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@article{1335871, author = {Islam, Barira and Stadlbauer, Petr and Krepl, Miroslav and Koča, Jaroslav and Neidle, Stephen and Haider, Shozeb and Šponer, Jiří}, article_location = {Oxford}, article_number = {18}, doi = {http://dx.doi.org/10.1093/nar/gkv785}, keywords = {TELOMERIC G-QUADRUPLEX; INTRAMOLECULAR DNA QUADRUPLEXES; GASTROINTESTINAL STROMAL TUMOR; PARALLEL G-QUADRUPLEXES; PARTICLE MESH EWALD; AMBER FORCE-FIELD; G-TRACT LENGTH; RNA LOOP-E; NUCLEIC-ACIDS; ION-BINDING}, language = {eng}, issn = {0305-1048}, journal = {Nucleic Acids Research}, title = {Extended molecular dynamics of a c-kit promoter quadruplex}, url = {http://nar.oxfordjournals.org/content/43/18/8673.full.pdf+html}, volume = {43}, year = {2015} }
TY - JOUR ID - 1335871 AU - Islam, Barira - Stadlbauer, Petr - Krepl, Miroslav - Koča, Jaroslav - Neidle, Stephen - Haider, Shozeb - Šponer, Jiří PY - 2015 TI - Extended molecular dynamics of a c-kit promoter quadruplex JF - Nucleic Acids Research VL - 43 IS - 18 SP - 8673-8693 EP - 8673-8693 PB - Oxford University Press SN - 03051048 KW - TELOMERIC G-QUADRUPLEX KW - INTRAMOLECULAR DNA QUADRUPLEXES KW - GASTROINTESTINAL STROMAL TUMOR KW - PARALLEL G-QUADRUPLEXES KW - PARTICLE MESH EWALD KW - AMBER FORCE-FIELD KW - G-TRACT LENGTH KW - RNA LOOP-E KW - NUCLEIC-ACIDS KW - ION-BINDING UR - http://nar.oxfordjournals.org/content/43/18/8673.full.pdf+html L2 - http://nar.oxfordjournals.org/content/43/18/8673.full.pdf+html N2 - The 22-mer c-kit promoter sequence folds into a parallel-stranded quadruplex with a unique structure, which has been elucidated by crystallographic and NMR methods and shows a high degree of structural conservation. We have carried out a series of extended (up to 10 mu s long, similar to 50 mu s in total) molecular dynamics simulations to explore conformational stability and loop dynamics of this quadruplex. Unfolding no-salt simulations are consistent with a multi-pathway model of quadruplex folding and identify the single-nucleotide propeller loops as the most fragile part of the quadruplex. Thus, formation of propeller loops represents a peculiar atomistic aspect of quadruplex folding. Unbiased simulations reveal mu s-scale transitions in the loops, which emphasizes the need for extended simulations in studies of quadruplex loops. We identify ion binding in the loops which may contribute to quadruplex stability. The long lateral-propeller loop is internally very stable but extensively fluctuates as a rigid entity. It creates a size-adaptable cleft between the loop and the stem, which can facilitate ligand binding. The stability gain by forming the internal network of GA base pairs and stacks of this loop may be dictating which of the many possible quadruplex topologies is observed in the ground state by this promoter quadruplex. ER -
ISLAM, Barira, Petr STADLBAUER, Miroslav KREPL, Jaroslav KOČA, Stephen NEIDLE, Shozeb HAIDER and Jiří ŠPONER. Extended molecular dynamics of a c-kit promoter quadruplex. \textit{Nucleic Acids Research}. Oxford: Oxford University Press, vol.~43, No~18, p.~8673-8693. ISSN~0305-1048. doi:10.1093/nar/gkv785. 2015.
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