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Conformational analysis of galanin using end to end distance distribution observed by Förster resonance energy transfer
- T. Kulinski, A. Wennerberg, +4 authors T. Bártfai
- Chemistry, MedicineEuropean Biophysics Journal
The coexistence of different structures of the neuropeptide galanin in trifluoroethanol solution was revealed by the model independent analysis of the distribution of relaxation times from the time-resolved resonance energy transfer data.
Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields.
- E. Fadrná, N. Špačková, +5 authors J. Šponer
- Chemistry, MedicineJournal of chemical theory and computation
- 19 August 2009
We have carried out a set of explicit solvent molecular dynamics (MD) simulations on two DNA quadruplex (G-DNA) molecules, namely the antiparallel d(G4T4G4)2 dimeric quadruplex with diagonal loops…
Conformations of Flanking Bases in HIV-1 RNA DIS Kissing Complexes Studied by Molecular Dynamics
The results suggest that bulged-out geometries are somewhat more preferred, which is in accord with recent experiments showing that they may mediate tertiary contacts in biomolecular assemblies or allow binding of aminoglycoside antibiotics.
Thermodynamic stability of RNA structures formed by CNG trinucleotide repeats. Implication for prediction of RNA structure.
- M. Broda, E. Kierzek, Z. Gdaniec, T. Kulinski, R. Kierzek
- Chemistry, MedicineBiochemistry
- 22 July 2005
For the first time, complete data concerning thermodynamic stabilities of RNA with CNG trinucleotide repeats is shown and improved thermodynamic parameters allow to predict much more accurately the thermodynamics stabilities and structures of CNG RNAs.
The Apical Loop of the HIV-1 TAR RNA Hairpin Is Stabilized by a Cross-loop Base Pair*
- T. Kulinski, M. Olejniczak, +5 authors R. Adamiak
- Biology, MedicineJournal of Biological Chemistry
- 3 October 2003
The TAR hairpin of the HIV-1 RNA genome is indispensable for trans-activation of the viral promoter and virus replication. The TAR structure has been studied extensively, but most attention has been…
Conformational dynamics of a 5S rRNA hairpin domain containing loop D and a single nucleotide bulge.
The results correlate with lead ion induced cleavage patterns in 5S rRNAs as the most rigid fragments independent of the localization of the bulge nucleotide are described.
Watson-Crick-like pairs in CCUG repeats: evidence for tautomeric shifts or protonation.
Crystal structures of two CCUG-containing oligomers show that the RNA strands associate into slipped duplexes that contain noncanonical C-U pairs that have apparently undergone tautomeric transition or protonation resulting in an unusual Watson-Crick-like pairing.
Modeling of the catalytic core of Arabidopsis thaliana Dicer-like 4 protein and its complex with double-stranded RNA
- A. Mickiewicz, J. Sarzynska, +6 authors J. Blazewicz
- Computer Science, BiologyComput. Biol. Chem.
- 1 February 2017
The results suggest that the spatial orientation of the Connector helix, Platform and PAZ relative to the RNase III domains is crucial for measuring dsRNAs of defined length, and can be helpful for understanding the mechanism of AtDCL4-mediated dsRNA recognition and binding.
Spectroscopic investigations of the single tryptophan residue and of riboflavin and 7-oxolumazine bound to lumazine apoprotein from Photobacterium leiognathi.
A new method is designed for evaluation of the rate constant of energy transfer by measuring the (picosecond) rise time of the acceptor fluorescence, which indicates no change in secondary structure on binding to the apoprotein.
A molecular dynamics computer simulation study of nucleotide analogues. Comparison of the hydration pattern of dithymidine phosphate with those of the dithymidine methylphosphonate diastereomers.
- K. Kulińska, T. Kulinski, J. Stawinski, A. Laaksonen
- Chemistry, MedicineJournal of biomolecular structure & dynamics
- 1 April 1998
The hydration pattern of thymidyl(3'->5') thymidine 1 and those of Rp and Sp diastereomers of the corresponding methylphosphonate analogue 2, have been studied using Molecular Dynamics (MD) computer…