About: Correlating the P-31 NMR Chemical Shielding Tensor and the (2)J(P,C) Spin-Spin Coupling Constants with Torsion Angles zeta and alpha in the Backbone of Nucleic Acids

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About: Correlating the P-31 NMR Chemical Shielding Tensor and the (2)J(P,C) Spin-Spin Coupling Constants with Torsion Angles zeta and alpha in the Backbone of Nucleic Acids Goto Sponge NotDistinct Permalink

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Description	Determination of nucleic acid (NA) structure with NMR spectroscopy is limited by the lack of restraints on conformation of NA phosphate. In this work, the P-31 chemical shielding tensor, the Gamma(P,C5'H5'1) and Gamma(P,C5'H5'2) cross-correlated relaxation rates, and the (2)J(P,C3'), (2)J(P,C5'), and (3)J(P,C4') coupling constants were calculated in dependence on NA backbone torsion angles zeta and alpha. While the orientation of the P-31 chemical shielding tensor was almost independent of the NA phosphate conformation, the principal tensor components varied by up to similar to 40 ppm. This variation and the dependence of the phosphate geometry on torsion angles zeta and alpha had only a minor influence on the calculated Gamma(P,C5'H5'1) and Gamma(P,C5'H5'2) cross-correlated relaxation rates, and therefore, the so-called rigid tensor approximation was here validated. For the first time, the (2)J(P,C) spin-spin coupling constants were correlated with the conformation of NA phosphate. Although each of the two J-couplings was significantly modulated by both torsions zeta and alpha, the (2)J(P,C3'), coupling could be structurally assigned to torsion zeta and the (2)J(P,C5') coupling to torsion alpha. We propose qualitative rules for their structural interpretation as loose reStraints on torsion angles zeta and alpha. The (3)J(P,C4') coupling assigned to torsion angle beta was found dependent also on torsions zeta and alpha, implying that the uncertainty in determination of beta with standard Karplus curves could be as large as similar to 25 degrees. The calculations provided a unified picture of NMR parameters applicable for the determination of NA phosphate conformation. Determination of nucleic acid (NA) structure with NMR spectroscopy is limited by the lack of restraints on conformation of NA phosphate. In this work, the P-31 chemical shielding tensor, the Gamma(P,C5'H5'1) and Gamma(P,C5'H5'2) cross-correlated relaxation rates, and the (2)J(P,C3'), (2)J(P,C5'), and (3)J(P,C4') coupling constants were calculated in dependence on NA backbone torsion angles zeta and alpha. While the orientation of the P-31 chemical shielding tensor was almost independent of the NA phosphate conformation, the principal tensor components varied by up to similar to 40 ppm. This variation and the dependence of the phosphate geometry on torsion angles zeta and alpha had only a minor influence on the calculated Gamma(P,C5'H5'1) and Gamma(P,C5'H5'2) cross-correlated relaxation rates, and therefore, the so-called rigid tensor approximation was here validated. For the first time, the (2)J(P,C) spin-spin coupling constants were correlated with the conformation of NA phosphate. Although each of the two J-couplings was significantly modulated by both torsions zeta and alpha, the (2)J(P,C3'), coupling could be structurally assigned to torsion zeta and the (2)J(P,C5') coupling to torsion alpha. We propose qualitative rules for their structural interpretation as loose reStraints on torsion angles zeta and alpha. The (3)J(P,C4') coupling assigned to torsion angle beta was found dependent also on torsions zeta and alpha, implying that the uncertainty in determination of beta with standard Karplus curves could be as large as similar to 25 degrees. The calculations provided a unified picture of NMR parameters applicable for the determination of NA phosphate conformation. (en)
Title	Correlating the P-31 NMR Chemical Shielding Tensor and the (2)J(P,C) Spin-Spin Coupling Constants with Torsion Angles zeta and alpha in the Backbone of Nucleic Acids Correlating the P-31 NMR Chemical Shielding Tensor and the (2)J(P,C) Spin-Spin Coupling Constants with Torsion Angles zeta and alpha in the Backbone of Nucleic Acids (en)
skos:prefLabel	Correlating the P-31 NMR Chemical Shielding Tensor and the (2)J(P,C) Spin-Spin Coupling Constants with Torsion Angles zeta and alpha in the Backbone of Nucleic Acids Correlating the P-31 NMR Chemical Shielding Tensor and the (2)J(P,C) Spin-Spin Coupling Constants with Torsion Angles zeta and alpha in the Backbone of Nucleic Acids (en)
skos:notation	RIV/61388963:_____/12:00379080!RIV13-AV0-61388963
http://linked.open...avai/predkladatel	Ústav organické chemie a biochemie AV ČR, v. v. i.
http://linked.open...avai/riv/aktivita	P Z
http://linked.open...avai/riv/aktivity	P(GA203/09/2037), P(GAP205/10/0228), P(GPP208/10/P398), Z(AV0Z40550506)
http://linked.open...iv/cisloPeriodika	12
http://linked.open...vai/riv/dodaniDat	2013
http://linked.open...aciTvurceVysledku	Benda, Ladislav Straka, Michal Sychrovský, Vladimír Sochorová Vokáčová, Zuzana
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	Ústav organické chemie a biochemie AV ČR, v. v. i.
http://linked.open...dnocenehoVysledku	128850
http://linked.open...ai/riv/idVysledku	RIV/61388963:_____/12:00379080
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	nucleic acids; phosphorus NMR; NMR calculations; cross-correlated relaxation; spin–spin coupling constants (en)
http://linked.open.../riv/klicoveSlovo	NMR calculations cross-correlated relaxation phosphorus NMR spin–spin coupling constants nucleic acids
http://linked.open...odStatuVydavatele	US - Spojené státy americké
http://linked.open...ontrolniKodProRIV	[19C6C1DA7708]
http://linked.open...i/riv/nazevZdroje	Journal of Physical Chemistry B
http://linked.open...in/vavai/riv/obor	CF
http://linked.open...ichTvurcuVysledku	4 (xsd:int)
http://linked.open...cetTvurcuVysledku	4 (xsd:int)
http://linked.open...vavai/riv/projekt	Multiscale modeling of endohedral fullerenes. Molecular dynamics, electronic structure, and molecular properties Structure and Dynaics of Bioinorganic Complexes Structural interpretation of the nuclear magnetic resonance spectroscopy parameters in nucleic acids and peptides
http://linked.open...UplatneniVysledku	2012
http://linked.open...v/svazekPeriodika	116
http://linked.open...iv/tvurceVysledku	Benda, Ladislav Straka, Michal Sychrovský, Vladimír Sochorová Vokáčová, Zuzana
http://linked.open...ain/vavai/riv/wos	000302051200018
http://linked.open...n/vavai/riv/zamer	Regulace biologických procesů: Chemické modulátory vybraných systémů významných pro medicínu a zemědělství
issn	1520-6106
number of pages	10 (xsd:int)
http://bibframe.org/vocab/doi	10.1021/jp2099043
is http://linked.open...avai/riv/vysledek of	Correlating the P-31 NMR Chemical Shielding Tensor and the (2)J(P,C) Spin-Spin Coupling Constants with Torsion Angles zeta and alpha in the Backbone of Nucleic Acids

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