Detail
Článek
Článek online
FT
Medvik - BMČ
  • Je něco špatně v tomto záznamu ?

Long-timescale dynamics of the Drew-Dickerson dodecamer

PD. Dans, L. Danilāne, I. Ivani, T. Dršata, F. Lankaš, A. Hospital, J. Walther, RI. Pujagut, F. Battistini, JL. Gelpí, R. Lavery, M. Orozco,

. 2016 ; 44 (9) : 4052-66. [pub] 20160415

Jazyk angličtina Země Anglie, Velká Británie

Typ dokumentu časopisecké články

Perzistentní odkaz   https://www.medvik.cz/link/bmc17031785

We present a systematic study of the long-timescale dynamics of the Drew-Dickerson dodecamer (DDD: d(CGCGAATTGCGC)2) a prototypical B-DNA duplex. Using our newly parameterized PARMBSC1 force field, we describe the conformational landscape of DDD in a variety of ionic environments from minimal salt to 2 M Na(+)Cl(-) or K(+)Cl(-) The sensitivity of the simulations to the use of different solvent and ion models is analyzed in detail using multi-microsecond simulations. Finally, an extended (10 μs) simulation is used to characterize slow and infrequent conformational changes in DDD, leading to the identification of previously uncharacterized conformational states of this duplex which can explain biologically relevant conformational transitions. With a total of more than 43 μs of unrestrained molecular dynamics simulation, this study is the most extensive investigation of the dynamics of the most prototypical DNA duplex.

Citace poskytuje Crossref.org

000      
00000naa a2200000 a 4500
001      
bmc17031785
003      
CZ-PrNML
005      
20171025115614.0
007      
ta
008      
171025s2016 enk f 000 0|eng||
009      
AR
024    7_
$a 10.1093/nar/gkw264 $2 doi
035    __
$a (PubMed)27084952
040    __
$a ABA008 $b cze $d ABA008 $e AACR2
041    0_
$a eng
044    __
$a enk
100    1_
$a Dans, Pablo D $u Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain Joint BSC-IRB Research Program in Computational Biology, Baldiri Reixac 10-12, 08028 Barcelona, Spain.
245    10
$a Long-timescale dynamics of the Drew-Dickerson dodecamer / $c PD. Dans, L. Danilāne, I. Ivani, T. Dršata, F. Lankaš, A. Hospital, J. Walther, RI. Pujagut, F. Battistini, JL. Gelpí, R. Lavery, M. Orozco,
520    9_
$a We present a systematic study of the long-timescale dynamics of the Drew-Dickerson dodecamer (DDD: d(CGCGAATTGCGC)2) a prototypical B-DNA duplex. Using our newly parameterized PARMBSC1 force field, we describe the conformational landscape of DDD in a variety of ionic environments from minimal salt to 2 M Na(+)Cl(-) or K(+)Cl(-) The sensitivity of the simulations to the use of different solvent and ion models is analyzed in detail using multi-microsecond simulations. Finally, an extended (10 μs) simulation is used to characterize slow and infrequent conformational changes in DDD, leading to the identification of previously uncharacterized conformational states of this duplex which can explain biologically relevant conformational transitions. With a total of more than 43 μs of unrestrained molecular dynamics simulation, this study is the most extensive investigation of the dynamics of the most prototypical DNA duplex.
650    _2
$a B-DNA $x chemie $x ultrastruktura $7 D059371
650    _2
$a molekulární modely $7 D008958
650    12
$a simulace molekulární dynamiky $7 D056004
650    12
$a konformace nukleové kyseliny $7 D009690
650    _2
$a chlorid draselný $x chemie $7 D011189
650    _2
$a chlorid sodný $x chemie $7 D012965
655    _2
$a časopisecké články $7 D016428
700    1_
$a Danilāne, Linda $u Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain Joint BSC-IRB Research Program in Computational Biology, Baldiri Reixac 10-12, 08028 Barcelona, Spain School of Chemistry, University of East Anglia (UEA), Norwich Research Park, Norwich NR4 7TJ, UK.
700    1_
$a Ivani, Ivan $u Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain Joint BSC-IRB Research Program in Computational Biology, Baldiri Reixac 10-12, 08028 Barcelona, Spain.
700    1_
$a Dršata, Tomáš $u Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám 2, 166 10 Prague, Czech Republic.
700    1_
$a Lankaš, Filip $u Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám 2, 166 10 Prague, Czech Republic Laboratory of Informatics and Chemistry, University of Chemistry and Technology Prague, Technická 5, 166 28 Prague, Czech Republic.
700    1_
$a Hospital, Adam $u Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain Joint BSC-IRB Research Program in Computational Biology, Baldiri Reixac 10-12, 08028 Barcelona, Spain.
700    1_
$a Walther, Jürgen $u Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain Joint BSC-IRB Research Program in Computational Biology, Baldiri Reixac 10-12, 08028 Barcelona, Spain.
700    1_
$a Pujagut, Ricard Illa $u Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain Joint BSC-IRB Research Program in Computational Biology, Baldiri Reixac 10-12, 08028 Barcelona, Spain.
700    1_
$a Battistini, Federica $u Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain Joint BSC-IRB Research Program in Computational Biology, Baldiri Reixac 10-12, 08028 Barcelona, Spain.
700    1_
$a Gelpí, Josep Lluis $u Department of Biochemistry and Molecular Biology, University of Barcelona, 08028 Barcelona, Spain.
700    1_
$a Lavery, Richard $u Bases Moléculaires et Structurales des Systèmes Infectieux, Université Lyon I/CNRS UMR 5086, IBCP, 7 Passage du Vercors, Lyon 69367, France.
700    1_
$a Orozco, Modesto $u Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain Joint BSC-IRB Research Program in Computational Biology, Baldiri Reixac 10-12, 08028 Barcelona, Spain Department of Biochemistry and Molecular Biology, University of Barcelona, 08028 Barcelona, Spain modesto.orozco@irbbarcelona.org.
773    0_
$w MED00003554 $t Nucleic acids research $x 1362-4962 $g Roč. 44, č. 9 (2016), s. 4052-66
856    41
$u https://pubmed.ncbi.nlm.nih.gov/27084952 $y Pubmed
910    __
$a ABA008 $b sig $c sign $y a $z 0
990    __
$a 20171025 $b ABA008
991    __
$a 20171025115656 $b ABA008
999    __
$a ok $b bmc $g 1255378 $s 992812
BAS    __
$a 3
BAS    __
$a PreBMC
BMC    __
$a 2016 $b 44 $c 9 $d 4052-66 $e 20160415 $i 1362-4962 $m Nucleic acids research $n Nucleic Acids Res $x MED00003554
LZP    __
$a Pubmed-20171025

Najít záznam

Citační ukazatele

Možnosti archivace