Molecular Interactions of Nucleic Acid Bases. A Review of Quantum-Chemical Studies (2003)
Ab initio quantum-chemical calculations with inclusion of electron correlation significantly contributed to our understanding of molecular interactions of DNA and RNA bases. Some of the most...
Réblová, Kamila, Špačková, Nad'a, Šponer, Judit E., Koča, Jaroslav, Šponer, Jiří
Explicit solvent molecular dynamics (MD) simulations were carried out for three RNA kissing–loop complexes. The theoretical structure of two base pairs (2 bp) complex of H3 stem–loop of Moloney...
Non-Watson-Crick Basepairing and Hydration in RNA Motifs: Molecular Dynamics of 5S rRNA Loop E
Réblová, Kamila, Špačková, Nad'a, Štefl, Richard, Csaszar, Kristina, Koča, Jaroslav, Leontis, Neocles B., ...
Explicit solvent and counterion molecular dynamics simulations have been carried out for a total of >80 ns on the bacterial and spinach chloroplast 5S rRNA Loop E motifs. The Loop E sequences form...
Štefl, Richard, Cheatham, Thomas E., Špačková, Nad'a, Fadrná, Eva, Berger, Imre, Koča, Jaroslav, ...
The formation of a cation-stabilized guanine quadruplex (G-DNA) stem is an exceptionally slow process involving complex kinetics that has not yet been characterized at atomic resolution. Here, we...
DNA Basepair Step Deformability Inferred from Molecular Dynamics Simulations
Lankaš, Filip, Šponer, Jiří, Langowski, Jörg, Cheatham, Thomas E.
The sequence-dependent DNA deformability at the basepair step level was investigated using large-scale atomic resolution molecular dynamics simulation of two 18-bp DNA oligomers:...
Molecular Dynamics Simulations of Guanine Quadruplex Loops: Advances and Force Field Limitations
Fadrná, Eva, Špačková, Nad'a, Štefl, Richard, Koča, Jaroslav, Cheatham, Thomas E., Šponer, Jiří
A computational analysis of d(GGGGTTTTGGGG)2 guanine quadruplexes containing either lateral or diagonal four-thymidine loops was carried out using molecular dynamics (MD) simulations in explicit...
Long-Residency Hydration, Cation Binding, and Dynamics of Loop E/Helix IV rRNA-L25 Protein Complex
Réblová, Kamila, Špačková, Nad'a, Koča, Jaroslav, Leontis, Neocles B., Šponer, Jiří
Molecular dynamics simulations of RNA-protein complex between Escherichia coli loop E/helix IV (LE/HeIV) rRNA and L25 protein reveal a qualitative agreement between the experimental and simulated...
Molecular dynamics simulations of sarcin–ricin rRNA motif
Explicit solvent molecular dynamics (MD) simulations were carried out for sarcin–ricin domain (SRD) motifs from 23S (Escherichia coli) and 28S (rat) rRNAs. The SRD motif consists of GAGA tetraloop,...
Rázga, Filip, Koča, Jaroslav, Šponer, Jiří, Leontis, Neocles B.
Kink-turn (K-turn) motifs are asymmetric internal loops found at conserved positions in diverse RNAs, with sharp bends in phosphodiester backbones producing V-shaped structures. Explicit-solvent...
Réblová, Kamila, Špačková, Nad'a, Šponer, Judit E., Koča, Jaroslav, Šponer, Jiří
Explicit solvent molecular dynamics (MD) simulations were carried out for three RNA kissing–loop complexes. The theoretical structure of two base pairs (2 bp) complex of H3 stem–loop of Moloney...
Non-Watson-Crick Basepairing and Hydration in RNA Motifs: Molecular Dynamics of 5S rRNA Loop E
Réblová, Kamila, Špačková, Nad'a, Štefl, Richard, Csaszar, Kristina, Koča, Jaroslav, Leontis, Neocles B., ...
Explicit solvent and counterion molecular dynamics simulations have been carried out for a total of >80 ns on the bacterial and spinach chloroplast 5S rRNA Loop E motifs. The Loop E sequences form...
Štefl, Richard, Cheatham, Thomas E., Špačková, Nad'a, Fadrná, Eva, Berger, Imre, Koča, Jaroslav, ...
The formation of a cation-stabilized guanine quadruplex (G-DNA) stem is an exceptionally slow process involving complex kinetics that has not yet been characterized at atomic resolution. Here, we...
DNA Basepair Step Deformability Inferred from Molecular Dynamics Simulations
Lankaš, Filip, Šponer, Jiří, Langowski, Jörg, Cheatham, Thomas E.
The sequence-dependent DNA deformability at the basepair step level was investigated using large-scale atomic resolution molecular dynamics simulation of two 18-bp DNA oligomers:...
Molecular Dynamics Simulations of Guanine Quadruplex Loops: Advances and Force Field Limitations
Fadrná, Eva, Špačková, Nad'a, Štefl, Richard, Koča, Jaroslav, Cheatham, Thomas E., Šponer, Jiří
A computational analysis of d(GGGGTTTTGGGG)2 guanine quadruplexes containing either lateral or diagonal four-thymidine loops was carried out using molecular dynamics (MD) simulations in explicit...
Long-Residency Hydration, Cation Binding, and Dynamics of Loop E/Helix IV rRNA-L25 Protein Complex
Réblová, Kamila, Špačková, Nad'a, Koča, Jaroslav, Leontis, Neocles B., Šponer, Jiří
Molecular dynamics simulations of RNA-protein complex between Escherichia coli loop E/helix IV (LE/HeIV) rRNA and L25 protein reveal a qualitative agreement between the experimental and simulated...
Rázga, Filip, Koča, Jaroslav, Šponer, Jiří, Leontis, Neocles B.
Kink-turn (K-turn) motifs are asymmetric internal loops found at conserved positions in diverse RNAs, with sharp bends in phosphodiester backbones producing V-shaped structures. Explicit-solvent...
Molecular dynamics simulations of sarcin–ricin rRNA motif
Explicit solvent molecular dynamics (MD) simulations were carried out for sarcin–ricin domain (SRD) motifs from 23S (Escherichia coli) and 28S (rat) rRNAs. The SRD motif consists of GAGA tetraloop,...
Trapped water molecules are essential to structural dynamics and function of a ribozyme
Rhodes, Maria M., Réblová, Kamila, Šponer, Jiří, Walter, Nils G.
Ribozymes are catalytically competent examples of highly structured noncoding RNAs, which are ubiquitous in the processing and regulation of genetic information. Combining explicit-solvent molecular...
Sefcikova, Jana, Krasovska, Maryna V., Šponer, Jiří, Walter, Nils G.
The genome of the human hepatitis delta virus (HDV) harbors a self-cleaving catalytic RNA motif, the genomic HDV ribozyme, whose crystal structure shows the dangling nucleotides 5′ of the cleavage...
Cations and Hydration in Catalytic RNA: Molecular Dynamics of the Hepatitis Delta Virus Ribozyme
Krasovska, Maryna V., Sefcikova, Jana, Réblová, Kamila, Schneider, Bohdan, Walter, Nils G., Šponer, Jiří
The hepatitis delta virus (HDV) ribozyme is an RNA enzyme from the human pathogenic HDV. Cations play a crucial role in self-cleavage of the HDV ribozyme, by promoting both folding and chemistry....
Rázga, Filip, Koča, Jaroslav, Mokdad, Ali, Šponer, Jiří
Explicit solvent molecular dynamics (MD) was used to describe the intrinsic flexibility of the helix 42–44 portion of the 23S rRNA (abbreviated as Kt-42+rGAC; kink-turn 42 and GTPase-associated...
Molecular dynamics simulations and their application to four-stranded DNA
This review provides a critical assessment of the advantages and limitations of modeling methods available for guanine quadruplex (G-DNA) molecules. We characterize the relations of simulations to...
Conformations of Flanking Bases in HIV-1 RNA DIS Kissing Complexes Studied by Molecular Dynamics
Réblová, Kamila, Fadrná, Eva, Sarzynska, Joanna, Kulinski, Tadeusz, Kulhánek, Petr, Ennifar, Eric, ...
Explicit solvent molecular dynamics simulations (in total almost 800 ns including locally enhanced sampling runs) were applied with different ion conditions and with two force fields (AMBER and...
Ditzler, Mark A., Šponer, Jiří, Walter, Nils G.
Despite numerous structural and biochemical investigations, the catalytic mechanism of hairpin ribozyme self-cleavage remains elusive. To gain insight into the coupling of active site dynamics with...