Réblová, Kamila, Spacková, Nada, Sponer, Judit E., Koca, Jaroslav, Sponer, Jirí
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...
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...
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...
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...
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...
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...
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....
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...