A Heterodimerizing Leucine Zipper Coiled Coil System for Examining the Specificity of a Position Interactions:  Amino Acids I, V, L, N, A, and K

Abstract

We use a heterodimerizing leucine zipper system to examine the contribution of the interhelical a-a' interaction to dimer stability for six amino acids (A, V, L, I, K, and N). Circular dichroism (CD) spectroscopy monitored the thermal denaturation of 36 heterodimers that generate six homotypic and 30 heterotypic a-a' interactions. Isoleucine (I-I) is the most stable homotypic a-a' interaction, being 9.2 kcal/mol per dimer more stable than the A-A interaction and 4.0 kcal/mol per dimer more stable than either the L-L or V-V interaction, and 7.0 kcal/mol per dimer more stable than the N-N interaction. Only lysine was less stable than alanine. An alanine-based double-mutant thermodynamic cycle calculated coupling energies between the a and a' positions in the heterodimer. The aliphatic amino acids L, V, and I prefer to form homotypic interactions with coupling energies of -0.6 to -0.9 kcal/mol per dimer, but the heterotypic aliphatic interactions have positive coupling energies of <1.0 kcal/mol per dimer. The asparagine homotypic interaction has a coupling energy of -0.5 kcal/mol per dimer, while heterotypic interactions with the aliphatic amino acids produce coupling energies ranging from 2.6 to 4.9 kcal/mol per dimer. The homotypic K-K interaction is 2.9 kcal/mol per dimer less stable than the A-A interaction, but the coupling energy is only 0.3 kcal/mol per dimer. Heterotypic interactions with lysine and either asparagine or aliphatic amino acids produce similar coupling energies ranging from -0.2 to -0.7 kcal/mol per dimer. Thus, of the amino acids that were examined, asparagine contributes the most to dimerization specificity because of the large positive coupling energies in heterotypic interactions with the aliphatic amino acids which results in the N-N homotypic interaction.

Preferred side-chain constellations at antiparallel coiled-coil interfaces

“…This limited set of rules has allowed considerable progress in the areas of coiled-coil prediction and design (1, 3), but our findings suggest that additional advances will be possible based on a more sophisticated treatment. Previously elucidated factors include lateral pairing of nonpolar side chains (9-16), which is driven by stereochemical complementarity, and lateral pairing of polar side chains (9)(10)(11)(12)(13)(14)(15)(16)33), which is driven by hydrogen bonding (at least for Asn-Asn pairs). In addition, pairing preferences are influenced by the electrostatic interactions (attractive or repulsive) between ionized side chains (34)(35)(36)(37)(38)(39).…”

“…Extensive work by Vinson et al, for example, has shown that the contribution of a given buried a side chain to parallel coiled-coil dimer stability depends on the identity of the lateral hydrophobic packing partner (a-aЈ interaction) (9,12). We have recently shown that lateral partners (a-dЈ) influence antiparallel coiled-coil stability (20).…”

“…The effects of sequence variation on coiled-coil stability have been widely studied (9)(10)(11)(12)(13)(14)(15)(16), but substantial gaps in our understanding remain. For example, the vast majority of prior efforts have focused on parallel coiled-coil homo dimers, but other coiled-coil states are seen in Nature.…”

The cytoplasmic coiled-coil mediates cooperative gating temperature sensitivity in the voltage-gated H+ channel Hv1

“…Given the reports from the GCN4 coiled-coil, a yeast leucine zipper protein [20][21][22] , the hydrophilic core residues, N231, could be a weakness of the core packing stability. Other structure features are the lack of inter-subunit polar interaction that stabilizes the assembly [23][24][25] ( Supplementary Fig. S2b) and the dual-conformation of Cys residues in the core, suggesting a possibility of switching of the disulfide bonding in response to redox ( Supplementary Fig.…”

Theindeterminate gametophyte1Gene of Maize Encodes a LOB Domain Protein Required for Embryo Sac and Leaf Development

“…Additionally, the Tyr and Gln residues of the SKYQ motif occupy the g and a positions, respectively, in the Leu zipper after this last Leu. The a, e, and g positions in the helix of Leu zippers determine the specificity of dimerization between Leu zippers (Acharya et al, 2002;Deppmann et al, 2004). Additionally, the presence of a positively charged amino acid in the a position of one of the heptads-Lys in ig1, ial1, Sbig1, Osig1, and AS2 and Arg in ial2, ial3, and Osial1-suggests that these proteins do not homodimerize.…”