Aryl–aryl interactions in designed peptide folds: Spectroscopic characteristics and optimal placement for structure stabilization

Abstract

We have extended our studies of Trp/Trp to other Aryl/Aryl through-space interactions that stabilize hairpins and other small polypeptide folds. Herein we detail the NMR and CD spectroscopic features of these types of interactions. NMR data remains the best diagnostic for characterizing the common T-shape orientation. Designated as an edge-to-face (EtF or FtE) interaction, large ring current shifts are produced at the edge aryl ring hydrogens and, in most cases, large exciton couplets appear in the far UV circular dichroic (CD) spectrum. The preference for the face aryl in FtE clusters is W≫Y≥F (there are some exceptions in the Y/F order); this sequence corresponds to the order of fold stability enhancement and always predicts the amplitude of the lower energy feature of the exciton couplet in the CD spectrum. The CD spectra for FtE W/W, W/Y, Y/W, and Y/Y pairs all include an intense feature at 225–232 nm. An additional couplet feature seen for W/Y, W/F, Y/Y and F/Y clusters, is a negative feature at 197–200 nm. Tyr/Tyr (as well as F/Y and F/F) interactions produce much smaller exciton couplet amplitudes. The Trp-cage fold was employed to search for the CD effects of other Trp/Trp and Trp/Tyr cluster geometries: several were identified. In this account, we provide additional examples of the application of cross-strand aryl/aryl clusters for the design of stable β-sheet models and a scale of fold stability increments associated with all possible FtE Ar/Ar clusters in several structural contexts.

Exciton circular dichroism couplet arising from nitrile-derivatized aromatic residues as a structural probe of proteins

“…[7] We chose these peptide systems because they all contain at least two Trp residues that have been shown to engage in exciton coupling and hence exhibit an exciton CD band. Finally, we investigated the Trp to Trp CN and Phe to Phe CN double mutant of another stable β-hairpin that was designed through “loop optimization” by Andersen and coworkers [20]. …”

“…In a recent study on the role of aryl-aryl interactions in β-hairpin folding, Andersen and coworkers [20] systematically examined the effect of various cross-strand interactions that can promote β-hairpin formation. In particular, they found that a peptide with the following sequence, KKYTFNPATGKWTVQE, can fold into a β-hairpin conformation at room temperature, due to a favorable Phe-Trp interaction with Trp occupying the face position and Phe at the edge position.…”

Biological consequences of improving the structural stability of hairpins that have antimicrobial activity

“…Cross‐strand Trp/Trp EtF interactions provide at least a 2.3–5 kJ/mol stabilization of hairpin folds . More recently, we have reported that end‐capping Trp/Trp EtF interactions produce a stabilization of 5–7 kJ/mol . Some stabilization also results from the interaction of the Gly‐H N with the indole ring of the C‐terminus Trp and the Thr hydroxyl group interacting with the C═O of the Trp‐alkanoyl peptide bond.…”

“…[13,18] More recently, we have reported that end-capping Trp/Trp EtF interactions produce a stabilization of 5-7 kJ/mol. [19] Some stabilization also results from the interaction of the Gly-H N with the indole ring of the C-terminus Trp and the Thr hydroxyl group interacting with the C═O of the Trpalkanoyl peptide bond. The stability of this cap has been shown to be higher, by~2 kJ/mol, than that conferred by some covalent stabilization strategies such as disulfide bonding.…”

A pH Switch for β‐Sheet Protein Folding

“…The WWst29 system was designed in‐house, starting as a truncated version of the wild type protein Pin1 with the inclusion of a Trp/Trp aromatic cluster flanking T1 . The cross‐strand Trp/Trp cluster also reports the stability of the overall structure as the amplitude of a circular dichroic exciton couplet with maximum at 228 nm . In addition to this spectroscopic feature, the WW domain has numerous specific and well‐dispersed structuring chemical shifts that can be quantitated by proton NMR.…”