Deuterium isotope effects on 15N backbone chemical shifts in proteins

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 D 15 N(D), are sensitive to backbone conformation and hydrogen bonding. A quantitative empirical model for 1 D 15 N(D) including the backbone dihedral angles, U and W, 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-HÁÁÁO 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 D 15 N(D) can provide insights into hydrogen bonding geometries.

Structure assignment and H/D-exchange behavior of several glycosylated polyphenols

“…47 In NMR spectroscopy, the IE terminology refers to differences in chemical shift for nuclei that are directly attached to the isotope or that are neighbors to the site of isotope substitution. In NMR spectroscopy, IEs have been generally reported for different classes of nuclei and substances, 48 have been used to describe conformational changes 49 and hydrogen-bonded systems, 50 and have been applied successfully to the structural description of small proteins in solution and in solid-state. 48 The absence of H/D-exchange at H6 and H8 for 5 and the progressing exchange of H6 and H8 in 5 is shown in Figure 7.…”

“…In NMR spectroscopy, IEs have been generally reported for different classes of nuclei and substances, 48 have been used to describe conformational changes 49 and hydrogen-bonded systems, 50 and have been applied successfully to the structural description of small proteins in solution and in solid-state. 48 The absence of H/D-exchange at H6 and H8 for 5 and the progressing exchange of H6 and H8 in 5 is shown in Figure 7. Increased deshielding in 5 shifted the resonances to over 7.0 ppm whereas they were shielded to below 7.0 ppm in 6.…”

Four‐bond deuterium isotope effects on the chemical shifts of amide nitrogens in proteins

“…5(a)) and the 4 ΔN(C β,i-1 D) shifts ( H-to-D replacement on the preceding or the following residue. However, inclusion of the terms accounting for hydrogen bond strengths and geometry as described for one-bond 15 N deuterium isotope shifts in ubiquitin previously, [29,33] did not statistically improve the fits in Eqns 4, 5. In summary, NMR methodology is developed for the measurements of four-bond deuterium isotope effects on the chemical shifts of backbone amide nitrogen nuclei in proteins.…”

“…The effects of proton-to-deuterium ( 1 H-to-D) substitution on the chemical shifts of 13 C α , 13 C β , and methyl 13 C nuclei 1-to-3 bonds away [17][18][19][20][21][22][23][24][25][26] and, more recently, 1-to-3-bond effects on the chemical shifts of the backbone 15 N, 13 CO, 13 C α , 13 C β , 1 H N and 1 H α , [27][28][29] Tyr 13 C ζ [30] and Cys 13 C β nuclei [31] have been quantified. Hydrogenbonding effects on one-bond isotope shifts of backbone 15 N, [32,33] side-chain 15 N of Asn, and Gln [34] as well as 15 N and 1 H N nuclei in NH 3 groups of lysine side-chains [35] have been investigated.…”

Estimating quadrupole couplings of amide deuterons in proteins from direct measurements of 2 H spin relaxation rates

“…The rigorous treatment can be found in Chung et al [22]. Once the electric field gradient tensor is assumed to be axially symmetric (g = 0) and collinear with the direction of the 15 N-D bond as above, the following Lipari-Szabo model-free spectral density function for the axially symmetric molecular tumbling can be used [23][24][25], 15 N-1 H amides as a result of a one-bond deuterium isotope shift [12,15,46]. Typical single-exponential decay curves of (b) D z , and (c) D + magnetization are shown for the amide deuterons of Glu 18 (dashed curves) and Gln 62 (solid curves) of ubiquitin.…”