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| Description
| - Study of the basic principles how molecular interactions influence folding and function of large RNAs, such as the ribosome. The research will be conducted using state of the art computational (explicit solvent simulations and quantum chemistry) and bioinformatics methods, in a close cooperation with experimental laboratories. It aims primarily at analysis of energies of molecular interactions and description of stochastic flexibilities of basic RNA building blocks. Both features are crucial for function of RNAs but are very difficult to assess by experiments. The research will mainly be directed to key medium-sized autonomous RNA building blocks, with the aim to rationalize covariation principles in RNA sequences, explain lack of certain isosteric substitutions during evolution, analyze motif swaps in homologous RNAs, classify RNA base stacking patterns with inclusion of the stacking energies, catalogue structural dynamics of RNA motifs and improve 2D predictions of internal RNA loops. (en)
- Studium základních principů, jak molekulové interakce ovlivňují folding a funkci velkých molekul RNA, jako je ribosom, s použítím nejmodernějších metod počítačové chemie (počítačových simulací s explicitním zahrnutím solventu a kvantové chemie) a bioinformatiky, v úzké spolupráci s experimentálními laboratořemi. Projekt je zaměřen na energetiku molekulových interakcí a stochastické pohyby základních stavebních modulů RNA. Jak energetika, tak stochastické pohyby jsou mimořádně důležité vlastnosti, které ale lze jen velmi omezeně charakterizovat dostupnými experimentálními metodami. Studovány budou zejména autonomní RNA moduly střední velikosti, tzv. RNA motivy. Cíle jsou mj. lépe pochopit pravidla, jimiž se řídí kovariace bází v sekvencích RNA, vysvětlit, proč některé isosterické substituce nejsou během evoluce téměř nikdy realizovány a proč někdy dochází k záměnám funkčních motivů v homologních molekulách RNA. Dále klasifikovat vertikální interakce bází v RNA se zahrnutím energií, katalogizovat strukturně-dynamické vlastnosti RNA motivů a zpřesnit 2D predikce interních RNA smyček.
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| Title
| - Structural dynamics, molecular interactions and function of key RNA motifs (en)
- Strukturní dynamika, molekulové interakce a funkce klíčových motivů RNA
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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...hodnoceniProjektu
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| http://linked.open...vai/cep/kategorie
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| http://linked.open.../cep/klicovaSlova
| - structure; and; function; of; RNA; molecular; dynamics; quantum; chemistry; bioinformatics; ribosome; base; pairs; RNA; motifs (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...jektu+dodavatelem
| - According to the main goal of the project, the work significantly contributed to an improvement of the knowledge of RNA modular building blocks, the physical chemistry of their molecular interactions, and their inclusion in larger RNA systems.The project was extremely successful. This is also documented by 49 publications in impacted journals. (en)
- Dle hlavního cíle projektu, řešitelský tým významně přispěl k prohloubení znalostí o RNA, fyzikální chemii molekulových interakcí modulárních částí RNA i o způsobech začlenění RNA do větších celků.Projekt byl vyřešen na vynikající úrovni. Dokladem je i 49 publikací v impaktovaných časopisech. (cs)
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| http://linked.open...tniCyklusProjektu
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| http://linked.open.../cep/klicoveSlovo
| - structure
- RNA
- and
- base
- bioinformatics
- chemistry
- dynamics
- function
- molecular
- of
- pairs
- quantum
- ribosome
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| is http://linked.open...vavai/riv/projekt
of | - Revisiting the planarity of nucleic acid bases: Pyramidilization at glycosidic nitrogen in purine bases is modulated by orientation of glycosidic torsion
- Large-scale compensation of errors in pairwise-additive empirical force fields: comparison of AMBER intermolecular terms with rigorous DFT-SAPT calculations
- Molecular dynamics and quantum mechanics of RNA: Conformational and chemical change we can believe in
- On the role of the cis Hoogsteen:sugar-edge family of base pairs in platforms and triplets-quantum chemical insights into RNA structural biology
- Structural dynamics of the box C/D RNA Kink-Turn and its complex with proteins: The role of the A-minor 0 interaction, long-residency water bridges, and structural ion-binding sites revealed by molecular simulations
- Molecular dynamics simulations suggest that RNA three-way junctions can act as flexible RNA structural elements in the ribosome
- Protonation states of the key active site residues and structural dynamics of the glmS riboswitch as revealed by molecular dynamics
- Structural dynamics of thrombin-binding DNA aptamer d(GGTTGGTGTGGTTGG) quadruplex DNA studied by large-scale explicit solvent simulations
- 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
- Quantum chemical studies of nucleic acids: Can we construct a bridge to the RNA structural biology and bioinformatics communities?
- Performance of molecular mechanics force fields for RNA simulations: Stability of UUCG and GNRA hairpins
- Explaining the varied glycosidic conformational, G-tract length and sequence preferences for anti-parallel G-quadruplexes
- Insight into G-DNA structural polymorphism and folding from sequence and loop connectivity through free energy analysis
- On the geometry and electronic structure of the As-DNA backbone
- On the stabilization of ribose by silicate minerals
- Prebiotic routes to nucleosides: A quantum chemical insight into the energetics of the multistep reaction pathways
- Understanding RNA flexibility using explicit solvent simulations: The ribosomal and group I intron reverse kink-turn motifs
- 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
- Theoretical modeling on the kinetics of the arsenate-ester hydrolysis: implications to the stability of As-DNA
- How does hydroxyl introduction influence the double helical structure: the stabilization of an altritol nucleic acid:ribonucleic acid duplex
- Reference Simulations of Noncanonical Nucleic Acids with Different chi Variants of the AMBER Force Field: Quadruplex DNA, Quadruplex RNA, and Z-DNA
- Simulations of A-RNA Duplexes. The Effect of Sequence, Solute Force Field, Water Model, and Salt Concentration
- A-minor tertiary interactions in RNA kink-turns. Molecular dynamics and quantum chemical analysis
- The DNA and RNA sugar-phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies
- Formamide-based prebiotic synthesis of nucleobases: A kinetically accessible reaction route
- Innovations in biomolecular modeling and simulations, Volume 2
- Molecular Mechanism of preQ(1) Riboswitch Action: A Molecular Dynamics Study
- A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA
- Conformational energies of DNA sugar-phosphate backbone: Reference QM calculations and a comparison with density functional theory and molecular mechanics
- Dynamics of the base of ribosomal A-site finger revealed by molecular dynamics simulations and Cryo-EM
- Extensive molecular dynamics simulations showing that canonical G8 and protonated A38H+ forms are most consistent with crystal structures of hairpin ribozyme
- Theoretical Studies on the Intermolecular Interactions of Potentially Primordial Base-Pair Analogues
- Cation binding to 15-TBA quadruplex DNA is a multiple-pathway cation-dependent process
- 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
- RNA 3D structure analysis and prediction
- Structure and mechanical properties of the ribosomal L1 stalk three-way junction
- Understanding the sequence preference of recurrent RNA building blocks using quantum chemistry: The intrastrand RNA dinucleotide platform
- QM/MM Studies of Hairpin Ribozyme Self-Cleavage Suggest the Feasibility of Multiple Competing Reaction Mechanisms
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| is http://linked.open...vavai/cep/projekt
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