Деформационное упрочнение начально-изотропных металлов при деформировании по траекториям малой кривизны

На примере стали мартенситного класса исследованы закономерности деформационного упрочнения при нагружении по траекториям, имеющим вид двухзвенных ломаных, которым соответствуют траектории деформирования малой кривизны. Показано, что поверхность нагружения, разделяющая области упругого и упругопластического деформирования, смещается в направлении вектора, который соединяет центр поверхности нагружения и изображающую точку на траектории нагружения, при этом не изменяется форма ее фронтальной части. Зависимость величины смещения центра поверхности нагружения от интенсивности накопленных пластических деформаций описывается кривой, инвариантной к виду траектории нагружения.На прикладі сталі мартенситного класу досліджено закономірності деформаційного зміцнення при навантаженні по траєкторіях, що мають вигляд дволанкових ламаних, яким відповідають траєкторії деформування малої кривини. Показано, що поверхня навантаження, яка розділяє області пружного та пружнопластичного деформування, зміщується у напрямку вектора, який з ’єднує центр поверхні навантаження та відображуючу точку на траєкторії навантаження, при цьому форма фронтальної частини не змінюється. Залежність величини зміщення центра поверхні навантаження від інтенсивності накопичених пластичних деформацій описується кривою, яка є інваріантною відносно траєкторії навантаження.By the example of martensitic steel we study regularities of strain hardening under loading along two-section broken lines corresponding to slightly curved strain paths. It is shown that the loading surface separating domains of elastic and elastoplastic strains (yield surface) is displaced in the direction of a vector connecting the surface center with the loading trajectory image point, while the shape of its frontal part remains unchanged. The yield surface center displacement versus the intensity of accumulated plastic strains is described by a curve invariant to the loading trajectory

Current challenges in software solutions for mass spectrometry-based quantitative proteomics

This work was in part supported by the PRIME-XS project, grant agreement number 262067, funded by the European Union seventh Framework Programme; The Netherlands Proteomics Centre, embedded in The Netherlands Genomics Initiative; The Netherlands Bioinformatics Centre; and the Centre for Biomedical Genetics (to S.C., B.B. and A.J.R.H); by NIH grants NCRR RR001614 and RR019934 (to the UCSF Mass Spectrometry Facility, director: A.L. Burlingame, P.B.); and by grants from the MRC, CR-UK, BBSRC and Barts and the London Charity (to P.C.

Mdm20 Stimulates PolyQ Aggregation via Inhibiting Autophagy Through Akt-Ser473 Phosphorylation

Mdm20 is an auxiliary subunit of the NatB complex, which includes Nat5, the catalytic subunit for protein N-terminal acetylation. The NatB complex catalyzes N-acetylation during de novo protein synthesis initiation; however, recent evidence from yeast suggests that NatB also affects post-translational modification of tropomyosin, which is involved in intracellular sorting of aggregated proteins. We hypothesized that an acetylation complex such as NatB may contribute to protein clearance and/or proteostasis in mammalian cells. Using a poly glutamine (polyQ) aggregation system, we examined whether the NatB complex or its components affect protein aggregation in rat primary cultured hippocampal neurons and HEK293 cells. The number of polyQ aggregates increased in Mdm20 over-expressing (OE) cells, but not in Nat5-OE cells. Conversely, in Mdm20 knockdown (KD) cells, but not in Nat5-KD cells, polyQ aggregation was significantly reduced. Although Mdm20 directly associates with Nat5, the overall cellular localization of the two proteins was slightly distinct, and Mdm20 apparently co-localized with the polyQ aggregates. Furthermore, in Mdm20-KD cells, a punctate appearance of LC3 was evident, suggesting the induction of autophagy. Consistent with this notion, phosphorylation of Akt, most notably at Ser473, was greatly reduced in Mdm20-KD cells. These results demonstrate that Mdm20, the so-called auxiliary subunit of the translation-coupled protein N-acetylation complex, contributes to protein clearance and/or aggregate formation by affecting the phosphorylation level of Akt indepenently from the function of Nat5

Proteomics of transcription factors

Peptide mass spectrometry (MS) is an invaluable analytical method in biological and medical research. It is the only technique that, when integrated with liquid chromatography (LC) and database search tools, allows a highly sensitive qualitative characterization and highly accurate quantitative comparison of proteomes. Although many proteomes are much more complex than their corresponding genomes, due to, for example, extreme differences in protein abundance and post-translational modifications, continuous technical advances in MS instrumentation and peptide pre-fractionation techniques lead to increasing fractions of proteomes that can be covered. Nevertheless, the targeted analysis of subsets of proteomes defined by post-translational modifications (PTMs), for example phosphorylation, acetylation, or glycosylation, using specialized enrichment techniques, is required to gain insight into cellular processes that would be inadequately covered by analysis of the full proteome alone. The technological progression in proteomics also benefits the analysis of protein complexes and other relatively small ensembles of proteins. With modern MS instrumentation, a targeted analysis is mostly not required to create a comprehensive picture of protein complexes, including PTMs and protein isoforms. Selected core technologies of proteomics are introduced in Chapter 1. It is mainly focused on MS instrumentation and database searching, but also covers aspects like peptide fragmentation and methods in quantitative proteomics. In this chapter we also give a brief introduction to the general transcription factors (GTFs) TFIID and SAGA and put them into their broader biological context

Effect of chemical modifications on peptide fragmentation behavior upon electron transfer induced dissociation.

In proteomics, proteolytic peptides are often chemically modified to improve MS analysis, peptide identification, and/or to enable protein/peptide quantification. It is known that such chemical modifications can alter peptide fragmentation in collision induced dissociation MS/MS. Here, we investigated the fragmentation behavior of such chemically modified peptides in MS/MS using the relatively new activation method electron transfer dissociation (ETD). We generated proteolytic peptides using the proteases Lys-N and trypsin and compared the fragmentation behavior of the unlabeled peptides with that of their chemically modified cognates. We investigated the effect of several commonly used modification reactions, namely, guanidination, dimethylation, imidazolinylation, and nicotinylation (ICPL). Of these guanidination and imidazolinylation specifically target the epsilon-amino groups of lysine residues in the peptides, whereas dimethylation and nicotinylation modify both N-termini and epsilon-amino groups of lysine residues. Dimethylation, guanidination, and particularly imidazolinylation of doubly charged Lys-N peptides resulted in a significant increase in peptide sequence coverage, resulting in more reliable peptide identification using ETD. This may be rationalized by the increased basicity and resulting positive charge at the N-termini of these peptides. Nicotinylation of the peptides, on the other hand, severely suppressed backbone fragmentation, hampering the use of this label in ETD based analysis. Doubly charged C-terminal lysine containing tryptic peptides also resulted in an enhanced observation of a single type of fragment ion series when guanidinated or imidazolinylated. These labels would thus facilitate the use of de novo sequencing strategies based on ETD for both arginine and lysine containing tryptic peptides. Since isotopic analogues of the labeling reagents applied in this work are commercially available, one can combine quantitation with improved ETD based peptide sequencing for both Lys-N and trypsin digested samples

Gaining efficiency by parallel quantification and identification of iTRAQ-labeled peptides using HCD and decision tree guided CID/ETD on an LTQ Orbitrap

Isobaric stable isotope labeling of peptides using iTRAQ is an important method for MS based quantitative proteomics. Traditionally, quantitative analysis of iTRAQ labeled peptides has been confined to beam-type instruments because of the weak detection capabilities of ion traps for low mass ions. Recent technical advances in fragmentation techniques on linear ion traps and the hybrid linear ion trap-orbitrap allow circumventing this limitation. Namely, PQD and HCD facilitate iTRAQ analysis on these instrument types. Here we report a method for iTRAQ-based relative quantification on the ETD enabled LTQ Orbitrap XL, which is based on parallel peptide quantification and peptide identification. iTRAQ reporter ion generation is performed by HCD, while CID and ETD provide peptide identification data in parallel in the LTQ ion trap. This approach circumvents problems accompanying iTRAQ reporter ion generation with ETD and allows quantitative, decision tree-based CID/ETD experiments. Furthermore, the use of HCD solely for iTRAQ reporter ion read out significantly reduces the number of ions needed to obtain informative spectra, which significantly reduces the analysis time. Finally, we show that integration of this method, both with existing CID and ETD methods as well as with existing iTRAQ data analysis workflows, is simple to realize. By applying our approach to the analysis of the synapse proteome from human brain biopsies, we demonstrate that it outperforms a latest generation MALDI TOF/TOF instrument, with improvements in both peptide and protein identification and quantification. Conclusively, our work shows how HCD, CID and ETD can be beneficially combined to enable iTRAQ-based quantification on an ETD-enabled LTQ Orbitrap XL. © The Royal Society of Chemistry 2010

Application of the MIDAS approach for analysis of lysine acetylation sites.

Multiple Reaction Monitoring Initiated Detection and Sequencing (MIDAS™) is a mass spectrometry-based technique for the detection and characterization of specific post-translational modifications (Unwin et al. 4:1134-1144, 2005), for example acetylated lysine residues (Griffiths et al. 18:1423-1428, 2007). The MIDAS™ technique has application for discovery and analysis of acetylation sites. It is a hypothesis-driven approach that requires a priori knowledge of the primary sequence of the target protein and a proteolytic digest of this protein. MIDAS essentially performs a targeted search for the presence of modified, for example acetylated, peptides. The detection is based on the combination of the predicted molecular weight (measured as mass-charge ratio) of the acetylated proteolytic peptide and a diagnostic fragment (product ion of m/z 126.1), which is generated by specific fragmentation of acetylated peptides during collision induced dissociation performed in tandem mass spectrometry (MS) analysis. Sequence information is subsequently obtained which enables acetylation site assignment. The technique of MIDAS was later trademarked by ABSciex for targeted protein analysis where an MRM scan is combined with full MS/MS product ion scan to enable sequence confirmation