Studies of Protein Post-translational Modifications Using High Resolution Tandem Mass Spectrometry PDF Download

Author: Huilin Li
Publisher:
ISBN:
Category :
Languages : en
Pages : 0

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Author: John R. Griffiths
Publisher: John Wiley & Sons
ISBN: 1119045851
Category : Science
Languages : en
Pages : 414

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Covers all major modifications, including phosphorylation, glycosylation, acetylation, ubiquitination, sulfonation and and glycation Discussion of the chemistry behind each modification, along with key methods and references Contributions from some of the leading researchers in the field A valuable reference source for all laboratories undertaking proteomics, mass spectrometry and post-translational modification research

Author: Oscar Alzate
Publisher: CRC Press
ISBN: 1420076264
Category : Medical
Languages : en
Pages : 356

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In this, the post-genomic age, our knowledge of biological systems continues to expand and progress. As the research becomes more focused, so too does the data. Genomic research progresses to proteomics and brings us to a deeper understanding of the behavior and function of protein clusters. And now proteomics gives way to neuroproteomics as we beg

Author: Christoph Kannicht
Publisher: Springer Science & Business Media
ISBN: 1592591817
Category : Science
Languages : en
Pages : 326

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Christoph Kannicht and a panel of highly experienced researchers describe readily reproducible methods for detecting and analyzing the posttranslational modifications of protein, particularly with regard to protein function, proteome research, and the characterization of pharmaceutical proteins.

Author: Zhou Li (Researcher in biological systems)
Publisher:
ISBN:
Category : Acid mine drainage
Languages : en
Pages : 175

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Mass spectrometry-based proteomics is focused on identifying the entire suite of proteins and their post-translational modifications (PTMs) in a cell, organism, or community. In particular, quantitative proteomics measures abundance changes of thousands of proteins among multiple samples and provides network-level insight into how biological systems respond to environmental perturbations. Various quantitative proteomics methods have been developed, including label-free, metabolic labeling, and isobaric chemical labeling. This dissertation starts with systematic comparison of these three methods, and shows that isobaric chemical labeling provides accurate, precise, and reproducible quantification for thousands of proteins. Based on these results, we applied this approach to characterizing the proteome of Arabidopsis seedlings treated with Strigolactones (SLs), a new class of plant hormones that modulate various developmental processes. Our study reveals that SLs regulate the expression of a range of proteins that have not been assigned to SL pathways, which provides novel targets for follow-up genetic and biochemical characterization of SL signaling. The same approach was also used to measure how elevated temperature impacts the physiology of individual microbial groups in an acid mine drainage (AMD) microbial community, and shows that related organisms differed in their abundance and functional responses to temperature. Elevated temperature repressed carbon fixation by two Leptospirillum genotypes, whereas carbon fixation was significantly up-regulated at higher temperature by a third member of this genus. Further, we developed a new proteomic approach that harnessed high-resolution mass spectrometry and supercomputing for direct identification and quantification of a broad range of PTMs from an AMD microbial community. We find that PTMs are extraordinarily diverse between different growth stages and highly divergent between closely related bacteria. The findings of this study motivate further investigation of the role of PTMs in the ecology and evolution of microbial communities. Finally, a computational approach has been developed to improve the sensitivity of phosphopeptide identification. Overall, the research presented in the dissertation not only reveals biological insights with existing quantitative proteomics methods, but also develops novel methodologies that open up new avenues in studying PTMs of proteins (e.g. PTM cross-talk).

Author: Jeremy Lynn Balsbaugh
Publisher:
ISBN:
Category :
Languages : en
Pages :

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Author: Qingchun Zhang
Publisher:
ISBN:
Category : Post-translational modification
Languages : en
Pages : 456

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Author: Liwen Wang
Publisher:
ISBN:
Category :
Languages : en
Pages :

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Abstract: This dissertation describes a proteomic workflow for the analysis of protein post-translational modifications (PTMs). The workflow combines the techniques for protein enrichment, multi-dimensional separations, mass spectrometry (MS) and automatic data analysis. The workflow was developed to improve the application of proteomic analysis in the realms of biomarker discovery and experimental therapeutic research. Chapter 2 presents an immunoaffinity chromatography method that was developed to enrich acetylated histones. A self-packed immunoaffinity capillary column was developed using commercial antibodies that could be recycled and used for on-line and off-line enrichment. The acetylated fractions were collected and identified by Matrix Assisted Laser Desorption (MALDI) MS and electrospray ionization (ESI) liquid chromatography tandem mass spectrometry (LC-MS/MS). In chapter 3 an optimized phosphoproteomic analysis workflow based on phosphopeptide enrichment, data-dependant neutral loss mass spectrometry and a novel hierarchical database searching is described. The combination of these approaches improved the confidence of phosphopeptide identifications. Chapter 4 describes the use of phosphoprotein enrichment and a tandem phosphoprotein and phosphopeptide enrichment to improve the identification of phosphoproteins and localization of the phosphorylation sites. Purification of global phosphoproteins from primary CLL B-cells was conducted by use of PhosTag Zn2 enrichment strategy at neutral pH. SDS-PAGE gel was used to separate the purified phosphoprotein fraction and Pro-Q diamond staining was employed to visualize those phosphoprotein bands. Shot-gun proteomic analysis was then performed to identify all the enriched phosphoproteins in the gel. Phosphopeptide enrichment was used in tandem to map phosphorylation sites of the enriched phosphoproteins. Chapter 5 describes the identification of tyrosine phosphoproteins associated with immunotherapy of malignant cells with the small modular immunopharmaceutical targeted against CD37 (CD37-SMIPTM). This drug induces apoptosis and antibody-dependent cellular cytotoxicity (ADCC) in primary Chronic Lymphocyte Leukemia (CLL) cells. Tyrosine phosphorylation of proteins was investigated as an early activation event for the cytotoxicity. Immunoprecipitation was used to purify the phosphotyrosine proteins from treated cell lysate and untreated cell lysate. Detection of modulation of tyrosine phosphorylation and identification of those tyrosine phosphoproteins after treatment by proteomic approaches revealed proteins associated with the signaling pathway activated by immunotherapy. Chapter 6 describes a direct application of the proteomic platform developed in Chapter 3 combined with LC-MS protein profiling. The modulation of histone phosphorylation isoforms induced by various chemotherapy drugs was detected by LC-MS screening. We detected the dephosphorylation of histones H1 and hyperphosphorylation of H2A.X associated with the different drug treatments.

Author: Henrik Molina
Publisher:
ISBN:
Category :
Languages : en
Pages : 160

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Author: Derek J. Chadwick
Publisher: John Wiley & Sons
ISBN: 0470514159
Category : Science
Languages : en
Pages : 282

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Book Description
How the amino acid sequence of a protein determines its three-dimensional structure is a major problem in biology and chemistry. Leading experts in the fields of NMR spectroscopy, X-ray crystallography, protein engineering and molecular modeling offer provocative insights into current views on the protein folding problem and various aspects for future progress.