Fr Francium

The inside cover picture shows that AuaA, a membrane-bound farnesyltransferase from Stigmatella aurantiaca, is responsible for the formation of aurachin D. This enzyme was successfully overproduced in E. coli and characterized biochemically. A number of C3-prenylated 4-hydroxyquinoline derivatives were produced by using cell extracts from the recombinant E. coli cells. For more details, see the paper by S.-M. Li et al. on p. 1724 ff.

The cover picture shows the selective binding of a synthetic naphthyridine-azaquinolone (NA) ligand to a CAG/CAG-triad-containing DNA. In humans, unusual expansion of the trinucleotide repeat is associated with a number of severe neurodegenerative diseases, such as Huntington's disease, spinobulbar muscular atrophy, and spinocerebellar ataxia. The d(CAG)_n expansion mutation in the Huntington gene results in the production of aberrant protein that leads to gradual damage to specific areas of the brain. Although the actual mechanism of repeat expansion remains uncertain, repeat instability of CAG/CTG might be related to the increased stability of an alternative DNA hairpin structure in the d(CAG) repeat sequences. On p. 1686 ff, K. Nakatani et al. show that NA stabilizes hairpin secondary structures on d(CAG)_n repeats, which efficiently interferes with DNA replication by Taq polymerase and human DNA polymerase A. Considering the selective sequence preference, the use of NA would be valuable in understanding the features of the genetic instabilities of CAG/CTG repeat sequences in genomes.

Despite their enormous diversity in biological function and structure, peptides and proteins are endowed with properties that have induced and stimulated the development of peptidomimetics. Clearly, peptides can be considered as the “stem” of a phylogenetic molecular development tree from which branches of oligomeric peptidomimetics such as peptoids, peptidosulfonamides, urea peptidomimetics, as well as β-peptides have sprouted. It is still a challenge to efficiently synthesize these oligomeric species, and study their structural and biological properties. Combining peptides and peptidomimetics led to the emergence of peptide–peptidomimetic hybrids in which one or more (proteinogenic) amino acid residues have been replaced with these mimetic residues. In scan-like approaches, the influence of these replacements on biological activity can then be studied, to evaluate to what extent a peptide can be transformed into a peptidomimetic structure while maintaining, or even improving, its biological properties. A central issue, especially with the smaller peptides, is the lack of secondary structure. Important approaches to control secondary structure include the introduction of α,α-disubstituted amino acids, or (di)peptidomimetic structures such as the Freidinger lactam. Apart from intra-amino acid constraints, inter-amino acid constraints for formation of a diversity of cyclic peptides have shaped a thick branch. Apart from the classical disulfide bridges, the repertoire has been extended to include sulfide and triazole bridges as well as the single-, double- and even triple-bond replacements, accessible by the extremely versatile ring-closing alkene/alkyne metathesis approaches. The latter approach is now the method of choice for the secondary structure that presents the greatest challenge for structural stabilization: the α-helix.

Building bridges: The design and development of peptidomimetics is an expanding research area and yields molecules that can improve on the function of their “natural” parent peptides—with tempting potential for novel therapeutics. We review here several different directions in exciting areas of oligomeric peptidomimetics, hybrids and covalent control of shape and secondary structure folding by alternatives to disulfide bridges.

An exo-β-xylosidase mutant with glycosynthase activity was created to aid in the synthesis of xylanase substrates and inhibitors. Simple monosaccharides were easily elaborated into di-, tri- and tetrasaccharides by using this enzyme. Some products proved to be surprisingly potent inhibitors of xylanases from glycoside hydrolase families 10 and 11.

Assembly by synthase: An exo-β-xylosidase mutant with glycosynthase activity greatly simplifies the synthesis of xylanase substrates and inhibitors (see scheme). Some of these glycosynthase products were found to be the most potent competitive inhibitors of glycoside hydrolase family 10 and 11 xylanases reported to date.

Crosslinkers that undergo large changes in length upon photoisomerization can produce large conformational changes, and thereby functional changes, in biomolecules. We have designed and synthesized extended and rigid bis-azobenzene crosslinkers: 4,4′-bis(4-(2-chloroacetamido)phenyl)diazenylbiphenyl (BPDB) and the water-soluble sulfonated analogue 4,4′-bis(4-(2-chloroacetamido)phenyl)diazenylbiphenyl-2,2′-disulfonate (BPDBS). These photoswitches can produce end-to-end distance changes of a minimum of ≈5 Å and a maximum of ≈23 Å upon trans/cis isomerization. They have high absorption coefficients (45–60 000 M⁻¹ cm⁻¹) and can produce up to ≈80 % cis isomers under favorable conditions. The photoswitching behavior of BPDBS-crosslinked peptides was found to be highly dependent on the crosslinker attachment site. Upon UV irradiation (365 nm), significant decreases in α-helix content were observed for peptides that were crosslinked with BPDBS through Cys residues at i,i+19, and i,i+21 positions. In contrast, large increases in α-helix content were exhibited by i,i+11 crosslinked peptides. BPDBS thus constitutes a particularly bright and effective photoswitch for biomolecule photocontrol.

More-remote control: Thiol-reactive bis-azo photoswitches enable photocontrol of peptide conformation over longer distances than previously possible. trans-to-cis photoisomerization of the bis-azo crosslinker enhances helical content in a peptide with cysteine residues spaced in a i,i+11 fashion.

Membrane integration enigmas: The two envelope membranes surrounding chloroplasts contain a plethora of integral proteins but not much is known about their targeting and integration processes. Here, we give a survey on accumulated knowledge concerning membrane protein integration and discuss methodological pitfalls.

Spanner in the works: The synthetic ligand, naphthyridine-azaquinolone (NA), can induce hairpin secondary structures on d(CAG)_n repeats and efficiently interfere with DNA replication by Taq DNA polymerase as well as the human DNA polymerase α (see figure). Considering its unique sequence preference, NA would be a valuable probe to understand the features of the genetic instabilities of CAG/CTG repeat sequences in genomes.