Untersuchungen Über α-Amino-N-carbonsäureanhydride,IV

Ohne Zusammenfassung     

Archimedes Revisited

Archimedes’ beautiful principle may be used to determine how an object floats in a vessel of liquid. This, in turn may be used to determine the global configuration associated with a floating object under the assumption that the surface of the liquid is planar. There are instances, however, in which capillary effects conspire to produce significantly nonplanar liquid interfaces and phenomena which is strikingly at odds with the predictions of the Archimedean principle. A most notable instance involves floatation of convex objects with density greater than that of the liquid. The effects of capillarity on liquid interface configurations invariably manifest themselves globally over the entire system, though the magnitude of such effects is often so small as to be overlooked. This phenomenon presents a major difficulty in obtaining an appropriate generalization of Archimedes’ principle which incorporates capillarity.     

Hausdorff dimension of self-similar sets with overlaps

We provide a simple formula to compute the Hausdorff dimension of the attractor of an overlapping iterated function system of contractive similarities satisfying a certain collection of assumptions. This formula is obtained by associating a non-overlapping infinite iterated function system to an iterated function system satisfying our assumptions and using the results of Moran to compute the Hausdorff dimension of the attractor of this infinite iterated function system, thus showing that the Hausforff dimension of the attractor of this infinite iterated function system agrees with that of the attractor of the original iterated function system. Our methods are applicable to some iterated function systems that do not satisfy the finite type condition recently introduced by Ngai and Wang.      

Spectral accuracy of molecular ions in an LTQ/Orbitrap mass spectrometer and implications for elemental composition determination

In addition to mass accuracy, the ability of a mass spectrometer to faithfully measure the isotopic distribution of an ion, defined as spectral accuracy, is also important. Although time-of-flight mass spectrometers are reported to possess high spectral accuracy capability compared with other mass spectrometers, the Orbitrap has not yet been investigated. Ten natural products (moxidectin, erythromycin, digoxin, rifampicin, amphotericin B, rapamycin, gramicidin S, cyclosporin A, vancomycin, and thiostrepton) ranging in molecular weight from 639 to 1663 Da were measured on an LTQ/Orbitrap mass spectrometer with resolving power settings of 7.5, 15, 30, 60, and 100 K. The difference in the observed profile isotope pattern compared with the theoretical calculation after peak shape calibration, denoted spectral error, was calculated using the program MassWorks (Cerno Bioscience, Danbury, CT, USA). Spectral errors were least at 7.5 K resolving power (≤3%) but exceeded 10% for some compounds at 100 K. The increasing spectral error observed at higher resolving power for compounds with complex fine structure might be explained by the phenomena of isotopic beat patterns as observed in FTICR. Several compounds with prominent doubly charged ions allowed comparison of spectral accuracies of singly-versus doubly-charged ions. When using spectral error to rank elemental compositions with formula constraints (C_0–100H_0–200N_0–50O_0–50Cl_0–5S_0–5) and a mass tolerance ≤2 parts-per-million, the correct formula was ranked first 35% of the time. However, spectral error considerations eliminated >99% of possible elemental formulas for compounds with molecular weight >900 Da.     

Identifying nonspecific ligand binding in electrospray ionization mass spectrometry using the reporter molecule method

The application of the reporter molecule (M_rep) method for identifying nonspecific complexes in the ES-MS analysis of protein-ligand and DNA-ligand interactions in vitro is described. To test the reliability of the method, it was applied to the ES-MS analysis of protein-carbohydrate complexes originating from specific interactions in solution and from nonspecific interactions in the ES process. These control experiments confirm the basic assumptions underlying the M_rep method, namely that nonspecific ligand binding is a random process, and that the ES droplet histories for specific and nonspecific complexes are distinct. The application of the M_rep method to the ES-MS analysis of the sequential binding of the ethidium cation, a DNA intercalator, to single and double strand oligodeoxynucleotides is also described, and highlights the general utility of the method.     

Differentiation of 3-O-sulfated heparin disaccharide isomers: Identification of structural aspects of the heparin CCL2 binding motif

The presence of 3-O-sulfated glucosamine residues in heparin or heparan sulfate plays a role in binding to antithrombin III and HSV infection. In this study, tandem mass spectrometry was used to differentiate between two heparin disaccharide isomers containing variable sulfate at C6 in a common disaccharide and C3 in a more rare one. The dissociation patterns shown by MS² and MS³ were clearly distinguishable between the isomers, allowing their differentiation and quantitation. Using this technique, we show that an octasaccharide with 11 sulfate groups with high affinity for inflammatory chemokine CCL2 does not contain 3-O-sulfated disaccharides.     

Accurate localization and relative quantification of arginine methylation using nanoflow liquid chromatography coupled to electron transfer dissociation and drbitrap mass spectrometry

Protein arginine (Arg) methylation serves an important functional role in eucaryotic cells, and typically occurs in domains consisting of multiple Arg in close proximity. Localization of methylarginine (MA) within Arg-rich domains poses a challenge for mass spectrometry (MS)-based methods; the peptides are highly charged under electrospray ionization (ESI), which limits the number of sequence-informative products produced by collision induced dissociation (CID), and loss of the labile methylation moieties during CID precludes effective fragmentation of the peptide backbone. Here the fragmentation behavior of Arg-rich peptides was investigated comprehensively using electron-transfer dissociation (ETD) and CID for both methylated and unmodified glycine-/Arg-rich peptides (GAR), derived from residues 679–695 of human nucleolin, which contains methylation motifs that are widely-represented in biological systems. ETD produced abundant information for sequencing and MA localization, whereas CID failed to provide credible identification for any available charge state (z=2–4). Nevertheless, CID produced characteristic neutral losses that can be employed to distinguish among different types of MA, as suggested by previous works and confirmed here with product ion scans of high accuracy/resolution by an LTQ/Orbitrap. To analyze MA-peptides in relatively complex mixtures, a method was developed that employs nano-LC coupled to alternating CID/ETD for peptide sequencing and MA localization/characterization, and an Orbitrap for accurate precursor measurement and relative quantification of MA-peptide stoichiometries. As proof of concept, GAR-peptides methylated in vitro by protein arginine N-methyltransferases PRMT1 and PRMT7 were analyzed. It was observed that PRMT1 generated a number of monomethylated (MMA) and asymmetric-dimethylated peptides, while PRMT7 produced predominantly MMA peptides and some symmetric-dimethylated peptides. This approach and the results may advance understanding of the actions of PRMTs and the functional significance of Arg methylation patterns.