The d′--d--d′ Vertical Triad Is Less Discriminating Than the a′--a--a′ Vertical Triad in the Antiparallel Coiled-Coil Dimer Motif

Abstract

Elucidating relationships between the amino-acid sequences of proteins and their three-dimensional structures, and uncovering non-covalent interactions that underlie polypeptide folding, are major goals in protein science. One approach toward these goals is to study interactions between selected residues, or among constellations of residues, in small folding motifs. The α-helical coiled coil has served as a platform for such studies because this folding unit is relatively simple in terms of both sequence and structure. Amino acid side chains at the helix-helix interface of a coiled coil participate in so-called ‘knobs-into-holes’ (KIH) packing whereby a side chain (the knob) on one helix inserts into a space (the hole) generated by four side chains on a partner helix. The vast majority of sequence-stability studies on coiled-coil dimers have focused on lateral interactions within these KIH arrangements, for example, between an a position on one helix and an a' position of the partner in a parallel coiled-coil dimer, or between a--d' pairs in an antiparallel dimer. More recently, it has been shown that vertical triads (specifically, a'--a--a' triads) in antiparallel dimers exhibit significant impact on pairing preferences. This observation provides impetus for analysis of other complex networks of side-chain interactions at the helix-helix interface. Here, we describe a combination of experimental and bioinformatics studies that show that d'--d--d' triads have much less impact on pairing preference than do a'--a--a' triads in a small, designed antiparallel coiled-coil dimer. However, the influence of the d'--d--d' triad depends on the lateral at a'--d interaction. Taken together, these results strengthen the emerging understanding that simple pair-wise interactions are not sufficient to describe side-chain interactions and overall stability in antiparallel coiled-coil dimers; higher-order interactions must be considered as well.

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

“…[39][40][41] In a comprehensive study, Vinson and colleagues determined the thermodynamic stabilities of 100 heterodimeric coiled-coil mutants varying a-a' residue pairs. They state: "the most extreme example of two amino acids regulating dimer preference has to do with Ile and Asn".…”

“…[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.…”

Unique Features of the Anti-parallel, Heterodimeric Coiled-coil Interaction between Methyl-cytosine Binding Domain 2 (MBD2) Homologues and GATA Zinc Finger Domain Containing 2A (GATAD2A/p66α)

“…The shorter valine side chain (as compared with isoleucine and leucine residues) allows close approximation of the two helices, which likely contributes to close intermolecular ionic interactions involving the glutamate residues. The conserved d-d interactions (28), which are composed of LQEV(A)LA, also place a valine (or alanine in MBD3L2) at the bend on the p66␣ helix near these same glutamate residues.…”

Coiled-Coil Response to Mechanical Force: Global Stability and Local Cracking

“…Both sets of interactions arise from interhelix complementarity due to the characteristic heptad-repeat structure, in which residues are typically labeled a-g. Using the designations of this repeat structure, the classic coiled coil has hydrophobic residues in locations a and d (15,16). These hydrophobic residues arrange themselves in a so-called knobs-in-the-hole packing such that their hydrophobic side chains are buried in close proximity to the corresponding heptad position from the other chain.…”