Conformational Flexibility of DNA sequences studied by Advanced
Molecular  Mechanics and Dynamics Tools

D 2003

Conformational Flexibility of DNA sequences studied by Advanced Molecular Mechanics and Dynamics Tools

FADRNÁ, Eva, Naděžda ŠPAČKOVÁ, Jiří ŠPONER a Jaroslav KOČA

Základní údaje

Originální název

Conformational Flexibility of DNA sequences studied by Advanced Molecular Mechanics and Dynamics Tools

Autoři

FADRNÁ, Eva (203 Česká republika, garant), Naděžda ŠPAČKOVÁ (203 Česká republika), Jiří ŠPONER (203 Česká republika) a Jaroslav KOČA (203 Česká republika)

Vydání

2003. vyd. Praha, Book of Abstracts, s. 20-20, 2003

Nakladatel

Workshop on Modeling Interactions in Biomolecules

Další údaje

Jazyk

angličtina

Typ výsledku

Stať ve sborníku

Obor

10403 Physical chemistry

Stát vydavatele

Česká republika

Utajení

není předmětem státního či obchodního tajemství

Kód RIV

RIV/00216224:14310/03:00009170

Organizační jednotka

Přírodovědecká fakulta

Klíčová slova anglicky

structure; dynamics; nucleic acids

Štítky

dynamics, nucleic acids, structure

Změněno: 21. 11. 2003 17:35, Mgr. Eva Fadrná, Ph.D.

Anotace

V originále

Molecular mechanics and dynamics is widely applied to various nucleic acids sequences in order to study their conformational behavior and flexibility. With increasing power of computational methods, it is possible to study structure-functional relationship in more detail. Wide range of methods has been applied to various G-DNA sequences that are able to form four-stranded arrangement. Taking part in controlling function of cells telomeras, these structures are in focus of biomolecular studies for more than 10 years. Computational methods contribute to the experimental ones and help them in prediction and explanation of structural features which can influence quadruplex formation, for example. Starting with conformational search of flexible parts of the molecule interesting conformational possibilities were found. Plain molecular dynamics as well as its modifications such as Locally Enhanced Sampling were used to study stability of geometries found by previous methods or described by experimental studies. Novel methods allow us to analyze the results in order to obtain free energy estimates. Some potential methodological pitfalls can be described by comparing free energy results and conformational preferences suggested for various structural sub-states. In contrast to experimentally observed results free energy analysis found different arrangement as the lowest energy one. Although the methods worked well until now, our results pointed out that still a lot of attention should be payed to methodological (force field) adjustments. Molecular dynamics is a powerful tool, but its routine use without careful attention to force field may be misleading. Anyway, our observations have shown big power of molecular dynamics and relative methods and pointed to potential course of the future methodological development.

Návaznosti

LN00A016, projekt VaV

Název: BIOMOLEKULÁRNÍ CENTRUM

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Biomolekulární centrum

Citovat

FADRNÁ, Eva, Naděžda ŠPAČKOVÁ, Jiří ŠPONER a Jaroslav KOČA. Conformational Flexibility of DNA sequences studied by Advanced Molecular Mechanics and Dynamics Tools. In Book of Abstracts. 2003. vyd. Praha: Workshop on Modeling Interactions in Biomolecules, 2003, s. 20.

@inproceedings{490425,
   author = {Fadrná, Eva and Špačková, Naděžda and Šponer, Jiří and Koča, Jaroslav},
   address = {Praha},
   booktitle = {Book of Abstracts},
   edition = {2003},
   keywords = {structure; dynamics; nucleic acids},
   language = {eng},
   location = {Praha},
   pages = {20-20},
   publisher = {Workshop on Modeling Interactions in Biomolecules},
   title = {Conformational Flexibility of DNA sequences studied by Advanced Molecular Mechanics and Dynamics Tools},
   year = {2003}
}

TY  - JOUR
ID  - 490425
AU  - Fadrná, Eva - Špačková, Naděžda - Šponer, Jiří - Koča, Jaroslav
PY  - 2003
TI  - Conformational Flexibility of DNA sequences studied by Advanced Molecular Mechanics and Dynamics Tools
PB  - Workshop on Modeling Interactions in Biomolecules
CY  - Praha
KW  - structure
KW  - dynamics
KW  - nucleic acids
N2  - Molecular mechanics and dynamics is widely applied to various nucleic acids sequences in order to study their conformational behavior and flexibility. With increasing power of computational methods, it is possible to study structure-functional relationship in more detail. Wide range of methods has been applied to various G-DNA sequences that are able to form four-stranded arrangement. Taking part in controlling function of cells telomeras, these structures are in focus of biomolecular studies for more than 10 years. Computational methods contribute to the experimental ones and help them in prediction and explanation of structural features which can influence quadruplex formation, for example. Starting with conformational search of flexible parts of the molecule interesting conformational possibilities were found. Plain molecular dynamics as well as its modifications such as Locally Enhanced Sampling were used to study stability of geometries found by previous methods or described by experimental studies. Novel methods allow us to analyze the results in order to obtain free energy estimates. Some potential methodological pitfalls can be described by comparing free energy results and conformational preferences suggested for various structural sub-states. In contrast to experimentally observed results free energy analysis found different arrangement as the lowest energy one. Although the methods worked well until now, our results pointed out that still a lot of attention should be payed to methodological (force field) adjustments. Molecular dynamics is a powerful tool, but its routine use without careful attention to force field may be misleading. Anyway, our observations have shown big power of molecular dynamics and relative methods and pointed to potential course of the future methodological development.
ER  -

FADRNÁ, Eva, Naděžda ŠPAČKOVÁ, Jiří ŠPONER a Jaroslav KOČA. Conformational Flexibility of DNA sequences studied by Advanced Molecular Mechanics and Dynamics Tools. In \textit{Book of Abstracts}. 2003. vyd. Praha: Workshop on Modeling Interactions in Biomolecules, 2003, s.~20.

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