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Deuterium isotope effects on 15N backbone chemical shifts in proteins.

Abildgaard J, Hansen PE, Manalo MN, LiWang A - J. Biomol. NMR (2009)

Bottom Line: The effect of hydrogen bonding is rationalized in part as an electric-field effect on the first derivative of the nuclear shielding with respect to N-H bond length.Another contributing factor is the effect of increased anharmonicity of the N-H stretching vibrational state upon hydrogen bonding, which results in an altered N-H/N-D equilibrium bond length ratio.For residues with uncharged side chains a very good prediction of isotope effects can be made.

View Article: PubMed Central - PubMed

Affiliation: Department of Science, Systems and Models, Roskilde University, Roskilde, Denmark.

ABSTRACT
Quantum mechanical calculations are presented that predict that one-bond deuterium isotope effects on the (15)N chemical shift of backbone amides of proteins, (1)Delta(15)N(D), are sensitive to backbone conformation and hydrogen bonding. A quantitative empirical model for (1)Delta(15)N(D) including the backbone dihedral angles, Phi and Psi, and the hydrogen bonding geometry is presented for glycine and amino acid residues with aliphatic side chains. The effect of hydrogen bonding is rationalized in part as an electric-field effect on the first derivative of the nuclear shielding with respect to N-H bond length. Another contributing factor is the effect of increased anharmonicity of the N-H stretching vibrational state upon hydrogen bonding, which results in an altered N-H/N-D equilibrium bond length ratio. The N-H stretching anharmonicity contribution falls off with the cosine of the N-H...O bond angle. For residues with uncharged side chains a very good prediction of isotope effects can be made. Thus, for proteins with known secondary structures, (1)Delta(15)N(D) can provide insights into hydrogen bonding geometries.

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Experimental 1Δ15N(D) values plotted against experimental 15N chemical shifts, δ15N, from human ubiquitin. The correlation line, 1Δ15N(D) = 0.0054 δ15N + 0.0754 ppm (R2 = 0.93), is for non-hydrogen bonded N–H groups. The 15N chemical shift data are not random coil corrected or corrected for neighboring residue offset
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Fig4: Experimental 1Δ15N(D) values plotted against experimental 15N chemical shifts, δ15N, from human ubiquitin. The correlation line, 1Δ15N(D) = 0.0054 δ15N + 0.0754 ppm (R2 = 0.93), is for non-hydrogen bonded N–H groups. The 15N chemical shift data are not random coil corrected or corrected for neighboring residue offset

Mentions: Shown in Fig. 4 is a plot of experimental 1Δ15N(D) versus δ15N. There seems to be a linear correlation between 1Δ15N(D) and δ15N in the non-hydrogen bonded N–H groups. This correlation, which is lost with hydrogen bonding, suggests that the intrinsic hydrogen–deuterium isotope effect is proportional to the heavy atom chemical shift, which has also been observed by Jaravine et al. (2004). 1Δ15N(D) values seem to group with secondary structure and hydrogen bonding with better separation in 1Δ15N(D) dimension than in the δ1HN or δ15N dimensions. Notice the small spread in the non-hydrogen bonded β-sheet values compared to the hydrogen bonded ones, both in 1Δ15N(D) and δ1HN (Supplemental Fig. 1), indicating a large effect of hydrogen bonding on these parameters. Clearly the separation between β-sheet and α-helix 1Δ15N(D) values is not as good as that observed for the chemical shift and coupling constants of the 13Cα group [δ1Hα, δ13Cα and 1JCαHα] (Spera and Bax 1991; Wishart et al. 1991; Vuister et al. 1992; Wishart et al. 1992), but the 1Δ15N(D) data seems to include hydrogen bonding information.Fig. 4


Deuterium isotope effects on 15N backbone chemical shifts in proteins.

Abildgaard J, Hansen PE, Manalo MN, LiWang A - J. Biomol. NMR (2009)

Experimental 1Δ15N(D) values plotted against experimental 15N chemical shifts, δ15N, from human ubiquitin. The correlation line, 1Δ15N(D) = 0.0054 δ15N + 0.0754 ppm (R2 = 0.93), is for non-hydrogen bonded N–H groups. The 15N chemical shift data are not random coil corrected or corrected for neighboring residue offset
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2697368&req=5

Fig4: Experimental 1Δ15N(D) values plotted against experimental 15N chemical shifts, δ15N, from human ubiquitin. The correlation line, 1Δ15N(D) = 0.0054 δ15N + 0.0754 ppm (R2 = 0.93), is for non-hydrogen bonded N–H groups. The 15N chemical shift data are not random coil corrected or corrected for neighboring residue offset
Mentions: Shown in Fig. 4 is a plot of experimental 1Δ15N(D) versus δ15N. There seems to be a linear correlation between 1Δ15N(D) and δ15N in the non-hydrogen bonded N–H groups. This correlation, which is lost with hydrogen bonding, suggests that the intrinsic hydrogen–deuterium isotope effect is proportional to the heavy atom chemical shift, which has also been observed by Jaravine et al. (2004). 1Δ15N(D) values seem to group with secondary structure and hydrogen bonding with better separation in 1Δ15N(D) dimension than in the δ1HN or δ15N dimensions. Notice the small spread in the non-hydrogen bonded β-sheet values compared to the hydrogen bonded ones, both in 1Δ15N(D) and δ1HN (Supplemental Fig. 1), indicating a large effect of hydrogen bonding on these parameters. Clearly the separation between β-sheet and α-helix 1Δ15N(D) values is not as good as that observed for the chemical shift and coupling constants of the 13Cα group [δ1Hα, δ13Cα and 1JCαHα] (Spera and Bax 1991; Wishart et al. 1991; Vuister et al. 1992; Wishart et al. 1992), but the 1Δ15N(D) data seems to include hydrogen bonding information.Fig. 4

Bottom Line: The effect of hydrogen bonding is rationalized in part as an electric-field effect on the first derivative of the nuclear shielding with respect to N-H bond length.Another contributing factor is the effect of increased anharmonicity of the N-H stretching vibrational state upon hydrogen bonding, which results in an altered N-H/N-D equilibrium bond length ratio.For residues with uncharged side chains a very good prediction of isotope effects can be made.

View Article: PubMed Central - PubMed

Affiliation: Department of Science, Systems and Models, Roskilde University, Roskilde, Denmark.

ABSTRACT
Quantum mechanical calculations are presented that predict that one-bond deuterium isotope effects on the (15)N chemical shift of backbone amides of proteins, (1)Delta(15)N(D), are sensitive to backbone conformation and hydrogen bonding. A quantitative empirical model for (1)Delta(15)N(D) including the backbone dihedral angles, Phi and Psi, and the hydrogen bonding geometry is presented for glycine and amino acid residues with aliphatic side chains. The effect of hydrogen bonding is rationalized in part as an electric-field effect on the first derivative of the nuclear shielding with respect to N-H bond length. Another contributing factor is the effect of increased anharmonicity of the N-H stretching vibrational state upon hydrogen bonding, which results in an altered N-H/N-D equilibrium bond length ratio. The N-H stretching anharmonicity contribution falls off with the cosine of the N-H...O bond angle. For residues with uncharged side chains a very good prediction of isotope effects can be made. Thus, for proteins with known secondary structures, (1)Delta(15)N(D) can provide insights into hydrogen bonding geometries.

Show MeSH