Jirí Sponer

Molecular dynamics suggest multifunctionality of an adenine imino group in acid-base catalysis of the hairpin ribozyme (2009)

Ditzler, Mark A., Sponer, Jirí, 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...

Elastic properties of ribosomal RNA building blocks: molecular dynamics of the GTPase-associated center rRNA (2007)

Rázga, Filip, Koca, Jaroslav, Mokdad, Ali, Sponer, Jirí

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...

The genomic HDV ribozyme utilizes a previously unnoticed U-turn motif to accomplish fast site-specific catalysis (2007)

Sefcikova, Jana, Krasovska, Maryna V., Sponer, Jirí, 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...

Molecular dynamics simulations of sarcin-ricin rRNA motif (2006)

Spacková, Nad'a, Sponer, Jirí

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,...

Molecular dynamics simulations of RNA kissing-loop motifs reveal structural dynamics and formation of cation-binding pockets (2003)

Réblová, Kamila, Spacková, Nad’a, 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...

Critical effect of the N2 amino group on structure, dynamics, and elasticity of DNA polypurine tracts.

Lankas, Filip, Cheatham, Thomas E, Spacková, Nad'a, Hobza, Pavel, Langowski, Jörg, Sponer, Jirí

Unrestrained 5-20-ns explicit-solvent molecular dynamics simulations using the Cornell et al. force field have been carried out for d[GCG(N)11GCG]2 (N, purine base) considering guanine*cytosine...

Critical effect of the N2 amino group on structure, dynamics, and elasticity of DNA polypurine tracts.

Lankas, Filip, Cheatham, Thomas E, Spacková, Nad'a, Hobza, Pavel, Langowski, Jörg, Sponer, Jirí

Unrestrained 5-20-ns explicit-solvent molecular dynamics simulations using the Cornell et al. force field have been carried out for d[GCG(N)11GCG]2 (N, purine base) considering guanine*cytosine...