Proteomic analysis in cells treated with pristine carbon nano-onions and its subcellular localization

2019 ◽  
Vol 10 (3) ◽  
pp. 035011
Author(s):  
Liudy Garcia-Hernández ◽  
Frank J Chao-Mujica ◽  
Jaques M Ferreira de Souza ◽  
Alan R Mól ◽  
Wagner Fontes ◽  
...  
Keyword(s):  
Subcellular Localization ◽  
Proteomic Analysis ◽  
In Cells

Imaging and proteomic study of a clickable iridium complex

Metallomics ◽  
2019 ◽  
Vol 11 (8) ◽  
pp. 1344-1352 ◽  
Author(s):  
Xiuxiu Wang ◽  
Jingyi Zhang ◽  
Xinyang Zhao ◽  
Wei Wei ◽  
Jing Zhao
Keyword(s):  
Proteomic Analysis ◽  
Click Reaction ◽  
Receptor Interaction ◽  
Iridium Complex ◽  
Quantitative Proteomic Analysis ◽  
Proteomic Study ◽  
In Cells

We synthesized a clickable iridium complex 2-N3 which can be imaged via click reaction in cells. Quantitative proteomic analysis revealed that ECM–receptor interaction pathway was activated and a series of celluar process was affected by 2-N3.

scholarly journals Split-TurboID enables contact-dependent proximity labeling in cells

2020 ◽  
Author(s):  
Kelvin F. Cho ◽  
Tess C. Branon ◽  
Sanjana Rajeev ◽  
Tanya Svinkina ◽  
Namrata D. Udeshi ◽  
...  
Keyword(s):  
Endoplasmic Reticulum ◽  
Protein Interaction ◽  
Proteomic Analysis ◽  
Protein Protein Interaction ◽  
Conventional Fractionation ◽  
Contact Sites ◽  
Biochemical Fractionation ◽  
Versatile Tool ◽  
Endogenous Proteins ◽  
In Cells

AbstractProximity labeling (PL) catalyzed by promiscuous enzymes such as TurboID have enabled the proteomic analysis of subcellular regions difficult or impossible to access by conventional fractionation-based approaches. Yet some cellular regions, such as organelle contact sites, remain out of reach for current PL methods. To address this limitation, we split the enzyme TurboID into two inactive fragments that recombine when driven together by a protein-protein interaction or membrane-membrane apposition. At endoplasmic reticulum (ER)-mitochondria contact sites, reconstituted TurboID catalyzed spatially-restricted biotinylation, enabling the enrichment and identification of >100 endogenous proteins, including many not previously linked to ER-mitochondria contacts. We validated eight novel candidates by biochemical fractionation and overexpression imaging. Overall, split-TurboID is a versatile tool for conditional and spatially-specific proximity labeling in cells.

scholarly journals Protein transduction of an antioxidant enzyme: subcellular localization of superoxide dismutase fusion protein in cells

BMB Reports ◽  
2008 ◽  
Vol 41 (2) ◽  
pp. 170-175 ◽  
Author(s):  
Dae-Won Kim ◽  
So-Young Kim ◽  
Hwa Lee ◽  
Yeum-Pyo Lee ◽  
Min-Jung Lee ◽  
...  
Keyword(s):  
Superoxide Dismutase ◽  
Fusion Protein ◽  
Subcellular Localization ◽  
Antioxidant Enzyme ◽  
Protein Transduction ◽  
In Cells

Proteomic Analysis Reveals Multiple Patterns of Response in Cells Exposed to a Toxin Mixture

2009 ◽  
Vol 22 (6) ◽  
pp. 1077-1085 ◽  
Author(s):  
Gian Luca Sala ◽  
Giuseppe Ronzitti ◽  
Makoto Sasaki ◽  
Haruhiko Fuwa ◽  
Takeshi Yasumoto ◽  
...  
Keyword(s):  
Proteomic Analysis ◽  
In Cells

scholarly journals Proteomics in Vaccinology and Immunobiology: An Informatics Perspective of the Immunone

2003 ◽  
Vol 2003 (5) ◽  
pp. 267-290 ◽  
Author(s):  
Irini A. Doytchinova ◽  
Paul Taylor
Keyword(s):  
Subcellular Localization ◽  
Data Management ◽  
Proteomic Analysis ◽  
Quantitative Methods ◽  
Host Pathogen Interactions ◽  
Subunit Vaccines ◽  
Host Pathogen ◽  
Experimental Process ◽  
The Impact

The postgenomic era, as manifest, inter alia, by proteomics, offers unparalleled opportunities for the efficient discovery of safe, efficacious, and novel subunit vaccines targeting a tranche of modern major diseases. A negative corollary of this opportunity is the risk of becoming overwhelmed by this embarrassment of riches. Informatics techniques, working to address issues of both data management and through prediction to shortcut the experimental process, can be of enormous benefit in leveraging the proteomic revolution. In this disquisition, we evaluate proteomic approaches to the discovery of subunit vaccines, focussing on viral, bacterial, fungal, and parasite systems. We also adumbrate the impact that proteomic analysis of host-pathogen interactions can have. Finally, we review relevant methods to the prediction of immunome, with special emphasis on quantitative methods, and the subcellular localization of proteins within bacteria.

scholarly journals Subcellular localization of drug distribution by super-resolution ion beam imaging

2019 ◽  
Author(s):  
Xavier Rovira-Clave ◽  
Sizun Jiang ◽  
Yunhao Bai ◽  
Graham Barlow ◽  
Salil Bhate ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Subcellular Localization ◽  
Small Molecules ◽  
Secondary Ion Mass Spectrometry ◽  
Ion Beam ◽  
Drug Distribution ◽  
Super Resolution ◽  
Active Regions ◽  
Nuclear Speckles ◽  
In Cells

AbstractTechnologies that visualize multiple biomolecules at the nanometer scale in cells will enable deeper understanding of biological processes that proceed at the molecular scale. Current fluorescence-based methods for microscopy are constrained by a combination of spatial resolution limitations, limited parameters per experiment, and detector systems for the wide variety of biomolecules found in cells. We present here super-resolution ion beam imaging (srIBI), a secondary ion mass spectrometry approach capable of high-parameter imaging in 3D of targeted biological entities and exogenously added small molecules. Uniquely, the atomic constituents of the biomolecules themselves can often be used in our system as the “tag”. We visualized the subcellular localization of the chemotherapy drug cisplatin simultaneously with localization of five other nuclear structures, with further carbon elemental mapping and secondary electron visualization, down to ∼30 nm lateral resolution. Cisplatin was preferentially enriched in nuclear speckles and excluded from closed-chromatin regions, indicative of a role for cisplatin in active regions of chromatin. These data highlight how multiplexed super-resolution techniques, such as srIBI, will enable studies of biomolecule distributions in biologically relevant subcellular microenvironments.One Sentence SummaryThree-dimensional multiplexed mass spectrometry-based imaging revealed the subcellular localization of proteins and small molecules at super-resolution.

Subcellular localization of GFP-myosin-V in live mouse melanocytes

1999 ◽  
Vol 112 (17) ◽  
pp. 2853-2865 ◽  
Author(s):  
V. Tsakraklides ◽  
K. Krogh ◽  
L. Wang ◽  
J.C. Bizario ◽  
R.E. Larson ◽  
...  
Keyword(s):  
Subcellular Localization ◽  
Actin Filaments ◽  
Expression Patterns ◽  
Intracellular Localization ◽  
Motor Domain ◽  
Chick Brain ◽  
Myosin V ◽  
Myosin Va ◽  
Myosin Vb ◽  
In Cells

Class-V myosins are two-headed actin-based mechanoenzymes that function in the transport and subcellular localization of organelles and possibly in the outgrowth of cellular processes. To determine which domains of myosin-V are involved in intracellular localization of this motor protein, we have expressed fusions of the green fluorescent protein with segments from two distinct myosin-V heavy chains. The expression patterns of constructs encoding four different domains of chick brain myosin-Va were compared to a single construct encoding the globular tail region of mouse myosin-Vb. In transfected mouse melanocytes, expression of the NH(2)-terminal head (catalytic domain) of chick brain myosin-Va codistributed with actin filaments throughout the cytoplasm. A similar construct encoding the myosin-Va head with the associated neck (light chain binding sites), also codistributed with actin filaments. The GFP-head-neck peptide was also highly concentrated in the tips of filopodia in B16 melanocytes wild type for myosin-Va (MYO5a gene), but was concentrated throughout the entire filopodia of S91-6 melanocytes derived from dilute mice with mutations in the MYO5a gene. Evidence is also presented that the globular tail of myosin-Va, but not myosin-Vb, targets this motor molecule to the centrosome as confirmed by colocalization in cells stained with antibodies to (gamma)-tubulin. Expression of the GFP-myosin-Va globular tail causes displacement of endogenous myosin-V from centrosomes as visualized by immunolabeling with antibodies to the head domain of myosin-V. Treatment with the microtubule-disrupting drug nocodazole markedly reduces myosin-V staining at the centrosome. In contrast, there was no detectable diminution of myosin-V staining at the centrosome in cells treated with the actin filament-disrupting drug cytochalasin D. Thus, while localization of the myosin-V motor domain to actin-rich regions is consistent with conventional models of actomyosin-based motility, localization to the centrosome occurs in the complete absence of the myosin-V motor domain and is dependent on intact microtubules.

scholarly journals Function of the MYND Domain and C-Terminal Region in Regulating the Subcellular Localization and Catalytic Activity of the SMYD Family Lysine Methyltransferase Set5

2019 ◽  
Vol 40 (2) ◽  
Author(s):  
Deepika Jaiswal ◽  
Rashi Turniansky ◽  
James J. Moresco ◽  
Sabeen Ikram ◽  
Ganesh Ramaprasad ◽  
...  
Keyword(s):  
Catalytic Activity ◽  
Subcellular Localization ◽  
Stress Responses ◽  
Genome Stability ◽  
Muscle Development ◽  
Mutational Analysis ◽  
Histone H4 ◽  
Nonhistone Proteins ◽  
Content Type ◽  
In Cells

ABSTRACT SMYD lysine methyltransferases target histones and nonhistone proteins for methylation and are critical regulators of muscle development and implicated in neoplastic transformation. They are characterized by a split catalytic SET domain and an intervening MYND zinc finger domain, as well as an extended C-terminal domain. Saccharomyces cerevisiae contains two SMYD proteins, Set5 and Set6, which share structural elements with the mammalian SMYD enzymes. Set5 is a histone H4 lysine 5, 8, and 12 methyltransferase, implicated in the regulation of stress responses and genome stability. While the SMYD proteins have diverse roles in cells, there are many gaps in our understanding of how these enzymes are regulated. Here, we performed mutational analysis of Set5, combined with phosphoproteomics, to identify regulatory mechanisms for its enzymatic activity and subcellular localization. Our results indicate that the MYND domain promotes Set5 chromatin association in cells and is required for its role in repressing subtelomeric genes. Phosphoproteomics revealed extensive phosphorylation of Set5, and phosphomimetic mutations enhance Set5 catalytic activity but diminish its ability to interact with chromatin in cells. These studies uncover multiple regions within Set5 that regulate its localization and activity and highlight potential avenues for understanding mechanisms controlling the diverse roles of SMYD enzymes.

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