Space in systems biology of signaling pathways - Towards intracellular molecular crowding in silico

Kouichi Takahashi, Satya Nanda Vel Arjunan, Masaru Tomita

Research output: Contribution to journalShort survey

179 Citations (Scopus)


How cells utilize intracellular spatial features to optimize their signaling characteristics is still not clearly understood. The physical distance between the cell-surface receptor and the gene expression machinery, fast reactions, and slow protein diffusion coefficients are some of the properties that contribute to their intricacy. This article reviews computational frameworks that can help biologists to elucidate the implications of space in signaling pathways. We argue that intracellular macromolecular crowding is an important modeling issue, and describe how recent simulation methods can reproduce this phenomenon in either implicit, semi-explicit or fully explicit representation.

Original languageEnglish
Pages (from-to)1783-1788
Number of pages6
JournalFEBS Letters
Issue number8
Publication statusPublished - 2005 Mar 21



  • Excluded volume effect
  • Intracellular space
  • Molecular crowding
  • Signaling pathway
  • Simulation
  • Systems biology

ASJC Scopus subject areas

  • Biophysics
  • Structural Biology
  • Biochemistry
  • Molecular Biology
  • Genetics
  • Cell Biology

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