Extensive regulation of enzyme activity by phosphorylation in Escherichia coli
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ABSTRACT: This project contains intact protein MS and PRM data for several central metabolic enzymes in E.coli. The enzymes are both wild-type and mutant for several
Project description:Here we investigate the role of acetyl phosphate-mediated acetylation in E. coli central metabolism. Out of 19 enzymes investigated from central metabolsim, only GapA and GpmA were acetylated at high stoichiometry.
Project description:New software-tool allowing an easy visualization of fragment ions and thus a rapid evaluation of key experimental parameters on the sequence coverage obtained for the MS/MS analysis of intact proteins. Our tool can deal with multiple fragmentation methods. We demonstrate that TDFragMapper can rapidly highlight the experimental fragmentation parameters that are critical to the characterization of intact proteins of various size using top-down proteomics.
Project description:In antibody-based drug research, regulatory agencies request a complete characterization of antibody proteoforms covering both the amino acid sequence and all post-translational modifications. The usual mass spectrometry-based approach to achieve this goal is bottom-up proteomics, which relies on the digestion of antibodies, but does not allow the diversity of proteoforms to be assessed. Middle-down and top-down approaches have recently emerged as attractive alternatives but are not yet mastered and thus used in routine by many analytical chemistry laboratories. The work described here aims at providing guidelines to achieve the best sequence coverage for the fragmentation of intact light and heavy chains generated from a simple reduction of intact antibodies using Orbitrap mass spectrometry. Three parameters were found crucial to this aim: the use of an electron-based activation technique, the multiplex selection of precursor ions of different charge states and the combination of replicates.
Project description:Periostin is a matricellular protein encoded by the POSTN gene that is alternatively spliced to produce ten different isoforms of periostin with a molecular weight ranging from 78 to 91 kDa. Periostin is known to promote fibrillogenesis, organize the extracellular matrix, and bind integrin-receptors to induce cell signaling. Periostin is a key component of the wound healing process but is also known to participate in the pathogenesis of different diseases including atopic dermatitis, asthma, and cancer. In both health and disease, the functions of the different periostin isoforms are largely unknown. The ability to precisely determine the isoform profile of a given human sample is fundamental for characterizing their functional significance. Identification of periostin isoforms is most often carried out at the transcriptional level using RT-PCR based approaches. Though, it must be recognized that periostin exerts it functions at the translational level and is an extracellular protein making it impossible to derive transcriptional information for e.g. plasma periostin that is spatially disconnected from the cell it was expressed by. Consequently, monitoring periostin isoforms at the protein level is highly advantageous. In the publication connected to this dataset we present a fully developed top down mass spectrometry assay for identification and quantification of periostin splice isoforms from any human sample at the protein level.
Project description:Photosynthesis drives all life on Earth by exploiting solar energy to split water molecules through the Photosystem (PS) II enzyme. In plant thylakoid membranes, PSII binds a modular set of light harvesting complexes (LHCII) to form different types of PSII-LHCII supercomplex (PSII-LHCIIsc). Plant PSII-LHCIIsc are localized in the stacked region of the thylakoid membranes called grana, from which they can be isolated in paired conformations of type (C2S2M2)x2 and (C2S2M)x2, with the two supercomplexes facing each other at their stromal surface. Although the atomic structure of PSII-LHCIIsc has recently been solved, there is still a lack of knowledge on their mutual interactions when facing each other within apposing thylakoid membranes, as well as their structural dynamics in response to light variations. The major challenges in the structural determination of the stromal interactions are posed not only by the dynamic nature of these over 2-megadalton assemblies, but also by the heterogeneity of the LHCII subunits and the high flexibility of their stromally exposed N-terminal loops. Here, we explored the potential of combining top-down mass spectrometry (TD-MS) and crosslinking mass spectrometry (XL-MS) to peek through the keyhole of the tight stromal gap between two facing supercomplexes, unveiling so far hidden structural details. A first goal of experiments was to identify the distinct sequence variants and proteoforms involved in PSII-LHCIIsc structural dynamics in response to light modulation. To investigate their structural interactions, we treated paired PSII-LHCIIsc isolated from the three light conditions with two complementary chemical cross-linkers, targeting different residues and producing partially overlapping distance restraints. Most interactions detected “in-vitro” on the isolated paired supercomplexes were further supported by XL-MS results obtained “in-situ” on the corresponding thylakoid membranes.
Project description:Calmodulin serves as a regulator for various proteins, such as enzymes, kinases or phosphatases. It can also serve as Ca2+-dependent adaptor protein. Due to the previous evidence that retroviruses use host cell calmodulin for their proliferation, we focused on the description of functional and structural patterns of the interaction between Mason-Pfizer monkey virus matrix and human calmodulin. One of the methods used was native mass spectrometry.
Project description:Top-down analysis of intact proteins by mass spectrometry provides an ideal platform for comprehensive proteoform characterization, in particular, for the identification and localization of post-translational modifications (PTM) co-occurring on a protein. One of the main bottlenecks in top-down proteomics is insufficient protein sequence coverage caused by incomplete protein fragmentation. Based on previous work on peptides, increasing sequence coverage and PTM localization by combining sequential ETD and HCD fragmentation in a single fragmentation event, we hypothesized that protein sequence coverage and phospho-proteoform characterization could be equally improved by this new dual fragmentation method termed EThcD, recently been made available on the Orbitrap Fusion. Here, we systematically benchmark the performance of several (hybrid) fragmentation methods for intact protein analysis on an Orbitrap Fusion, using as a model system a 17.5 kDa N-terminal fragment of the mitotic regulator Bora. During cell division Bora becomes multiply phosphorylated by a variety of cell cycle kinases, including Aurora A and Plk1, albeit at distinctive sites. Here, we monitor the phosphorylation of Bora by Aurora A and Plk1, analyzing the generated distinctive phospho-proteoforms by top-down fragmentation. We show that EThcD and ETciD on a Fusion are feasible and capable of providing richer fragmentation spectra compared to HCD or ETD alone, increasing protein sequence coverage, and thereby facilitating phosphosite localization and the determination of kinase specific phosphorylation sites in these phospho-proteoforms.
Project description:Protamine 1 (P1) and protamine 2 family (P2) are the most abundant nuclear basic spermspecific proteins, packing 85-95% of the paternal DNA. P1 is synthesized as a mature form, whereas P2 components (HP2, HP3 and HP4) arise from the proteolysis of the precursor (pre-P2). Due to the particular protamine physical-chemical properties, their identification by standardized bottom-up mass spectrometry (MS) strategies are not straightforward. Therefore, the aim of this study was to identify the sperm protamine proteoforms profile including P1 and P2 members and their post-translational modifications in normozoospermic individuals using two complementary strategies, a top-down MS approach and a proteinase K-digestion based bottom-up MS approach. By top-down MS approach, both described and new truncated P1 and pre-P2 proteoforms were identified. Likewise, intact P1, pre-P2, and P2 mature forms and their phosphorylation pattern were detected, as well as a +61 Da modification in different proteoforms. Additionally, the bottom-up MS approach revealed phosphorylated residues for pre-P2 and the new P2 isoform 2, which is not annotated at UniProtKB database. Implementing these strategies in comparative studies of different infertile phenotypes would permit to determine alterations in the protamine proteoforms pattern and elucidate the role of phosphorylation/dephosphorylation dynamics in male fertility.
Project description:Senescent cells are increasingly recognized as major contributors to age-related diseases, primarily through the secretion of bioactive molecules known as the senescence-associated secretory phenotype (SASP). The SASP plays a crucial role in promoting various age-related conditions, including neurodegeneration and type-2 diabetes. While bottom-up proteomic profiling has been instrumental in elucidating senescence heterogeneity and linking SASP factors to aging and obesity, the complexity of protein modifications in SASP remains underexplored. Notably, proteoform-level analysis has not yet been applied to study SASP profiles in detail. In this study, we employ top-down proteomics to capture proteoform diversity in the secretomes of senescent and healthy lung fibroblasts (IMR90).
Project description:Cysteine disulfide bridges can be reduced by chemical methods, like an incubation with DTT. However, reduction with an electrochemical method has also been demonstrated. Electrochemical reduction can be implemented online, after LC separation and before mass spectrometry. For the study of antibody molecules, reduction of the intermolecular disulfide bridges between heavy and light chains has been demonstrated in literature. However, the reduction of intramolecular disulfide bridges has remained elusive. Here, we demonstrate the online electrochemical reduction of a therapeutic monoclonal antibody. The complete reduction of these molecules will facilitate the study of recombinant or natural antibodies by MS and MS/MS.