Stability of 100 Homo and Heterotypic Coiled−Coil a−a‘ Pairs for Ten Amino Acids (A, L, I, V, N, K, S, T, E, and R)

Abstract

We present the thermal stability monitored by circular dichroism (CD) spectroscopy at 222 nm of 100 heterodimers that contain all possible coiled-coil a-a' pairs for 10 amino acids (I, V, L, N, A, K S, T, E, and R). This includes the stability of 36 heterodimers for 6 amino acids (I, V, L, N, A, and K) previously described and 64 new heterodimers including the 4 amino acids (S, T, E, and R). We have calculated a double mutant alanine thermodynamic cycle to determine a-a' pair coupling energies to evaluate which a-a' pairs encourage specific dimerization partners. The four new homotypic a-a' pairs (T-T, S-S, R-R, E-E) are repulsive relative to A-A and have destabilizing coupling energies. Among the 90 heterotypic a-a' pairs, the stabilizing coupling energies contain lysine or arginine paired with either an aliphatic or a polar amino acid. The range in coupling energies for each amino acid reveals its potential to regulate dimerization specificity. The a-a' pairs containing isoleucine and asparagine have the greatest range in coupling energies and thus contribute dramatically to dimerization specificity, which is to encourage homodimerization. In contrast, the a-a' pairs containing charged amino acids (K, R, and E) show the least range in coupling energies and promiscuously encourage heterodimerization.

N@a and N@d: Oligomer and Partner Specification by Asparagine in Coiled-Coil Interfaces

“…Building on the point about incomplete layers, and following the experimental work of Vinson, 39 we also analyzed the partnering of 33 Asn residues found in the 81 heterodimeric coiled coils of CC+, Table 2b. In these, one third (11) of the examples with N@a made AsnAsn pairs; approximately one quarter (9) did not make complete, reciprocated knobs-intoholes interactions; and the remainder (13) paired with a range of other and predominantly polar residues (…”

“…[35][36][37][38] Studies have also been performed to quantify the contribution of these Asn-Asn pairs to dimer stability at least. [39][40][41] To summarize a large body of literature, N@a is destabilising, but it specifies parallel dimer over alternative states such as antiparallel dimer and parallel trimer. Asn inclusions do occur in trimers, though less frequently than in dimers.…”

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.…”

Structural specificity in coiled-coil interactions

“…Acharya et al report a tour de force of 100 measurements of homo and heterotypic substitutions at a-a'-position pairs in a model bZIPlike coiled-coil heterodimer [40]. These data illustrate homotypic preferences for most hydrophobic residues and Asn, and heterotypic preferences for other polar or charged residues: Thr, Lys, Arg and Glu.…”

“…A simpler sequence-based model for scoring different coiled-coil dimers involves summing up relevant interhelical coupling energies [40,41]. However, this does not work well for predicting bZIP pairs [48].…”