Literature DB >> 16815898

Funneled landscape leads to robustness of cellular networks: MAPK signal transduction.

Jin Wang1, Bo Huang, Xuefeng Xia, Zhirong Sun.   

Abstract

We uncover the underlying potential energy landscape for a cellular network. We find that the potential energy landscape of the mitogen-activated protein-kinase signal transduction network is funneled toward the global minimum. The funneled landscape is quite robust against random perturbations. This naturally explains robustness from a physical point of view. The ratio of slope versus roughness of the landscape becomes a quantitative measure of robustness of the network. Funneled landscape is a realization of the Darwinian principle of natural selection at the cellular network level. It provides an optimal criterion for network connections and design. Our approach is general and can be applied to other cellular networks.

Mesh:

Year:  2006        PMID: 16815898      PMCID: PMC1544318          DOI: 10.1529/biophysj.106.086777

Source DB:  PubMed          Journal:  Biophys J        ISSN: 0006-3495            Impact factor:   4.033


  11 in total

1.  Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades.

Authors:  B N Kholodenko
Journal:  Eur J Biochem       Date:  2000-03

2.  The large-scale organization of metabolic networks.

Authors:  H Jeong; B Tombor; R Albert; Z N Oltvai; A L Barabási
Journal:  Nature       Date:  2000-10-05       Impact factor: 49.962

Review 3.  Network dynamics and cell physiology.

Authors:  J J Tyson; K Chen; B Novak
Journal:  Nat Rev Mol Cell Biol       Date:  2001-12       Impact factor: 94.444

4.  The yeast cell-cycle network is robustly designed.

Authors:  Fangting Li; Tao Long; Ying Lu; Qi Ouyang; Chao Tang
Journal:  Proc Natl Acad Sci U S A       Date:  2004-03-22       Impact factor: 11.205

Review 5.  Thermodynamics of stoichiometric biochemical networks in living systems far from equilibrium.

Authors:  Hong Qian; Daniel A Beard
Journal:  Biophys Chem       Date:  2004-12-22       Impact factor: 2.352

6.  The energy landscapes and motions of proteins.

Authors:  H Frauenfelder; S G Sligar; P G Wolynes
Journal:  Science       Date:  1991-12-13       Impact factor: 47.728

7.  Stochastic mechanisms in gene expression.

Authors:  H H McAdams; A Arkin
Journal:  Proc Natl Acad Sci U S A       Date:  1997-02-04       Impact factor: 11.205

Review 8.  Navigating the folding routes.

Authors:  P G Wolynes; J N Onuchic; D Thirumalai
Journal:  Science       Date:  1995-03-17       Impact factor: 47.728

9.  Ultrasensitivity in the mitogen-activated protein kinase cascade.

Authors:  C Y Huang; J E Ferrell
Journal:  Proc Natl Acad Sci U S A       Date:  1996-09-17       Impact factor: 11.205

10.  Calculating biological behaviors of epigenetic states in the phage lambda life cycle.

Authors:  X-M Zhu; L Yin; L Hood; P Ao
Journal:  Funct Integr Genomics       Date:  2004-02-05       Impact factor: 3.410

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  17 in total

1.  Emerging of Stochastic Dynamical Equalities and Steady State Thermodynamics from Darwinian Dynamics.

Authors:  P Ao
Journal:  Commun Theor Phys       Date:  2008-05-15       Impact factor: 1.968

2.  Communications: Hamiltonian regulated cell signaling network.

Authors:  Ge Wang; Muhammad H Zaman
Journal:  J Chem Phys       Date:  2010-03-28       Impact factor: 3.488

3.  Stable stochastic dynamics in yeast cell cycle.

Authors:  Yurie Okabe; Masaki Sasai
Journal:  Biophys J       Date:  2007-08-17       Impact factor: 4.033

4.  Potential landscape and flux framework of nonequilibrium networks: robustness, dissipation, and coherence of biochemical oscillations.

Authors:  Jin Wang; Li Xu; Erkang Wang
Journal:  Proc Natl Acad Sci U S A       Date:  2008-08-21       Impact factor: 11.205

5.  Robustness of integrin signaling network.

Authors:  Mark Kness; Ge Wang; Muhammad H Zaman
Journal:  J Chem Phys       Date:  2009-06-21       Impact factor: 3.488

6.  Robustness and coherence of a three-protein circadian oscillator: landscape and flux perspectives.

Authors:  Jin Wang; Li Xu; Erkang Wang
Journal:  Biophys J       Date:  2009-12-02       Impact factor: 4.033

7.  Relationship among phenotypic plasticity, phenotypic fluctuations, robustness, and evolvability; Waddington's legacy revisited under the spirit of Einstein.

Authors:  Kunihiko Kaneko
Journal:  J Biosci       Date:  2009-10       Impact factor: 1.826

8.  Cancer as robust intrinsic state of endogenous molecular-cellular network shaped by evolution.

Authors:  Ping Ao; David Galas; Leroy Hood; Xiaomei Zhu
Journal:  Med Hypotheses       Date:  2007-09-04       Impact factor: 1.538

Review 9.  Signalling mechanisms involved in renal pathological changes during cisplatin-induced nephropathy.

Authors:  Siddesh Jaiman; Arun Kumar Sharma; Kulwant Singh; Deepa Khanna
Journal:  Eur J Clin Pharmacol       Date:  2013-08-09       Impact factor: 2.953

10.  Borges dilemma, fundamental laws, and systems biology.

Authors:  Ping Ao
Journal:  Bioinform Biol Insights       Date:  2008-04-10
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