The origin of the stability of isolated β-hairpins in aqueous solution is unclear with contrasting opinions as to the relative importance of interstrand hydrogen bonding, hydrophobic interactions, and conformational preferences, the latter being associated largely with the turn sequence. We have designed an unconstrained 16-residue peptide that we show folds autonomously in water to form a β-hairpin that mimics the two-stranded anti-parallel β-sheet DNA binding motif of the met repressor dimer. The designed peptide, with a type I‘ turn (INGK), is shown by CD and a range of NMR parameters to be appreciably folded (≈50% at 303 K) in aqueous solution with the predicted alignment of the peptide backbone. We show that the folding transition approximates to a two-state model. The hairpin has a marked temperature-dependent stability, reaching a maximum value at 303 K in water with both lower and higher temperatures destabilizing the folded structure. Van't Hoff analysis of Hα chemical shifts, reveals that folding is endothermic and entropy-driven in aqueous solution with a large negative ΔC p, all of which are reminiscent of proteins with hydrophobic cores, pointing to the hydrophobic effect as the dominant stabilizing interaction in water. We have examined the conformational properties of the C-terminal β-strand (residues 9−16) in isolation and have shown that 3 J α N values and backbone intra- and inter-residue Hα-NH NOE intensities deviate from those predicted for a random coil, indicating that the β-strand has a natural predisposition to adopt an extended conformation in the absence of secondary structure interactions. A family of β-hairpin structures calculated from 200 (distance and torsion angle) restraints using molecular dynamics shows that the conformation of the hairpin mimics closely the DNA binding face of the met repressor dimer (backbone RMSD between corresponding β-strands of 1.0 ± 0.2 Å).

No abstract

The extracellular siderophore from Mycobacterium smegmatis, exochelin MS, was isolated from iron-deficiently grown cultures and purified to > 98% by a combination of ion-exchange chromatography and h.p.l.c. The material is unextractable into organic solvents, is basic (pI = 9.3-9.5), has a lambda max at 420 nm and a probable Ks for Fe3+ of between 10(25) and 10(30). Its structure has been determined by examination of desferri- and ferri-exochelin and its gallium complex. The methods used were electrospray-m.s. and one- and two-dimensional (NOESY, DQF-COSY and TOCSY) 1H n.m.r. The constituent amino acids were examined by chiral g.l.c analysis of N-trifluoroacetyl isopropyl and N-pentafluoropropionyl methyl esters after hydrolysis, and reductive HI hydrolysis, of the siderophore. The exochelin is a formylated pentapeptide: N-(delta-N-formyl,delta N-hydroxy-R-ornithyl) -beta-alaninyl-delta N-hydroxy-R-ornithinyl-R-allo-threoninyl-delta N-hydroxy-S-ornithine. The linkages involving the three ornithine residues are via their delta N(OH) and alpha-CO groups leaving three free alpha-NH2 groups. Although there are two peptide bonds, these involve the three R (D)-amino acids. Thus the molecule has no conventional peptide bond, and this suggests that it will be resistant to peptidase hydrolysis. The co-ordination centre with Fe3+ is hexadenate in an octahedral structure involving the three hydroxamic acid groups. Molecular modelling shows it to have similar features to other ferric trihydroxamate siderophores whose three-dimensional structures have been established. The molecule is shown to have little flexibility around the iron chelation centre, although the terminal (Orn-3) residue, which is not involved in iron binding except at its delta N atom, has more motional freedom.

Exochelin MN has some structural features in common with other siderophores, but has a unique three-dimensional structure, which is presumably important for its specific activity in M. leprae. Exochelin MN may be a target for drug design in the fight against infection with this pathogen.

No abstract

The solution structure of the dodecamer duplex d(CTTTTGCAAAAG)(2)and its 2:1 complex with the bis -benzimidazole Hoechst 33258 has been investigated by NMR and NOE-restrained molecular dynamics (rMD) simulations. Drug molecules are bound in each of the two A-tracts with the bulky N-methylpiperazine ring of each drug located close to the central TG (CA) step, binding essentially to the narrow minor groove of each A-tract. MD simulations over 1 ns, using an explicit solvation model, reveal time-averaged sequence-dependent narrowing of the minor groove from the 3'-end towards the 5'-end of each TTTT sequence. Distinct junctions at the TpG (CpA) steps, characterised by large positive roll, low helical and propeller twists and rapid AT base pair opening rates, add to the widening of the groove at these sites and appear to account for the bound orientation of the two drug molecules with the N-methylpiperazine ring binding in the wider part of the groove close to the junctions. Comparisons between the free DNA structure and the 2:1 complex (heavy atom RMSD 1.55 A) reveal that these sequence-dependent features persist in both structures. NMR studies of the sequence d(GAAAAGCTTTTC)(2), in which the A-tracts have been inverted with the elimination of the TpG junctions, results in loss of orientational specificity of Hoechst 33258 and formation of multiple bound species in solution, consistent with the drug binding in a number of different orientations.

We present reference data and a javascript web page which allow the rapid identification and quantification of residual solvents by NMR. The data encompass all of the ICH-prescribed solvents and were obtained for a number of NMR solvents. We also present an example of its application.

No abstract