The human plasma membrane peripherome: visualization and analysis of interactions

Biomed Res Int. 2014;2014:397145. doi: 10.1155/2014/397145. Epub 2014 Jun 25.

Abstract

A major part of membrane function is conducted by proteins, both integral and peripheral. Peripheral membrane proteins temporarily adhere to biological membranes, either to the lipid bilayer or to integral membrane proteins with noncovalent interactions. The aim of this study was to construct and analyze the interactions of the human plasma membrane peripheral proteins (peripherome hereinafter). For this purpose, we collected a dataset of peripheral proteins of the human plasma membrane. We also collected a dataset of experimentally verified interactions for these proteins. The interaction network created from this dataset has been visualized using Cytoscape. We grouped the proteins based on their subcellular location and clustered them using the MCL algorithm in order to detect functional modules. Moreover, functional and graph theory based analyses have been performed to assess biological features of the network. Interaction data with drug molecules show that ~10% of peripheral membrane proteins are targets for approved drugs, suggesting their potential implications in disease. In conclusion, we reveal novel features and properties regarding the protein-protein interaction network created by peripheral proteins of the human plasma membrane.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Cell Membrane / chemistry*
  • Cluster Analysis
  • Computational Biology / methods*
  • Databases, Protein
  • Humans
  • Lipid Bilayers / chemistry
  • Pharmaceutical Preparations / chemistry
  • Protein Interaction Mapping / methods*
  • Proteome*
  • Software

Substances

  • Lipid Bilayers
  • Pharmaceutical Preparations
  • Proteome