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@article{1185380,
author = {Gkionis, Konstantinos and Kruse, Holger and Platts, James and Mládek, Arnošt and Koča, Jaroslav and Šponer, Jiří},
article_location = {Washington DC},
article_number = {3},
doi = {http://dx.doi.org/10.1021/ct4009969},
keywords = {MOLECULAR-DYNAMICS SIMULATIONS; GAUSSIAN-BASIS SETS; TETRAMOLECULAR G-QUADRUPLEXES; HUMAN TELOMERIC QUADRUPLEX; AIM TOPOLOGICAL ANALYSIS; FORCE-FIELD; STRUCTURAL DYNAMICS; NUCLEIC-ACIDS; ELECTRONIC DENSITY; DIELECTRIC MEDIUM},
language = {eng},
issn = {1549-9618},
journal = {Journal of Chemical Theory and Computation},
title = {Ion Binding to Quadruplex DNA Stems. Comparison of MM and QM Descriptions Reveals Sizable Polarization Effects Not Included in Contemporary Simulations},
url = {http://pubs.acs.org/doi/pdf/10.1021/ct4009969},
volume = {10},
year = {2014}
}
TY - JOUR
ID - 1185380
AU - Gkionis, Konstantinos - Kruse, Holger - Platts, James - Mládek, Arnošt - Koča, Jaroslav - Šponer, Jiří
PY - 2014
TI - Ion Binding to Quadruplex DNA Stems. Comparison of MM and QM Descriptions Reveals Sizable Polarization Effects Not Included in Contemporary Simulations
JF - Journal of Chemical Theory and Computation
VL - 10
IS - 3
SP - 1326-1340
EP - 1326-1340
PB - American Chemical Society
SN - 15499618
KW - MOLECULAR-DYNAMICS SIMULATIONS
KW - GAUSSIAN-BASIS SETS
KW - TETRAMOLECULAR G-QUADRUPLEXES
KW - HUMAN TELOMERIC QUADRUPLEX
KW - AIM TOPOLOGICAL ANALYSIS
KW - FORCE-FIELD
KW - STRUCTURAL DYNAMICS
KW - NUCLEIC-ACIDS
KW - ELECTRONIC DENSITY
KW - DIELECTRIC MEDIUM
UR - http://pubs.acs.org/doi/pdf/10.1021/ct4009969
L2 - http://pubs.acs.org/doi/pdf/10.1021/ct4009969
N2 - Molecular mechanical (MM) force fields are commonly employed for biomolecular simulations. Despite their success, the nonpolarizable nature of contemporary additive force fields limits their performance, especially in long simulations and when strong polarization effects are present. Guanine quadruplex D(R)NA molecules have been successfully studied by MM simulations in the past. However, the G-stems are stabilized by a chain of monovalent cations that create sizable polarization effects. Indeed, simulation studies revealed several problems that have been tentatively attributed to the lack of polarization. Here, we provide a detailed comparison between quantum chemical (QM) DFT-D3 and MM potential energy surfaces of ion binding to G-stems and assess differences that may affect MM simulations. We suggest that MM describes binding of a single ion to the G-stem rather well. However, polarization effects become very significant when a second ion is present. We suggest that the MM approximation substantially limits accuracy of description of energy and dynamics of multiple ions inside the G-stems and binding of ions at the stem loop junctions. The difference between QM and MM descriptions is also explored using symmetry-adapted perturbation theory and quantum theory of atoms in molecules analyses, which reveal a delicate balance of electrostatic and induction effects.
ER -
GKIONIS, Konstantinos, Holger KRUSE, James PLATTS, Arnošt MLÁDEK, Jaroslav KOČA and Jiří ŠPONER. Ion Binding to Quadruplex DNA Stems. Comparison of MM and QM Descriptions Reveals Sizable Polarization Effects Not Included in Contemporary Simulations. \textit{Journal of Chemical Theory and Computation}. Washington DC: American Chemical Society, 2014, vol.~10, No~3, p.~1326-1340. ISSN~1549-9618. Available from: https://dx.doi.org/10.1021/ct4009969.
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