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4 Computational Methods in Science and Technology

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Parametrization of 2-thiouracil and 4-thiouracil in CHARMM all-atom empirical force field

100%

Sarzyńska J. , Kuliński T.

Computational Methods in Science and Technology

2005

tom Vol. 11, nr 1

49-55

A new set of force field parameters complementing the CHARMM27 all atom empirical force field for nucleic acids was developed for 2-thiouracil and 4-thiouracil, two naturally modified RNA bases. The new parameters allow for molecular modeling and molecular dynamics simulations of RNA containing 2-thiouracil and 4-thiouracil.

Molecular dynamics of RNA structural motif. Temperature enhanced sampling of the conformational space

100%

Kuliński T. , Kulińska K.

Computational Methods in Science and Technology

2002

tom Vol. 8, nr 2

37--45

Temperature Enhanced Molecular Dynamics (TEMD) simulations were applied for the sampling of the conformational space of the RNA structural motif. During MD experiments run in explicit water and ions we observed at the atomic level the switching of the RNA tetraloop structures from the unusual conformations found in the crystal form to the conformation characteristic for the f r e e molecule in the solution. TEMD simulations prove to be useful for the exploration of the possible conformational switches, kinetic traps in RNA folding, the detection of the barriers on folding energy surfaces as well as reviling the role of water molecules and counter ions in the stabilization of RNA structure.

Parametrization of 2 - aminopurine and purine in charmm all - atom empirical force field

80%

Sarzyńska J. , Kulińska K. , Kuliński T.

Computational Methods in Science and Technology

2003

tom Vol. 9, nr 1-2

127-135

Molecular dynamics simulations based on empirical force fields are commonly used in studies of large and complex biological systems. A new set of force field parameters complementing the CHARMM27 all atom empirical force field for nucleic acid was developed for 2-aminopurine and purine, two nucleobase analogues extensively used to probe the nucleic acids structure and dynamics.

Flexibility of Dicer Studied by Implicit Solvent Molecular Dynamics Simulations

61%

Sarzyńska J. , Mickiewicz A. , Miłostan M. , Łukasiak P. , Błażewicz J. , Figlerowicz M. , Kuliński T.

Computational Methods in Science and Technology

2010

tom Vol. 16, No. 1

97-104

Dicer is an enzyme responsible for processing double-stranded RNAs and plays a key role in an RNAi mechanism. Structural insight into the Dicer is provided by the crystal structure of eukaryotic Dicer from Giardia intestinalis. It has been proposed that the structure has three structurally rigid regions that are connected by the flexible hinges. Flexibility of the Dicer is believed to be a critical feature for its function. Spatial arrangement of the RNA-recognition and the catalytic regions is crucial for producing small RNAs of defined length. It has been suggested that in the Giardia Dicer a Platform domain may help in specific arrangement of these regions. To learn more about the role of the Platform domain in Giardia Dicer, we have performed molecular dynamics (MD) simulations of the whole Dicer (WT Dicer) and the Dicer with a deleted platform domain (delta Plf Dicer). The MD simulations were carried out in an implicit solvent model with two implementations of analytic Generalized Born (GB) solvation model in CHARMM: GBMV (Generalized Born using Molecular Volume) and GBSW (Generalized Born with simple Switching). To detect the key global motions of the Dicer, a principal component analysis (PCA) of the obtained MD trajectories has been used. To further explore the motion of the Dicer, we performed a domain motion analysis with the DYNDOM program. The simulations show that both WT Dicer and delta Plf Dicer display flexibility which can be described as a movement of two or three domains. The removal of the Platform substantially changed the flexibility and arrangement of these domains. During the MD simulations of delta Plf Dicer an large movement of the RNA-recognition domain was observed.