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

Kouichi Takahashi; Satya Nanda Vel Arjunan; Masaru Tomita

doi:10.1016/j.febslet.2005.01.072

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

Kouichi Takahashi, Satya Nanda Vel Arjunan, Masaru Tomita

Faculty of Environment and Information Studies

Research output: Contribution to journal › Short survey › peer-review

187 Citations (Scopus)

Abstract

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 language	English
Pages (from-to)	1783-1788
Number of pages	6
Journal	FEBS Letters
Volume	579
Issue number	8
DOIs	https://doi.org/10.1016/j.febslet.2005.01.072
Publication status	Published - 2005 Mar 21

Keywords

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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10.1016/j.febslet.2005.01.072

Cite this

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title = "Space in systems biology of signaling pathways - Towards intracellular molecular crowding in silico",

abstract = "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.",

keywords = "Excluded volume effect, Intracellular space, Molecular crowding, Signaling pathway, Simulation, Systems biology",

author = "Kouichi Takahashi and {Vel Arjunan}, {Satya Nanda} and Masaru Tomita",

note = "Funding Information: We thank Dr. Kirsten Benjamin for critical reading. K.T. acknowledges Dr. Roger Brent and Dr. Dan Gillespie for stimulating discussions. Michiko Abe helped us in preparing the figure. This work was supported by CREST/JST, and the Ministry of Education, Culture, Sports, Science and Technology (Leading Project for Biosimulation, The 21st Century COE Program, and The Monbukagakusho Scholarship Program).",

year = "2005",

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doi = "10.1016/j.febslet.2005.01.072",

language = "English",

volume = "579",

pages = "1783--1788",

journal = "FEBS Letters",

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number = "8",

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TY - JOUR

T1 - Space in systems biology of signaling pathways - Towards intracellular molecular crowding in silico

AU - Takahashi, Kouichi

AU - Vel Arjunan, Satya Nanda

AU - Tomita, Masaru

N1 - Funding Information: We thank Dr. Kirsten Benjamin for critical reading. K.T. acknowledges Dr. Roger Brent and Dr. Dan Gillespie for stimulating discussions. Michiko Abe helped us in preparing the figure. This work was supported by CREST/JST, and the Ministry of Education, Culture, Sports, Science and Technology (Leading Project for Biosimulation, The 21st Century COE Program, and The Monbukagakusho Scholarship Program).

PY - 2005/3/21

Y1 - 2005/3/21

N2 - 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.

AB - 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.

KW - Excluded volume effect

KW - Intracellular space

KW - Molecular crowding

KW - Signaling pathway

KW - Simulation

KW - Systems biology

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U2 - 10.1016/j.febslet.2005.01.072

DO - 10.1016/j.febslet.2005.01.072

M3 - Short survey

C2 - 15763552

AN - SCOPUS:14844321288

SN - 0014-5793

VL - 579

SP - 1783

EP - 1788

JO - FEBS Letters

JF - FEBS Letters

IS - 8

ER -

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

Abstract

Keywords

ASJC Scopus subject areas

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