Biologistics-Diffusion coefficients for complete proteome of Escherichia coli

Bioinformatics

Volumn 28, Issue 22, 2012, Pages 2971-2978

  Kalwarczyk, Tomasz ^a   Tabaka, Marcin ^a   Holyst, Robert ^a  

^a INSTITUTE OF PHYSICAL CHEMISTRY   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

ESCHERICHIA COLI; EUKARYOTA; PROKARYOTA;

ESCHERICHIA COLI PROTEIN; PROTEOME;

ARTICLE; CHEMISTRY; CYTOLOGY; DIFFUSION; ESCHERICHIA COLI; EUKARYOTIC CELL; FACTUAL DATABASE; METABOLISM; MOLECULAR WEIGHT; PROTEIN DATABASE; TRANSPORT AT THE CELLULAR LEVEL;

BIOLOGICAL TRANSPORT; DATABASES, FACTUAL; DATABASES, PROTEIN; DIFFUSION; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; EUKARYOTIC CELLS; MOLECULAR WEIGHT; PROTEOME;

EID: 84869393388     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts537     Document Type: Article

References (44)

1. Apweiler, R. et al. (2011) Ongoing and future developments at the universal protein resource. Nucleic Acids Res., 39, D214-D219.
2. Bakshi, S. et al. (2012) Superresolution imaging of ribosomes and RNA polymerase in live Escherichia coli cells. Mol. Microbiol., 85, 21-38.
3. Blattner, F. et al. (1997) The complete genome sequence of Escherichia coli k-12. Science, 277, 1453-1462. (Pubitemid 27449228)
4. Campbell, C.S. and Mullins, R.D. (2007) In vivo visualization of type ii plasmid segregation: bacterial actin filaments pushing plasmids. J. Cell Biol., 179, 1059-1066. (Pubitemid 350223498)
5. Capoulade, J. et al. (2011) Quantitative fluorescence imaging of protein diffusion and interaction in living cells. Nat. Biotechnol., 29, 835-842.
6. Cluzel, P. et al. (2000) An ultrasensitive bacterial motor revealed by monitoring signaling proteins in single cells. Science, 287, 1652-1655. (Pubitemid 30127766)
7. Derman, A.I. et al. (2008) Intracellular mobility of plasmid DNA is limited by the para family of partitioning systems. Mol. Microbiol., 67, 935-946. (Pubitemid 351207325)
8. Dill, K.A. et al. (2011) Physical limits of cells and proteomes. Proc. Natl. Acad. Sci. USA, 108, 17876-17882.
9. Driessen, A.J.M. and Nouwen, N. (2008) Protein translocation across the bacterial cytoplasmic membrane. Annu. Rev. Biochem., 77, 643-667.
10. Elf, J. et al. (2007) Probing transcription factor dynamics at the single-molecule level in a living cell. Science, 316, 1191-1194. (Pubitemid 46877481)
11. Elowitz, M. et al. (1999) Protein mobility in the cytoplasm of Escherichia coli. J. Bacteriol., 181, 197-203. (Pubitemid 29013671)
12. English, B.P. et al. (2011) Single-molecule investigations of the stringent response machinery in living bacterial cells. Proc. Natl. Acad. Sci. USA, 108, E365-E373.
13. Golding, I. and Cox, E. (2004) RNA dynamics in live Escherichia coli cells. Proc. Natl Acad. Sci. USA, 101, 11310-11315. (Pubitemid 39038343)
14. Holyst, R. et al. (2009) Scaling form of viscosity at all length-scales in poly(ethylene glycol) solutions studied by fluorescence correlation spectroscopy and capillary electrophoresis. Phys. Chem. Chem. Phys., 11, 9025-9032.
15. Hou, S. et al. (2012) Characterization of Caulobacter crescentus ftsz protein using dynamic light scattering. J. Biol. Chem., 287, 23878-23886.
16. Jain, E. et al. (2009) Infrastructure for the life sciences: design and implementation of the uniprot website. BMC Bioinformatics, 10, 136.
17. Jasnin, M. et al. (2008) Down to atomic-scale intracellular water dynamics. EMBO Rep., 9, 543-547. (Pubitemid 351772917)
18. Jennifer, L.-S. et al. (2001) Studying protein dynamics in living cells. Nat. Rev. Mol. Cell Biol., 2, 444-456.
19. Kalwarczyk, T. et al. (2011) Comparative analysis of viscosity of complex liquids and cytoplasm of mammalian cells at the nanoscale. Nano Lett., 11, 2157-2163.
20. Kim, J. et al. (2004) Fundamental structural units of the Escherichia coli nucleoid revealed by atomic force microscopy. Nucleic Acids Res., 32, 1982-1992. (Pubitemid 38842538)
21. Konopka, M.C. et al. (2006) Crowding and confinement effects on protein diffusion in vivo. J. Bacteriol., 188, 6115-6123. (Pubitemid 44448553)
22. Kubitschek, H. (1990) Cell-volume increase in Escherichia coli after shifts to richer media. J. Bacteriol., 172, 94-101. (Pubitemid 20016819)
23. Kumar, M. et al. (2010) Mobility of cytoplasmic, membrane, and DNA-binding proteins in Escherichia coli. Biophys. J., 98, 552-559.
24. Li, G.-W. et al. (2009) Effects of macromolecular crowding and DNA looping on gene regulation kinetics. Nat. Phys., 5, 294-297.
25. Lukacs, G. et al. (2000) Size-dependent DNA mobility in cytoplasm and nucleus. J. Biol. Chem., 275, 1625-1629. (Pubitemid 30060778)
26. McGuffee, S.R. and Elcock, A.H. (2010) Diffusion, crowding & protein stability in a dynamic molecular model of the bacterial cytoplasm. PLoS Comput. Biol., 6, e1000694.
27. Mika, J.T. and Poolman, B. (2011) Macromolecule diffusion and confinement in prokaryotic cells. Curr. Opin. Biotechnol., 22, 117-126.
28. Mika, J.T. et al. (2010) Molecular sieving properties of the cytoplasm of Escherichia coli and consequences of osmotic stress. Mol. Microbiol., 77, 200-207.
29. Mullineaux, C. et al. (2006) Diffusion of green fluorescent protein in three cell environments in Escherichia coli. J. Bacteriol., 188, 3442-3448. (Pubitemid 43726207)
30. Nenninger, A. et al. (2010) Size dependence of protein diffusion in the cytoplasm of Escherichia coli. J. Bacteriol., 192, 4535-4540.
31. Ochab-Marcinek, A. and Holyst, R. (2011) Scale-dependent diffusion of spheres in solutions of flexible and rigid polymers: mean square displacement and autocorrelation function for FCS and DLS measurements. Soft Matter, 7, 7366-7374.
32. Pederson, T. (2000) Diffusional protein transport within the nucleus: a message in the medium. Nat. Cell Biol., 2, E73-E74.
33. Pogliano, J. (2008) The bacterial cytoskeleton. Curr. Opin. Cell Biol., 20, 19-27.
34. Robertson, R.M. et al. (2006) Diffusion of isolated DNA molecules: dependence on length and topology. Proc. Natl. Acad. Sci. USA, 103, 7310-7314. (Pubitemid 43727829)
35. Sargent, F. (2007) The twin-arginine transport system: moving folded proteins across membranes. Biochem. Soc. Trans., 35(Part 5), 835-847. (Pubitemid 350206379)
36. Shih, Y.-L. and Rothfield, L. (2006) The bacterial cytoskeleton. Microbiol. Mol. Biol. Rev., 70, 729-754. (Pubitemid 44484691)
37. Slade, K.M. et al. (2009) Quantifying green fluorescent protein diffusion in Escherichia coli by using continuous photobleaching with evanescent illumination. J. Phys. Chem. B, 113, 4837-4845.
38. Szymań ski, J. et al. (2006a) Movement of proteins in an environment crowded by surfactant micelles: anomalous versus normal diffusion. J. Phys. Chem. B, 110, 7367-7373.
39. Szymań ski, J. et al. (2006b) Diffusion and viscosity in a crowded environment: from nano-to macroscale. J. Phys. Chem. B, 110, 25593-25597.
40. Vale, R. (2003) The molecular motor toolbox for intracellular transport. Cell, 112, 467-480. (Pubitemid 36263080)
41. van den Bogaart, G. et al. (2007) Protein mobility and diffusive barriers in Escherichia coli: consequences of osmotic stress. Mol. Microbiol., 64, 858-871. (Pubitemid 46653224)
42. Vandesande, W. and Persoons, A. (1985) The size and shape of macromolecular structures-determination of the radius, the length, and the persistence length of rodlike micelles of dodecyldimethylammonium chloride and bromide. J. Phys. Chem., 89, 404-406.
43. Werner, A. (2011) Predicting translational diffusion of evolutionary conserved RNA structures by the nucleotide number. Nucleic Acids Res., 39, e17.
44. Zhao, Y.H. et al. (2003) Fast calculation of van der Waals volume as a sum of atomic and bond contributions and its application to drug compounds. J. Org. Chem., 68, 7368-7373. (Pubitemid 37122487)