Документ взят из кэша поисковой машины. Адрес оригинального документа : http://dualopt1.cmm.msu.ru/pub/Projects/ParmBsc0/nar.ciw Дата изменения: Wed Apr 18 20:46:44 2012 Дата индексирования: Fri Feb 28 20:17:55 2014 Кодировка:

FN Thomson Reuters Web of Knowledge
VR 1.0
PT J
AU Reshetnikov, RV
Sponer, J
Rassokhina, OI
Kopylov, AM
Tsvetkov, PO
Makarov, AA
Golovin, AV
AF Reshetnikov, Roman V.
Sponer, Jiri
Rassokhina, Olga I.
Kopylov, Alexei M.
Tsvetkov, Philipp O.
Makarov, Alexander A.
Golovin, Andrey V.
TI Cation binding to 15-TBA quadruplex DNA is a multiple-pathway
cation-dependent process
SO NUCLEIC ACIDS RESEARCH
LA English
DT Article
ID MOLECULAR-DYNAMICS SIMULATIONS; APTAMER D(GGTTGGTGTGGTTGG); STRUCTURAL
DYNAMICS; HIV-1 INTEGRASE; FORCE-FIELD; LOOP-LENGTH; METAL-IONS;
STABILITY; THROMBIN; SEQUENCE
AB A combination of explicit solvent molecular dynamics simulation (30
simulations reaching 4 mu s in total), hybrid quantum
mechanics/molecular mechanics approach and isothermal titration
calorimetry was used to investigate the atomistic picture of ion binding
to 15-mer thrombin-binding quadruplex DNA (G-DNA) aptamer. Binding of
ions to G-DNA is complex multiple pathway process, which is strongly
affected by the type of the cation. The individual ion-binding events
are substantially modulated by the connecting loops of the aptamer,
which play several roles. They stabilize the molecule during time
periods when the bound ions are not present, they modulate the route of
the ion into the stem and they also stabilize the internal ions by
closing the gates through which the ions enter the quadruplex. Using our
extensive simulations, we for the first time observed full spontaneous
exchange of internal cation between quadruplex molecule and bulk solvent
at atomistic resolution. The simulation suggests that expulsion of the
internally bound ion is correlated with initial binding of the incoming
ion. The incoming ion then readily replaces the bound ion while
minimizing any destabilization of the solute molecule during the
exchange.
C1 [Sponer, Jiri] Acad Sci Czech Republic, Inst Biophys, CS-61265 Brno, Czech Republic.
[Reshetnikov, Roman V.; Golovin, Andrey V.] Lomonosov Moscow State Univ, Dept Boiengn & Bioinformat, Moscow 119991, Russia.
[Reshetnikov, Roman V.; Golovin, Andrey V.] Apto Pharm LLC, Moscow 115446, Russia.
[Rassokhina, Olga I.; Kopylov, Alexei M.] Lomonosov Moscow State Univ, Dept Chem, Leninskie Gory, Russia.
[Tsvetkov, Philipp O.; Makarov, Alexander A.] Russian Acad Sci, Engelhardt Inst Mol Biol, Moscow 119991, Russia.
RP Sponer, J (reprint author), Acad Sci Czech Republic, Inst Biophys, Kralovopolska 135, CS-61265 Brno, Czech Republic
EM sponer@ncbr.chemi.muni.cz
golovin@belozersky.msu.ru
FU Russian Foundation for Basic Research[11-04-02084-a]; Ministry of
Education and Science of Russian Federation[16.512.11.2009]; Russian
Academy of Sciences; Grant Agency of the Academy of Sciences of the
Czech Republic (CR)[IAA400040802]; Grant Agency of the CR[203/09/1476,
P208/11/1822]; Ministry of Education of the CR[LC06030]; Academy of
Sciences of the CR[AV0Z50040507, AV0Z50040702]
FX Funding for open access charge: Russian Foundation for Basic Research
grant (11-04-02084-a); Ministry of Education and Science of Russian
Federation grant (16.512.11.2009); Molecular and Cellular Biology
Program of the Russian Academy of Sciences; Grant Agency of the Academy
of Sciences of the Czech Republic (CR) grant (IAA400040802 to J.S.);
Grant Agency of the CR grants (203/09/1476, P208/11/1822); Ministry of
Education of the CR LC06030 and Academy of Sciences of the CR grants
(AV0Z50040507, AV0Z50040702).
NR 79
TC 0
Z9 0
PU OXFORD UNIV PRESS
PI OXFORD
PA GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND
SN 0305-1048
J9 NUCLEIC ACIDS RES
JI Nucleic Acids Res.
PD DEC
PY 2011
VL 39
IS 22
BP 9789
EP 9802
DI 10.1093/nar/gkr639
PG 14
WC Biochemistry & Molecular Biology
SC Biochemistry & Molecular Biology
GA 863RT
UT WOS:000298186000034
ER
EF