Variable Stability Heterodimeric Coiled-Coils from Manipulation of Electrostatic Interface Residue Chain Length

Abstract

The design of variable-stability coiled-coil heterodimers is described. The electrostatic interface between helices, formed by contact between side chains in heptad e/g positions, is manipulated to produce complexes ranging in stability from ones that are essentially unstructured to those that cannot be thermally denatured. The tuning is accomplished by incremental extension or contraction of parent glutamic acid and lysine side chains by single methylene units, producing peptides that bear either carboxylic acids or amines separated from the peptide backbone by one to four CH2 groups. Detailed examination of all homodimers and electrostatically compatible heterodimers generates interesting combinations, particularly those in which longer-chain acids are incorporated into peptides paired with lysine-bearing ones. The discovery of very stable dimers allows exchange experiments in which one strand of an original heterodimer is specifically replaced by an added one, even in cases where the original complex features the native-like glutamic acid/lysine pairing. The reported results add significantly to the available design templates for coiled-coil construction and enable the future implementation of various triggered-recognition strategies.

Preferred side-chain constellations at antiparallel coiled-coil interfaces

“…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). Our findings indicate that vertical interactions must be considered as well if we are to understand the origins of dimerization selectivity among natural coiled-coil sequences and expand current abilities to predict and design such interactions.…”

Structural specificity in coiled-coil interactions

“…Adding methylene groups to lysine and glutamate side chains at e and g positions in an ACID/BASE heterodimer significantly increased coiled-coil stability [38]. Modulating the length of guanidinium-functionalized side chains at a central a position had less effect.…”

Disruption of Bcr-Abl Coiled Coil Oligomerization by Design

“…1, red and blue residues). Because charged residues are routinely found at the g and e positions, mutating these residues in a rational manner to add salt bridges to favor formation of hetero-oligomers (10 -12) and charge-charge repulsions to reduce the formation of homo-oligomers (13,14) can change the affinity and specificity of the coiled coil dimer.…”

“…However, although this provides more salt bridges in the hetero-oligomer, these mutations alone are undesirable as they allow the formation of a greater number of salt bridges in the homo-oligomer. To reduce homo-oligomerization in the mutant coiled coil, residues proximal to charged residues on the opposing helix were considered as candidates for mutation to introduce chargecharge repulsion (13,14). Leu-45 and Glu-48 were identified as two such residues (Fig.…”