Ion pairs in alpha helices

A survey of 47 globular proteins was made to determine the probability of occurrence of ion pairs separated by 1, 2, 3,... and 8 residues in the alpha helices. As a control, the probability of occurrence of like charged pairs was also determined. The survey showed that ion pairs of the type i, i±3 and i, i±4 are the most predominant. Such a preference was not observed for like charged pairs. The observed frequency of ion pairs is significantly greater than their expected frequency. The normalized frequencies of occurrence of the ion pairs were also found to increase generally with the helix length. These results indicate that the ion pairs may contribute to the stability of solvent-exposed alpha helices. Since the stabilization of protein secondary structure, these results may throw light on the mechanism of protein folding

Stabilization of alpha helices by ion pairs

A survey of 50 protein structures (47 globular and 3 fibrous) indicates that intrahelical ion pairs between oppositely charged residues (Glu-, Asp-/Lys+, Arg+) 3 or 4 residues apart along the helix may have a stabilizing effect on alpha helices exposed to solvent. It is found that the i, i ± 3/4 types of ion pairs are the most predominant, and their observed frequencies are significantly greater than their expected frequencies. Such a preference is not seen for the like-charged pairs which served as a control. It was found that the normalized frequencies of these ion pairs increased with the helix length. An analysis of the distances between the charged groups in ion pairs suggests that only about 20% of the ion pairs are stabilized by hydrogen bonding (salt bridged), about 40% by electrostatic interactions, and the remaining may be stabilized by solvation: forming water bridges or plumes of water molecules around the charged groups. The fibrous proteins, which have a proportionately larger solvent exposed area than the globular proteins, have a higher density of intrahelical or secondary structural ion pairs. They are distinguished from the globular proteins which contain fewer ion pairs/charged residues because of their smaller solvent exposed area. The results indicate that the ion pairs may have a stabilizing effect on alpha helices exposed to solvent

Closely related antibody receptors exploit fundamentally different strategies for steroid recognition

Molecular recognition by the adaptive immune system relies on specific high-affinity antibody receptors that are generated from a restricted set of starting sequences through homologous recombination and somatic mutation. The steroid binding antibody DB3 and the catalytic Diels–Alderase antibody 1E9 derive from the same germ line sequences but exhibit very distinct specificities and functions. However, mutation of only two of the 36 sequence differences in the variable domains, LeuH47Trp and ArgH100Trp, converts 1E9 into a high-affinity steroid receptor with a ligand recognition profile similar to DB3. To understand how these changes switch binding specificity and function, we determined the crystal structures of the 1E9 LeuH47Trp/ArgH100Trp double mutant (1E9dm) as an unliganded Fab at 2.05 Å resolution and in complex with two configurationally distinct steroids at 2.40 and 2.85 Å. Surprisingly, despite the functional mimicry of DB3, 1E9dm employs a distinct steroid binding mechanism. Extensive structural rearrangements occur in the combining site, where residue H47 acts as a specificity switch and H100 adapts to different ligands. Unlike DB3, 1E9dm does not use alternative binding pockets or different sets of hydrogen-bonding interactions to bind configurationally distinct steroids. Rather, the different steroids are inserted more deeply into the 1E9dm combining site, creating more hydrophobic contacts that energetically compensate for the lack of hydrogen bonds. These findings demonstrate how subtle mutations within an existing molecular scaffold can dramatically modulate the function of immune receptors by inducing unanticipated, but compensating, mechanisms of ligand interaction