title: Modelling reaction kinetics inside cells.
abstract: In the past decade, advances in molecular biology such as the development of non-invasive single molecule imaging techniques have given us a window into the intricate biochemical activities that occur inside cells. In this chapter we review four distinct theoretical and simulation frameworks: (i) non-spatial and deterministic, (ii) spatial and deterministic, (iii) non-spatial and stochastic and (iv) spatial and stochastic. Each framework can be suited to modelling and interpreting intracellular reaction kinetics. By estimating the fundamental length scales, one can roughly determine which models are best suited for the particular reaction pathway under study. We discuss differences in prediction between the four modelling methodologies. In particular we show that taking into account noise and space does not simply add quantitative predictive accuracy but may also lead to qualitatively different physiological predictions, unaccounted for by classical deterministic models.
authors.affiliation: Institute for Mathematical Sciences, Imperial College, London, U.K.
authors.forename: Ramon
authors.initials: R
authors.lastname: Grima
authors.forename: Santiago
authors.initials: S
authors.lastname: Schnell
mesh_terms: D000818:Animals; D002477:Cells / Q000378:metabolism*; D007700:Kinetics; D008954:Models, Biological; D013269:Stochastic Processes
references.citation: Annu Rev Phys Chem. 2007;58:35-55
references.pmid: 17037977
references.citation: Annu Rev Biophys Biomol Struct. 1997;26:373-99
references.pmid: 9241424
references.citation: Mol Biol Cell. 2000 Jan;11(1):369-91
references.pmid: 10637314
references.citation: Methods. 2001 Jun;24(2):181-90
references.pmid: 11384193
references.citation: Proc Natl Acad Sci U S A. 2003 Jun 10;100(12):6940-5
references.pmid: 12771378
references.citation: Int Rev Cytol. 2000;192:189-221
references.pmid: 10553280
references.citation: Biophys J. 2003 May;84(5):2841-51
references.pmid: 12719218
references.citation: Science. 2005 Jul 15;309(5733):446-51
references.pmid: 16020730
references.citation: Nat Chem Biol. 2006 Feb;2(2):87-94
references.pmid: 16415859
references.citation: Trends Biotechnol. 2001 Oct;19(10):401-6
references.pmid: 11587765
references.citation: Phys Rev E Stat Nonlin Soft Matter Phys. 2005 Apr;71(4 Pt 1):041103
references.pmid: 15903653
references.citation: Bioinformatics. 2005 Jun 15;21(12):2923-4
references.pmid: 15817692
references.citation: Biophys J. 1994 Feb;66(2 Pt 1):394-401
references.pmid: 8161693
references.citation: J Bioinform Comput Biol. 2005 Apr;3(2):415-36
references.pmid: 15852513
references.citation: Phys Rev E Stat Nonlin Soft Matter Phys. 2004 Aug;70(2 Pt 1):020901
references.pmid: 15447471
references.citation: Phys Biol. 2004 Dec;1(3-4):137-51
references.pmid: 16204833
references.citation: J Mol Biol. 2003 May 30;329(2):291-309
references.pmid: 12758077
references.citation: Science. 1997 Dec 19;278(5346):2075-80
references.pmid: 9405336
references.citation: Prog Biophys Mol Biol. 2004 Sep;86(1):77-112
references.pmid: 15261526
references.citation: Comput Biol Chem. 2004 Jul;28(3):165-78
references.pmid: 15261147
references.citation: Mol Syst Biol. 2006;2:56
references.pmid: 17047663
references.citation: J Neurosci. 2005 Mar 2;25(9):2181-91
references.pmid: 15745944
references.citation: Eur J Biochem. 2000 Sep;267(17):5313-29
references.pmid: 10951190
references.citation: Biotechnol Bioeng. 1999 Jul 20;64(2):200-12
references.pmid: 10397856
references.citation: BMC Bioinformatics. 2004 Mar 08;5:24
references.pmid: 15113411
references.citation: Syst Biol (Stevenage). 2004 Jun;1(1):129-38
references.pmid: 17052123
references.citation: Phys Rev Lett. 2006 Mar 10;96(9):098102
references.pmid: 16606319
references.citation: Proc Natl Acad Sci U S A. 2005 Jan 11;102(2):321-4
references.pmid: 15626756
references.citation: J Theor Biol. 2004 Oct 7;230(3):301-12
references.pmid: 15302540
references.citation: Bioinformatics. 2003 Feb 12;19(3):435-6
references.pmid: 12584138
references.citation: Proc Natl Acad Sci U S A. 1997 Feb 4;94(3):814-9
references.pmid: 9023339
references.citation: Proc Natl Acad Sci U S A. 1996 Jun 11;93(12):5747-52
references.pmid: 8650164
references.citation: Science. 2002 Aug 16;297(5584):1183-6
references.pmid: 12183631
references.citation: Prog Biophys Mol Biol. 2004 Jun-Jul;85(2-3):235-60
references.pmid: 15142746
references.citation: Bioessays. 1995 Nov;17(11):987-97
references.pmid: 8526893
references.citation: Biophys J. 2005 May;88(5):3720-30
references.pmid: 15749770
references.citation: Annu Rev Biophys Biophys Chem. 1985;14:131-60
references.pmid: 3890878
references.citation: Nat Cell Biol. 2000 Mar;2(3):168-72
references.pmid: 10707088
references.citation: Proc Natl Acad Sci U S A. 2002 Jan 22;99(2):673-8
references.pmid: 11792856
references.citation: Biophys J. 2000 Jul;79(1):163-83
references.pmid: 10866945
references.citation: Am J Physiol. 1984 Feb;246(2 Pt 2):R133-51
references.pmid: 6364846
references.citation: EMBO J. 2000 Mar 1;19(5):892-901
references.pmid: 10698931
references.citation: J Phys Chem B. 2005 Oct 20;109(41):19068-81
references.pmid: 16853459
references.citation: Proteomics. 2007 Mar;7(6):828-38
references.pmid: 17370261
references.citation: Proc Natl Acad Sci U S A. 2005 Feb 15;102(7):2310-5
references.pmid: 15701703
references.citation: Science. 2001 Oct 26;294(5543):864-7
references.pmid: 11679673
references.citation: Phys Rev Lett. 2006 Jul 28;97(4):048302
references.pmid: 16907618
references.citation: Trends Genet. 1999 Feb;15(2):65-9
references.pmid: 10098409
references.citation: Biophys J. 2004 Nov;87(5):3518-24
references.pmid: 15339818
references.citation: J Biol Chem. 1999 May 28;274(22):15293-6
references.pmid: 10336412
references.citation: J Mol Biol. 2000 May 12;298(4):677-89
references.pmid: 10788329
references.citation: Science. 2002 Feb 8;295(5557):1083-6
references.pmid: 11834838