Literature DB >> 27429713

Napoleon Is in Equilibrium.

Rob Phillips1.   

Abstract

It has been said that the cell is the test tube of the twenty-first century. If so, the theoretical tools needed to quantitatively and predictively describe what goes on in such test tubes lag sorely behind the stunning experimental advances in biology seen in the decades since the molecular biology revolution began. Perhaps surprisingly, one of the theoretical tools that has been used with great success on problems ranging from how cells communicate with their environment and each other to the nature of the organization of proteins and lipids within the cell membrane is statistical mechanics. A knee-jerk reaction to the use of statistical mechanics in the description of cellular processes is that living organisms are so far from equilibrium that one has no business even thinking about it. But such reactions are probably too hasty given that there are many regimes in which, because of a separation of timescales, for example, such an approach can be a useful first step. In this article, we explore the power of statistical mechanical thinking in the biological setting, with special emphasis on cell signaling and regulation. We show how such models are used to make predictions and describe some recent experiments designed to test them. We also consider the limits of such models based on the relative timescales of the processes of interest.

Entities:  

Keywords:  MWC model; allostery; biophysics; gene regulation; transcription

Year:  2015        PMID: 27429713      PMCID: PMC4946674          DOI: 10.1146/annurev-conmatphys-031214-014558

Source DB:  PubMed          Journal:  Annu Rev Condens Matter Phys        ISSN: 1947-5454            Impact factor:   16.109


  60 in total

1.  Stochasticity in transcriptional regulation: origins, consequences, and mathematical representations.

Authors:  T B Kepler; T C Elston
Journal:  Biophys J       Date:  2001-12       Impact factor: 4.033

2.  Receptor sensitivity in bacterial chemotaxis.

Authors:  Victor Sourjik; Howard C Berg
Journal:  Proc Natl Acad Sci U S A       Date:  2001-12-11       Impact factor: 11.205

3.  Chemosensing in Escherichia coli: two regimes of two-state receptors.

Authors:  Juan E Keymer; Robert G Endres; Monica Skoge; Yigal Meir; Ned S Wingreen
Journal:  Proc Natl Acad Sci U S A       Date:  2006-01-30       Impact factor: 11.205

4.  Signal processing by the HOG MAP kinase pathway.

Authors:  Pascal Hersen; Megan N McClean; L Mahadevan; Sharad Ramanathan
Journal:  Proc Natl Acad Sci U S A       Date:  2008-05-14       Impact factor: 11.205

5.  The OR control system of bacteriophage lambda. A physical-chemical model for gene regulation.

Authors:  M A Shea; G K Ackers
Journal:  J Mol Biol       Date:  1985-01-20       Impact factor: 5.469

Review 6.  Transcription by the numbers redux: experiments and calculations that surprise.

Authors:  Hernan G Garcia; Alvaro Sanchez; Thomas Kuhlman; Jane Kondev; Rob Phillips
Journal:  Trends Cell Biol       Date:  2010-12       Impact factor: 20.808

7.  A systems-level analysis of perfect adaptation in yeast osmoregulation.

Authors:  Dale Muzzey; Carlos A Gómez-Uribe; Jerome T Mettetal; Alexander van Oudenaarden
Journal:  Cell       Date:  2009-07-10       Impact factor: 41.582

8.  Quantitative model for gene regulation by lambda phage repressor.

Authors:  G K Ackers; A D Johnson; M A Shea
Journal:  Proc Natl Acad Sci U S A       Date:  1982-02       Impact factor: 11.205

9.  Induction of ectopic eyes by targeted expression of the eyeless gene in Drosophila.

Authors:  G Halder; P Callaerts; W J Gehring
Journal:  Science       Date:  1995-03-24       Impact factor: 47.728

10.  Trade-offs and constraints in allosteric sensing.

Authors:  Bruno M C Martins; Peter S Swain
Journal:  PLoS Comput Biol       Date:  2011-11-03       Impact factor: 4.475

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  15 in total

1.  Chromosome-refolding model of mating-type switching in yeast.

Authors:  Barış Avşaroğlu; Gabriel Bronk; Kevin Li; James E Haber; Jane Kondev
Journal:  Proc Natl Acad Sci U S A       Date:  2016-10-24       Impact factor: 11.205

2.  Monod-Wyman-Changeux Analysis of Ligand-Gated Ion Channel Mutants.

Authors:  Tal Einav; Rob Phillips
Journal:  J Phys Chem B       Date:  2017-02-21       Impact factor: 2.991

Review 3.  In search of lost time: Enhancers as modulators of timing in lymphocyte development and differentiation.

Authors:  Jonathan M Chu; Nicholas A Pease; Hao Yuan Kueh
Journal:  Immunol Rev       Date:  2021-03-18       Impact factor: 12.988

Review 4.  Figure 1 Theory Meets Figure 2 Experiments in the Study of Gene Expression.

Authors:  Rob Phillips; Nathan M Belliveau; Griffin Chure; Hernan G Garcia; Manuel Razo-Mejia; Clarissa Scholes
Journal:  Annu Rev Biophys       Date:  2019-05-06       Impact factor: 12.981

5.  Is a super-enhancer greater than the sum of its parts?

Authors:  Noah Dukler; Brad Gulko; Yi-Fei Huang; Adam Siepel
Journal:  Nat Genet       Date:  2016-12-28       Impact factor: 38.330

6.  A stochastic epigenetic switch controls the dynamics of T-cell lineage commitment.

Authors:  Kenneth Kh Ng; Mary A Yui; Arnav Mehta; Sharmayne Siu; Blythe Irwin; Shirley Pease; Satoshi Hirose; Michael B Elowitz; Ellen V Rothenberg; Hao Yuan Kueh
Journal:  Elife       Date:  2018-11-20       Impact factor: 8.140

7.  Statistical Mechanics of Allosteric Enzymes.

Authors:  Tal Einav; Linas Mazutis; Rob Phillips
Journal:  J Phys Chem B       Date:  2016-04-29       Impact factor: 2.991

8.  Anticipating response function in gene regulatory networks.

Authors:  Pankaj Gautam; Sudipta Kumar Sinha
Journal:  J R Soc Interface       Date:  2021-06-02       Impact factor: 4.293

9.  Intrinsic limits to gene regulation by global crosstalk.

Authors:  Tamar Friedlander; Roshan Prizak; Călin C Guet; Nicholas H Barton; Gašper Tkačik
Journal:  Nat Commun       Date:  2016-08-04       Impact factor: 14.919

10.  PTRE-seq reveals mechanism and interactions of RNA binding proteins and miRNAs.

Authors:  Kyle A Cottrell; Hemangi G Chaudhari; Barak A Cohen; Sergej Djuranovic
Journal:  Nat Commun       Date:  2018-01-19       Impact factor: 14.919

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