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| Description
| - The non-coding RNAs play decisive roles in expression and regulation of genetic information. Among them catalytic RNAs (ribozymes) have high biological and biotechnological relevance. Still, more than a quarter-century after their discovery, the understanding of physical-chemistry of RNA catalysis lags behind that of proteins. The project suggests major step forward in physical-chemistry understanding of RNA catalysis, based on integrated application of state-of-the art computational tools, mainly large-scale classical and quantum-classical simulations. Applicability and limitations of the methodology will be established, including its tuning. Three crystallographically and biochemically best characterized small ribozymes, the hairpin, hepatitis delta virus and glmS ribozymes will be studied and complemented by study of protein CRISPR Csy4 endonuclease, which also catalyzes RNA self-cleavage. The interdisciplinary project will improve atomistic-resolution understanding of the RNA catalysis and contribute to the development of advanced computational tools to tackle RNA. (en)
- Nekódující RNA hrají zásadní úlohu při údržbě, regulaci a modifikaci genetické informace. Klíčovými molekulami jsou RNA enzymy (ribozymy), které mají významné biologické a biotechnologické funkce. Přesto více než čtvrt století po jejich objevu jsou znalosti o RNA katalýze nedostatečné ve srovnání s katalytickými bílkovinami. Projekt navrhuje výrazný krok vpřed ve fyzikálně-chemickém pochopení RNA katalýzy. Je založen na integrované aplikaci nejmodernějších počítačových metod, především masívní aplikaci klasických a kvantově-klasických simulací. Bude určena použitelnost a limitace metod, včetně jejich testování a adjustace. Studovány budou tři nejlépe krystalograficky a biochemicky charakterizované RNA enzymy, vlásenkový, HDV a glmS ribozym. Projekt dále zahrnuje CRISPR Csy4 endonukleázu, což je bílkovina, jež rovněž katalyzuje štěpení cukr-fosfátové páteře RNA. Tento interdisciplinární projekt bude mít podstatný přínos k základnímu pochopení fyzikální chemie RNA katalýzy na atomární úrovni a přispěje rovněž k vývoji moderních počítačových metod vhodných ke studiu RNA.
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| Title
| - Catalytic strategies of RNA and RNP enzymes studied by multi-scale computational approach (en)
- Katalytická strategie RNA a RNP enzymů studovaná širokým spektrem výpočetních metod
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| skos:notation
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| http://linked.open...avai/cep/aktivita
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| http://linked.open...kovaStatniPodpora
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| http://linked.open...ep/celkoveNaklady
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| http://linked.open...datumDodatniDoRIV
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| http://linked.open...i/cep/druhSouteze
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| http://linked.open...ep/duvernostUdaju
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| http://linked.open.../cep/fazeProjektu
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| http://linked.open...ai/cep/hlavniObor
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| http://linked.open...vai/cep/kategorie
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| http://linked.open.../cep/klicovaSlova
| - RNA enzyme catalysis QM/MM quantum chemistry molecular dynamics (en)
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| http://linked.open...ep/partnetrHlavni
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| http://linked.open...inujicichPrijemcu
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| http://linked.open...cep/pocetPrijemcu
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| http://linked.open...ocetSpoluPrijemcu
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| http://linked.open.../pocetVysledkuRIV
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| http://linked.open...enychVysledkuVRIV
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| http://linked.open...lneniVMinulemRoce
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| http://linked.open.../prideleniPodpory
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| http://linked.open...iciPoslednihoRoku
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| http://linked.open...atUdajeProjZameru
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| http://linked.open.../vavai/cep/soutez
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| http://linked.open...usZobrazovaneFaze
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| http://linked.open...ai/cep/typPojektu
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| http://linked.open...ep/ukonceniReseni
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| http://linked.open.../cep/vedlejsiObor
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| http://linked.open...ep/zahajeniReseni
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| http://linked.open...tniCyklusProjektu
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| is http://linked.open...vavai/riv/projekt
of | - Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape
- Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome
- 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
- Computer Folding of RNA Tetraloops? Are We There Yet?
- Nature and Magnitude of Aromatic Base Stacking in DNA and RNA: Quantum Chemistry, Molecular Mechanics, and Experiment
- A Novel Approach for Deriving Force Field Torsion Angle Parameters Accounting for Conformation-Dependent Solvation Effects
- Can We Accurately Describe the Structure of Adenine Tracts in B-DNA? Reference Quantum-Chemical Computations Reveal Overstabilization of Stacking by Molecular Mechanics
- The role of an active site Mg2+ in HDV ribozyme self-cleavage: insights from QM/MM calculations
- How to understand quantum chemical computations on DNA and RNA systems? A practical guide for non-specialists
- Simulations of A-RNA Duplexes. The Effect of Sequence, Solute Force Field, Water Model, and Salt Concentration
- The DNA and RNA sugar-phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies
- Molecular Mechanism of preQ(1) Riboswitch Action: A Molecular Dynamics Study
- RNA 3D structure analysis and prediction
- Structure and mechanical properties of the ribosomal L1 stalk three-way junction
- Are Waters around RNA More than Just a Solvent? - An Insight from Molecular Dynamics Simulations
- Comparison of ab Initio, DFT, and Semiempirical QM/MM Approaches for Description of Catalytic Mechanism of Hairpin Ribozyme
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| is http://linked.open...vavai/cep/projekt
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