Spatial Control of Biochemical Modification Cascades and Pathways

Biophysical Journal

Volumn 108, Issue 12, 2015, Pages 2912-2924

  Alam Nazki, Aiman ^a   Krishnan, J ^a  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CELL COMPARTMENTALIZATION; METABOLOME; PROTEIN PROCESSING; SIGNAL TRANSDUCTION; THEORETICAL MODEL;

CELL COMPARTMENTATION; METABOLOME; MODELS, THEORETICAL; PROTEIN PROCESSING, POST-TRANSLATIONAL; SIGNAL TRANSDUCTION;

EID: 84931292161     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2015.05.012     Document Type: Article

References (45)

1. S. Hurtley Spatial cell biology. Location, location, location. Introduction Science 326 2009 1205
2. L. Shapiro, H.H. McAdams, and R. Losick Why and how bacteria localize proteins Science 326 2009 1225 1228
3. L.C. Kam, K. Shen, and M.L. Dustin Micro- and nanoscale engineering of cell signaling Annu. Rev. Biomed. Eng. 15 2013 305 326
4. A.H. Chen, and P.A. Silver Designing biological compartmentalization Trends Cell Biol. 22 2012 662 670
5. M. Knudsen, E. Feliu, and C. Wiuf Exact analysis of intrinsic qualitative features of phosphorelays using mathematical models J. Theor. Biol. 300 2012 7 18
6. A. Alam-Nazki, and J. Krishnan Covalent modification cycles through the spatial prism Biophys. J. 105 2013 1720 1731
7. C.-Y. Huang, and J.E. Ferrell Jr. Ultrasensitivity in the mitogen-activated protein kinase cascade Proc. Natl. Acad. Sci. USA 93 1996 10078 10083
8. A.C. Ventura, J.A. Sepulchre, and S.D. Merajver A hidden feedback in signaling cascades is revealed PLOS Comput. Biol. 4 2008 e1000041
9. A. Goldbeter, and D.E. Koshland Jr. An amplified sensitivity arising from covalent modification in biological systems Proc. Natl. Acad. Sci. USA 78 1981 6840 6844
10. K. Takahashi, S. Tanase-Nicola, and P.R. ten Wolde Spatiooral correlations can drastically change the response of a MAPK pathway Proc. Natl. Acad. Sci. USA 107 2010 2473 2478
11. Y.E. Chen, and C.G. Tsokos M.T. Laub Dynamics of two Phosphorelays controlling cell cycle progression in Caulobacter crescentus J. Bacteriol. 191 2009 7417 7429
12. F. Marks, U. Klingmuller, and K. Muller-Decker Cellular signal processing: an introduction to the molecular mechanisms of signal transduction 2009 Garland Science New York
13. N. Vartak, and P. Bastiaens Spatial cycles in G-protein crowd control EMBO J. 29 2010 2689 2699
14. G.C. Brown, and B.N. Kholodenko Spatial gradients of cellular phospho-proteins FEBS Lett. 457 1999 452 454
15. B.N. Kholodenko Cell-signalling dynamics in time and space Nat. Rev. Mol. Cell Biol. 7 2006 165 176
16. G. Laloux, and C. Jacobs-Wagner How do bacteria localize proteins to the cell pole? J. Cell Sci. 127 2014 11 19
17. M.S. Cyert Regulation of nuclear localization during signaling J. Biol. Chem. 276 2001 20805 20808
18. D.Z. Rudner, Q. Pan, and R.M. Losick Evidence that subcellular localization of a bacterial membrane protein is achieved by diffusion and capture Proc. Natl. Acad. Sci. USA 99 2002 8701 8706
19. K. Kondoh, S. Torii, and E. Nishida Control of MAP kinase signaling to the nucleus Chromosoma 114 2005 86 91
20. A. Eijkelenboom, and B.M.T. Burgering FOXOs: signalling integrators for homeostasis maintenance Nat. Rev. Mol. Cell Biol. 14 2013 83 97
21. J. Blenis, and M.D. Resh Subcellular localization specified by protein acylation and phosphorylation Curr. Opin. Cell Biol. 5 1993 984 989
22. C. Walsh Post-translational Modification of Proteins:Expanding Nature's Inventory 2005 Roberts Greenwood Village, CO
23. K. Engel, A. Kotlyarov, and M. Gaestel Leptomycin B-sensitive nuclear export of MAPKAP kinase 2 is regulated by phosphorylation EMBO J. 17 1998 3363 3371
24. P. Goyal, D. Pandey, and W. Siess Phosphorylation-dependent regulation of unique nuclear and nucleolar localization signals of LIM kinase 2 in endothelial cells J. Biol. Chem. 281 2006 25223 25230
25. P. Cohen The regulation of protein function by multisite phosphorylation - a 25 year update Trends Biochem. Sci. 25 2000 596 601
26. M. Thanbichler Spatial regulation in Caulobacter crescentus Curr. Opin. Microbiol. 12 2009 715 721
27. A. Csikász-Nagy, and O.S. Soyer Adaptive dynamics with a single two-state protein J. R. Soc. Interface 5 Suppl 1 2008 S41 S47
28. T. Drengstig, and I.W. Jolma P. Ruoff A basic set of homeostatic controller motifs Biophys. J. 103 2012 2000 2010
29. L. Kerkeb, and I. Mukherjee E.L. Connolly Iron-induced turnover of the Arabidopsis IRON-REGULATED TRANSPORTER1 metal transporter requires lysine residues Plant Physiol. 146 2008 1964 1973
30. U.S. Bhalla Trafficking motifs as the basis for two-compartment signaling systems to form multiple stable states Biophys. J. 101 2011 21 32
31. A.M. Berezhkovskii, M. Coppey, and S.Y. Shvartsman Signaling gradients in cascades of two-state reaction-diffusion systems Proc. Natl. Acad. Sci. USA 106 2009 1087 1092
32. H.A. Harrington, and E. Feliu M.P.H. Stumpf Cellular compartments cause multistability and allow cells to process more information Biophys. J. 104 2013 1824 1831
33. A. Alam-Nazki, and J. Krishnan An investigation of spatial signal transduction in cellular networks BMC Syst. Biol. 6 2012 83
34. N.E. Buchler, and M. Louis Molecular titration and ultrasensitivity in regulatory networks J. Mol. Biol. 384 2008 1106 1119
35. D. Del Vecchio, A.J. Ninfa, and E.D. Sontag Modular cell biology: retroactivity and insulation Mol. Syst. Biol. 4 2008 161
36. E. Feliu, and C. Wiuf Enzyme-sharing as a cause of multi-stationarity in signalling systems J. R. Soc. Interface 9 2012 1224 1232
37. N. Blüthgen, and F.J. Bruggeman B.N. Kholodenko Effects of sequestration on signal transduction cascades FEBS J. 273 2006 895 906
38. D.D. Seaton, and J. Krishnan The coupling of pathways and processes through shared components BMC Syst. Biol. 5 2011 103
39. C.E. Shannon A mathematical theory of communication Bell Syst. Tech. J. 27 1948 379 423
40. M.C. Good, J.G. Zalatan, and W.A. Lim Scaffold proteins: hubs for controlling the flow of cellular information Science 332 2011 680 686
41. C.M. Agapakis, P.M. Boyle, and P.A. Silver Natural strategies for the spatial optimization of metabolism in synthetic biology Nat. Chem. Biol. 8 2012 527 535
42. G. Sachdeva, and A. Garg P.A. Silver In vivo co-localization of enzymes on RNA scaffolds increases metabolic production in a geometrically dependent manner Nucleic Acids Res. 42 2014 9493 9503
43. R.J.R.W. Peters, and M. Marguet S. Lecommandoux Cascade reactions in multicompartmentalized polymersomes Angew. Chem. Int. Ed. Engl. 53 2014 146 150
44. T. Nakano, A.W. Eckford, and T. Haraguchi Molecular Communication 2013 Cambridge University Press Cambridge, United Kingdom
45. E. Katz Biomolecular Information Processing: From Logic Systems to Smart Sensors and Actuators 2012 Wiley Hoboken, NJ