Daptomycin is a lipopeptide antibiotic produced by a nonribosomal peptide synthetase (NRPS) in Streptomyces roseosporus. The holoenzyme is composed of three subunits, encoded by the dptA, dptBC, and dptD genes, each responsible for incorporating particular amino acids into the peptide. We introduced expression plasmids carrying dptD or NRPS genes encoding subunits from two related lipopeptide biosynthetic pathways into a daptomycin nonproducing strain of S. roseosporus harboring a deletion of dptD. All constructs successfully complemented the deletion in trans, generating three peptide cores related to daptomycin. When these were coupled with incomplete methylation of 1 amino acid and natural variation in the lipid side chain, 18 lipopeptides were generated. Substantial amounts of nine of these compounds were readily obtained by fermentation, and all displayed antibacterial activity against gram-positive pathogens.

Daptomycin is a 13 amino acid, cyclic lipopeptide produced by a non-ribosomal peptide synthetase (NRPS) mechanism in Streptomyces roseosporus. A 128 kb region of S. roseosporus DNA was cloned and verified by heterologous expression in Streptomyces lividans to contain the daptomycin biosynthetic gene cluster (dpt). The cloned region was completely sequenced and three genes (dptA, dptBC, dptD) encoding the three subunits of an NRPS were identified. The catalytic domains in the subunits, predicted to couple five, six or two amino acids, respectively, included a novel activation domain and amino-acid-binding pocket for incorporating the unusual amino acid l-kynurenine (Kyn), three types of condensation domains and an extra epimerase domain (E-domain) in the second module. Novel genes (dptE, dptF) whose products likely work in conjunction with a unique condensation domain to acylate the first amino acid, as well as other genes (dptI, dptJ) probably involved in supply of the non-proteinogenic amino acids l-3-methylglutamic acid and Kyn, were located next to the NRPS genes. The unexpected E-domain suggested that daptomycin would have d-Asn, rather than l-Asn, as originally assigned, and this was confirmed by comparing stereospecific synthetic peptides and the natural product both chemically and microbiologically.

Peptide fragments taken from residues 18‒54 of short consensus repeat 3 (SCR3) from the human complement receptor CR1 have been found in aqueous solution to slowly aggregate and form fibrils. NMR studies of the monomeric form of these peptides show that they are essentially unfolded in aqueous solution and that they all have an increased helicity in TFE solutions. The behaviour of residues 28‒31 from SCR3 is particularly interesting. These residues have a high β -sheet propensity in the native protein and a seven peptide containing their sequence is found to form fibrils despite its short length. However, NMR studies show that these residues adopt a well-defined α -helix in 80% TFE and under these conditions fibril formation has not been observed. These data demonstrate the strong dependence of conformational propensities on environment.

At the heart of the pathogenesis of transmissible spongiform encephalopathies (TSEs), such as BSE, scrapie, and Creutzfeldt–Jakob disease, lies a poorly understood structural rearrangement of PrP, an abundant glycoprotein of the nervous and lymphoid systems. The normal form (PrPC), rich in α‐helix, converts into an aberrant β‐sheet‐dominated form (PrPSc), which seems to be at the center of the pathotoxic symptoms observed in TSEs. To understand this process better at a molecular level, we have studied the interactions between different peptides derived from bovine PrP and their structural significance. We show that two unstructured peptides derived from the central region of bovine PrP, residues 115–133 and 140–152, respectively, interact stoichiometrically under physiological conditions to generate β‐sheet‐dominated fibrils. However, when both peptides are incubated in the presence of a third peptide derived from an adjoining α‐helical region (residues 153–169), the formation of β‐sheet‐rich fibrils is abolished. These data indicate that native PrPC helix 1 might inhibit the strong intrinsic β‐sheet‐forming propensity of sequences immediately N‐terminal to the globular core of PrPC, by keeping in place intrachain interactions that would prevent these amyloidogenic regions from triggering aggregation. Moreover, these results indicate new ways in which PrPSc formation could be prevented.

Under solution conditions where the native state is destabilized, the largely helical polypeptide hormone insulin readily aggregates to form amyloid fibrils with a characteristic cross-β structure. However, there is a lack of information relating the 4.8 Å β-strand repeat to the higher order assembly of amyloid fibrils. We have used cryo-electron microscopy (EM), combining single particle analysis and helical reconstruction, to characterize these fibrils and to study the three-dimensional (3D) arrangement of their component protofilaments. Low-resolution 3D structures of fibrils containing 2, 4, and 6 protofilaments reveal a characteristic, compact shape of the insulin protofilament. Considerations of protofilament packing indicate that the cross-β ribbon is composed of relatively flat β-sheets rather than being the highly twisted, β-coil structure previously suggested by analysis of globular protein folds. Comparison of the various fibril structures suggests that very small, local changes in β-sheet twist are important in establishing the long-range coiling of the protofilaments into fibrils of diverse morphology.

Sodium dodecyl sulphate (SDS), a detergent that mimics some characteristics of biological membranes, has been found to affect significantly fibril formation by a peptide from human complement receptor 1. In aqueous solution the peptide is unfolded but slowly aggregates to form fibrils. In sub‐micellar concentrations of SDS the peptide is initially α‐helical but converts rapidly to a β‐sheet structure and large quantities of fibrils form. In SDS above the critical micellar concentration the peptide adopts a stable α‐helical structure and no fibrils are observed. These findings demonstrate the sensitivity of fibril formation to solution conditions and suggest a possible role for membrane components in amyloid fibril formation in living systems.

The substitution of alanines for the two cysteines which form thioether linkages to the haem group in cytochrome c 552 from Hydogenobacter thermophilus destabilises the native protein fold. The holo form of this variant slowly converts into a partially folded apo state that over prolonged periods of time aggregates into fibrillar structures. Characterisation of these structures by electron microscopy and thioflavin‐T binding assays shows that they are amyloid fibrils. The data demonstrate that when the native state of this cytochrome is destabilised by loss of haem, even this highly α‐helical protein can form β‐sheet structures of the type most commonly associated with protein deposition diseases.

Fourier transform infrared spectroscopy (FTIR), circular dichroism (CD), and electron microscopy (EM) have been used simultaneously to follow the temperature-induced formation of amyloid fibrils by bovine insulin at acidic pH. The FTIR and CD data confirm that, before heating, insulin molecules in solution at pH 2.3 have a predominantly native-like alpha-helical structure. On heating to 70 degrees C, partial unfolding occurs and results initially in aggregates that are shown by CD and FT-IR spectra to retain a predominantly helical structure. Following this step, changes in the CD and FTIR spectra occur that are indicative of the extensive conversion of the molecular conformation from alpha-helical to beta-sheet structure. At later stages, EM shows the development of fibrils with well-defined repetitive morphologies including structures with a periodic helical twist of approximately 450 A. The results indicate that formation of fibrils by insulin requires substantial unfolding of the native protein, and that the most highly ordered structures result from a slow evolution of the morphology of the initially formed fibrillar species.

The self-assembly and aggregation of insulin molecules has been investigated by means of nanoflow electrospray mass spectrometry. Hexamers of insulin containing predominantly two, but up to four, Zn(2+) ions were observed in the gas phase when solutions at pH 4.0 were examined. At pH 3.3, in the absence of Zn(2+), dimers and tetramers are observed. Spectra obtained from solutions of insulin at millimolar concentrations at pH 2.0, conditions under which insulin is known to aggregate in solution, showed signals from a range of higher oligomers. Clusters containing up to 12 molecules could be detected in the gas phase. Hydrogen exchange measurements show that in solution these higher oligomers are in rapid equilibrium with monomeric insulin. At elevated temperatures, under conditions where insulin rapidly forms amyloid fibrils, the concentration of soluble higher oligomers was found to decrease with time yielding insoluble high molecular weight aggregates and then fibrils. The fibrils formed were examined by electron microscopy and the results show that the amorphous aggregates formed initially are converted to twisted, unbranched fibrils containing several protofilaments. Fourier transform infrared spectroscopy shows that both the soluble form of insulin and the initial aggregates are predominantly helical, but that formation of beta-sheet structure occurs simultaneously with the appearance of well-defined fibrils.

The binding of sodium ions to the transmembrane channel peptide gramicidin A has permitted the use of electrospray ionization mass spectrometry to study its conformation in different solvent environments. The mass spectra of the peptide in the various solvents suggest that different conformations of gramicidin A differ in their ability to bind metal ions. The data are consistent with monomeric behavior of gramicidin A in trifluoroethanol and dimethyl sulfoxide solutions, but reveal the presence of noncovalent intermolecular interactions in ethanol solution through the observation of heterodimers formed between the naturally occurring variants of the peptide. The addition of 50% v/v of water to the ethanolic solution causes changes in the circular dichroism spectrum of the peptide, suggestive of a shift in the equilibrium mixture of conformers present toward monomeric species, a result supported by its mass spectrum. The structure of gramicidin A in trifluoroethanol has also been investigated by hydrogen exchange measurements monitored by mass spectrometry. The observation of significant protection against exchange suggests that the monomeric peptide is highly structured in trifluoroethanol. The results indicate that mass spectrometry has the potential to probe the conformational behavior of neutral hydrophobic peptides in environments that mimic their functional states.

We have investigated the effect of gramicidin A on the dynamics of two model membranes: dimyristoylphosphatidylcholine (DMPC) in the lamellar phase at a lipid-to-peptide molar ratio of 10:1 and dioleoylphosphatidylcholine (DOPC) in the hexagonal HII phase at a lipid-to-peptide molar ratio of 5:1. Natural abundance 13C nuclear magnetic resonance (NMR) spectroscopy was used in combination with magic angle spinning to increase the spectral resolution, therefore allowing the different regions of the lipid bilayers to be investigated from the same spectra. 31P NMR was also used to detect and confirm the formation of the DOPC HII phase in the presence of gramicidin A. In order to examine the effect of gramicidin A on both the fast and slow motions of DMPC and DOPC, the 1H spin-lattice relaxation times in the laboratory frame (HT1) as well as the 1H spin-lattice relaxation times in the rotating frame (HT1ρ) were calculated for each resolved protonated lipid resonance in the 13C spectra. For both DMPC and DOPC, we found that the presence of gramicidin A does not significantly affect the fast motions of the lipid acyl chains but increases slightly the fast motions of the polar head group. However, the HT1ρ are significantly decreased, this effect being more pronounced for DOPC most likely due to a decrease in the rate of the lipid lateral diffusion.

We have investigated in the present study the interaction between G-actin and various types of liposomes, zwitterionic, positively charged, and negatively charged. To investigate at the molecular level the conformation of actin in the presence of lipids, we have selectively attached a fluorinated probe, 3-bromo-1,1,1-trifluoropropanone, to the actin cysteine residues 10, 285, and 374 and used high-resolution 19F nuclear magnetic resonance spectroscopy to investigate the probe resonances. The results indicate a change in the mobility of the 19F labels when G-actin is in the presence of positively charged liposomes made of DMPC and stearylamine and in the presence of DMPG, a negatively charged lipid. No conformational change was observed in the actin molecule in the presence of neutral liposomes. Electron micrographs of these systems reveal the formation of paracrystalline arrays of actin filaments at the surface of the positively charged liposomes, while no evidence of actin polymerization or paracrystallization was observed in the presence of DMPG. The interaction between actin and the lipid polar headgroup has also been investigated using solid-state phosphorus and deuterium NMR. The results indicate no evidence of interaction between actin and zwitterionic liposomes but show an interaction between the positively charged liposomes and a negative charge on the actin molecules. Interestingly, the negatively charged liposomes interact with a positive charge, which is most likely associated with the three residues (His-Arg-Lys) preceding the cysteine 374 residue in the protein.

Fourier transform infrared spectroscopy (FTIR) and deuterium nuclear magnetic resonance spectroscopy (2H-NMR) have been used to study the location of two odorants, beta-ionone and menthone, in a model membrane of dimyristoylphosphatidylcholine, as well as the effect of the odorants on the structure and dynamics of the phospholipids. The interaction has been investigated for two lipid-to-odorant molar ratios, 10:1 and 1:1. The two odorants were found to affect the fluidity of the membrane. More specifically, the 2H-NMR results indicate that at a lipid-to-odorant molar ratio of 10:1, both beta-ionone and menthone increase the order of the deuterons in the interfacial and headgroup regions of the lipid while the incorporation of the odorants at a lipid-to-odorant molar ratio of 1:1 decreases the order of both the lipid headgroup and acyl chains. On the other hand, the infrared results show that the incorporation of beta-ionone and menthone decreases the phase transition temperature and cooperativity of the lipid acyl chains. The results suggest that the site of incorporation of beta-ionone and menthone is very similar in DMPC membranes.

One- and two-dimensional solid-state 1H nuclear magnetic resonance spectra of gramicidin A incorporated in a dimyristoylphosphatidylcholine membrane have been obtained with use of high-speed magic angle spinning. By rotating the sample at 13 kHz, it is possible to observe signals in the 1H spectra between 6.0 and 9.0 ppm attributable to the aromatic protons of the tryptophan residues and the formyl group proton of gramicidin A. Two-dimensional solid-state COSY spectra provided information for the peak assignments. Moreover, changes in the 1H spectra have been observed as a function of the co-solubilization solvent initially used to prepare the samples and therefore as a function of the conformation adopted by gramicidin A. Three organic solvents have been used: trifluoroethanol, a mixture of methanol/chloroform (1:1 v/v), and ethanol. The conformational interconversion of gramicidin A from the double helix conformation to the channel structure for the sample prepared from ethanol was confirmed by following the time evolution of the proton spectra.

We have investigated the interactions between gramicidin and a model membrane composed of one phospholipid, dimyristoylphosphatidylcholine, as a function of the cosolubilization solvent and incubation time used in the sample preparation. Three organic solvents have been used; trifluoroethanol, a mixture of methanol/chloroform (1:1 v/v), and ethanol. Using Fourier transform infrared spectroscopy, we have demonstrated that the conformation adopted by gramicidin in the membrane is dependent upon the cosolubilization solvent used, and, only with trifluoroethanol, it is possible to incorporate gramicidin entirely as a beta 6.3-helix. Moreover, Raman spectroscopy results indicate that the orientation of the tryptophan side chains in gramicidin and their interaction with the hydrocarbon chains and the carbonyl groups of the lipids are also dependent on the cosolubilization solvent. On the other hand, the effect of the incorporation of gramicidin on the thermotropism of the lipid bilayer was found to be dependent upon the conformation of gramicidin in the lipid bilayers.