scholarly journals Regional diversity in the postsynaptic proteome of the mouse brain

2018 ◽  
Author(s):  
Marcia Roy ◽  
Oksana Sorokina ◽  
Colin McLean ◽  
Silvia Tapia-González ◽  
Javier DeFelipe ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Human Brain ◽  
Protein Interaction ◽  
Protein Interaction Networks ◽  
Interaction Networks ◽  
Excitatory Synapses ◽  
Vertebrate Species ◽  
Biochemical Pathways ◽  
Disease Protein ◽  
The Brain

AbstractThe proteome of the postsynaptic terminal of excitatory synapses comprises over one thousand proteins in vertebrate species and plays a central role in behavior and brain disease. The brain is organized into anatomically distinct regions and whether the synapse proteome differs across these regions is poorly understood. Postsynaptic proteomes were isolated from seven forebrain and hindbrain regions in mice and their composition determined using proteomic mass spectrometry. Seventy-four percent of proteins showed differential expression and each region displayed a unique compositional signature. These signatures correlated with the anatomical divisions of the brain and their embryological origins. Biochemical pathways controlling plasticity and disease, protein interaction networks and individual proteins involved with cognition all showed differential regional expression. Combining proteomic and connectomic data shows that interconnected regions have specific proteome signatures. Diversity in synapse proteome composition is key feature of mouse and human brain structure.

scholarly journals Regional Diversity in the Postsynaptic Proteome of the Mouse Brain

Proteomes ◽  
2018 ◽  
Vol 6 (3) ◽  
pp. 31 ◽  
Author(s):  
Marcia Roy ◽  
Oksana Sorokina ◽  
Colin McLean ◽  
Silvia Tapia-González ◽  
Javier DeFelipe ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Human Brain ◽  
Protein Interaction ◽  
Protein Interaction Networks ◽  
Interaction Networks ◽  
Excitatory Synapses ◽  
Vertebrate Species ◽  
Biochemical Pathways ◽  
Disease Protein ◽  
The Brain

The proteome of the postsynaptic terminal of excitatory synapses comprises over one thousand proteins in vertebrate species and plays a central role in behavior and brain disease. The brain is organized into anatomically distinct regions and whether the synapse proteome differs across these regions is poorly understood. Postsynaptic proteomes were isolated from seven forebrain and hindbrain regions in mice and their composition determined using proteomic mass spectrometry. Seventy-four percent of proteins showed differential expression and each region displayed a unique compositional signature. These signatures correlated with the anatomical divisions of the brain and their embryological origins. Biochemical pathways controlling plasticity and disease, protein interaction networks and individual proteins involved with cognition all showed differential regional expression. Combining proteomic and connectomic data shows that interconnected regions have specific proteome signatures. Diversity in synapse proteome composition is key feature of mouse and human brain structure.

scholarly journals XlinkCyNET: a Cytoscape application for visualization of protein interaction networks based on cross-linking mass-spectrometry identifications

2020 ◽  
Author(s):  
Diogo Borges Lima ◽  
Ying Zhu ◽  
Fan Liu
Keyword(s):  
Mass Spectrometry ◽  
Protein Interaction ◽  
Large Scale ◽  
Interaction Network ◽  
Protein Interaction Networks ◽  
Interaction Networks ◽  
Cross Linking ◽  
Protein Interaction Data ◽  
Interaction Data ◽  
Link Type

ABSTRACTSoftware tools that allow visualization and analysis of protein interaction networks are essential for studies in systems biology. One of the most popular network visualization tools in biology is Cytoscape, which offers a large selection of plugins for interpretation of protein interaction data. Chemical cross-linking coupled to mass spectrometry (XL-MS) is an increasingly important source for such interaction data, but there are currently no Cytoscape tools to analyze XL-MS results. In light of the suitability of Cytoscape platform but also to expand its toolbox, here we introduce XlinkCyNET, an open-source Cytoscape Java plugin for exploring large-scale XL-MS-based protein interaction networks. XlinkCyNET offers rapid and easy visualization of intra and intermolecular cross-links and the locations of protein domains in a rectangular bar style, allowing subdomain-level interrogation of the interaction network. XlinkCyNET is freely available from the Cytoscape app store: http://apps.cytoscape.org/apps/xlinkcynet and at https://www.theliulab.com/software/xlinkcynet.

scholarly journals Thermodynamic Measures of Human Brain Development from Fetal Stage to Adulthood

2019 ◽  
Author(s):  
Edward A. Rietman ◽  
Sophie Taylor ◽  
Hava T. Siegelmann ◽  
Marco Cavaglia ◽  
Jack A. Tuszynski
Keyword(s):  
Free Energy ◽  
Brain Development ◽  
Gibbs Free Energy ◽  
Protein Interaction ◽  
Brain Regions ◽  
Protein Interaction Networks ◽  
Interaction Networks ◽  
Protein Protein Interaction ◽  
Protein Protein Interaction Networks ◽  
The Brain

AbstractThis paper analyzes the data obtained from tissue samples of the human brains containing protein expression values. The data have been processed for their thermodynamic measure in terms of the Gibbs free energy of the corresponding protein-protein interaction networks. We have investigated the functional dependence of the Gibbs free energies on age and found consistent trends for most of the 16 main brain areas. The peak of the Gibbs energy values is found at birth with a trend toward plateauing at the age of maturity. We have also compared the data for males and females and uncovered functional differences for some of the brain regions.Significance StatementIn this paper we briefly outline the theoretical basis for a novel analysis of brain development in terms of a thermodynamic measure (Gibbs free energy) for the corresponding protein-protein interaction networks. We analyzed the overall developmental patterns for Gibbs free energy as a function of age across all brain regions. Of particular note was the significant upward trend in the fetal stages, which is generally followed by a sharp dip at birth and a plateau at maturity. We then compared the trends for female and male samples. A crossover pattern was observed for most of the brain regions, where the Gibbs free energy of the male samples were lower than the female samples at prenatal and neonatal ages, but higher at ages 8-40.

Analysis of protein interaction networks using mass spectrometry compatible techniques

2006 ◽  
Vol 564 (1) ◽  
pp. 10-18 ◽  
Author(s):  
Martin Ethier ◽  
Jean-Philippe Lambert ◽  
Julian Vasilescu ◽  
Daniel Figeys
Keyword(s):  
Mass Spectrometry ◽  
Protein Interaction ◽  
Protein Interaction Networks ◽  
Interaction Networks

scholarly journals Using XlinkCyNET to visualize protein cross-links in Cytoscape software

2020 ◽  
Author(s):  
Diogo Borges Lima ◽  
Ying Zhu ◽  
Fan Liu
Keyword(s):  
Mass Spectrometry ◽  
Complex Networks ◽  
Open Source ◽  
Protein Interaction ◽  
High Performance ◽  
Protein Interaction Networks ◽  
Interaction Networks ◽  
Cross Linking ◽  
Interactive Interface ◽  
Cross Links

Abstract We present a high-performance app for Cytoscape to visualize cross-linking mass-spectrometry (XL-MS) data. XlinkCyNET is an open-source Java plugin that generates residue-to-residue connections provided by XL-MS in protein interaction networks. Importantly, it provides an interactive interface for the exploration of cross-links and offers various options to display protein domains. XlinkCyNET works well in complex networks containing thousands of proteins.

Sign in / Sign up

Export Citation Format

Share Document