Ion Binding to Quadruplex DNA Stems. Comparison of MM and QM
Descriptions Reveals Sizable Polarization Effects Not Included
in Contemporary Simulations

J 2014

Ion Binding to Quadruplex DNA Stems. Comparison of MM and QM Descriptions Reveals Sizable Polarization Effects Not Included in Contemporary Simulations

GKIONIS, Konstantinos, Holger KRUSE, James PLATTS, Arnošt MLÁDEK, Jaroslav KOČA et. al.

Základní údaje

Originální název

Ion Binding to Quadruplex DNA Stems. Comparison of MM and QM Descriptions Reveals Sizable Polarization Effects Not Included in Contemporary Simulations

Autoři

GKIONIS, Konstantinos (300 Řecko, domácí), Holger KRUSE (276 Německo, domácí), James PLATTS (826 Velká Británie a Severní Irsko), Arnošt MLÁDEK (203 Česká republika), Jaroslav KOČA (203 Česká republika, domácí) a Jiří ŠPONER (203 Česká republika, garant, domácí)

Vydání

Journal of Chemical Theory and Computation, Washington DC, American Chemical Society, 2014, 1549-9618

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10403 Physical chemistry

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 5.498

Kód RIV

RIV/00216224:14740/14:00075657

Organizační jednotka

Středoevropský technologický institut

DOI

http://dx.doi.org/10.1021/ct4009969

UT WoS

000332913500041

Klíčová slova anglicky

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

Štítky

kontrola MP, MP, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 12. 8. 2014 10:11, Martina Prášilová

Anotace

V originále

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.

Návaznosti

ED1.1.00/02.0068, projekt VaV

Název: CEITEC - central european institute of technology

286154, interní kód MU

Název: SYLICA - Synergies of Life and Material Sciences to Create a New Future (Akronym: SYLICA)

Investor: Evropská unie, SYLICA - Synergies of Life and Material Sciences to Create a New Future, Kapacity

Citovat

GKIONIS, Konstantinos, Holger KRUSE, James PLATTS, Arnošt MLÁDEK, Jaroslav KOČA a Jiří ŠPONER. Ion Binding to Quadruplex DNA Stems. Comparison of MM and QM Descriptions Reveals Sizable Polarization Effects Not Included in Contemporary Simulations. Journal of Chemical Theory and Computation. Washington DC: American Chemical Society, 2014, roč. 10, č. 3, s. 1326-1340. ISSN 1549-9618. Dostupné z: https://dx.doi.org/10.1021/ct4009969.

@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 a 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, roč.~10, č.~3, s.~1326-1340. ISSN~1549-9618. Dostupné z: https://dx.doi.org/10.1021/ct4009969.

Podrobný výpis o publikaci