necessary experimental feedback. State-of-the-art computational facilities are available not only in our laboratory but also in cooperating laboratories abroad. The exact topic will be specified based on the discussion with the applicant and her/his scientific interests and capabilities. Currently available specific themes include for example multiscale studies of protein-RNA complexes, RNA catalysis, structural dynamics and folding of quadruplex DNA and large-scale QM studies of complete nucleic acids building blocks.

2. Computational Modeling of Processes Relevant to the Origin of Life

Supervisor: prof. RNDr. Jiří Šponer, DrSc.
Consultants: Judit Šponerová, PhD.

Annotation:

Formation of the very first oligonucleotide sequences is one of the greatest mysteries surrounding life’s origin. In the last few years computational chemistry is more and more frequently used to aid experiments at unraveling those simple chemical transformations which could give rise to the emergence of functional biomolecules from an inanimate matter. This PhD project will focus on the application of modern quantum chemistry and molecular dynamics simulations to help understanding the abiogenesis of RNA. The research will be carried out in a close cooperation with leading experimental laboratories using the state-of-the-art computational facilities available in our laboratory. The exact topic will be specified based on discussion with the applicant and her/his scientific interests and capabilities. Currently available specific themes include for example modelling of (i) chemical mechanisms leading to the prebiotic synthesis of nucleotides, (ii) nonenzymatic template-free oligomerizations, as well as (iii) the emergence of the catalytic activity of short oligonucleotide sequences.

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