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JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
Published on: October 19, 2021
Exploring the spatial and temporal organization of a cell's proteome
Martin Beck1, Maya Topf, Zachary Frazier
1European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany.
Journal of Structural Biology
|November 25, 2010
Summary
Understanding cellular processes requires mapping the proteome
Area of Science:
- Cellular Biology
- Structural Biology
- Computational Biology
Background:
- Cellular processes like signaling and division depend on the proteome's organization.
- Understanding proteome organization requires data across atomic to cellular scales.
- New technologies enhance spatial information on molecular organization in living cells.
Purpose of the Study:
- To review methods for determining macromolecular structure and spatial organization.
- To integrate structural, spatial, and dynamic data of the proteome.
- To advance towards a predictive model of cellular processes.
Main Methods:
- Structure determination of macromolecular assemblies using electron microscopy.
- Visualization of spatial distributions via cryo-electron tomography and image processing.
- Spatial modeling of proteome dynamics, including reaction-diffusion simulations.
Main Results:
- Advances in determining atomic structures of macromolecular assemblies.
- Improved visualization of protein complex distribution within cells.
- Development of methods for simulating proteome dynamics in crowded cellular environments.
Conclusions:
- Integrating diverse proteome organization data is crucial for understanding cellular functions.
- Combining structural, spatial, and dynamic information advances predictive cell modeling.
- This integrated approach aims to create a spatially explicit model of cellular processes.
Related Concept Videos
01:33Proteomics
A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...
01:32Subcellular Fractionation
The homogenate obtained after cell lysis contains various membrane-bound organelles that can be further separated into pure fractions by subcellular fractionation. These isolates are used to study specific cellular components, analyze localized protein activity, and are even employed in diagnostics. Fractionation is typically achieved using centrifugation methods, the most common being density-gradient and differential centrifugation.
Differential Centrifugation
Differential centrifugation is...
Differential Centrifugation
Differential centrifugation is...
01:19Protein Dynamics in Living Cells
Different fluorescence-based techniques are used to study the protein dynamics in living cells. These techniques include FRAP, FRET, and PET.
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...
02:24Ribosome Profiling
Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
02:26Protein Networks
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...