Investigation of the NMR spin-spin coupling constants across the hydrogen bonds in ubiquitin: the nature of the hydrogen bond as reflected by the coupling mechanism

C.T. Tuttle, E. Kraka, A. Wu, D. Cremer

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Abstract

The indirect scalar NMR spin−spin coupling constants across the H-bonds of the protein ubiquitin were calculated, including the Fermi contact, the diamagnetic spin−orbit, the paramagnetic spin−orbit, and the spin dipole term, employing coupled perturbed density functional theory in combination with the B3LYP functional and different basis sets:  (9s,5p,1d/5s,1p)[6s,4p,1d/3s,1p] and (11s,7p,2d/5s,1p)[7s,6p,2d/4s,2p]. Four different models based on either the crystal or the aqueous solution structure of ubiquitin were used to describe H-bonding for selected residue pairs of ubiquitin. Calculated and measured 3hJ(NC‘) coupling constants differ depending on the model used, which is due to the fact that the geometry of ubiquitin is different in the solid state and in aqueous solution. Also, conformational averaging leads to a decrease of the magnitude of the measured 3hJ(NC‘) constants, which varies locally (larger for β-sheets, smaller for α-helix). Two different spin−spin coupling mechanisms were identified. While mechanism I transmits spin polarization via an electric field effect, mechanism II involves also electron delocalization from the lone pair of the carbonyl oxygen to the antibonding orbital of the N−H bond. Mechanism I is more important in the crystal structure of ubiquitin, while in aqueous solution, mechanism II plays a larger role. It is possible to set up simple relationships between the spin−spin coupling constants associated with the H bond in proteins and the geometrical features of these bonds. The importance of the 3hJ(NC‘) and 1J(N−H) constants as descriptors for the H-bond is emphasized.
LanguageEnglish
Pages5093-5107
Number of pages15
JournalJournal of the American Chemical Society
Volume126
Issue number16
DOIs
Publication statusPublished - 2004

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Ubiquitin
Hydrogen
Hydrogen bonds
Nuclear magnetic resonance
Orbits
Electric field effects
Proteins
Orbit
Spin polarization
Density functional theory
Crystal structure
Crystals
Oxygen
Geometry
Electrons

Keywords

  • NMR Spin−Spin Coupling
  • hydrogen bonds
  • ubiquitin

Cite this

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title = "Investigation of the NMR spin-spin coupling constants across the hydrogen bonds in ubiquitin: the nature of the hydrogen bond as reflected by the coupling mechanism",
abstract = "The indirect scalar NMR spin−spin coupling constants across the H-bonds of the protein ubiquitin were calculated, including the Fermi contact, the diamagnetic spin−orbit, the paramagnetic spin−orbit, and the spin dipole term, employing coupled perturbed density functional theory in combination with the B3LYP functional and different basis sets:  (9s,5p,1d/5s,1p)[6s,4p,1d/3s,1p] and (11s,7p,2d/5s,1p)[7s,6p,2d/4s,2p]. Four different models based on either the crystal or the aqueous solution structure of ubiquitin were used to describe H-bonding for selected residue pairs of ubiquitin. Calculated and measured 3hJ(NC‘) coupling constants differ depending on the model used, which is due to the fact that the geometry of ubiquitin is different in the solid state and in aqueous solution. Also, conformational averaging leads to a decrease of the magnitude of the measured 3hJ(NC‘) constants, which varies locally (larger for β-sheets, smaller for α-helix). Two different spin−spin coupling mechanisms were identified. While mechanism I transmits spin polarization via an electric field effect, mechanism II involves also electron delocalization from the lone pair of the carbonyl oxygen to the antibonding orbital of the N−H bond. Mechanism I is more important in the crystal structure of ubiquitin, while in aqueous solution, mechanism II plays a larger role. It is possible to set up simple relationships between the spin−spin coupling constants associated with the H bond in proteins and the geometrical features of these bonds. The importance of the 3hJ(NC‘) and 1J(N−H) constants as descriptors for the H-bond is emphasized.",
keywords = "NMR Spin−Spin Coupling , hydrogen bonds , ubiquitin",
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year = "2004",
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journal = "Journal of the American Chemical Society",
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T1 - Investigation of the NMR spin-spin coupling constants across the hydrogen bonds in ubiquitin: the nature of the hydrogen bond as reflected by the coupling mechanism

AU - Tuttle, C.T.

AU - Kraka, E.

AU - Wu, A.

AU - Cremer, D.

PY - 2004

Y1 - 2004

N2 - The indirect scalar NMR spin−spin coupling constants across the H-bonds of the protein ubiquitin were calculated, including the Fermi contact, the diamagnetic spin−orbit, the paramagnetic spin−orbit, and the spin dipole term, employing coupled perturbed density functional theory in combination with the B3LYP functional and different basis sets:  (9s,5p,1d/5s,1p)[6s,4p,1d/3s,1p] and (11s,7p,2d/5s,1p)[7s,6p,2d/4s,2p]. Four different models based on either the crystal or the aqueous solution structure of ubiquitin were used to describe H-bonding for selected residue pairs of ubiquitin. Calculated and measured 3hJ(NC‘) coupling constants differ depending on the model used, which is due to the fact that the geometry of ubiquitin is different in the solid state and in aqueous solution. Also, conformational averaging leads to a decrease of the magnitude of the measured 3hJ(NC‘) constants, which varies locally (larger for β-sheets, smaller for α-helix). Two different spin−spin coupling mechanisms were identified. While mechanism I transmits spin polarization via an electric field effect, mechanism II involves also electron delocalization from the lone pair of the carbonyl oxygen to the antibonding orbital of the N−H bond. Mechanism I is more important in the crystal structure of ubiquitin, while in aqueous solution, mechanism II plays a larger role. It is possible to set up simple relationships between the spin−spin coupling constants associated with the H bond in proteins and the geometrical features of these bonds. The importance of the 3hJ(NC‘) and 1J(N−H) constants as descriptors for the H-bond is emphasized.

AB - The indirect scalar NMR spin−spin coupling constants across the H-bonds of the protein ubiquitin were calculated, including the Fermi contact, the diamagnetic spin−orbit, the paramagnetic spin−orbit, and the spin dipole term, employing coupled perturbed density functional theory in combination with the B3LYP functional and different basis sets:  (9s,5p,1d/5s,1p)[6s,4p,1d/3s,1p] and (11s,7p,2d/5s,1p)[7s,6p,2d/4s,2p]. Four different models based on either the crystal or the aqueous solution structure of ubiquitin were used to describe H-bonding for selected residue pairs of ubiquitin. Calculated and measured 3hJ(NC‘) coupling constants differ depending on the model used, which is due to the fact that the geometry of ubiquitin is different in the solid state and in aqueous solution. Also, conformational averaging leads to a decrease of the magnitude of the measured 3hJ(NC‘) constants, which varies locally (larger for β-sheets, smaller for α-helix). Two different spin−spin coupling mechanisms were identified. While mechanism I transmits spin polarization via an electric field effect, mechanism II involves also electron delocalization from the lone pair of the carbonyl oxygen to the antibonding orbital of the N−H bond. Mechanism I is more important in the crystal structure of ubiquitin, while in aqueous solution, mechanism II plays a larger role. It is possible to set up simple relationships between the spin−spin coupling constants associated with the H bond in proteins and the geometrical features of these bonds. The importance of the 3hJ(NC‘) and 1J(N−H) constants as descriptors for the H-bond is emphasized.

KW - NMR Spin−Spin Coupling

KW - hydrogen bonds

KW - ubiquitin

U2 - 10.1021/ja030246e

DO - 10.1021/ja030246e

M3 - Article

VL - 126

SP - 5093

EP - 5107

JO - Journal of the American Chemical Society

T2 - Journal of the American Chemical Society

JF - Journal of the American Chemical Society

SN - 0002-7863

IS - 16

ER -