2007
Human telomeric G-DNA - a test example for force field adjustment
FADRNÁ, Eva, Naděžda ŠPAČKOVÁ, Daniel SVOZIL, Jiří ŠPONER, Jaroslav KOČA et. al.Základní údaje
Originální název
Human telomeric G-DNA - a test example for force field adjustment
Název česky
Lidská telomerní G-DNA - testovací příklad pro vývoj silových polí
Autoři
FADRNÁ, Eva (203 Česká republika, garant), Naděžda ŠPAČKOVÁ (203 Česká republika), Daniel SVOZIL (203 Česká republika), Jiří ŠPONER (203 Česká republika) a Jaroslav KOČA (203 Česká republika)
Vydání
Albany, Journal Of Biomolecular Structure and Dynamics, od s. 709-709, 1 s. 2007
Nakladatel
Adenine Press
Další údaje
Jazyk
angličtina
Typ výsledku
Stať ve sborníku
Obor
10403 Physical chemistry
Stát vydavatele
Spojené státy
Utajení
není předmětem státního či obchodního tajemství
Impakt faktor
Impact factor: 2.389
Kód RIV
RIV/00216224:14310/07:00022918
Organizační jednotka
Přírodovědecká fakulta
ISSN
UT WoS
000247289600160
Klíčová slova anglicky
G-DNA; force field; human telomere
Štítky
Příznaky
Mezinárodní význam
Změněno: 23. 6. 2008 15:37, prof. RNDr. Jiří Šponer, DrSc.
V originále
Our interest has been focused on molecular modelling studies of DNA quadruplexes. Since these four-stranded arrangements play important role in cell cycle, they are currently extensively studied by means of experimental and computational techniques. Human telomeric sequence was extensively studied by means of molecular modelling tools. Starting from the X-ray structure we tested the influence of various ion types and radii on molecular dynamics, Locally Enhanced Sampling, free energy estimations, etc. Results have shown a strong influence of ion radius on conformational behavior during the trajectories. Greater computational force brings not only larger simulation timescale, but also cumulation of force-field imbalancies which can lead to some artifacts. Simple model of ion description influences entire potential energy surface and may shift the molecule from experimetal geometry. Slight changes in ion parameters force the simulation to completely different area of conformational space. Some (ir)reversible backbone changes of alpha-beta-gamma torsion angles (switches) have been observed in all trajectories that pointed out at some imbalancies in the force field parametrisation. Our study brought a contribution to some methodological tasks such as inclusions of proper ions type or backbone torsions switches. It has shown that human telomere sequence can be used as a testing example for recent methodological problems, because some imbalancies appear in it in relativelly short simulation time.
Česky
Our interest has been focused on molecular modelling studies of DNA quadruplexes. Since these four-stranded arrangements play important role in cell cycle, they are currently extensively studied by means of experimental and computational techniques. Human telomeric sequence was extensively studied by means of molecular modelling tools. Starting from the X-ray structure we tested the influence of various ion types and radii on molecular dynamics, Locally Enhanced Sampling, free energy estimations, etc. Results have shown a strong influence of ion radius on conformational behavior during the trajectories. Greater computational force brings not only larger simulation timescale, but also cumulation of force-field imbalancies which can lead to some artifacts. Simple model of ion description influences entire potential energy surface and may shift the molecule from experimetal geometry. Slight changes in ion parameters force the simulation to completely different area of conformational space. Some (ir)reversible backbone changes of alpha-beta-gamma torsion angles (switches) have been observed in all trajectories that pointed out at some imbalancies in the force field parametrisation. Our study brought a contribution to some methodological tasks such as inclusions of proper ions type or backbone torsions switches. It has shown that human telomere sequence can be used as a testing example for recent methodological problems, because some imbalancies appear in it in relativelly short simulation time.
Návaznosti
| LC06030, projekt VaV |
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| MSM0021622413, záměr |
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