Phospho‐tyrosine dependent protein–protein interaction network

Großmann, Arndt; Benlasfer, Nouhad; Birth, Petra; Hegele, Anna; Wachsmuth, Franziska; Apelt, Luise; Stelzl, Ulrich

doi:10.15252/msb.20145968

Cited by 78 publications

(91 citation statements)

References 65 publications

(148 reference statements)

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“…In a recent study, we generated yeast strains individually expressing human NRTKs for the systematic analysis of phospho-tyrosine (pY) dependent interactions (Grossmann et al, 2015). We expressed active full-length NRTKs at very low levels and did not observe toxicity of the L40c-Y2H S. cerevisiae strain under conditions of fast growth (Suppl.…”

Section: Measuring Tyrosine Phosphorylation By Human Kinases In Yeastmentioning

confidence: 99%

Defining Human Tyrosine Kinase Phosphorylation Networks Using Yeast as an In Vivo Model Substrate

et al. 2017

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Systematic assessment of tyrosine kinase-substrate relationships is fundamental to a better understanding of cellular signaling and its profound alterations in human diseases such as cancer. In human cells, complex signaling networks, feedback loops, conditional activity and intra-kinase redundancy combine to confound systematic attempts to address this topic. We leveraged the model organism S. cerevisiae to individually express human non-receptor tyrosine kinases (NRTKs) and exploited the full yeast proteome as an in vivo model substrate. For 16 NRTKs, we recorded 3,279 kinase-substrate relationships involving 1,351 yeast pY-sites. From this data we generated a set of new linear kinase motifs and assigned ~1,300 known human pY-sites to specific NRTKs. Furthermore, experimentally defined pY-sites for each individual kinase were shown to cluster within the yeast interactome network irrespective of linear motif information. We therefore applied a network inference approach to predict kinase-substrate relationships for more than 3,500 human proteins, marking a substantial step forward in our understanding of kinase biology.. Corwin et al., revised3 7/25/2017 3

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Section: Measuring Tyrosine Phosphorylation By Human Kinases In Yeastmentioning

confidence: 99%

Defining Human Tyrosine Kinase Phosphorylation Networks Using Yeast as an In Vivo Model Substrate

et al. 2017

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“…Using these HTP-PPI mapping approaches, relatively large proteomewide data sets have been generated (22). Also, more focused approaches were successful in systematically mapping specific cellular processes, selected functional groups of proteins, multiprotein complexes, or specific types of interactions (23,24). Y2H approaches result in binary interaction information that is complementary to copurification-based approaches and thus often provide hints as to how complexes assemble or dynamically remodel in the course of cellular processes (25).…”

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confidence: 99%

Systematic Protein–Protein Interaction Analysis Reveals Intersubcomplex Contacts in the Nuclear Pore Complex

Apelt

Knockenhauer

Leksa

et al. 2016

Molecular & Cellular Proteomics

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The nuclear pore complex (NPC) enables transport across the nuclear envelope. It is one of the largest multiprotein assemblies in the cell, built from about 30 proteins called nucleoporins (Nups), organized into distinct subcomplexes. Structure determination of the NPC is a major research goal. The assembled ϳ40 -112 MDa NPC can be visualized by cryoelectron tomography (cryo-ET), while Nup subcomplexes are studied crystallographically. Docking the crystal structures into the cryo-ET maps is difficult because of limited resolution. Further, intersubcomplex contacts are not well characterized. Here, we systematically investigated direct interactions between Nups. In a comprehensive, structurebased, yeast two-hybrid interaction matrix screen, we mapped protein-protein interactions in yeast and human. Benchmarking against crystallographic and coaffinity purification data from the literature demonstrated the high coverage and accuracy of the data set. Novel intersubcomplex interactions were validated biophysically in microscale thermophoresis experiments and in intact cells through protein fragment complementation. These intersubcomplex interaction data provide direct experimental evidence toward possible structural arrangements of architectural elements within the assembled NPC, or they may point to assembly intermediates. Our data favors an assembly model in which major architectural elements of the NPC, notably the Y-complex, exist in different structural contexts within the scaffold. Molecular & Cellular

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“…Generally, primary lung cancer is characterized into two types such as, Small Cell Lung Cancer (SCLC) and NonSmall Cell Lung Cancer (NSCLC) [2]. Whereas, the most common types of NSCLC are squamous cell carcinoma, large cell carcinoma and adenocarcinoma.…”

Section: Introductionmentioning

confidence: 99%

Identification of Lung Cancer Related Genes Using Enhanced Floyd Warshall Algorithm in a Protein to Protein Interaction Network

Patil¹,

Patil²,

Manickam³

2018

IJIES

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Lung cancer is defined as an uncontrolled cell growing in the tissues of lung, which is also said to be lung tumor. The lung cancer is curable in the starting stage, but identifying the lung cancer in starting stage is very difficult. In recent decades, researchers showed great interest on gene level lung cancer identification using shortest path between the lung cancer related genes. Many research has been done to identify the shortest path between the genes, but the conventional methods consumes more time for processing the data. In this research, Protein to Protein Interaction (PPI) structure is constructed from the weighted protein present in the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database. For identifying the shortest path between the genes in PPI, an effective algorithm: enhanced Floyd warshall algorithm is proposed. Floyd warshall is efficient in finding the shortest path between the genes and also solves all pairs of shortest path problem. A major drawback of Floyd warshall algorithm is, it works slower than other conventional algorithms designed to perform the same task. To improve the performance of traditional Floyd warshall algorithm, an iterative matrix is used for eliminating the invalid path. Then, the comparison between the proposed method and existing system is given in the experimental result. Experimental outcome shows that the proposed approach improved the time consumption up to 2-3 sec compared to the existing methods: Dijkstra's algorithm and Floyd warshall algorithm.Keywords: Dijkstra's algorithm, Enhanced Floyd warshall algorithm, Protein to protein interaction, Search tool for the retrieval of interacting genes/proteins.

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Phospho‐tyrosine dependent protein–protein interaction network

Cited by 78 publications

References 65 publications

Defining Human Tyrosine Kinase Phosphorylation Networks Using Yeast as an In Vivo Model Substrate

Defining Human Tyrosine Kinase Phosphorylation Networks Using Yeast as an In Vivo Model Substrate

Systematic Protein–Protein Interaction Analysis Reveals Intersubcomplex Contacts in the Nuclear Pore Complex

Identification of Lung Cancer Related Genes Using Enhanced Floyd Warshall Algorithm in a Protein to Protein Interaction Network

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