Design of Functional Globular β-Sheet Miniproteins

The design of discrete β-sheet peptides is far less advanced than e. g. the design of α-helical peptides. The reputation of β-sheet peptides as being poorly soluble and aggregation-prone often hinders active design efforts. Here, we show that this reputation is unfounded. We demonstrate this by looking at the β-hairpin and WW domain. Their structure and folding have been extensively studied and they have long served as model systems to investigate protein folding and folding kinetics. The resulting fundamental understanding has led to the development of hyperstable β-sheet scaffolds that fold at temperatures of 100 °C or high concentrations of denaturants. These have been used to design functional miniproteins with protein or nucleic acid binding properties, in some cases with such success that medical applications are conceivable. The β-sheet scaffolds are not always completely rigid, but can be specifically designed to respond to changes in pH, redox potential or presence of metal ions. Some engineered β-sheet peptides also exhibit catalytic properties, although not comparable to those of natural proteins. Previous reviews have focused on the design of stably folded and non-aggregating β-sheet sequences. In our review, we now also address design strategies to obtain functional miniproteins from β-sheet folding motifs.

The Effects of Charged Amino Acid Side-Chain Length on Diagonal Cross-Strand Interactions between Carboxylate- and Ammonium-Containing Residues in a β-Hairpin

The β-sheet is one of the common protein secondary structures, and the aberrant aggregation of β-sheets is implicated in various neurodegenerative diseases. Cross-strand interactions are an important determinant of β-sheet stability. Accordingly, both diagonal and lateral cross-strand interactions have been studied. Surprisingly, diagonal cross-strand ion-pairing interactions have yet to be investigated. Herein, we present a systematic study on the effects of charged amino acid side-chain length on a diagonal ion-pairing interaction between carboxylate- and ammonium-containing residues in a β-hairpin. To this end, 2D-NMR was used to investigate the conformation of the peptides. The fraction folded population and the folding free energy were derived from the chemical shift data. The fraction folded population for these peptides with potential diagonal ion pairs was mostly lower compared to the corresponding peptide with a potential lateral ion pair. The diagonal ion-pairing interaction energy was derived using double mutant cycle analysis. The Asp2-Dab9 (Asp: one methylene; Dab: two methylenes) interaction was the most stabilizing (−0.79 ± 0.14 kcal/mol), most likely representing an optimal balance between the entropic penalty to enable the ion-pairing interaction and the number of side-chain conformations that can accommodate the interaction. These results should be useful for designing β-sheet containing molecular entities for various applications.

The impact of α-hydrazino acids embedded in short fluorescent peptides on peptide interactions with DNA and RNA

A series of novel hydrazino-based peptidomimetics and analogues comprising N-terminal lysine and C-terminal phenanthridinyl-l-alanine were prepared. The presented results demonstrate the up to now unknown possibility to finely modulate peptide interactions with DNA/RNA by α-hydrazino group insertion and how the different positioning of two α-hydrazino groups in peptides controls binding to various double stranded and single stranded DNA and RNA. All peptidomimetics bind with 1-10 micromolar affinity to ds-DNA/RNA, whereby the binding mode is a combination of electrostatic interactions and hydrophobic interactions within DNA/RNA grooves. Insertion of the α-hydrazino group into the peptide systematically decreased its fluorimetric response to DNA/RNA binding in the order: mono-hydrazino < alternating-hydrazino < sequential-hydrazino group. Binding studies of ss-polynucleotides suggest intercalation of phenanthridine between polynucleotide bases, whereby affinity and fluorimetric response decrease with the number of α-hydrazino groups in the peptide sequence. Particularly interesting was the interaction of two sequential α-hydrazino acids-peptidomimetic with poly rG, characterised by a specific strong increase of CD bands, while all other peptide/ssRNA combinations gave only a CD-band decrease. All mentioned interactions could also be reversibly controlled by adjusting the pH, due to the protonation of the fluorophore.

Coupling the folding of a β-hairpin with chelation-enhanced luminescence of Tb(III) and Eu(III) ions for specific sensing of a viral RNA

Rational modification of a natural RNA-binding peptide with a lanthanide EDTA chelator, and a phenanthroline ligand yields a highly selective luminescent sensor. The sensing mechanism relies on the RNA-triggered folding of the peptide into a β-hairpin, which promotes the coordination of the phenanthroline sensitizer, and the efficient sensitization of complexed lanthanide ions.

Separation of peptide fragments of a protein kinase C substrate fused to a β-hairpin by capillary electrophoresis

Synthetic peptides incorporating well-folded β-hairpin peptides possess advantages in a variety of cell biology applications by virtue of increased resistance to proteolytic degradation. In this study, the WKpG β-hairpin peptide fused to a protein kinase C (PKC) substrate was synthesized, and capillary-electrophoretic separation conditions for this peptide and its proteolytic fragments were developed. Fragments of WKpG-PKC were generated by enzymatic treatment with trypsin and Pronase E to produce standards for identification of degradation fragments in a cellular lysate. A simple buffer system of 250 mM H3PO4, pH 1.5 enabled separation of WKpG-PKC and its fragments by capillary electrophoresis in less than 16 min. Using a cellular lysate produced from Ba/F3 cells, the β-hairpin-conjugated substrate and its PKCα-phosphorylated product could be detected and separated from peptidase-generated fragments produced in a cell lysate. The method has potential application for identification and quantification of WKpG-PKC and its fragments in complex biological systems when the peptide is used as a reporter to assay PKC activity.

Design of monomeric water-soluble β-hairpin and β-sheet peptides

Since the first report in 1993 (JACS 115, 5887-5888) of a peptide able to form a monomeric β-hairpin structure in aqueous solution, the design of peptides forming either β-hairpins (two-stranded antiparallel β-sheets) or three-stranded antiparallel β-sheets has become a field of growing interest and activity. These studies have yielded great insights into the principles governing the stability and folding of β-hairpins and antiparallel β-sheets. This chapter provides an overview of the reported β-hairpin/β-sheet peptides focussed on the applied design criteria, reviews briefly the factors contributing to β-hairpin/β-sheet stability, and describes a protocol for the de novo design of β-sheet-forming peptides based on them. Guidelines to select appropriate turn and strand residues and to avoid self-association are provided. The methods employed to check the success of new designed peptides are also summarized. Since NMR is the best technique to that end, NOEs and chemical shifts characteristic of β-hairpins and three-stranded antiparallel β-sheets are given.

Tryptophan residues: scarce in proteins but strong stabilizers of β-hairpin peptides

Tryptophan plays important roles in protein stability and recognition despite its scarcity in proteins. Except as fluorescent groups, they have been used rarely in peptide design. Nevertheless, Trp residues were crucial for the stability of some designed minimal proteins. In 2000, Trp-Trp pairs were shown to contribute more than any other hydrophobic interaction to the stability of β-hairpin peptides. Since then, Trp-Trp pairs have emerged as a paradigm for the design of stable β-hairpins, such as the Trpzip peptides. Here, we analyze the nature of the stabilizing capacity of Trp-Trp pairs by reviewing the β-hairpin peptides containing Trp-Trp pairs described up to now, the spectroscopic features and geometry of the Trp-Trp pairs, and their use as binding sites in β-hairpin peptides. To complete the overview, we briefly go through the other relevant β-hairpin stabilizing Trp-non-Trp interactions and illustrate the use of Trp in the design of short peptides adopting α-helical and mixed α/β motifs. This review is of interest in the field of rational design of proteins, peptides, peptidomimetics, and biomaterials.

beta-hairpin-forming peptides; models of early stages of protein folding

Formation of beta-hairpins is considered the initial step of folding of many proteins and, consequently, peptides constituting the beta-hairpin sequence of proteins (the beta-hairpin-forming peptides) are considered as models of early stages of protein folding. In this article, we discuss the results of experimental studies (circular-dichroism, infrared and nuclear magnetic resonance spectroscopy, and differential scanning calorimetry) of the structure of beta-hairpin-forming peptides excised from the B1 domain of protein G, which are known to fold on their own. We demonstrate that local interactions at the turn sequence and hydrophobic interactions between nonpolar residues are the dominant structure-determining factors, while there is no convincing evidence that stable backbone hydrogen bonds are formed in these peptides in aqueous solution. Consequently, the most plausible mechanism for folding of the beta-hairpin sequence appears to be the broken-zipper mechanism consisting of the following three steps: (i) bending the chain at the turn sequence owing to favorable local interactions, (ii) formation of loose hydrophobic contacts between nonpolar residues, which occur close to the contacts in the native structure of the protein but not exactly in the same position and, finally, (iii) formation of backbone hydrogen bonds and locking the hydrophobic contacts in the native positions as a hydrophobic core develops, sufficient to dehydrate the backbone peptide groups. This mechanism provides sufficient uniqueness (contacts form between residues that become close together because the chain is bent at the turn position) and robustness (contacts need not occur at once in the native positions) for folding a beta-hairpin sequence.