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

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About: Ion Binding to Quadruplex DNA Stems. Comparison of MM and QM Descriptions Reveals Sizable Polarization Effects Not Included in Contemporary Simulations Goto Sponge NotDistinct Permalink

An Entity of Type : http://linked.opendata.cz/ontology/domain/vavai/Vysledek, within Data Space : linked.opendata.cz associated with source document(s)

Attributes	Values
rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
rdfs:seeAlso	http://pubs.acs.org/doi/pdf/10.1021/ct4009969
Description	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. 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. (en)
Title	Ion Binding to Quadruplex DNA Stems. Comparison of MM and QM Descriptions Reveals Sizable Polarization Effects Not Included in Contemporary Simulations Ion Binding to Quadruplex DNA Stems. Comparison of MM and QM Descriptions Reveals Sizable Polarization Effects Not Included in Contemporary Simulations (en)
skos:prefLabel	Ion Binding to Quadruplex DNA Stems. Comparison of MM and QM Descriptions Reveals Sizable Polarization Effects Not Included in Contemporary Simulations Ion Binding to Quadruplex DNA Stems. Comparison of MM and QM Descriptions Reveals Sizable Polarization Effects Not Included in Contemporary Simulations (en)
skos:notation	RIV/00216224:14740/14:00075657!RIV15-MSM-14740___
http://linked.open...avai/riv/aktivita	I P
http://linked.open...avai/riv/aktivity	I, P(ED1.1.00/02.0068), P(GAP208/11/1822)
http://linked.open...iv/cisloPeriodika	3
http://linked.open...vai/riv/dodaniDat	2015
http://linked.open...aciTvurceVysledku	Gkionis, Konstantinos Šponer, Jiří Koča, Jaroslav Kruse, Holger
http://linked.open.../riv/druhVysledku	J - Článek v odborném periodiku
http://linked.open...iv/duvernostUdaju	S - Úplné a pravdivé údaje nepodléhající ochraně podle zvláštních právních předpisů
http://linked.open...titaPredkladatele	Masarykova univerzita / Středoevropský technologický institut
http://linked.open...dnocenehoVysledku	22819
http://linked.open...ai/riv/idVysledku	RIV/00216224:14740/14:00075657
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	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 (en)
http://linked.open.../riv/klicoveSlovo	FORCE-FIELD TETRAMOLECULAR G-QUADRUPLEXES AIM TOPOLOGICAL ANALYSIS DIELECTRIC MEDIUM ELECTRONIC DENSITY HUMAN TELOMERIC QUADRUPLEX STRUCTURAL DYNAMICS GAUSSIAN-BASIS SETS NUCLEIC-ACIDS MOLECULAR-DYNAMICS SIMULATIONS
http://linked.open...odStatuVydavatele	US - Spojené státy americké
http://linked.open...ontrolniKodProRIV	[B4030FF1FF66]
http://linked.open...i/riv/nazevZdroje	Journal of Chemical Theory and Computation
http://linked.open...in/vavai/riv/obor	CF
http://linked.open...ichTvurcuVysledku	4 (xsd:int)
http://linked.open...cetTvurcuVysledku	6 (xsd:int)
http://linked.open...vavai/riv/projekt	Central european institute of technology Structure and dynamics of DNA. Advanced computational studies.
http://linked.open...UplatneniVysledku	2014
http://linked.open...v/svazekPeriodika	10
http://linked.open...iv/tvurceVysledku	Koča, Jaroslav Šponer, Jiří Mládek, Arnošt Gkionis, Konstantinos Kruse, Holger Platts, James
http://linked.open...ain/vavai/riv/wos	000332913500041
issn	1549-9618
number of pages	15 (xsd:int)
http://bibframe.org/vocab/doi	10.1021/ct4009969
http://localhost/t...ganizacniJednotka	14740

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