Semisynthetic, site-specific ubiquitin modification of α-synuclein reveals differential effects on aggregation

The process of neurodegeneration in Parkinson's Disease is intimately associated with the aggregation of the protein α-synuclein into toxic oligomers and fibrils. Interestingly, many of these protein aggregates are found to be post-translationally modified by ubiquitin at several different lysine residues. However, the inability to generate homogeneously ubiquitin modified α-synuclein at each site has prevented the understanding of the specific biochemical consequences. We have used protein semisynthesis to generate nine site-specifically ubiquitin modified α-synuclein derivatives and have demonstrated that different ubiquitination sites have differential effects on α-synuclein aggregation.     

Reliable automatic protein identification from matrix-assisted laser desorption/ionization mass spectrometric peptide fingerprints

Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry of protein samples from two-dimensional (2-D) gels in conjunction with protein sequence database searches is frequently used to identify proteins. Moreover, the automatic analysis of complete 2-D gels with hundreds and even thousands of protein spots ("proteome analysis") is possible, without human intervention, with the availability of highly accurate mass spectrometry instruments, and high-throughput facilities for preparation and handling of protein samples from 2-D gels. However, the lack of software for precise automatic analysis and annotation of mass spectra, as well as software for in-batch sequence database queries, is increasingly becoming a significant bottleneck for the proteomics work flow. In the present paper we outline an algorithm for reliable, accurate, and automatic evaluation of mass spectrometric data and database searches. We show here that simply selecting from the sequence database the protein that has the most matching fragment masses often leads to false-positive results. Reliable protein identification is dependent on several parameters: the accuracy of fragment mass determination, the number of masses submitted for query, the mass distribution of query masses, the number of masses matching between sample and database protein, the size of the sequence database, and the kind and number of modifications considered. Using these parameters, we derive a simple statistical estimation that can be used to calculate the probability of true-positive protein identification.     

Backward electroproduction of π+ mesons in the second and third nucleon resonance region

The reactionep→enπ ⁺ has been studied in the invariant mass range of 1.44≦W≦1.83 GeV. The outgoing pion was detected in the backward direction (cosλ _π ^* ≦-0.94) with respect to the virtual photon at four-momentum transfers of 0.4≦q ²≦0.7 (GeV/c)². The values of the helicity-1/2-partial wave amplitudesA _2?(D ₁₃(1520)) andA _3?(F ₁₅(1688)) were determined by a phenomenological analysis and compared with single quark transition models (S.Q.T.M.).     

A-X and A′-X progressions in dissociative excitation of matrix-isolated I2: Rare gas effect on lifetimes and intensities

The A-X and A′-X progressions of I₂ in Ne, Ar, Kr and Xe matrices have been time resolved and analyzed, and the matrix effects interpreted in terms of repulsive interactions in Ne and Ar, which become increasingly attractive in Kr and Xe. The Franck-Condon distributions in rare gas solids are compared with gas phase data. Combination of this information with new lifetime measurements yields matrix-independent transition moments, R_e(A-X)=0.17±0.02 D and R_e(A′-X)=0.010±0.001 D. The estimated transition moment R_e(A-X) in the gas phase is 0.20 D. Intensity ratios of the A-X and A′-X progressions were evaluated, yielding rations of 62:38, 75:25, 63:37, and 58:42 for the A and A′ state populations from dissociatively excited I₂ in Ne, Ar, Kr, and Xe. These results are in conflict with a previously proposed “cage size” model. An alternative relaxation scheme is proposed which accounts for observed A/A′ state population rations in the dissociative excitation of matrix-isolated I₂, Br₂, and Cl₂.     

Identification of differentially expressed, tumor-associated proteins in oral squamous cell carcinoma by proteomic analysis

Oral squamous cellular carcinoma is a malignant tumor with poor prognosis and therefore the discovery of early markers to discriminate malignant from normal cells would be of critical importance in clinical diagnosis. Subcellular fractions from oral squamous cell carcinoma (OSCC) and control samples, enriched in mitochondrial and cytosolic proteins, were analyzed by 2-DE, followed by MALDI-TOF-MS. Twenty proteins showed altered expression levels in OSCC; 14 were up- and 6 were down-regulated in comparison with the control samples. For 11 proteins, cofilin, C-reactive protein precursor, creatine kinase m-chain, fatty acid-binding protein, keratin type II, myosin light chain 2 and 3, nucleoside diphosphate kinase A, phosphoglycerate mutase 1, plakoglobulin, and retinoic acid-binding protein II, it is shown for the first time that they are differentially expressed in OSCC. Proteins with highly up-regulated levels may be of interest as potential diagnostic markers and consequently of clinical interest.     

Soil collapse computations with finite elements

Summary The elastic-plastic finite element method is reviewed with a view to predict collapse loads of geotechnical constructions. The basic technique of using an incremental-iterative approach with a constant stiffness matrix is well-known, but we fill a gap by proving that the procedure converges not only for small steps but also for large load increments. Here restriction is made to associated plasticity, as uniqueness of solution is not ensured for non-associated plasticity problems. Differences between associated and nonassociated problems are illustrated by showing results of numerical analyses. Finally, a number of practical aspects associated with the method are discussed.

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Finite-Element-Berechnungen des Versagens von Böden

Übersicht Im Hinblick auf die Vorhersage der Versagenlasten von Erdbauten wird ein Überblick über die elastisch-plastische Finite-Element-Methode gegeben. Das grundlegende Verfahren mit inkrementelliterativem Vorgehen mit einer konstanten Steifigkeitsmatrix ist wohlbekannt. Durch den Beweis, daß das Verfahren nicht nur bei kleinen Schrittweiten, sondern auch bei großen Laststufen konvergiert, werden jedoch neuartige Erkenntnisse vorgestellt. Hierbei muß einschränkend assoziierte Plastizität gelten, da bei nicht-assoziierter Plastizität die Eindeutigkeit von Lösungen nicht gewährleistet ist. Anhand von numerischen Ergebnissen werden Unterschiede zwischen Aufgabenstellungen mit assoziierter und nichtassoziierter Plastizität aufgezeigt. Schließlich werden auch noch praktische Gesichtspunkte des Verfahrens erörtert.

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Presented at the workshop on Limit Analysis and Bifurcation Theory, held at the University of Karlsruhe (FRG), February 22–25, 1988