Chiroptical labeling of folded polypeptide conformations: The thioamide probe

Modulation of SpyCatcher Ligation Kinetics by SpyTag Thioamide Substitution

Thioamide substitutions have been shown to impart valuable properties on peptides for biophysical experiments as well as cell or in vivo studies, but a rational understanding of thioamide effects on protein structure and protein-protein interactions is lacking. To elucidate their effects in β-sheet structures, we have used SpyCatcher003-SpyTag003 as a host-guest system to study individual thioamide incorporation at eight different positions in the SpyTag peptide. We have demonstrated that incorporating thioamides into SpyTag at specific positions can result in a ∼2-fold faster ligating complex, as well as >2000-fold slower ligating complex. Biophysical analysis and structural modeling provide a reasonable explanation for most of the thioamide effects, altering hydrogen bond networks as well as modulating an n→π* interaction within the SpyTag peptide. Our findings have important implications for potential applications of thioamide SpyTag variants, where the thioamide could impart protease stability in cells while also controlling the rate of ligation to SpyCatcher. These SpyCatcher-SpyTag host-guest experiments will also help to build a database for predicting thioamide effects on protein structure and function.

Structural impact of thioamide incorporation into a β-hairpin

The thioamide is a naturally-occurring single atom substitution of the canonical amide bond. The exchange of oxygen to sulfur alters the amide's physical and chemical characteristics, thereby expanding its functionality. Incorporation of thioamides in prevalent secondary structures has demonstrated that they can either have stabilizing, destabilizing, or neutral effects. We performed a systematic investigation of the structural impact of thioamide incorporation in a β-hairpin scaffold with nuclear magnetic resonance (NMR). Thioamides as hydrogen bond donors did not increase the foldedness of the more stable "YKL" variant of this scaffold. In the less stable "HPT" variant of the scaffold, the thioamide could be stabilizing as a hydrogen bond donor and destabilizing as a hydrogen bond acceptor, but the extent of the perturbation depended upon the position of incorporation. To better understand these effects we performed structural modelling of the macrocyclic folded HPT variants. Finally, we compare the thioamide effects that we observe to previous studies of both side-chain and backbone perturbations to this β-hairpin scaffold to provide context for our observations.

Folding and Unfolding of the Tryptophan Zipper in the Presence of Two Thioamide Substitutions

We studied the stability and folding and unfolding kinetics of the tryptophan zipper, containing different double thioamide subsitutions. Conformation change was triggered by photoisomerization of an integrated AMPP photoswitch in the turn region of the hairpin, and transient spectra were recorded in the deep UV and the mid-IR, covering the time window of the (un)folding transition from picoseconds to tens of microseconds. Thio-substitution of inward-pointing backbone carbonyls was found to strongly destabilize the β-hairpin structures, whereas molecules with two outward pointing thio-carbonyls showed similar or enhanced stability with respect to the unsubstituted sequence, which we attribute to stronger interstrand hydrogen bonding. Thiolation of the two Trp residues closest to the turn can even prevent the opening of the hairpin after cis-trans isomerization of the switch. The circular dichroism due to the two thioamide ππ* transitions is spectrally well-separated from the aromatic tryptophan signal. It changes upon photoswitching, reflecting a local change in coupling and geometry.

Broad-Band Ultraviolet CD Spectroscopy of Ultrafast Peptide Backbone Conformational Dynamics

The far-UV spectral window widely used for the conformational analysis of biomolecules is not easily covered with broad-band lasers. This has made it difficult to use circular dichroism (CD) spectroscopy to directly follow fast structure changes. By combining transient CD spectroscopy in the deep-UV with thioamide substitution, we demonstrate a method to overcome this difficulty. We investigated a dipeptide whose two carbonyl oxygen atoms were replaced by sulfur, red-shifting the strong lowest-lying ππ* transitions into the more accessible 250-370 nm spectral window. Coupling of the two thioamide units cannot be resolved by achiral 2D-UV spectroscopy, but it gives rise to a pronounced bisignate CD spectrum. The transient CD spectra reveal weakening of this coupling in the electronically excited state, where conformational constraints are released. Our results show that direct local probing of fast backbone conformational change via CD spectroscopy is possible in combination with site-selective thio substitution in peptides and proteins.

Thioamides in the collagen triple helix

To probe noncovalent interactions within the collagen triple helix, backbone amides were replaced with a thioamide isostere. This subtle substitution is the first in the collagen backbone that does not compromise thermostability. A triple helix with a thioamide as a hydrogen bond donor was found to be more stable than triple helices assembled from isomeric thiopeptides.

Synthesis of thioester peptides for the incorporation of thioamides into proteins by native chemical ligation

Thioamides can be used as photoswitches, as reporters of local environment, as inhibitors of enzymes, and as fluorescence quenchers. We have recently demonstrated the incorporation of thioamides into polypeptides and proteins using native chemical ligation (NCL). In this protocol, we describe procedures for the synthesis of a thioamide precursor and an NCL-ready thioamide-containing peptide using Dawson's N-acyl-benzimidazolinone (Nbz) process. We include a description of the synthesis by NCL of a thioamide-labeled fragment of the neuronal protein α-synuclein.

Thionoglycine as a multifunctional spectroscopic reporter of screw-sense preference in helical foldamers

A single thionoglycine (glycine thioamide, -HNCH2C(=S)-) residue inserted into a peptide foldamer provides both a pair of germinal protons for use as a (1)H NMR stereochemical probe and a chromophore giving rise to a well defined Cotton effect in CD. Comparison of the response of these two features to a local helically chiral environment validates them as independent methods for quantifying the conformational screw-sense preference of a helical oligomer, in this case a peptide made of repeated Aib units. The sign of the Cotton effect provides a measure of the sign of the screw-sense preference, while both the chemical shift separation of the anisochronous signals of the glycine CH2 group and the magnitude of the Cotton effect give an estimate of the helicity excess of the oligomer. The thionoglycine unit is readily introduced synthetically by a thionation of a BocGlyAibOMe dipeptide.

Partial thioamide scan on the lipopeptaibiotic trichogin GA IV. Effects on folding and bioactivity

Backbone modification is a common chemical tool to control the conformation of linear peptides and to explore potentially useful effects on their biochemical and biophysical properties. The thioamide, ψ[CS-NH], group is a nearly isosteric structural mimic of the amide (peptide) functionality. In this paper, we describe the solution synthesis, chemical characterization, preferred conformation, and membrane and biological activities of three, carefully selected, peptide analogues of the lipopeptaibiotic [Leu¹¹-OMe] trichogin GA IV. In each analogue, a single thioamide replacement was incorporated. Sequence positions near the N-terminus, at the center, and near the C-terminus were investigated. Our results indicate that (i) a thioamide linkage is well tolerated in the overall helical conformation of the [Leu¹¹-OMe] lipopeptide analogue and (ii) this backbone modification is compatible with the preservation of its typical membrane leakage and antibiotic properties, although somewhat attenuated.

Native chemical ligation of thioamide-containing peptides: development and application to the synthesis of labeled α-synuclein for misfolding studies

Thioamide modifications of the peptide backbone are used to perturb secondary structure, to inhibit proteolysis, as photoswitches, and as spectroscopic labels. Thus far, their incorporation has been confined to single peptides synthesized on solid phase. We have generated thioamides in C-terminal thioesters or N-terminal Cys fragments and examined their compatibility with native chemical ligation conditions. Most sequence variants can be coupled in good yields with either TCEP or DTT as the reductant, though some byproducts are observed with prolonged TCEP incubations. Furthermore, we find that thioamides are compatible with thiazolidine protection of an N-terminal Cys, so that multiple ligations can be used to construct larger proteins. Since the acid-lability of the thioamide prohibits on-resin thioester synthesis using Boc chemistry, we devised a method for the synthesis of thioamide peptides with a masked C-terminal thioester that is revealed in situ. Finally, we have shown that thioamidous peptides can be coupled to expressed protein fragments to generate large proteins with backbone thioamide labels by synthesizing labeled versions of the amyloid protein α-synuclein for protein folding studies. In a proof-of-principle experiment, we demonstrated that quenching of fluorescence by thioamides can be used to track conformational changes during aggregation of labeled α-synuclein.

Compatibility of the thioamide functional group with beta-sheet secondary structure: incorporation of a thioamide linkage into a beta-hairpin peptide

[structure: see text]. We report the incorporation of a thioamide linkage between the i + 2 and i + 3 residues of the type II' beta-turn of a peptide known to fold into a beta-hairpin conformation. Two-dimensional NMR spectroscopy and circular dichroism spectroscopy indicate that the thioxo peptide adopts a hairpin conformation similar to that of the oxo peptide and that the hairpin conformation persists at elevated temperatures. The results show that a thioamide linkage is compatible with beta-sheet secondary structure.