Orchestration of discoid polyketide cyclization in the resistomycin pathway

Resistomycin is a bacterial polyphenolic metabolite from Streptomyces resistomycificus with a unique pentacyclic "discoid" ring system that clearly differs from the typical linear or angular architectures of aromatic polyketides. The first comprehensive cyclase amino acid sequence-function correlation revealed that the enzymes directing the nascent polyketide chain into a peri-fused system clearly differ from canonical linear and angular cyclases. All genes that are required and sufficent for resistomycin (rem) biosynthesis were identified through systematic dissection and reconstitution of the type II polyketide synthase (PKS) complex. The minimal rem PKS and the first cyclase were successfully cross-complemented with orthologues from the linear tetracenomycin polyketide pathway, indicating that both dekaketide pathways share early biosynthetic steps. In total three cyclases that are involved in discoid cyclization (RemI, RemF, and RemL) were identified by mutational analyses and in vivo pathway reconstitution. Analyses of the metabolic profiles of mutants expressing incomplete gene sets led to the discovery of a novel tetracenomycin derivative, TcmR1. The most surprising finding is that only the concerted action of the PKS and all three cyclases leads to the discoid ring structure. These results provide strong support for a model according to which the multienzyme complex forms a cage in which the polyketide is shaped, rather than a sequential cyclization of the polyketide chain by individual enzymes.     

Fast and efficient in silico 3D screening: toward maximum computational efficiency of pharmacophore-based and shape-based approaches

In continuation of our recent studies on the quality of conformational models generated with CATALYST and OMEGA we present a large-scale survey focusing on the impact of conformational model quality and several screening parameters on pharmacophore-based and shape-based virtual high throughput screening (vHTS). Therefore, we collected known active compounds of CDK2, p38 MAPK, PPAR-gamma, and factor Xa and built a set of druglike decoys using ilib:diverse. Subsequently, we generated 3D structures using CORINA and also calculated conformational models for all compounds using CAESAR, CATALYST FAST, and OMEGA. A widespread set of 103 structure-based pharmacophore models was developed with LigandScout for virtual screening with CATALYST. The performance of both database search modes (FAST and BEST flexible database search) as well as the fit value calculation procedures (FAST and BEST fit) available in CATALYST were analyzed in terms of their ability to discriminate between active and inactive compounds and in terms of efficiency. Moreover, these results are put in direct comparison to the performance of the shape-based virtual screening platform ROCS. Our results prove that high enrichment rates are not necessarily in conflict with efficient vHTS settings: In most of the experiments, we obtained the highest yield of actives in the hit list when parameter sets for the fastest search algorithm were used.     

Improved STR typing of telogen hair root and hair shaft DNA

Today the STR typing of telogen hair and hair shafts is regarded as a challenge. The small DNA quantity in the hair is highly degraded. Another problem are PCR inhibitors in the hair. In particular hair pigments, the melanins, are known to inhibit PCR. Hairs are exposed to sunlight and partly to chemical oxidation processes, which make them even more difficult to analyze. To increase the chances of a correct typing of hair, the small amount of DNA must be successfully isolated and the inhibitors have to be removed or neutralized. Furthermore, miniSTR typing improves the analysis of stains with degraded DNA like it is the case with hair. We introduce a nonorganic extraction method and in addition a miniSTR concept which is promising in typing stains with little and degraded DNA, especially hairs. The miniSTR concept including five database STRs (SE33, VWA, TH01, FGA, D3S1358) and the gender typing system Amelogenin was optimized for the amplification of hair DNA. Compared to commercial STR kits, this approach resulted in considerably higher success rates.     

Classification of malignant gliomas by infrared spectroscopic imaging and linear discriminant analysis

Infrared (IR) spectroscopy provides a sensitive molecular fingerprint for tissue without external markers. Supervised classification models can be trained to identify the tissue type based on the spectroscopic fingerprint. Infrared imaging spectrometers equipped with multi-channel detectors combine the spectral and spatial information. Tissue areas of 4 x 4 mm(2) can be analyzed within a few minutes in the macroscopic imaging mode. An approach is described to apply this methodology to human astrocytic gliomas, which are graded according to their malignancy from one to four. Multiple IR images of three tissue sections from one patient with a malignant glioma are acquired and assigned to the six classes normal brain tissue, astrocytoma grade II, astrocytoma grade III, glioblastoma multiforme grade IV, hemorrhage, and other tissue by a linear discriminant analysis model which was trained by data from a single-channel detector. Before the model is applied here, the spectra are shown to be virtually identical. The first specimen contained approximately 95% malignant glioma regions, that means astrocytoma grade III or glioblastoma. The smaller percentage of 12-34% malignant glioma in the second specimen is consistent with its location at the tumor periphery. The detection of less than 0.2% malignant glioma in the third specimen points to a location outside the tumor. The results were correlated with the cellularity of the tissue which was obtained from the histopathologic gold standard. Potential applications of IR spectroscopic imaging as a rapid tool to complement established diagnostic methods are discussed.     

Picosecond multidimensional fluorescence spectroscopy: a tool to measure real-time protein dynamics during function

Advanced multidimensional time-correlated single photon counting (mdTCSPC) and picosecond time-resolved fluorescence in combination with site-directed fluorescence labeling are valuable tools to study the properties of membrane protein surface segments on the pico- to nanoseconds time scale. Time-resolved fluorescence anisotropy changes of protein bound fluorescent probes reveal changes in protein dynamics and steric restriction. In addition, the change in fluorescence lifetime and intensity of the covalently bound fluorescent dye is indicative of environmental changes at the protein surface. In this study, we have measured the changes in fluorescence lifetime traces of the fluorescent dye fluorescein covalently bound to the first cytoplasmic loop of bacteriorhodopsin (bR) after light activation of protein function. The fluorescence is excited by a picosecond laser pulse. The retinylidene chromophore of bR is light-activated by a 10 ns laser pulse, which in turn triggers recording of a sequence of fluorescence lifetime traces in the mdTCSPC-module. The fluorescence decay changes upon protein function occur predominantly in the 100 ps time range. The kinetics of these changes shows two transitions between three intermediate states in the second part of the bR photocycle. Correlation with photocycle kinetics allows for the determination of reaction intermediates at the proteins surface which are coupled to changes in the retinal binding pocket.     

Synthesis and characterization of semifluorinated polymers and block copolymers

The goal of the investigation presented here was to evaluate the influence of semifluorinated side chains on the bulk structure and the surface properties of polysulfones with different chain structure. Thus, segmented block copolymers consisting of polysulfone and semifluorinated aromatic polyester segments as well as polysulfones having semifluorinated side chains randomly distributed over the polymer backbone were synthesized and characterized. Oxydecylperfluorodecyl side chains were used because of their strong tendency for self-organization. The influence of the chain architecture on the self-organization as well as on the surface properties, particularly the wetting behavior, was examined. It could be shown that despite of the higher self-organizing tendency of block copolymers the surface properties of both polymer types are comparable and depend only on the concentration of side chains.     

Darstellung,Eigenschaften und Reaktionsverhalten von 2-(Dimethylaminomethyl)phenyl- und 8-(Dimethylamino)naphthylsubstituierten Lithiumhydridosilylamiden – Bildung von Silaniminen durch Lithiumhydrideliminierung

Preparation, Properties, and Reaction Behaviour of 2-(Dimethylaminomethyl)phenyl- and 8-(Dimethylamino)naphthylsubstituted Lithium Hydridosilylamides – Formation of Silanimines by Elimination of Lithium Hydride The hydridosilylamines Ar(R)Si(H)–NHR′ ( 2 a : Ar = 2-Me₂NCH₂C₆H₄, R = Me, R′ = CMe₃; 2 b : Ar = 2-Me₂NCH₂C₆H₄, R = Ph, R′ = CMe₃; 2 c : Ar = 2-Me₂NCH₂C₆H₄, R = Me, R′ = SiMe₃; 2 d : Ar = 8-Me₂NC₁₀H₆, R = Me, R′ = CMe₃; 2 e : Ar = 8-Me₂NC₁₀H₆, R = Ph, R′ = CMe₃; 2 f : Ar = 8-Me₂NC₁₀H₆, R = Me, R′ = SiMe₃) have been synthesized from the appropriate chlorosilanes Ar(R)SiHCl either by reaction with the stoichiometric amount of Me₃CNHLi ( 2 a , 2 b , 2 d , 2 e ) or by coammonolysis in liquid NH₃ with chlorotrimethylsilane in molar ratio 1 : 3 ( 2 c , 2 f ). Treatment of 2 a–2 f with n-butyllithium in equimolar ratio in n-hexane resulted in the lithiumhydridosilylamides Ar(R)Si(H)–N(Li)R′ 3 a–3 f . The frequencies of the Si–H stretching vibration and ²⁹Si–¹H coupling constants in the amides are smaller than in the analogous amines indicating a higher hydride character for the hydrogen atom of the Si–H group in the amides compared to the amines. Results of NMR spectroscopic studies point to the existence of a (Me₂)N → Si coordination bond in the 8-(dimethylamino)naphthyl-substituted amines and amides. The amides 3 a–3 c are stable under refluxing in m-xylene. At the same conditions 3 d and 3 e eliminate LiH and the silanimines 8-Me₂NC₁₀H₆(R)Si=NCMe₃ ( 4 d : R = Me, 4 e : R = Ph) are formed. The amides 3 a–3 d und 3 f react with chlorotrimethylsilane in THF to give the corresponding N-substitution products Ar(R)Si(H)–N(SiMe₃)R′ 6 a–6 d and 6 f in good yields. 4 d is formed as a byproduct in the reaction of 3 d with chlorotrimethylsilane. In n-hexane and m-xylene these amides are little reactive opposite to chlorotrimethylsilane. 6 a–6 d and 6 f are obtained in very small amounts. In the case of 3 d besides the N-substitution product 6 d the silanimine 4 d is obtained. In contrast to chlorotrimethylsilane the amides 3 a and 3 f react well with chlorodimethylsilane in m-xylene producing 2-Me₂NCH₂C₆H₄(H) SiMe–N(SiHMe₂)CMe₃ ( 7 a ) and 8-Me₂NC₁₀H₆(H)SiMe–N(SiHMe₂)SiMe₃ ( 7 f ).     

Pattern avoidance and Boolean elements in the Bruhat order on involutions

We show that the principal order ideal of an element w in the Bruhat order on involutions in a symmetric group is a Boolean lattice if and only if w avoids the patterns 4321, 45312 and 456123. Similar criteria for signed permutations are also stated. Involutions with this property are enumerated with respect to natural statistics. In this context, a bijective correspondence with certain Motzkin paths is demonstrated. This article is largely based on results from the second author’s M.Sc. thesis [15].