Molecular dynamics simulations of guanine quadruplex loops:Advances and force field limitations

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14310%2F03%3A00009338" target="_blank" >RIV/00216224:14310/03:00009338 - isvavai.cz</a>

Alternative codes found

RIV/68081707:_____/04:00104620 RIV/00216224:14310/04:00010228

Result on the web

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DOI - Digital Object Identifier

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Result language

angličtina

Original language name

Molecular dynamics simulations of guanine quadruplex loops:Advances and force field limitations

Original language description

A computational analysis of d(GGGGTTTTGGGG)2 guanine quadruplexes containing both lateral and diagonal four-thymidine loops was carried out using Molecular Dynamics (MD) simulations in explicit solvent, Locally Enhanced Sampling (LES) simulations, systematic conformational search, and free energy Molecular Mechanics, Poisson Boltzmann, Surface Area calculations with explicit inclusion of structural monovalent cations. The study provides, within the approximations of the applied all-atom additive force field, a qualitatively complete analysis of the available loop conformational space. The results are independent of the starting structures. Major conformational transitions not seen in conventional MD simulations are observed when LES is applied. The favored LES structures consistently provide lower free energies (as estimated by MM-PBSA) than other structures. Unfortunately, the predicted optimal structure for the diagonal loop arrangement differs substantially from the atomic resolutio

Czech name

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Czech description

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Type

J_x - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)

CEP classification

CF - Physical chemistry and theoretical chemistry

OECD FORD branch

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Project

<a href="/en/project/LN00A016" target="_blank" >LN00A016: BIOMOLECULAR CENTER</a><br>

Continuities

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year

2004

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Biophysical Journal

ISSN

0006-3495

e-ISSN

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Volume of the periodical

2003

Issue of the periodical within the volume

1

Country of publishing house

US - UNITED STATES

Number of pages

20

Pages from-to

1-20

UT code for WoS article

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EID of the result in the Scopus database

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