The relationship between amide proton chemical shifts and secondary structure in proteins

Abstract

The parameters for HN chemical shift calculations of proteins have been determined using data from high-resolution crystal structures of 15 proteins. Employing these chemical shift calculations for HN protons, the observed secondary structure chemical shift trends of HN protons, i.e., upfield shifts on helix formation and downfield shifts on β-sheet formation, are discussed. Our calculations suggest that the main reason for the difference in NH chemical shifts in helices and sheets is not an effect from the directly hydrogen-bonded carbonyl, which gives rise to downfield shifts in both cases, but arises from an additional upfield shift predicted in helices and originating in residues i-2 and i-3. The calculations also explain the well-known relationship between amide proton shifts and hydrogen-bond lengths. In addition, the HN chemical shifts of the distorted amphipathic helices of the GCN4 leucine zipper are calculated and used to characterise the solution structure of the helices. By comparing the calculated and experimental shifts, it is shown that in general the agreement is good between residues 15 and 28. The most interesting observation is that in the N-terminal half of the zipper, although both calculated and experimental shifts show clear periodicity, they are no longer in phase. This suggests that for the N-terminal half, in the true average solution structure the period of the helix coil is longer by roughly one residue compared to the NMR structures.

The plug domain of FepA, a TonB-dependent transport protein from Escherichia coli , binds its siderophore in the absence of the transmembrane barrel domain

“…4) are significantly shifted downfield from the region where the other backbone amides are clustered. The 1 H chemical shifts of these peaks strongly suggest that they participate in secondary structure in an extended conformation (23). However, the low intensity of these peaks (Ϸ10-20% of the Trp indole NH), suggests they exist only in part of the population of molecules of the sample, so that even this small segment of secondary structure is only partially formed.…”

Unusual1H NMR chemical shifts support (His) Cɛ1—H⋅⋅⋅O⩵C H-bond: Proposal for reaction-driven ring flip mechanism in serine protease catalysis

“…Three contemporary models that have been applied to calculation of both C ␣ OH and amide N-H protons shielding in proteins are those of Ö sapay and Case (48), Herranz et al (49), and Williamson and Asakura (50) [also Asakura et al (51)]. A detailed analysis is given in the supplementary material.…”

NMR reveals hydrogen bonds between oxygen and distal histidines in oxyhemoglobin

“…Thus, these amino acid residues can serve as probes of the heme-pocket conformation. The HMQC spectra can be correlated with the structure of Hb with the aid of a computer program, TOTAL.F, which, given a protein's structure in the form of a PDB file, predicts the 1 H chemical shifts (42,43). The predicted chemical shifts of the proximal and distal histidines are compared with our experimental results in Table 1.…”