Dynamic proteomics in modeling of the living cell. Protein-protein interactions

@article{Terentiev2009DynamicPI,
  title={Dynamic proteomics in modeling of the living cell. Protein-protein interactions},
  author={A. A. Terentiev and N. T. Moldogazieva and K. Shaitan},
  journal={Biochemistry (Moscow)},
  year={2009},
  volume={74},
  pages={1586-1607}
}
This review is devoted to describing, summarizing, and analyzing of dynamic proteomics data obtained over the last few years and concerning the role of protein-protein interactions in modeling of the living cell. Principles of modern high-throughput experimental methods for investigation of protein-protein interactions are described. Systems biology approaches based on integrative view on cellular processes are used to analyze organization of protein interaction networks. It is proposed that… Expand
Network-Based Protein-Protein Interaction Analysis
TLDR
The-state-of-art of network-based strategies and applications to infer protein interactions are described, which are critical for the development of powerful, efficient prediction methods for the structure and function analysis of protein interaction network. Expand
Protein–protein interactions: switch from classical methods to proteomics and bioinformatics-based approaches
TLDR
A strong case is made as to why unraveling the interactome is the next challenge in the field of proteomics and classical methods of investigation of PPIs and structure-based bioinformatics approaches are presented. Expand
Proteomics and Non-proteomics Approaches to Study Stable and Transient Protein-Protein Interactions.
TLDR
The proteomics and non-proteomics approaches to study stable and transient PPIs to identify proteins, their sequence and known modifications as well as their quantitation in a biological sample for the purpose of understanding biological processes, protein cellular functions and their physiological and pathological involvement in diseases. Expand
Investigation of stable and transient protein–protein interactions: Past, present, and future
TLDR
An overview of the literature and a review of recent advances in the analysis of stable and transient protein–protein interactions (PPIs) with a focus on their function within cells, organs, and organisms is presented. Expand
PCD-GED: Protein complex detection considering PPI dynamics based on time series gene expression data.
TLDR
The proposed method generates a series of time-sequenced subnetworks according to the time that the interactions are activated, and finds the protein complexes by employing the weighted clustering coefficient and maximal weighted density concepts. Expand
A survey of computational methods in protein–protein interaction networks
TLDR
The network properties of protein–protein interaction networks are discussed and how they can be exploited to identify protein complexes and functional modules, as well as help classify proteins as essential. Expand
A method for predicting protein complex in dynamic PPI networks
TLDR
The experimental results show that the dynamic active information significantly improves the performance of protein complex prediction and the method can effectively make good use of both the dynamicactive information and the topology structure information of dynamic PPI networks to achieve state-of-the-artprotein complex prediction capabilities. Expand
BiCAMWI: A Genetic-Based Biclustering Algorithm for Detecting Dynamic Protein Complexes
TLDR
Experimental results confirm that BiCAMWI effectively models the dynamicity inherent in static PPI networks and achieves significantly better results than state-of-the-art methods and are suggested as a more reliable method for protein complex detection. Expand
A conceptual review on systems biology in health and diseases: from biological networks to modern therapeutics
TLDR
A concept of cell-to-human framework comprising of five modules ( data mining, networking, modeling, experimental and validation) for addressing human physiology and diseases based on a paradigm of system level analysis is put forth. Expand
Reconstruction of Bio-molecular Networks
TLDR
This chapter introduces how to construct bio-molecular networks and facilitates the further mathematical modeling, dynamical analysis, and statistical analysis on the related life systems. Expand
...
1
2
3
4
...

References

SHOWING 1-10 OF 230 REFERENCES
Analyzing protein-protein interactions using two-hybrid system.
TLDR
This chapter presents the analysis of protein–protein interactions using two-hybrid system, a yeast-based genetic assay for detecting protein– protein interactions in vivo and the basis for this method and the protocols that are necessary to use this system. Expand
Studying the interactome with the yeast two-hybrid system and mass spectrometry.
  • B. Causier
  • Chemistry, Medicine
  • Mass spectrometry reviews
  • 2004
TLDR
This review introduces the yeast two-hybrid system to those unfamiliar with the technique, and discusses how it can be used in combination with MS to unravel the network of protein interactions that occur in a cell. Expand
Roles for the Two-hybrid System in Exploration of the Yeast Protein Interactome*
TLDR
The yeast two-hybrid system can be used for the mapping of the interaction domains and the isolation of interaction-defective mutants, it would serve as a technical basis for the latter purpose, thereby playing another important role in the next phase of protein interactome research. Expand
Global analysis of protein localization in budding yeast
TLDR
The construction and analysis of a collection of yeast strains expressing full-length, chromosomally tagged green fluorescent protein fusion proteins helps reveal the logic of transcriptional co-regulation, and provides a comprehensive view of interactions within and between organelles in eukaryotic cells. Expand
Proteomic analysis of protein complexes
TLDR
While advances in technology have had a huge impact, sample preparation issues related to the isolation of protein complexes remains a critical factor in determining the success of these types of studies. Expand
Interactome: gateway into systems biology.
TLDR
Although far from complete, currently available maps provide insight into how biochemical properties of proteins and protein complexes are integrated into biological systems, and are also a useful resource to predict the function(s) of thousands of genes. Expand
Functional organization of the yeast proteome by systematic analysis of protein complexes
TLDR
The analysis provides an outline of the eukaryotic proteome as a network of protein complexes at a level of organization beyond binary interactions, which contains fundamental biological information and offers the context for a more reasoned and informed approach to drug discovery. Expand
Proteomics Technologies and Challenges
  • W. Cho
  • Computer Science, Medicine
  • Genom. Proteom. Bioinform.
  • 2007
TLDR
A snapshot of contemporary issues in proteomics technologies is discussed, including mining low abundant proteins and integration of proteomics with genomics and metabolomics data. Expand
Examining multiprotein signaling complexes from all angles
TLDR
The intensive investigation of LAT highlights how the systematic use of complementary techniques leads to an integrated understanding of the formation, composition and function of multiprotein signaling complexes that occur at receptors, adapter proteins and effector molecules. Expand
Dynamic proteomics in mammalian cells: capabilities and challenges.
  • R. Milo
  • Biology, Medicine
  • Molecular bioSystems
  • 2007
TLDR
One approach is reviewed, incorporating random endogenous gene tagging, high-throughput incubated time-lapse microscopy, and automated image analysis, that can provide information on, for example, the accumulation rates of proteins throughout the cell cycle and the variability of protein level expression. Expand
...
1
2
3
4
5
...