Stabilizing capping motif for β-hairpins and sheets

Abstract

Although much has been learned about the design of models of β-sheets during the last decade, modest fold stabilities in water and terminal fraying remain a feature of most β-hairpin peptides. In the case of hairpin capping, nature did not provide guidance for solving the problem. Some observations from prior turn capping designs, with further optimization, have provided a generally applicable, "unnatural" beta cap motif (alkanoyl-Trp at the N terminus and Trp-Thr-Gly at the C terminus) that provides a net contribution of 6 þ kJ∕mol to β-hairpin stability, surpassing all other interactions that stabilize β-hairpins including the covalent disulfide bond. The motif, made up entirely of natural residues, is specific to the termini of antiparallel β-strands and reduces fraying at the ends of hairpins and other β-sheet models. Utilizing this motif, 10-to 22-residue peptide scaffolds of defined stereochemistry that are greater than 98% folded in water have been prepared. The β-cap can also be used to staple together short antiparallel β-strands connected by a long flexible loop.beta sheets | capping stabilization | peptide hairpins | Trp/Trp interactions C apping motifs are well-known features of protein and peptide secondary structure; specifically, terminal alpha helix caps (especially N caps) are common both in proteins and designed peptides (1-4). The basis for helix capping is straightforward: countering the helix macrodipole and providing additional H-bonding interactions (1). Caps increase the fold population of isolated α-helical peptides and have been a boon to the design of α-helix models. β-Structures have capping requirements wholly different from those of helices; the ends of canonical β-sheets and hairpins do not have dipole moments or unsatisfied H bonds.The a priori design of model β-sheet systems (5), focused on hairpins, has lagged behind that of α-helix counterparts. The key discoveries that improved β-hairpin stabilities outside of protein contexts have been sequences with good turn propensities, for example D-Pro-Gly (pG) (6), heterochiral pP (7), and Aib-Gly (8) [or less favorably, Asn-Gly (NG) (5, 9)] and the incorporation of optimized cross-strand pairings [most notably Trp/Trp pairs flanking the turn (10-14)]. However, longer hairpin models are typically still frayed at the termini; to date, fully folded spectroscopic reference values have only been attained via cyclization (15-17). With the exception of cyclization, mutations at terminal sites have yielded only modest changes in hairpin stability; terminal coulombic effects (ΔΔG U ¼ 1.5-2.5 kJ∕mol) standing as the only generally observed capping effect (11,18,19). Pi-cation interactions have also been shown to provide significant hairpin stabilization (20), but instances in which the interaction appears near the ends of hairpins have provided only marginal stability increases (18,(21)(22)(23)). An unnatural π-cation interaction has also been shown to stabilize the turn in a tripeptide (24). There has been limited evidence for hairpin fold sta...

Binding interactions of agents that alter α-synuclein aggregation

“…The concentration range examined was 0 – 8 or 0 –20 vol-% HFIP. In most cases, there was an increase in β structure stability observed at 8 or 20 vol-% HFIP as has previously been observed for other β hairpins 63–67 .…”

Binding of a pleurotolysin ortholog from Pleurotus eryngii to sphingomyelin and cholesterol-rich membrane domains

“…The location of the relatively close C terminus was not altered due to a stabilizing salt bridge between K25 and D132. In both models, W92 and W103 exhibit an edge-to-face orientation, indicating their importance to stabilize aryl/aryl cross-strand interactions ( 46 ). This is in good agreement with the unsuccessful expression of W92A and W103A, possibly due to a failure of the mutants to acquire the correct folding state.…”

β‐Hairpin Peptides: Heme Binding, Catalysis, and Structure in Detergent Micelles

“…Model b-hairpin peptides with aromatic (and especially Trp) residues have been observed to yield similar CD spectra arising from exciton coupling contribution of Trp side chain. [21,23,40] There were no significant changes in the CD spectra of IV8 and IV8FA in the presence of cofactor, indicating peptides do not undergo any major conformational rearrangement in complex with heme (Supporting Information, Figure S6). Further, binding of heme with the designed peptides produces an induced CD band for heme at the Soret region of the absorption spectra, indicating that the heme is experiencing a chiral environment (Supporting Information, Figure S7).…”