Investigation of a protein complex network

  title={Investigation of a protein complex network},
  author={Alireza Mashaghi and Abolfazl Ramezanpour and Vahid Karimipour},
  journal={The European Physical Journal B - Condensed Matter and Complex Systems},
Abstract.The budding yeast Saccharomyces cerevisiae is the first eukaryote whose genome has been completely sequenced. It is also the first eukaryotic cell whose proteome (the set of all proteins) and interactome (the network of all mutual interactions between proteins) has been analyzed. In this paper we study the structure of the yeast protein complex network in which weighted edges between complexes represent the number of shared proteins. It is found that the network of protein complexes is… 

Global organization of protein complexome in the yeast Saccharomyces cerevisiae

This work analyzes the topological network structure of protein complexes and their component proteins in the budding yeast in terms of the bipartite network and its projections, where the complexes and proteins are its two distinct components.

Predicting Physical Interactions between Protein Complexes*

A method to computationally predict physical interactions between protein complexes, applied to both humans and yeast, and designed a statistical method to identify pairs of protein complexes where the number of protein interactions between a complex pair is due to an actual physical interaction between the complexes.

From proteomes to complexomes in the era of systems biology

It is envisioned that improved integration of proteomics and systems biology, incorporating the dynamics of protein complexes in space and time, may lead to more predictive models of cell signaling networks for effective modulation.

The architectonic fold similarity network in protein fold space

It seems that this model can be used to depict the divergent evolution and expanding progress of protein fold space.

Protein Signaling Pathway: Network Centrality Analysis

A dynamic study of a new bigger network composed of the most important nodes of these two elementary nodes to better predict all these vital proteins' effects on other elements, inside or outside the network.


The starting point of this work has been the study of the properties of contacts between protein residues, since they constrain protein folding and characterize different protein structures, and introduced a Hidden Markov Model (HMM), which outperforms all the existing programs and can be adopted for the coiled-coil prediction and for large-scale genome annotation.

A topology framework for macromolecular complexes and condensates

A circuit topology-based formalism is proposed to define the topology of a complex consisting of linear polymeric chains with inter- and intrachain interactions to aid analysis and predictions of mechanistic and evolutionary principles in the design of macromolecular assemblies.

The effect of backbone on the small-world properties of protein contact maps

By randomly mimicking the protein collapse, the covalent structure of the protein chain significantly contributes to the small-world behavior of the inter-residue contact graphs.

Reconstruction of Bio-molecular Networks

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.



The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes.

  • A. Wagner
  • Biology
    Molecular biology and evolution
  • 2001
The structure and evolution of the protein interaction network of the yeast Saccharomyces cerevisiae is analyzed and it is shown that the persistence of redundant interaction partners is the exception rather than the rule.

Functional organization of the yeast proteome by systematic analysis of protein complexes

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.

A comprehensive two-hybrid analysis to explore the yeast protein interactome

The comprehensive analysis using a system to examine two-hybrid interactions in all possible combinations between the budding yeast Saccharomyces cerevisiae is completed and would significantly expand and improve the protein interaction map for the exploration of genome functions that eventually leads to thorough understanding of the cell as a molecular system.

Lethality and centrality in protein networks

It is demonstrated that the phenotypic consequence of a single gene deletion in the yeast Saccharomyces cerevisiae is affected to a large extent by the topological position of its protein product in the complex hierarchical web of molecular interactions.

Specificity and Stability in Topology of Protein Networks

It is found that for both interaction and regulatory networks, links between highly connected proteins are systematically suppressed, whereas those between a highly connected and low-connected pairs of proteins are favored.

Modeling of Protein Interaction Networks

A graph-generating model aimed at representing the evolution of protein interaction networks based on the hypothesis of evolution by duplication and divergence of the genes which produce proteins is introduced.

Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry

Comparison of the HMS-PCI data set with interactions reported in the literature revealed an average threefold higher success rate in detection of known complexes compared with large-scale two-hybrid studies.

A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae

Examination of large-scale yeast two-hybrid screens reveals interactions that place functionally unclassified proteins in a biological context, interactions between proteins involved in the same biological function, and interactions that link biological functions together into larger cellular processes.