H-Bonds in Proteins

Recently it has been found that couplings between and C across H-bonds, e.g. in systems containing N—H..-0= C units (in proteins), can be directly detected and provide evidence for H-bonds in proteins and nucleic acids [89]. Although this technology is now standard for larger biomolecules it is rarely used for smaller molecules [90]. 

The predominant H-bond in proteins is the bridge between the backbone amide proton of one amino acid and the backbone carbonyl oxygen atom of a second amino acid (see insert to Fig. 9.3). Although scalar couplings across H-bonds to the magnetic isotope 170 are conceivable, the fast relaxation of this quadrupolar nucleus would prevent such observations in... 

Fig. 1.12. Examples for the H-bonds in protein-nucleic add complexes. A) H-bond contacts of the X,-repressor in complex with its operator sequence. After Jordan Pabo, (1988). B) H-bonds in the complex between the Zinc fingers of Zif268 with the cognate recognition helix. Zif268 contacts the DNA with three Zn-fingers (finger 1-3 in Fig. 1.5). Shown are the H-bond contacts formed between the fingers and the base pairs of the recognition sequence. After Pavletich Pabo, (1991).

To a large extent, the complex molecules in living matter have structures and properties that are determined by intramolecular H bonds. Although this type of H bond has some features in common with inter-molecular H bonds, there are appreciable differences. We have already mentioned some of these differences, but it will be useful to codify the variations before discussing H bonding in proteins. 

Pelupessy P, Ravindranathan S, Bodenhausen G (2003) Correlated motions of successive amide N-H bonds in proteins. J Biomol NMR 25 265-280... 

A thorough theoretical investigation of the spin-spin coupling mechanism across a H-bond in proteins, N-H - 0 = C, has been performed by Cremer and co-workers. ° An analysis of the data obtained for the protein ubiquitin has shown that there are simple relationships between the spin-spin couplings associated with the H bond in proteins and the geometrical features of these bonds. In particular, the authors emphasized the importance of the and Jhn couplings as descriptors of the H-bond. 

Steinberg, I. Z., Sckeraga, H. A. Influence of water structure and of hydrophobic interactions on the strength of side-chain H-bonds in proteins. Eiopolymers 1, 43 (1963). 

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