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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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A small region of the 2D HA(CACO)N spectrum of human ubiquitin at pH 4.7 labeled with deuterium at the NH group ([D2O]/[H2O] = 1.6) recorded at 600 MHz 1H frequency, 25°C. For each backbone amide group, the upfield and downfield peaks originate from the deuterated and protonated isotopomers, respectively. The residue labels are according to the 15N chemical shifts
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Fig2: A small region of the 2D HA(CACO)N spectrum of human ubiquitin at pH 4.7 labeled with deuterium at the NH group ([D2O]/[H2O] = 1.6) recorded at 600 MHz 1H frequency, 25°C. For each backbone amide group, the upfield and downfield peaks originate from the deuterated and protonated isotopomers, respectively. The residue labels are according to the 15N chemical shifts

Mentions: Two-dimensional deuterium-decoupled HA(CACO)N experiments (Wang et al. 1995; Ottiger and Bax 1997) were recorded on a sample of commercially obtained human ubiquitin, uniformly enriched in 13C and 15N (VLI Research, PA, USA) and dissolved in a solution of [D2O]/[H2O] = 1.6, prepared in a manner similar to that described previously (LiWang and Bax 1996). Two spectra were collected as 512* (t1) × 256* (t2) data sets (where n* refers to n complex data points), with acquisition times of 389 ms (t1) and 85 ms (t2), where t1 refers to the 15N dimension and t2 to the 1H dimension. The total measuring time was 8 h for each experiment. Prior to Fourier transformation, the data were apodized with sine bell and squared sine bell functions shifted by 60° in both dimensions, and then zero-filled to 2,048* and 1,024* in the t1 and t2 dimensions, respectively. Data were processed using the program nmrPipe (Delaglio et al. 1995), and the peak positions and intensities for non-overlapping resonances were determined interactively using the program PIPP (Garrett et al. 1991; Fig. 2).Fig. 2


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

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

A small region of the 2D HA(CACO)N spectrum of human ubiquitin at pH 4.7 labeled with deuterium at the NH group ([D2O]/[H2O] = 1.6) recorded at 600 MHz 1H frequency, 25°C. For each backbone amide group, the upfield and downfield peaks originate from the deuterated and protonated isotopomers, respectively. The residue labels are according to the 15N chemical shifts
© Copyright Policy
Related In: Results  -  Collection

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

Fig2: A small region of the 2D HA(CACO)N spectrum of human ubiquitin at pH 4.7 labeled with deuterium at the NH group ([D2O]/[H2O] = 1.6) recorded at 600 MHz 1H frequency, 25°C. For each backbone amide group, the upfield and downfield peaks originate from the deuterated and protonated isotopomers, respectively. The residue labels are according to the 15N chemical shifts
Mentions: Two-dimensional deuterium-decoupled HA(CACO)N experiments (Wang et al. 1995; Ottiger and Bax 1997) were recorded on a sample of commercially obtained human ubiquitin, uniformly enriched in 13C and 15N (VLI Research, PA, USA) and dissolved in a solution of [D2O]/[H2O] = 1.6, prepared in a manner similar to that described previously (LiWang and Bax 1996). Two spectra were collected as 512* (t1) × 256* (t2) data sets (where n* refers to n complex data points), with acquisition times of 389 ms (t1) and 85 ms (t2), where t1 refers to the 15N dimension and t2 to the 1H dimension. The total measuring time was 8 h for each experiment. Prior to Fourier transformation, the data were apodized with sine bell and squared sine bell functions shifted by 60° in both dimensions, and then zero-filled to 2,048* and 1,024* in the t1 and t2 dimensions, respectively. Data were processed using the program nmrPipe (Delaglio et al. 1995), and the peak positions and intensities for non-overlapping resonances were determined interactively using the program PIPP (Garrett et al. 1991; Fig. 2).Fig. 2

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