PubMed Health⌕ Search

Biomedical subjects

Thomas Schrader

Publications and source records attributed to Thomas Schrader.

At least 19 recordsLinked to original sources
PubMed2006

Color fingerprinting of proteins by calixarenes embedded in lipid/polydiacetylene vesicles.

"Naked eye" color detection of proteins was achieved by embedding calixarene receptors within vesicles comprising phospholipids and the chromatic polymer polydiacetylene. Dramatic visible absorbance changes were induced through electrostatic interactions between the protein surface and the vesicle-incorporated hosts. The colorimetric responses could be induced by micromolar protein concentrations, and furthermore, specific protein fingerprints could be obtained by incorporating different receptors within the vesicles. Fluorescence and circular dichroism experiments confirmed the relationship between the colorimetric phenomena and protein docking on the surface of the chromatic vesicles. The colorimetric assay constitutes a generic platform for high-sensitivity detection of soluble proteins and for evaluation of protein surface charge distribution.

Calixarenes↗
PubMed2006

Molecular tweezer and clip in aqueous solution: unexpected self-assembly, powerful host-guest complex formation, quantum chemical 1H NMR shift calculation.

The newly prepared water-soluble naphthalene tweezer 2a and anthracene clip 4a (substituted both with lithium methanephosphonate groups in the central spacer unit) undergo an unexpected self-assembly in aqueous solution. The highly ordered intertwined structures of the self-assembled dimers [2a]2 and [4a]2 were elucidated by quantum chemical 1H NMR shift calculations. 2a and 4a form extremely stable host-guest complexes with N-methylnicotinamide 8 in methanol and water as well. According to the thermodynamic parameters determined by 1H NMR titration experiments at various temperatures the self-assembly of 2a and 4a and their strong binding to NMNA 8 observed in aqueous solution are enthalpy driven (DeltaH << 0); the enthalpic driving force is partially compensated by an unfavorable entropy (TDeltaS < 0). Self-assembly and the host-guest binding are therefore beautiful examples of the nonclassical hydrophobic effect.

Journal Article↗
PubMed2006

Arginine- and lysine-specific polymers for protein recognition and immobilization.

Free radical polymerization of methacrylamide-based bisphosphonates turns weak arginine binders into powerful polymeric protein receptors. Dansyl-labeled homo- and copolymers with excellent water solubility are accessible through a simple copolymerization protocol. Modeling studies point to a striking structural difference between the stiff rodlike densely packed homopolymer 1 and the flexible copolymer 2 with spatially separated bisphosphonate units. Fluorescence titrations in buffered aqueous solution (pH = 7.0) confirm the superior affinity of the homopolymer toward oligoarginine peptides reaching nanomolar K(D) values for the Tat peptide. Basic proteins are bound almost equally well by 1 and 2 with micromolar affinities, with the latter producing much more soluble complexes. The Arg selectivity of the monomer is transferred to the polymer, which binds Arg-rich proteins 1 order of magnitude tighter than lysine-rich pendants of comparable pI, size, and (Arg/Lys vs Glu/Asp) ratio. Noncovalent deposition of both polymers on glass substrates via polyethyleneimine layers results in new materials suitable for peptide and protein immobilization. RIfS measurements allow calculation of association constants K(a) as well as dissociation kinetics k(D). They generally confirm the trends already found in free solution. Close inspection of electrostatic potential surfaces suggest that basic domains favor protein binding on the flat surface. The high specificity of the bisphosphonate polymers toward basic proteins is demonstrated by comparison with polyvinyl sulfate, which has almost no effect in RIfS experiments. Thus, copolymerization of few different comonomer units without cross-linking enables surface recognition of basic proteins in free solution as well as their effective immobilization on surfaces.

Acrylamides↗
PubMed2005

Inclusion of thiamine diphosphate and S-adenosylmethionine at their chemically active sites.

[structure: see text] Molecular clips functionalized by phosphonate or phosphate groups bind thiamine diphosphate (TPP) and S-adenosylmethionine (SAM) with high affinity in water; both sulfur-based cofactors transfer organic groups to biomolecules. For TPP, various analytical tools point toward a simultaneous insertion of both heterocyclic rings into the electron-rich clip cavity. Similarly, SAM is also embedded with its sulfonium moiety inside the receptor cavity. This paves the way for enzyme models and direct interference with enzymatic processes.

Binding Sites↗
PubMed2005

A molecular tweezer for lysine and arginine.

Lysine and arginine play a key role in numerous biological recognition processes controlling, inter alia, gene regulation, glycoprotein targeting and vesicle transport. They are also found in signaling peptide sequences responsible, e.g. for bacterial cell wall biosynthesis, Alzheimer peptide aggregation and skin regeneration. Almost none of all artificial receptor structures reported to date are selective and efficient for lysine residues in peptides or proteins. An artificial molecular tweezer is introduced which displays an exceptionally high affinity for lysine (K(a) approximately 5000 in neutral phosphate buffer). It features an electron-rich torus-shaped cavity adorned with two peripheral anionic phosphonate groups. Exquisite selectivity for arginine and lysine is achieved by threading the whole amino acid side chain through the cavity and subsequent locking by formation of a phosphonate-ammonium/guanidinium salt bridge. This pseudorotaxane-like geometry is also formed in small basic signaling peptides, which can be bound with unprecedented affinity in buffered aqueous solution. NMR titrations, NOESY and VT experiments as well as ITC measurements and Monte Carlo simulations unanimously point to an enthalpy-driven process utilizing a combination of van der Waals interactions and substantial electrostatic contributions for a conformational lock. Since DMSO and acetonitrile compete with the amino acid guest inside the cavity, a simple change in the cosolvent composition renders the whole complexation process reversible.

Acetonitriles↗
PubMed2005

Selective detection of catecholamines by synthetic receptors embedded in chromatic polydiacetylene vesicles.

A new detection scheme for catecholamines was constructed through embedding synthetic receptors within vesicles comprising phospholipids and polydiacetylene. Fluorescence emission of the polydiacetylene was induced through specific interactions between the soluble ligands and the vesicle-incorporated hosts. The system demonstrated remarkable selectivity among structurally similar ligands and achieved much lower detection thresholds compared to that of other reported catecholamine sensors. The chromatic assembly provides a generic route for high sensitivity detection of ligand-receptor interactions.

Acetylene↗
PubMed2005

beta-Sheet ligands in action: KLVFF recognition by aminopyrazole hybrid receptors in water.

Little is known about the precise mechanism of action of beta-sheet ligands, hampered by the notorious solubility problems involved with protein misfolding and amyloid formation. Recently the nucleation site for the pathogenic aggregation of the Alzheimer's peptide was identified as the KLVFF sequence in the central region of Abeta. A combination of two aminopyrazole ligands with di- or tripeptides taken from this key fragment now furnished water-soluble Abeta-specific ligands which allow model investigations in water. A detailed conformational analysis provides experimental evidence for an increased beta-sheet content induced in the peptide. Strong indications were also found for the peptide backbone recognition via hydrogen bonds plus hydrophobic contributions between aminopyrazole nuclei and Phe residues. The affinity of these new ligands toward the KKLVFF fragment is highly dependent on their sequence and composition from natural and artificial amino acids. Thus, for the first time, detailed insight is gained into the complexation of beta-sheet ligands with model peptides taken directly from Abeta.

Amyloid beta-Peptides↗
PubMed2005

Nanomolar protein sensing with embedded receptor molecules.

A new concept of protein sensing at the air-water interface is introduced, based on amphiphilic receptor molecules embedded in a lipid monolayer. The process begins with incorporation of a small amount (0.13 equiv) of one or two different calix[4]arenes, adorned with charged functional groups at their upper rims, into a stearic acid monolayer. These doped monolayers are subsequently shown to attract peptides and proteins from the aqueous subphase. Depending on the host structure, the monolayers can be made selective for basic or acidic proteins. A working model is proposed, which explains the large observed p/A shifts with reincorporation of excess receptor molecules into the lipid monolayer after complex formation with the oppositely charged protein. This requires a self-assembly of multiple calixarene units over the protein surface, which bind the protein in a cooperative fashion. Oppositely charged calixarene derivatives do not form molecular capsules inside the monolayer, but rather remain separate inside the lipid layer, adopting a perpendicular orientation. They combine their hydrogen bond donor and acceptor capacities, and thus markedly enhance the sensitivity of the sensor system toward proteins, pushing the detection limits to 10 pM concentrations. The response pattern obtained from various receptor units inside the monolayer toward the same protein creates a fingerprint for this protein, which can hence be selectively detected at nanomolar concentrations (pattern recognition).

Amino Acids↗
PubMed2005

Selective complexation of N-alkylpyridinium salts: binding of NAD+ in water.

A new class of receptor molecules is presented that is highly selective for N-alkylpyridinium ions and electron-poor aromatics. Its key feature is the combination of a well-preorganized molecular clip with an electron-rich inner cavity and strategically placed, flanking bis-phosphonate monoester anions. This shape and arrangement of binding sites attracts predominantly flat electron-poor aromatics in water, binds them mainly by pi-cation, pi-pi, CH-pi, and hydrophobic interactions, and leads to their highly efficient desolvation. NAD(+) and NADP, the important cofactors of many redox enzymes, are recognized by the new receptor molecule, which embraces the catalytically active nicotinamide site and the adenine unit. Even nucleosides such as adenosine are likewise drawn into the clip's cavity. Complex formation and structures were examined by one- and two-dimensional NMR spectroscopy, Job plot analyses, and isothermal titration microcalorimetric (ITC) measurements, as well as quantum chemical calculations of (1)H NMR shifts. The new receptor molecule is a promising tool for controlling enzymatic oxidation processes and for DNA chemistry.

Calorimetry↗
PubMed2004

On the role of PIII ligands in the conjugate addition of diorganozinc derivatives to enones.

A mechanistic study on the conjugate addition of diethylzinc to cyclohexenone catalyzed by various chiral PIII ligands, provides new insights into its mechanism. Complete in situ conversion of the catalytic amount of Cu(OTf)2 into CuI species by excess ZnEt2 is demonstrated by EPR spectroscopy. Experimental evidence is presented in favor of a critical ternary 1:1:1 complex between enone, Et2Zn and catalyst, supporting a rate-limiting reductive elimination or carbocupration from a preformed mixed Cu/Zn cluster carrying one- or two-ligand molecules. A crystal structure has been obtained for a CuIL2 complex, which shows catalytic turnover on addition of reagent and substrate. NMR spectroscopic analyses and VT experiments reveal that steric hindrance may prevent complexation of a second ligand molecule on the CuI cation, leading to extremely fast precatalysts based on CuX.L species.

Journal Article↗
PubMed2004

Relative binding affinities of molecular capsules investigated by ESI-mass spectrometry.

ESI-MS(/MS) has been used as a method which allows the fast, unambiguous and sensitive simultaneous detection and relative stability approximation of supramolecular assemblies in mixtures. In spite of the obvious fundamental differences between solution and gas phase, ESI-MS in the case of self-assembled molecular capsules has been shown to produce very similar results to single binding experiments monitored by NMR titrations as well as conformational searches performed by Monte-Carlo simulations. MS/MS experiments reveal the same relative order of gas phase stabilities as previously found in solution. Moreover, proton transfer reactions which lead to new molecular capsules, are not detectable in the time-averaged NMR spectrum. However, the newly produced species are found in the complex mixtures by ESI-MS and can be conveniently characterized by subsequent MS/MS experiments: in a collision-induced dissociation the single half-spheres are easily discovered and structurally assigned. Thus, ESI-MS has worked as a valuable tool for the rapid screening of complex supramolecular mixtures and in combination with MS/MS experiments elucidated both the path of unexpected side reactions as well as the thermodynamic gas-phase stabilities of all components in the mixture.

Journal Article↗
PubMed2004

Adrenaline recognition in water.

Host molecule 1 displays a high affinity in water towards catecholamines and especially related structures such as beta-blockers with extended aromatic pi-faces (up to 7x10(3) M(-1) for each single complexation step or 5x10(7) M(-2) for both steps). The amphiphilic structural design leads to an extensive self-association of host molecules through their aromatic flanks. Above a cmc (critical micelle concentration) of 3x10(-4) M, host 1 forms micelles that produce a favorable microenvironment for hydrophobic interactions with the included guest molecules. Electrostatic attraction of the ammonium alcohol by the phosphonate anions is thus combined with hydrophobic contributions between the aromatic moieties. Ionic hydrogen bonds with polar OH or NH groups of the guest enforce the non-covalent interactions, and finally lead to increased specificity. Both its affinity and its selectivity towards adrenergic receptor substrates are greatly enhanced if the receptor molecule 1 is transferred from water into a lipid monolayer. Catecholamines and beta-blockers lead to drastically different effects at concentrations approaching the micromolar regime. Especially beta-blockers with minute structural changes can be easily distinguished from each other. In both cases, extensive hydrophobic interactions with a self-associated and/or self-organized microenvironment are largely responsible for the observed high efficiency and specificity.

Adrenergic beta-Antagonists↗
PubMed2004

Prevention of Alzheimer's disease-associated Abeta aggregation by rationally designed nonpeptidic beta-sheet ligands.

A new concept is introduced for the rational design of beta-sheet ligands, which prevent protein aggregation. Oligomeric acylated aminopyrazoles with a donor-acceptor-donor (DAD) hydrogen bond pattern complementary to that of a beta-sheet efficiently block the solvent-exposed beta-sheet portions in Abeta-(1-40) and thereby prevent formation of insoluble protein aggregates. Density gradient centrifugation revealed that in the initial phase, the size of Abeta aggregates was efficiently kept between the trimeric and 15-meric state, whereas after 5 days an additional high molecular weight fraction appeared. With fluorescence correlation spectroscopy (FCS) exactly those two, i.e. a dimeric aminopyrazole with an oxalyl spacer and a trimeric head-to-tail connected aminopyrazole, of nine similar aminopyrazole ligands were identified as efficient aggregation retardants whose minimum energy conformations showed a perfect complementarity to a beta-sheet. The concentration dependence of the inhibitory effect of a trimeric aminopyrazole derivative allowed an estimation of the dissociation constant in the range of 10(-5) m. Finally, electrospray ionization mass spectrometry (ESI-MS) was used to determine the aggregation kinetics of Abeta-(1-40) in the absence and in the presence of the ligands. From the comparable decrease in Abeta monomer concentration, we conclude that these beta-sheet ligands do not prevent the initial oligomerization of monomeric Abeta but rather block further aggregation of spontaneously formed small oligomers. Together with the results from density gradient centrifugation and fluorescence correlation spectroscopy it is now possible to restrict the approximate size of soluble Abeta aggregates formed in the presence of both inhibitors from 3- to 15-mers.

Alzheimer Disease↗
PubMed2004

PEG-supported synthesis of pyrazole oligoamides with peptide beta-sheet affinity.

Pyrazole amino acid oligoamides were prepared on polyethylene glycol starting from nitro pyrazole carboxylic acids or protected pyrazole amino acids. The polymer support facilitates product isolation during synthesis and makes the target oligoamides soluble in chloroform and water. This allows the determination of their binding properties towards peptides. Moderate affinity, which increases with the number of pyrazole units, is observed in chloroform and water.

Journal Article↗
PubMed2004

Teleconsultation in diagnostic pathology: experience from Iran and Germany with the use of two European telepathology servers.

Eighty pathology cases were sent independently to each of two telepathology servers. Cases were submitted from the Department of Pathology at the University of Kerman in Iran (40 cases) and from the Institute of Pathology in Berlin, Germany (40 cases). The telepathology servers were located in Berlin (the UICC server) and Basel in Switzerland (the iPATH server). A scoring system was developed to quantify the differences between the diagnoses of the referring pathologist and the remote expert. Preparation of the cases, as well as the submission of images, took considerably longer from Kerman than from Berlin; this was independent of the server system. The Kerman delay was mainly associated with a slower transmission rate and longer image preparation. The diagnostic gap between referrers' and experts' diagnoses was greater with the iPATH system, but not significantly so. The experts' response time was considerably shorter for the iPATH system. The results showed that telepathology is feasible for requesting pathologists working in a developing country or in an industrialized country. The key factor in the quality of the service is the work of the experts: they should be selected according to their diagnostic expertise, and their commitment to the provision of telepathology services is critical.

Germany↗