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MIPDB: a relational database dedicated to MIP family proteins

Khalid El Karkouri1, Hervé Gueuné, Christian Delamarche

  • 1UMR CNRS 6026 Interactions Cellulaires et Moléculaires, Université de Rennes 1, équipe SDM (Structure et Dynamique des Macromolécules), Campus de Beaulieu, Bât. 13, 35042 Rennes Cedex, France.

Biology of the Cell
|April 27, 2005
PubMed
Abstract

Insights

MIPDB is a new database for major intrinsic proteins (MIPs), including aquaporins (AQPs), that classifies these membrane transport proteins and aids in predicting their function and location. This resource facilitates large-scale analysis of MIPs across diverse organisms.

Area of Science:

  • Membrane biology
  • Bioinformatics
  • Protein science

Background:

  • Major intrinsic proteins (MIPs) are crucial membrane proteins facilitating the transport of water and small solutes.
  • Aquaporins (AQPs), a subset of MIPs, are key to understanding cellular membrane permeability.
  • MIPs are found across Archaea, Bacteria, and Eukaryota, necessitating comprehensive databases for analysis.

Purpose of the Study:

  • To develop MIPDB, a relational database for MIP proteins.
  • To enable large-scale analysis of MIP sequences for functional and evolutionary insights.
  • To provide a centralized resource for studying the MIP protein family.

Main Methods:

  • Integrated data on 785 MIP proteins from over 200 organisms.
  • Developed a motif-oriented database containing 230 distinct sequence motifs.
  • Classified MIP proteins into functional subgroups: AQPs, glycerol-uptake facilitators, and aquaglyceroporins.

Main Results:

  • MIPDB classifies MIP proteins into three functional subgroups.
  • Plant MIPs are further categorized by subcellular localization (plasma membrane, tonoplast, symbiosome membrane).
  • Identified selective motifs can predict the transport function and subcellular localization of unknown MIP proteins.

Conclusions:

  • MIPDB provides a user-friendly interface for accessing MIP resources and analysis tools.
  • The database is publicly accessible as a web application.
  • MIPDB supports research on membrane transport and protein function.

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