| 1. |
- Astorga-Wells, Juan
(författare)
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Microfluidic electrocapture technology in protein and peptide analysis
- 2004
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- After sequencing the genomes of several organisms, science in the postgenomic era now aims at a thorough study of the proteins present in a given tissue or organism. Since this task requires an enormous analytical effort, integrated microfluidic systems are envisioned as the solution to automated high throughput analysis of biomolecules. This thesis is focused on a microfluidic methodology and device that present several advantages over present technologies. The microfluidic device utilizes an electric field to capture molecules traveling in a flow stream. After capture, another medium is injected into the system that is of a desirable chemical composition or carries reagents, which are brought into contact with the captured molecules. The microfluidic device was employed as a concentrator for capillary electrophoresis (CE). Samples containing a mixture of proteins were concentrated and injected into a CE instrument. Detection limits were thereby improved from µM to nM protein levels. The device was further applied to desalting and removal of contaminants before MALDI-MS analysis. Polypeptides were captured followed by the injection of a solvent suitable for NIS analysis. Significant desalting and removal of CHAPS detergent was obtained for efficient analysis of peptides and proteins by MALDI-MS. In further study, the utilization of the electrocapture device to carry out microreactions is described. After the capture of a target protein, another medium containing enzymes and/or reagents is injected. Reduction, alkylation, and trypsin digestion, as well as sample cleanup, were carried out for peptide mass mapping by MALDI-MS. The use of the electrocapture device as a separation tool is also described. The separation process involves the capture and subsequent sequential release of peptides according to their electrophoretic mobility. Tryptic peptides from digestion of a mixture of proteins were separated and analyzed by MALDI-MS. A final study concerns the capture mechanism. It was found that negatively charged molecules are in fact immobilized in the flow stream due to a steady-state phenomenon created by the generation of areas with different electric field strengths along the fluidic channel. Herein we describe a flexible microfluidic device capable of processing polypeptides to resolve key analytical problems in protein and peptide analysis.
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| 2. |
- Crona, Mikael, et al.
(författare)
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Biochemical Characterization of the Split Class II Ribonucleotide Reductase from Pseudomonas aeruginosa
- 2015
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 10:7
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Tidskriftsartikel (refereegranskat)abstract
- The opportunistic pathogen Pseudomonas aeruginosa can grow under both aerobic and anaerobic conditions. Its flexibility with respect to oxygen load is reflected by the fact that its genome encodes all three existing classes of ribonucleotides reductase (RNR): the oxygen-dependent class I RNR, the oxygen-indifferent class II RNR, and the oxygen-sensitive class III RNR. The P. aeruginosa class II RNR is expressed as two separate polypeptides (NrdJa and NrdJb), a unique example of a split RNR enzyme in a free-living organism. A split class II RNR is also found in a few closely related gamma-Proteobacteria. We have characterized the P. aeruginosa class II RNR and show that both subunits are required for formation of a biologically functional enzyme that can sustain vitamin B12-dependent growth. Binding of the B12 coenzyme as well as substrate and allosteric effectors resides in the NrdJa subunit, whereas the NrdJb subunit mediates efficient reductive dithiol exchange during catalysis. A combination of activity assays and activity-independent methods like surface plasmon resonance and gas phase electrophoretic macromolecule analysis suggests that the enzymatically active form of the enzyme is a (NrdJa-NrdJb) 2 homodimer of heterodimers, and a combination of hydrogen-deuterium exchange experiments and molecular modeling suggests a plausible region in NrdJa that interacts with NrdJb. Our detailed characterization of the split NrdJ from P. aeruginosa provides insight into the biochemical function of a unique enzyme known to have central roles in biofilm formation and anaerobic growth.
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| 3. |
- Jornvall, Hans, et al.
(författare)
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Oligomerization and insulin interactions of proinsulin C-peptide : Threefold relationships to properties of insulin
- 2010
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Ingår i: Biochemical and Biophysical Research Communications - BBRC. - : Elsevier BV. - 0006-291X .- 1090-2104. ; 391:3, s. 1561-1566
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Tidskriftsartikel (refereegranskat)abstract
- Three principally different sites of action have been reported for proinsulin C-peptide, at surface-mediated, intracellular, and extracellular locations. Following up on the latter, we now find that (i) mass spectrometric analyses reveal the presence of the C-peptide monomer in apparent equilibrium with a low-yield set of oligomers in weakly acidic or basic aqueous solutions, even at low peptide concentrations (sub-mu M). It further shows not only C-peptide to interact with insulin oligomers (known before), but also the other way around. (ii) Polyacrylamide gel electrophoresis of C-peptide shows detectable oligomers upon Western blotting. Formation of thioflavin T positive material was also detected. (iii) Cleavage patterns of analogues are compatible with C-peptide as a substrate of insulin degrading enzyme. Combined, the results demonstrate three links with insulin properties, in a manner reminiscent of amyloidogenic peptides and their chaperons in other systems. If so, peripheral C-peptide/insulin interactions, absolute amounts of both peptides and their ratios may be relevant to consider in diabetic and associated diseases.
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| 4. |
- Jung, Taeyang, et al.
(författare)
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The Polyglutamine Expansion at the N-Terminal of Huntingtin Protein Modulates the Dynamic Configuration and Phosphorylation of the C-Terminal HEAT Domain
- 2020
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Ingår i: Structure. - : Cell Press. - 0969-2126 .- 1878-4186. ; 28:9, s. 1035-1050.e8
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Tidskriftsartikel (refereegranskat)abstract
- The polyQ expansion in huntingtin protein (HTT) is the prime cause of Huntington's disease (HD). The recent cryoelectron microscopy (cryo-EM) structure of HTT-HAP40 complex provided the structural information on its HEAT-repeat domains. Here, we present analyses of the impact of polyQ length on the structure and function of HTT via an integrative structural and biochemical approach. The cryo-EM analysis of normal (Q23) and disease (Q78) type HTTs shows that the structures of apo HTTs significantly differ from the structure of HTT in a HAP40 complex and that the polyQ expansion induces global structural changes in the relative movements among the HTT domains. In addition, we show that the polyQ expansion alters the phosphorylation pattern across HTT and that Ser2116 phosphorylation in turn affects the global structure and function of HTT These results provide a molecular basis for the effect of the polyQ segment on HTT structure and activity, which may be important for HTT pathology.
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| 5. |
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| 6. |
- Saei, Amir Ata, et al.
(författare)
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System-wide identification and prioritization of enzyme substrates by thermal analysis
- 2021
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 12:1
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Tidskriftsartikel (refereegranskat)abstract
- Despite the immense importance of enzyme-substrate reactions, there is a lack of general and unbiased tools for identifying and prioritizing substrate proteins that are modified by the enzyme on the structural level. Here we describe a high-throughput unbiased proteomics method called System-wide Identification and prioritization of Enzyme Substrates by Thermal Analysis (SIESTA). The approach assumes that the enzymatic post-translational modification of substrate proteins is likely to change their thermal stability. In our proof-of-concept studies, SIESTA successfully identifies several known and novel substrate candidates for selenoprotein thioredoxin reductase 1, protein kinase B (AKT1) and poly-(ADP-ribose) polymerase-10 systems. Wider application of SIESTA can enhance our understanding of the role of enzymes in homeostasis and disease, opening opportunities to investigate the effect of post-translational modifications on signal transduction and facilitate drug discovery.
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| 7. |
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| 8. |
- Shariatgorji, Mohammadreza, 1974-
(författare)
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Novel clean-up, concentration and laser desorption/ionization strategies for mass spectrometry
- 2010
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Despite valuable advantages of mass spectrometry (MS) techniques they still have drawbacks that need to be overcome, notably their sensitivity to various kinds of interfering substances and associated difficulties involved in detecting signals from analytes present in trace quantities. Thus, high quality analytical data could be acquired by improving sample pre-treatment techniques and/or ionization methods to increase ionization yields and/or avoid the generation of unwanted ions. In the studies this thesis is based upon, a microfluidic electrocapture system capable of trapping charged proteins/polypeptides while non-charged species such as non-ionic detergents are swept out, was used to decrease the concentration of detergent in samples containing soluble and membrane associated proteins/polypeptide. Subsequent mass spectrometric analysis yielded well-resolved mass spectra of the target analytes. In addition, it was found that solid phase extraction (SPE) sorbents such as graphitized carbon black (GCB), can efficiently assist the laser desorption ionization of small molecules without generating any interfering ions which inspired the fabrication of μ-traps and discs. Other matrix-free approaches demonstrated the utility of silicon nitride and oxidized GCB nanoparticles as versatile media for surface-assisted laser desorption ionization (SALDI) of small molecules. In this thesis it is discussed that small molecule analytes such as Polyphenols present in red wine and quaternary protoberberine alkaloids with highly conjugated systems and acidic/permanently charged functional groups can be readily analyzed without any matrix or assisting-surface. In summary, the microfluidic electrocapture, new laser desorption ionization methods and surfaces, as well as integrated SALDI and SPE platforms, introduced in this work extend the MS strategies allowing coverage of a wider range of samples.
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| 9. |
- Shariatgorji, Mohammadreza, et al.
(författare)
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Trends in the bioanalytical applications of microfluidic electrocapture
- 2011
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Ingår i: Analytical and Bioanalytical Chemistry. - : Springer Science and Business Media LLC. - 1618-2642 .- 1618-2650. ; 399:1, s. 191-195
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Downscaled analytical tools for sample preparation have offered benefits such as higher throughput, easier automation and lower sample/reagent consumption. Microfluidic electrocapture, which is a newly developed sample preparation/manipulation system, uses an electric field to trap and separate charged species without using any solid sorbent. The feasibility of using microfluidic electrocapture is reported for separation, clean-up, concentration, microreactions and complexation studies of proteins, peptides and other biologically important biomolecules. The instrumentation and applications of microfluidic electrocapture are reviewed and an overview is provided of future perspectives offered by the current and envisaged platforms.
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| 10. |
- Visnes, Torkild, et al.
(författare)
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Small-molecule inhibitor of OGG1 suppresses proinflammatory gene expression and inflammation
- 2018
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 362:6416, s. 834-
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Tidskriftsartikel (refereegranskat)abstract
- The onset of inflammation is associated with reactive oxygen species and oxidative damage to macromolecules like 7,8-dihydro-8-oxoguanine (8-oxoG) in DNA. Because 8-oxoguanine DNA glycosylase 1 (OGG1) binds 8-oxoG and because Ogg1-deficient mice are resistant to acute and systemic inflammation, we hypothesized that OGG1 inhibition may represent a strategy for the prevention and treatment of inflammation. We developed TH5487, a selective active-site inhibitor of OGG1, which hampers OGG1 binding to and repair of 8-oxoG and which is well tolerated by mice. TH5487 prevents tumor necrosis factor-alpha-induced OGG1-DNA interactions at guanine-rich promoters of proinflammatory genes. This, in turn, decreases DNA occupancy of nuclear factor kappa B and proinflammatory gene expression, resulting in decreased immune cell recruitment to mouse lungs. Thus, we present a proof of concept that targeting oxidative DNA repair can alleviate inflammatory conditions in vivo.
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