Mechanical Stability and Unfolding Pathways of Parallel Tetrameric G-Quadruplexes Probed by Pulling Simulations
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F68081707%3A_____%2F24%3A00586249" target="_blank" >RIV/68081707:_____/24:00586249 - isvavai.cz</a>
Alternative codes found
RIV/00216224:14740/24:00138701 RIV/61989100:27740/24:10254884
Result on the web
<a href="https://pubs.acs.org/doi/10.1021/acs.jcim.4c00227" target="_blank" >https://pubs.acs.org/doi/10.1021/acs.jcim.4c00227</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1021/acs.jcim.4c00227" target="_blank" >10.1021/acs.jcim.4c00227</a>
Alternative languages
Result language
angličtina
Original language name
Mechanical Stability and Unfolding Pathways of Parallel Tetrameric G-Quadruplexes Probed by Pulling Simulations
Original language description
Guanine quadruplex (GQ) is a noncanonical nucleic acid structure formed by guanine-rich DNA and RNA sequences. Folding of GQs is a complex process, where several aspects remain elusive, despite being important for understanding structure formation and biological functions of GQs. Pulling experiments are a common tool for acquiring insights into the folding landscape of GQs. Herein, we applied a computational pulling strategy-steered molecular dynamics (SMD) simulations-in combination with standard molecular dynamics (MD) simulations to explore the unfolding landscapes of tetrameric parallel GQs. We identified anisotropic properties of elastic conformational changes, unfolding transitions, and GQ mechanical stabilities. Using a special set of structural parameters, we found that the vertical component of pulling force (perpendicular to the average G-quartet plane) plays a significant role in disrupting GQ structures and weakening their mechanical stabilities. We demonstrated that the magnitude of the vertical force component depends on the pulling anchor positions and the number of G-quartets. Typical unfolding transitions for tetrameric parallel GQs involve base unzipping, opening of the G-stem, strand slippage, and rotation to cross-like structures. The unzipping was detected as the first and dominant unfolding event, and it usually started at the 3 '-end. Furthermore, results from both SMD and standard MD simulations indicate that partial spiral conformations serve as a transient ensemble during the (un)folding of GQs.
Czech name
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Czech description
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Classification
Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
10608 - Biochemistry and molecular biology
Result continuities
Project
<a href="/en/project/GA21-23718S" target="_blank" >GA21-23718S: The fascinating physical chemistry of DNA studied by advanced computations</a><br>
Continuities
I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace
Others
Publication year
2024
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
Journal of Chemical Information and Modeling
ISSN
1549-9596
e-ISSN
1549-960X
Volume of the periodical
64
Issue of the periodical within the volume
9
Country of publishing house
US - UNITED STATES
Number of pages
16
Pages from-to
3896-3911
UT code for WoS article
001204966100001
EID of the result in the Scopus database
2-s2.0-85190742372