Evidence for a monomeric structure of nonribosomal Peptide synthetases

Nonribosomal peptide synthetases (NRPS) are multimodular biocatalysts that bacteria and fungi use to assemble many complex peptides with broad biological activities. The same modular enzymatic assembly line principles are found in fatty acid synthases (FAS), polyketide synthases (PKS), and most recently in hybrid NRPS/PKS multienzymes. FAS as well as PKS are known to function as homodimeric enzyme complexes, raising the question of whether NRPS may also act as homodimers. To test this hypothesis, biophysical methods (size exclusion chromatography, analytical equilibrium ultracentrifugation, and chemical crosslinking) and biochemical methods (two-affinity-tag-system and complementation studies with enzymes being inactivated in different catalytic domains) were applied to NRPS subunits from the gramicidin S (GrsA-ATE), tyrocidine (TycB(1)-CAT and TycB(2-3)-AT.CATE), and enterobactin (EntF-CATTe) biosynthetic systems. These methods had revealed the dimeric structure of FAS and PKS previously, but all three NRPS systems investigated are functionally active as monomers.     

Synthesis and derivatization of daptomycin: a chemoenzymatic route to acidic lipopeptide antibiotics

Daptomycin is a branched cyclic nonribosomally assembled acidic lipopeptide, which is the first clinically approved antibiotic of this class. Here we show that the recombinant cyclization domain of the Streptomyces coelicolor calcium-dependent antibiotic (CDA) nonribosomal peptide synthetase (NRPS) is a versatile tool for the chemoenzymatic generation of daptomycin derivatives. Linear CDA undecapeptide thioesters with single exchanges at six daptomycin-specific residues were successfully cyclized by CDA cyclase. Simultaneous incorporation of all six of these residues into the peptide backbone and elongation of the N-terminus of CDA by two residues yielded a daptomycin derivative that lacked only the beta-methyl group of l-3-methylglutamate. Bioactivity studies with several substrate analogues revealed a significant role of nonproteinogenic constituents for antibacterial potency. In accordance with acidic lipopeptides, the bioactivity of the chemoenzymatic assembled daptomycin analogue is dependent on the concentration of calcium ions. Single deletions of the four acidic residues in the peptide backbone suggest that only two aspartic acid residues are essential for antimicrobial potency. These two residues are strictly conserved among other nonribosomal acidic lipopeptides and the EF-motif of ribosomally assembled calmodulin. Based on these findings CDA cyclase is a versatile catalyst that can be used to generate novel daptomycin derivatives that are otherwise difficult to obtain by chemical modification of the parental tridecapeptide to improve further its therapeutic activity.     

Synthesis and characterization of a new family of bi-, tri-, tetra-, and pentanuclear ferric complexes

Nine members of a new family of polynuclear ferric complexes have been synthesized and characterized. The reaction of Fe(O(2)CMe)(2) with polydentate Schiff base proligands (H(2)L) derived from salicylidene-2-ethanolamine, followed in some cases by reaction with carboxylic acids, has afforded new complexes of general formulas [Fe(2)(pic)(2)(L)(2)] (where pic(-) is the anion of 2-picolinic acid), [Fe(3)(O(2)CMe)(3)(L)(3)], [Fe(4)(OR)(2)(O(2)CMe)(2)(L)(4)], and [Fe(5)O(OH)(O(2)CR)(4)(L)(4)]. The tri-, tetra-, and pentanuclear complexes all possess unusual structures and novel core topologies. M?ssbauer spectroscopy confirms the presence of high-spin ferric centers in the tri- and pentanuclear complexes. Variable-temperature magnetic measurements suggest spin ground states of S = 0, 1/2, 0, and 5/2 for the bi-, tri-, tetra-, and pentanuclear complexes, respectively. Fits of the magnetic susceptibility data have provided the magnitude of the exclusively antiferromagnetic exchange interactions. In addition, an easy-axis-type magnetic anisotropy has been observed for the pentanuclear complexes, with D values of approximately -0.4 cm(-)(1) determined from modeling the low-temperature magnetization data. A low-temperature micro-SQUID study of one of the pentanuclear complexes reveals magnetization hysteresis at nonzero field. This is attributed to an anisotropy-induced energy barrier to magnetization reversal that is of molecular origin. Finally, an inelastic neutron scattering study of one of the trinuclear complexes has revealed that the magnetic behavior arises from two distinct species.     

Are the Interactions between Recombinant Prion Proteins and Polymeric Surfaces Related to the Hydrophilic/Hydrophobic Balance?

New non‐fouling tubes are developed and their influence on the adhesion of neuroproteins is studied. Recombinant prion proteins are considered as a single component representative of hydrophobic proteins. Samples are stored for 24 h at 4 °C in tubes coated with two different coatings: poly(N‐isopropylacrylamide) as a hydrophilic surface and a plasma‐fluorinated coating as a hydrophobic one. The protein adhesion is monitored by ELISA tests, XPS and confocal microscopy. It appears that the highest recovery of recombinant prion protein in the liquid phase is obtained with the hydrophilic surface while the hydrophobic character of the storage tube induces an important amount of biological loss. However, the recovery is not complete even for tubes coated with poly(N‐isopropylacrylamide).

     

Improvement of cyclosporin A determination in whole blood by reversed-phase high-performance liquid chromatography

A chromatographic method was developed for the determination of cyclosporin A in human whole blood using reversed-phase HPLC at room temperature. Most previous reports carried out this liquid chromatographic separation at temperatures above 70 degrees C. The present procedure greatly improves the detection limit by controlling peak broadening effects, as well as the lifetime of the column at room temperature. Under optimal conditions and using ketoconazole as an internal standard, the calibration graph was linear in the range of 16-1000 microg/L with a relative standard deviation of 3.72% at 150 microg/L and 2.45% at 300 microg/L (n = 11) of cyclosporin A. The detection limit was of 5.0 microg/L cyclosporin A. By this procedure, cyclosporin A pharmacokinetic parameters in healthy Chinese subjects were studied. The developed method could be applied to the quantification of cyclosporin A in human blood samples and allows the study of its pharmacokinetics in routine laboratories.     

Identification of Structure–Activity Relationships from Screening a Structurally Compact DNA‐Encoded Chemical Library

Methods for the rapid and inexpensive discovery of hit compounds are essential for pharmaceutical research and DNA‐encoded chemical libraries represent promising tools for this purpose. We here report on the design and synthesis of DAL‐100K, a DNA‐encoded chemical library containing 103 200 structurally compact compounds. Affinity screening experiments and DNA‐sequencing analysis provided ligands with nanomolar affinities to several proteins, including prostate‐specific membrane antigen and tankyrase 1. Correlations of sequence counts with binding affinities and potencies of enzyme inhibition were observed and enabled the identification of structural features critical for activity. These results indicate that libraries of this type represent a useful source of small‐molecule binders for target proteins of pharmaceutical interest and information on structural features important for binding.     

Separation of purine and pyrimidine bases by ion chromatography with direct conductivity detection

A simple, rapid and accurate method for the simultaneous determination of four purine and pyrimidine bases (cytosine, 5-methylcytosine, adenine and N6-methyladenine) has been developed. The quantitative determination of these bases was accomplished by ion chromatography (IC) with direct conductivity detection (CD) based on their ionization in acidic medium without chemical suppression. The recovery of cytosine, 5-methylcytosine, and adenine in calf thymus DNA was more than 98% (n=3) and the relative standard deviation (RSD, n=5) less than 2.4%. In a single chromatographic run, the four bases could be separated and determined in less than 10 min. The detection limits were found to be 0.05 microg/mL for cytosine, 0.08 microg/mL for 5-methylcytosine, 0.07 microg/mL for adenine, and 0.07 microg/mL for N6-methyladenine. Linear ranges were 0.2-95.1 microg/mL for cytosine (r2=0.9996), 0.3-196.6 microg/mL for 5-methylcytosine (r2=0.9994), 0.3-105.5 microg/mL for adenine (r2=0.9998), and 0.3-159.1 microg/mL for N6-methyladenine (r2=0.9999). With the proposed method, purine and pyrimidine bases could be successfully detected in calf thymus DNA. We also determined these bases in calf thymus DNA using RP-HPLC. Compared to RP-HPLC, the IC method offers advantages such as high selectivity and simple mobile phase.     

Studies of finite molecular chains: synthesis, structural, magnetic and inelastic neutron scattering studies of hexa- and heptanuclear chromium horseshoes

We report the synthesis and structural characterisation of a family of finite molecular chains, specifically [{[R(2)NH(2)](3)[Cr(6)F(11)(O(2)CCMe(3))(10)]}(2)] (in which R=nPr 1, Et 2, nBu 3), [{Et(2)NH}(2){[Et(2)NH(2)](3)[Cr(7)F(12)(O(2)CCMe(3))(12)][HO(2)CCMe(3)](2)}(2)] (4), [{[Me(2)NH(2)](3)[Cr(6)F(11)(O(2)CCMe(3))(10)]2.5 H(2)O}(4)] (5) and [{[iPr(2)NH(2)](3)[Cr(7)F(12)(O(2)CCMe(3))(12)]}(2)] (6). The structures all contain horseshoes of chromium centres, with each Cr...Cr contact within the horseshoe bridged by a fluoride and two pivalates. The horseshoes are linked through hydrogen bonds to the secondary ammonium cations in the structure, leading to di- and tetra-horseshoe structures. Through magnetic measurements and inelastic neutron scattering studies we have determined the exchange coupling constants in 1 and 6. In 1 it is possible to distinguish two exchange interactions, J(A)=-1.1 meV and J(B)=-1.4 meV; J(A) is the exchange interactions at the tips of the horseshoe and J(B) is the exchange within the body of the horseshoe (1 meV=8.066 cm(-1)). For 6 only one interaction was needed to model the data: J=-1.18 meV. The single-ion anisotropy parameters for Cr(III) were also derived for the two compounds as: for 1, D(Cr)=-0.028 meV and |E(Cr)|=0.005 meV; for 6, D(Cr)=-0.031 meV. Magnetic-field-dependent inelastic neutron scattering experiments on 1 allowed the Zeeman splitting of the first two excited states and level crossings to be observed. For the tetramer of horseshoes (5), quantum Monte Carlo calculations were used to fit the magnetic susceptibility behaviour, giving two exchange interactions within the horseshoe (-1.32 and -1.65 meV) and a weak inter-horseshoe coupling of +0.12 meV. Multi-frequency variable-temperature EPR studies on 1, 2 and 6 have also been performed, allowing further characterisation of the spin Hamiltonian parameters of these chains.     

Smoothing and passivation of special Si(111) substrates: studied by SPV,PL, AFM and SEM measurements

Surface sensitive techniques, the field-modulated surface photovoltage, photoluminescence measurements, atomic force microscopy and scanning electron microscopy, were employed to yield detailed information on the influence of wet-chemical treatments on the preparation induced microroughness and electronic properties of wet-chemically passivated Si(111) substrates with special surface morphology. Stepped substrates with evenly distributed atomically flat terraces were prepared and passivated by thin oxide layers, which were used as a starting point for the subsequent H-termination after long storage in air. It was shown that their surface morphology and electronic properties do not degrade. Applying this preparation method to solar cell substrates with randomly distributed Si(111) pyramids, we achieved significantly lower densities of surface states and reduced recombination loss at a-Si:H/c-Si interfaces, compared with conventional pretreatments. The surface microroughness, the density of rechargeable states and the resulting recombination loss on a-Si:H/c-Si heterojunctions were found to be mainly influenced by two steps of surface pretreatment: firstly, the wet-chemical smoothing procedure of structured substrates and, secondly, the removal of native and wet-chemical oxides during the final etching in HF- or NH₄F- containing solutions. Figure After wet-chemical oxidation in H₂SO₄/H₂O₂ and storage in air