Limits...
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.

Show MeSH
Calculated and experimental 1Δ15N(D) values for aliphatic and glycine residues of ubiquitin. Experimental values are shown in yellow and were collected using the 2H-decoupled HA(CACO)N experiment described earlier (Wang et al. 1995) on a sample of human ubiquitin equilibrated in a [D2O]/[H2O] = 1.6 solvent mixture, pH 4.7, 25°C. QM calculations using N-formylaminoacid-amides (Fig. 1) without hydrogen bond partners are shown in blue. Inclusion of electric-field effects of hydrogen bonding and the Morse calculated value of 0.0071 Å for ΔRN–H(D) yields the calculated 1Δ15N(D) values shown in black
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC2697368&req=5

Fig5: Calculated and experimental 1Δ15N(D) values for aliphatic and glycine residues of ubiquitin. Experimental values are shown in yellow and were collected using the 2H-decoupled HA(CACO)N experiment described earlier (Wang et al. 1995) on a sample of human ubiquitin equilibrated in a [D2O]/[H2O] = 1.6 solvent mixture, pH 4.7, 25°C. QM calculations using N-formylaminoacid-amides (Fig. 1) without hydrogen bond partners are shown in blue. Inclusion of electric-field effects of hydrogen bonding and the Morse calculated value of 0.0071 Å for ΔRN–H(D) yields the calculated 1Δ15N(D) values shown in black

Mentions: Using Eq. 11Δ15N(D) can be calculated provided the first derivative of the shielding constant (see Supplemental Table 3) and the change in the NH bond length upon deuteriation are known. In order to get a feeling for the importance of the various factors we have done the following. Calculations using a bond length change of 0.0061 Å (see above) and amino acid geometries obtained from the X-ray crystal structure but neglecting hydrogen bonding show a poor correlation between calculated and experimental 1Δ15N(D) values (blue bars, Fig. 5). Including formamide as hydrogen-bond acceptor and the Morse calculated value of ΔRN–H(D) = 0.0071 Å for the hydrogen bonded amino acids the calculated values are in slightly better agreement with experimental results (black bars, Fig. 5). However, it is obvious that none of the calculated values are very good as a standard bond extension has been used. Obviously, for each hydrogen bonded pair a value has to be calculated. This is not very practical and very time consuming. We have therefore taken different approach, see below.Fig. 5


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

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

Calculated and experimental 1Δ15N(D) values for aliphatic and glycine residues of ubiquitin. Experimental values are shown in yellow and were collected using the 2H-decoupled HA(CACO)N experiment described earlier (Wang et al. 1995) on a sample of human ubiquitin equilibrated in a [D2O]/[H2O] = 1.6 solvent mixture, pH 4.7, 25°C. QM calculations using N-formylaminoacid-amides (Fig. 1) without hydrogen bond partners are shown in blue. Inclusion of electric-field effects of hydrogen bonding and the Morse calculated value of 0.0071 Å for ΔRN–H(D) yields the calculated 1Δ15N(D) values shown in black
© Copyright Policy
Related In: Results  -  Collection

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

Fig5: Calculated and experimental 1Δ15N(D) values for aliphatic and glycine residues of ubiquitin. Experimental values are shown in yellow and were collected using the 2H-decoupled HA(CACO)N experiment described earlier (Wang et al. 1995) on a sample of human ubiquitin equilibrated in a [D2O]/[H2O] = 1.6 solvent mixture, pH 4.7, 25°C. QM calculations using N-formylaminoacid-amides (Fig. 1) without hydrogen bond partners are shown in blue. Inclusion of electric-field effects of hydrogen bonding and the Morse calculated value of 0.0071 Å for ΔRN–H(D) yields the calculated 1Δ15N(D) values shown in black
Mentions: Using Eq. 11Δ15N(D) can be calculated provided the first derivative of the shielding constant (see Supplemental Table 3) and the change in the NH bond length upon deuteriation are known. In order to get a feeling for the importance of the various factors we have done the following. Calculations using a bond length change of 0.0061 Å (see above) and amino acid geometries obtained from the X-ray crystal structure but neglecting hydrogen bonding show a poor correlation between calculated and experimental 1Δ15N(D) values (blue bars, Fig. 5). Including formamide as hydrogen-bond acceptor and the Morse calculated value of ΔRN–H(D) = 0.0071 Å for the hydrogen bonded amino acids the calculated values are in slightly better agreement with experimental results (black bars, Fig. 5). However, it is obvious that none of the calculated values are very good as a standard bond extension has been used. Obviously, for each hydrogen bonded pair a value has to be calculated. This is not very practical and very time consuming. We have therefore taken different approach, see below.Fig. 5

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