Section 22.2.3.1. Proteins

The hydrogen-bonding capacities of the various hydrogen-bonding groups in proteins are shown in Fig. 22.2.3.1. All, with the exception of the peptide NH and Trp side-chain NH groups, can participate in more than one hydrogen-bond interaction. Peptide and side-chain C=O groups, for example, can act as acceptors for two hydrogen bonds by using both lone pairs of electrons on the sp²-hybridized oxygen. Likewise, the —OH groups of Ser or Thr can act as donors through their single H atom, and acceptors through their two lone pairs. In Tyr side chains, the C—O bond has some double-bond character, and the phenolic —OH is thus likely to prefer only two hydrogen bonds, both in the ring plane. The carboxylate groups of Asp and Glu are normally ionized above pH 4 and their C—O bonds also have partial double-bond character; each carboxylate oxygen should then be able to accept two hydrogen bonds, although the restriction to two may be less severe than for C=O.

Figure 22.2.3.1| top | pdf | Hydrogen-bonding potential of protein functional groups. Potential hydrogen bonds are shown with broken lines. Arg, Lys, Asp and Glu side chains are shown in their ionized forms.

Several uncertainties exist. Crystallographically, it is not usually possible to distinguish the amide oxygen and nitrogen atoms of Asn and Gln, and the decision as to which is which has to be made on environmental grounds by considering what hydrogen bonds would be made in each of the two possible arrangements. Likewise, two possibilities exist for His side chains by rotating 180° about C^β—C^γ. This problem has been analysed by McDonald & Thornton (1994b), and corrections can be made with HBPLUS .

For some side chains, the ionization state is uncertain. Arg and Lys are assumed to be fully protonated, as in Fig. 22.2.3.1, and Asp and Glu are assumed to be fully ionized. Nevertheless, a survey by Flocco & Mowbray (1995) has shown that a small but significant number of short O···O distances between Asp and Glu side chains must represent O—H···O hydrogen bonds, with one carboxyl group protonated. His side chains, in addition to the orientational uncertainty, have a pK_a (∼6.5) that implies that they may be in either their neutral or their protonated form, depending on pH and environment. In the neutral form, only one N atom is protonated (more often , but sometimes ), but in the protonated form both N atoms carry protons; again, the actual state has to be deduced from their environment.